1
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Deshmukh VA, Kühne TD, Gámez JA. GAFF-AIC: reoptimisation of the GAFF force field for realistic densities and viscosities in aromatic isocyanates. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2023.2178234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
| | - Thomas D. Kühne
- Department of Chemistry, Universität Paderborn, Paderborn, Germany
| | - José A. Gámez
- Global Innovation – Digital R&D 2, Covestro Deutschland AG, Leverkusen, Germany
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2
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Dissolving salt is not equivalent to applying a pressure on water. Nat Commun 2022; 13:822. [PMID: 35145131 PMCID: PMC8831556 DOI: 10.1038/s41467-022-28538-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Salt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water’s structure is drastically changed by dissolved ions is still debated. Based on density functional theory, we employ machine learning based molecular dynamics to model sodium chloride, potassium chloride, and sodium bromide solutions at different concentrations. The resulting reciprocal-space structure factors agree quantitatively with neutron diffraction data. Here we provide clear evidence that the ions in salt water do not distort the structure of water in the same way as neat water responds to elevated pressure. Rather, the computed structural changes are restricted to the ionic first solvation shells intruding into the hydrogen bond network, beyond which the oxygen radial-distribution function does not undergo major change relative to neat water. Our findings suggest that the widely cited pressure-like effect on the solvent in Hofmeister series ionic solutions should be carefully revisited. By advanced machine learning techniques, first-principles simulations find that dissolving salt in water does not change water structure drastically. It is contrary to the notion of “pressure effect” which has been widely applied over past 25 years.
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3
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Taherivardanjani S, Elfgen R, Reckien W, Suarez E, Perlt E, Kirchner B. Benchmarking the Computational Costs and Quality of Vibrational Spectra from Ab Initio Simulations. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shima Taherivardanjani
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Roman Elfgen
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Werner Reckien
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Estela Suarez
- Institute for Advanced Simulation Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH Wilhelm‐Johnen‐Straße Jülich D‐52425 Germany
| | - Eva Perlt
- Otto Schott Institute of Materials Research Faculty of Physics and Astronomy Friedrich‐Schiller‐Universität Jena Löbdergraben 32 Jena D‐07743 Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
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4
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Teh S, Hsu PJ, Kuo JL. Size of the hydrogen bond network in liquid methanol: a quantum cluster equilibrium model with extensive structure search. Phys Chem Chem Phys 2021; 23:9166-9175. [PMID: 33885093 DOI: 10.1039/d1cp00427a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies have debated what is a favorable cluster size in liquid methanol. Applications of the quantum cluster equilibrium (QCE) model on a limited set of cluster structures have demonstrated the dominance of cyclic hexamers in liquid methanol. In this study, we examined the aforementioned question by integrating our implementation of QCE with a molecular-dynamics-based structural searching scheme. QCE simulations were performed using a database comprising extensively searched stable conformers of (MeOH)n for n = 2-14, which were optimized by B3LYP/6-31+G(d,p) with and without the dispersion correction. Our analysis indicated that an octamer structure can contribute significantly to cluster probability. By reoptimizing selected conformers with high probability at the MP2 level, we found that the aforementioned octamer became the dominant species due to favorable vibrational free energy, which was attributed to modes of intermolecular vibration.
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Affiliation(s)
- Soon Teh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan.
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5
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Evaluation test of the most popular models of methanol using selected thermodynamic, dynamic and structural properties. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Mosaddeghi H, Alavi S, Kowsari MH, Najafi B, Az'hari S, Afshar Y. Molecular dynamics simulations of nano-confined methanol and methanol-water mixtures between infinite graphite plates: Structure and dynamics. J Chem Phys 2019; 150:144510. [PMID: 30981262 DOI: 10.1063/1.5088030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Molecular dynamics simulations are used to investigate microscopic structures and dynamics of methanol and methanol-water binary mixture films confined between hydrophobic infinite parallel graphite plate slits with widths, H, in the range of 7-20 Å at 300 K. The initial geometric densities of the liquids were chosen to be the same as bulk methanol at the same temperature. For the two narrowest slit widths, two smaller initial densities were also considered. For the nano-confined system with H = 7 Å and high pressure, a solid-like hexagonal arrangement of methanol molecules arranged perpendicular to the plates is observed which reflects the closest packing of the molecules and partially mirrors the structure of the underlying graphite structure. At lower pressures and for larger slit widths, in the contact layer, the methanol molecules prefer having the C-O bond oriented parallel to the walls. Layered structures of methanol parallel to the wall were observed, with contact layers and additional numbers of central layers depending on the particular slit width. For methanol-water mixtures, simulations of solutions with different composition were performed between infinite graphite slits with H = 10 and 20 Å at 300 K. For the nanoslit with H = 10 Å, in the solution mixtures, three layers of molecules form, but for all mole fractions of methanol, methanol molecules are excluded from the central fluid layer. In the nanopore with H = 20 Å, more than three fluid layers are formed and methanol concentrations are enhanced near the confining plates walls compared to the average solution stoichiometry. The self-diffusion coefficients of methanol and water molecules in the solution show strong dependence on the solution concentration. The solution mole fractions with minimal diffusivity are the same in confined and non-confined bulk methanol-water mixtures.
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Affiliation(s)
- Hamid Mosaddeghi
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Saman Alavi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Mohammad H Kowsari
- Department of Chemistry and Center for Research in Climate Change and Global Warming (CRCC), Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Bijan Najafi
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Sara Az'hari
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Yaser Afshar
- Department of Aerospace Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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7
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Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput 2019; 15:402-423. [PMID: 30512951 PMCID: PMC6467725 DOI: 10.1021/acs.jctc.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics force fields define how the energy and forces in a molecular system are computed from its atomic positions, thus enabling the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parametrization, considerable human expertise is required to develop or extend force fields. In particular, human input has long been required to define atom types, which encode chemically unique environments that determine which parameters will be assigned. However, relying on humans to establish atom types is suboptimal. Human-created atom types are often developed without statistical justification, leading to over- or under-fitting of data. Human-created types are also difficult to extend in a systematic and consistent manner when new chemistries must be modeled or new data becomes available. Finally, human effort is not scalable when force fields must be generated for new (bio)polymers, compound classes, or materials. To remedy these deficiencies, our long-term goal is to replace human specification of atom types with an automated approach, based on rigorous statistics and driven by experimental and/or quantum chemical reference data. In this work, we describe novel methods that automate the discovery of appropriate chemical perception: SMARTY allows for the creation of atom types, while SMIRKY goes further by automating the creation of fragment (nonbonded, bonds, angles, and torsions) types. These approaches enable the creation of move sets in atom or fragment type space, which are used within a Monte Carlo optimization approach. We demonstrate the power of these new methods by automating the rediscovery of human defined atom types (SMARTY) or fragment types (SMIRKY) in existing small molecule force fields. We assess these approaches using several molecular data sets, including one which covers a diverse subset of the DrugBank database.
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Affiliation(s)
- Camila Zanette
- Department of Pharmaceutical Sciences, University of California, Irvine
| | | | | | - Josh Fass
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine
- Department of Chemistry, University of California, Irvine
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8
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Visscher KM, Vosmeer CR, Luirink RA, Geerke DP. A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. J Comput Chem 2018; 38:508-517. [PMID: 28133840 DOI: 10.1002/jcc.24702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 11/05/2022]
Abstract
In this work, parameters are optimized for a charge-on-spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico-chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed-phase polarizabilities, and starting from the non-polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure-liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure-liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen-bonding and non-hydrogen-bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Koen M Visscher
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - C Ruben Vosmeer
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - Rosa A Luirink
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
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9
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Muñoz-Muñoz YM, Guevara-Carrion G, Vrabec J. Molecular Insight into the Liquid Propan-2-ol + Water Mixture. J Phys Chem B 2018; 122:8718-8729. [DOI: 10.1021/acs.jpcb.8b05610] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Jadran Vrabec
- Thermodynamics and Energy Technology, University of Paderborn, 33098 Paderborn, Germany
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10
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Kelley MP, Yang P, Clark SB, Clark AE. Competitive Interactions Within Cm(III) Solvation in Binary Water/Methanol Solutions. Inorg Chem 2018; 57:10050-10058. [PMID: 30067015 DOI: 10.1021/acs.inorgchem.8b01214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Competitive forces exist in multicomponent solutions, and within electrolytes they consist of both ion-solvent and solvent-solvent interactions. These can influence a myriad of processes, including ligand complexation. In the case of water/alcohol solutions, recent work revealed an interesting dilemma regarding the overall solution dynamics and organization as compared to solute-solvent interactions. This is particularly true for highly charged ions in solution, whose ion-solvent interactions were demonstrated to be highly sensitive to the composition of the immediate solvation environment. Faster solvent exchange should be observed about the ion, considering that second-order Møller-Plesset perturbation theory predicts an average decrease in ion-solvent dissociation energy when methanol enters the first solvation shell of Cm3+(aq). Yet the addition of methanol to water causes the dynamic features of the hydrogen-bond network of the entire solution to slow. The apparent competition between these contrary forces was examined using a combination of electronic structure calculations with both ab initio and classical molecular dynamics simulations, using binary water/methanol solutions and Cm3+ as a representative solute. This combination of theoretical methods predicts that, among the competitive effects of the solvent-solvent and ion-solvent interactions, the solution-phase dynamics imparted by the addition of methanol to water kinetically restricts the solvation exchange rates about Cm3+ in these binary solutions.
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Affiliation(s)
- Morgan P Kelley
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico , United States
| | - Ping Yang
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico , United States
| | - Sue B Clark
- Pacific Northwest National Laboratory , Richland , Washington , United States
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11
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Fujii A, Sugawara N, Hsu PJ, Shimamori T, Li YC, Hamashima T, Kuo JL. Hydrogen bond network structures of protonated short-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:14971-14991. [DOI: 10.1039/c7cp08072g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.
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Affiliation(s)
- Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Natsuko Sugawara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Takuto Shimamori
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Toru Hamashima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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12
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Trumm M, Adam C, Koke C, Maiwald M, Höfener S, Skerencak-Frech A, Panak PJ, Schimmelpfennig B. The influence of polarity in binary solvent mixtures on the conformation of bis-triazinyl-pyridine in solution. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Michael Trumm
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
| | - Christian Adam
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
| | - Carsten Koke
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
- Physikalisch-Chemisches Institut, Ruprecht Karls Universität Heidelberg, Heidelberg, Germany
| | - Martin Maiwald
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
- Physikalisch-Chemisches Institut, Ruprecht Karls Universität Heidelberg, Heidelberg, Germany
| | - Sebastian Höfener
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Karlsruhe, Germany
| | - Andrej Skerencak-Frech
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
- Physikalisch-Chemisches Institut, Ruprecht Karls Universität Heidelberg, Heidelberg, Germany
| | - Petra J. Panak
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
- Physikalisch-Chemisches Institut, Ruprecht Karls Universität Heidelberg, Heidelberg, Germany
| | - Bernd Schimmelpfennig
- Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie, Karlsruhe, Germany
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13
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Besford QA, Christofferson AJ, Liu M, Yarovsky I. Long-range dipolar order and dispersion forces in polar liquids. J Chem Phys 2017; 147:194503. [DOI: 10.1063/1.5005581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | | | - Maoyuan Liu
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria 3001, Australia
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14
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Kohns M, Horsch M, Hasse H. Activity coefficients from molecular simulations using the OPAS method. J Chem Phys 2017; 147:144108. [DOI: 10.1063/1.4991498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Maximilian Kohns
- Laboratory of Engineering Thermodynamics, University of Kaiserslautern, Erwin-Schrödinger Str. 44, D-67663 Kaiserslautern, Germany
| | - Martin Horsch
- Laboratory of Engineering Thermodynamics, University of Kaiserslautern, Erwin-Schrödinger Str. 44, D-67663 Kaiserslautern, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics, University of Kaiserslautern, Erwin-Schrödinger Str. 44, D-67663 Kaiserslautern, Germany
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15
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Naserifar S, Brooks DJ, Goddard WA, Cvicek V. Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids. J Chem Phys 2017; 146:124117. [DOI: 10.1063/1.4978891] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Saber Naserifar
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - Daniel J. Brooks
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - Vaclav Cvicek
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
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16
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González-Salgado D, Zemánková K, Noya EG, Lomba E. Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol. J Chem Phys 2017; 144:184505. [PMID: 27179493 DOI: 10.1063/1.4948611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion by the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.
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Affiliation(s)
- D González-Salgado
- Departamento de Física Aplicada, Universidad de Vigo, Campus del Agua, Edificio Manuel Martínez-Risco, E-32004 Ourense, Spain
| | - K Zemánková
- Departamento de Física Aplicada, Universidad de Vigo, Campus del Agua, Edificio Manuel Martínez-Risco, E-32004 Ourense, Spain
| | - E G Noya
- Instituto de Química Física Rocasolano, CSIC, Calle Serrano 119, E-28006 Madrid, Spain
| | - E Lomba
- Instituto de Química Física Rocasolano, CSIC, Calle Serrano 119, E-28006 Madrid, Spain
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17
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Albertí M, Amat A, Aguilar A, Pirani F. Methanol–methanol and methanol–water systems: the intermolecular interactions controlling the transition from small clusters to the liquid phase. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02919e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present paper focuses on the characterization of the properties of methanol and water molecules in gas and liquid enviroments.
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Affiliation(s)
- Margarita Albertí
- IQTCUB
- Departament de Ciència de Materials i Química Física
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Anna Amat
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO)
- CNR-ISTM
- 06123 Perugia
- Italy
| | - Antonio Aguilar
- IQTCUB
- Departament de Ciència de Materials i Química Física
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Fernando Pirani
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- 06123 Perugia and Istituto di Nanotecnologia (CNR, NANOTEC)
- 70126 Bari
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18
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Lafond PG, Izvekov S. Multiscale Coarse-Graining of Polarizable Models through Force-Matched Dipole Fluctuations. J Chem Theory Comput 2016; 12:5737-5750. [DOI: 10.1021/acs.jctc.6b00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick G. Lafond
- Weapons and Materials Research
Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Sergei Izvekov
- Weapons and Materials Research
Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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19
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Garate JA, Perez-Acle T. From dimers to collective dipoles: Structure and dynamics of methanol/ethanol partition by narrow carbon nanotubes. J Chem Phys 2016; 144:064105. [PMID: 26874480 DOI: 10.1063/1.4941331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Alcohol partitioning by narrow single-walled carbon nanotubes (SWCNTs) holds the promise for the development of novel nanodevices for diverse applications. Consequently, in this work, the partition of small alcohols by narrow tubes was kinetically and structurally quantified via molecular dynamics simulations. Alcohol partitioning is a fast process in the order of 10 ns for diluted solutions but the axial-diffusivity within SWCNT is greatly diminished being two to three orders of magnitude lower with respect to bulk conditions. Structurally, alcohols form a single-file conformation under confinement and more interestingly, they exhibit a pore-width dependent transition from dipole dimers to a single collective dipole, for both methanol and ethanol. Energetic analyses demonstrate that this transition is the result of a detailed balance between dispersion and electrostatics interactions, with the latter being more pronounced for collective dipoles. This transition fully modifies the reorientational dynamics of the loaded particles, generating stable collective dipoles that could find usage in signal-amplification devices. Overall, the results herein have shown distinct physico-chemical features of confined alcohols and are a further step towards the understanding and development of novel nanofluidics within SWCNTs.
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Affiliation(s)
- Jose A Garate
- Computational Biology Laboratory, Fundación Ciencia and Vida, Santiago, Chile
| | - Tomas Perez-Acle
- Computational Biology Laboratory, Fundación Ciencia and Vida, Santiago, Chile
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20
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Ploetz EA, Rustenburg AS, Geerke DP, Smith PE. To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures. J Chem Theory Comput 2016; 12:2373-87. [DOI: 10.1021/acs.jctc.5b01115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ariën S. Rustenburg
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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21
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Affiliation(s)
- Victor H. Rusu
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Stephan Bachmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland
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22
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Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG. Polarization Effects in Aqueous and Nonaqueous Solutions. J Chem Theory Comput 2015; 3:2055-67. [PMID: 26636201 DOI: 10.1021/ct7001539] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Polarization effects in aqueous and nonaqueous solutions were analyzed for nine neutral and three charged organic solutes by the SM8 universal implicit solvation model and class IV partial atomic charges based on Charge Model 4M (CM4M) with the M06-2X density functional. The CM4M partial atomic charges in neutral and ionic solutes and in the corresponding clustered solutes (supersolutes), which included one solute molecule and one or two solvent molecules, were modeled in three solvents (benzene, methylene chloride, and water) and compared to those in the gas phase. The use of the supersolute approach (microsolvation) allows one to account for charge transfer from the solute to the solvent, and we find charge transfers as large as 0.06 atomic units for neutral solutes (pyridine in water) and 0.32 atomic units for ions (methoxide anion in water). Relaxation of the electronic structure of the solute in the presence of solvent increases the polarization free energy of the neutral solutes studied here, on average, by 16% in benzene, 30% in methylene chloride, and 43% in water. The increase for the ions in water averaged 43%.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Adam C Chamberlin
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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23
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Excess properties of non-ideal binary mixtures containing water, methanol and ethanol by molecular simulation. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.08.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Abstract
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany
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25
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Bachmann SJ, van Gunsteren WF. An improved simple polarisable water model for use in biomolecular simulation. J Chem Phys 2015; 141:22D515. [PMID: 25494786 DOI: 10.1063/1.4897976] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.
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Affiliation(s)
- Stephan J Bachmann
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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26
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Szklarczyk OM, Arvaniti E, van Gunsteren WF. Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. J Comput Chem 2015; 36:1311-21. [DOI: 10.1002/jcc.23929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Oliwia M. Szklarczyk
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology ETH; 8093 Zürich Switzerland
| | - Eirini Arvaniti
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology ETH; 8093 Zürich Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology ETH; 8093 Zürich Switzerland
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27
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Vosmeer CR, Kiewisch K, Keijzer K, Visscher L, Geerke DP. A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities. Phys Chem Chem Phys 2015; 16:17857-62. [PMID: 25042275 DOI: 10.1039/c4cp02401j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects.
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Affiliation(s)
- C Ruben Vosmeer
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands.
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28
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Lin Z, van Gunsteren WF. Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide. J Chem Theory Comput 2015; 11:1983-6. [DOI: 10.1021/acs.jctc.5b00210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhixiong Lin
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Zürich, Switzerland
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29
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Lin Z, Bachmann SJ, van Gunsteren WF. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2. J Chem Phys 2015; 142:094117. [DOI: 10.1063/1.4913955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhixiong Lin
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
| | - Stephan J. Bachmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
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30
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Shilov IY. Molecular dynamics simulation of dielectric constant and cluster structure of liquid methanol: the role of cluster–cluster dipole correlations. Mol Phys 2014. [DOI: 10.1080/00268976.2014.960496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ignat Yu. Shilov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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31
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Huang W, van Gunsteren WF. Challenge of Representing Entropy at Different Levels of Resolution in Molecular Simulation. J Phys Chem B 2014; 119:753-63. [DOI: 10.1021/jp505045m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei Huang
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland
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32
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Kollipost F, Domanskaya AV, Suhm MA. Microscopic Roots of Alcohol–Ketone Demixing: Infrared Spectroscopy of Methanol–Acetone Clusters. J Phys Chem A 2014; 119:2225-32. [DOI: 10.1021/jp503999b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Franz Kollipost
- Institut
für Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Alexandra V. Domanskaya
- Institut
für Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut
für Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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33
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Takahashi KZ, Yasuoka K. A determination of liquid–vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.913791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Fennell CJ, Wymer KL, Mobley DL. A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. J Phys Chem B 2014; 118:6438-46. [PMID: 24702668 PMCID: PMC4064691 DOI: 10.1021/jp411529h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a simple optimization strategy for incorporating experimental dielectric response information on neat liquids in classical molecular models of alcohol. Using this strategy, we determine simple and transferable hydroxyl modulation rules that, when applied to an existing molecular parameter set, result in a newly dielectric corrected (DC) parameter set. We applied these rules to the general Amber force field (GAFF) to form an initial set of GAFF-DC parameters, and we found this to lead to significant improvement in the calculated dielectric constant and hydration free energy values for a wide variety of small molecule alcohol models. Tests of the GAFF-DC parameters in the SAMPL4 blind prediction event for hydration show these changes improve agreement with experiment. Surprisingly, these simple modifications also outperform detailed quantum mechanical electric field calculations using a self-consistent reaction field environment coupling term. This work provides a potential benchmark for future developments in methods for representing condensed-phase environments in electronic structure calculations.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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35
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Nagasaka M, Mochizuki K, Leloup V, Kosugi N. Local Structures of Methanol–Water Binary Solutions Studied by Soft X-ray Absorption Spectroscopy. J Phys Chem B 2014; 118:4388-96. [DOI: 10.1021/jp4091602] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masanari Nagasaka
- The
Institute
for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- The Graduate University
for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan
| | - Kenji Mochizuki
- The Graduate University
for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan
| | - Valentin Leloup
- The
Institute
for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Nobuhiro Kosugi
- The
Institute
for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- The Graduate University
for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan
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36
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Kumar P, Bojarowski S, Jarzembska KN, Domagała S, Vanommeslaeghe K, MacKerell AD, Dominiak PM. A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers. J Chem Theory Comput 2014; 10:1652-1664. [PMID: 24803869 PMCID: PMC3985931 DOI: 10.1021/ct4011129] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Indexed: 11/29/2022]
Abstract
Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ≈ 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ≈ 0.93 on average). The RSMEs do not exceed 3.2 kcal mol-1 for the UBDB and are in the range of 3.7-7.6 kcal mol-1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications to macromolecules.
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Affiliation(s)
- Prashant Kumar
- Department
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | | | | | - Sławomir Domagała
- Department
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, 20 Penn
Street HSF II, Baltimore, Maryland 21201, United
States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, 20 Penn
Street HSF II, Baltimore, Maryland 21201, United
States
| | - Paulina M. Dominiak
- Department
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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37
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Van Houteghem M, Ghysels A, Verstraelen T, Poelmans W, Waroquier M, Van Speybroeck V. Critical analysis of the accuracy of models predicting or extracting liquid structure information. J Phys Chem B 2014; 118:2451-70. [PMID: 24512612 DOI: 10.1021/jp411737s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.
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Affiliation(s)
- Marc Van Houteghem
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
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38
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Szklarczyk OM, Bachmann SJ, van Gunsteren WF. A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. J Comput Chem 2014; 35:789-801. [PMID: 26248885 DOI: 10.1002/jcc.23551] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/22/2013] [Accepted: 01/13/2014] [Indexed: 12/17/2022]
Abstract
Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge-on-spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united-atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self-diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force-field parameters for CH2, CH3, and CH4 moieties.
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Affiliation(s)
- Oliwia M Szklarczyk
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
| | - Stephan J Bachmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
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39
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Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Curr Pharm Des 2014; 20:3281-92. [PMID: 23947650 PMCID: PMC4026342 DOI: 10.2174/13816128113199990600] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022]
Abstract
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This paper introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The paper ends with a brief overview of common force fields in CSBDD.
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Affiliation(s)
- Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
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40
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Kulschewski T, Pleiss J. A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.769680] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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41
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Li W. Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions. J Chem Phys 2013; 138:014106. [DOI: 10.1063/1.4773011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Lee S, Park SS. Thermodynamic and dynamic properties in binary mixtures of propylene carbonate with dimethyl carbonate and ethylene carbonate. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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Daub CD, Cann NM. Molecular Dynamics Simulations to Examine Structure, Energetics, and Evaporation/Condensation Dynamics in Small Charged Clusters of Water or Methanol Containing a Single Monatomic Ion. J Phys Chem A 2012; 116:10488-95. [DOI: 10.1021/jp308217q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Christopher D. Daub
- Department of Chemistry, Queen’s University, 90 Bader
Lane, Kingston,
Ontario, Canada K7L3N6
| | - Natalie M. Cann
- Department of Chemistry, Queen’s University, 90 Bader
Lane, Kingston,
Ontario, Canada K7L3N6
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44
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Van Houteghem M, Verstraelen T, Ghysels A, Vanduyfhuys L, Waroquier M, Van Speybroeck V. Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol. J Chem Phys 2012; 137:104506. [PMID: 22979873 DOI: 10.1063/1.4749929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.
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Affiliation(s)
- Marc Van Houteghem
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
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45
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Vosmeer CR, Rustenburg AS, Rice JE, Horn HW, Swope WC, Geerke DP. QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation. J Chem Theory Comput 2012; 8:3839-53. [PMID: 26593025 DOI: 10.1021/ct300085z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Accounting for electronic polarization effects in biomolecular simulation (by using a polarizable force field) can increase the accuracy of simulation results. However, the use of gas-phase estimates of atomic polarizabilities αi usually leads to overpolarization in condensed-phase systems. In the current work, a combined QM/MM approach has been employed to obtain condensed-phase estimates of atomic polarizabilities for water and methanol (QM) solutes in the presence of (MM) solvents of different polarity. In a next step, the validity of the linear response and isotropy assumptions were evaluated based on the observed condensed-phase distributions of αi values. The observed anisotropy and low average values for the polarizability of methanol's carbon atom in polar solvents was explained in terms of strong solute-solvent interactions involving its adjacent hydroxyl group. Our QM/MM estimates for atomic polarizabilities were found to be close to values used in previously reported polarizable water and methanol models. Using our estimate for αO of methanol, a single set of polarizable force field parameters was obtained that is directly transferable between environments of different polarity.
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Affiliation(s)
- C Ruben Vosmeer
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ariën S Rustenburg
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Julia E Rice
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - Hans W Horn
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - Daan P Geerke
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Lee S, Park SS. Dielectric Properties of Organic Solvents from Non-Polarizable Molecular Dynamics Simulation with Electronic Continuum Model and Density Functional Theory. J Phys Chem B 2011; 115:12571-6. [DOI: 10.1021/jp207658m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanghun Lee
- Corporate R&D Center, Samsung SDI Co. Ltd., Yongin, Gyunggido, 446-577, South Korea
| | - Sung Soo Park
- Corporate R&D Center, Samsung SDI Co. Ltd., Yongin, Gyunggido, 446-577, South Korea
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Ren P, Wu C, Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput 2011; 7:3143-3161. [PMID: 22022236 PMCID: PMC3196664 DOI: 10.1021/ct200304d] [Citation(s) in RCA: 337] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chuanjie Wu
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
| | - Jay W. Ponder
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
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Marie C, Miguirditchian M, Guillaumont D, Tosseng A, Berthon C, Guilbaud P, Duvail M, Bisson J, Guillaneux D, Pipelier M, Dubreuil D. Complexation of Lanthanides(III), Americium(III), and Uranium(VI) with Bitopic N,O Ligands: an Experimental and Theoretical Study. Inorg Chem 2011; 50:6557-66. [DOI: 10.1021/ic200271e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cécile Marie
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Manuel Miguirditchian
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Dominique Guillaumont
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Arnaud Tosseng
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Claude Berthon
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Philippe Guilbaud
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Magali Duvail
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Julia Bisson
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Denis Guillaneux
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, SCPS, F-30207 Bagnols-sur-Cèze, France
| | - Muriel Pipelier
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UFR des Sciences et des Techniques, Université de Nantes, UMR CNRS 6230, 2 rue de la Houssinière, F-44322 Nantes, France
| | - Didier Dubreuil
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UFR des Sciences et des Techniques, Université de Nantes, UMR CNRS 6230, 2 rue de la Houssinière, F-44322 Nantes, France
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Wang J, Tingjun H. Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization. J Chem Theory Comput 2011; 7:2151-2165. [PMID: 21857814 DOI: 10.1021/ct200142z] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their "ideal" values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper.
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Affiliation(s)
- Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
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50
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Abroshan H, Akbarzadeh H, Taherkhani F, Parsafar G. Effect of water–methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; a molecular dynamics study. Mol Phys 2011. [DOI: 10.1080/00268976.2010.549846] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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