1
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Wei Y, Shen YR. Interfacial local field and surface response coefficients. J Chem Phys 2024; 161:124117. [PMID: 39329309 DOI: 10.1063/5.0231281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
The interfacial local field is of critical importance in data analysis to deduce intrinsic surface responses from optical measurements of interfaces of condensed media but has not yet been well interrogated. We present here a simple approach to find local fields approximately at various interfaces of isotropic or nearly isotropic media. We divide a medium into atomic planes or molecular layers. It is found that the dipolar field contribution to the local field in a plane or layer from induced dipoles residing in planes beyond the nearest neighbor planes or layers is negligible; in many cases, the contribution is dominated by in-plane dipoles and the local field has a simple expression very much like that for an isotropic bulk. This finding allows us to calculate approximate local field variation at various interfaces. With the interfacial local field known, intrinsic surface response coefficients can be extracted from the optically measured surface responses.
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Affiliation(s)
- Yuxuan Wei
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structure (MOE), Fudan University, Shanghai 200433, China
| | - Y R Shen
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structure (MOE), Fudan University, Shanghai 200433, China
- Physics Department, University of California, Berkeley, California 94707, USA
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2
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Villard J, Bircher MP, Rothlisberger U. Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder. Chem Sci 2024; 15:4434-4451. [PMID: 38516095 PMCID: PMC10952088 DOI: 10.1039/d3sc05828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.
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Affiliation(s)
- Justin Villard
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
| | - Martin P Bircher
- Computational and Soft Matter Physics, Universität Wien Wien A-1090 Austria
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
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3
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Jin J, Schweizer KS, Voth GA. Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship. J Chem Phys 2023; 158:034103. [PMID: 36681649 DOI: 10.1063/5.0116299] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural properties, assessing dynamic properties in CG modeling is often unfeasible due to the accelerated dynamics of the CG models, which allows for more efficient structural sampling. Therefore, the ultimate goal of the present series of articles is to establish a better correspondence between the FG and CG dynamics. To assess and compare dynamical properties in the FG and the corresponding CG models, we utilize the excess entropy scaling relationship. For Paper I of this series, we provide evidence that the FG and the corresponding CG counterpart follow the same universal scaling relationship. By carefully reviewing and examining the literature, we develop a new theory to calculate excess entropies for the FG and CG systems while accounting for entropy representability. We demonstrate that the excess entropy scaling idea can be readily applied to liquid water and methanol systems at both the FG and CG resolutions. For both liquids, we reveal that the scaling exponents remain unchanged from the coarse-graining process, indicating that the scaling behavior is universal for the same underlying molecular systems. Combining this finding with the concept of mapping entropy in CG models, we show that the missing entropy plays an important role in accelerating the CG dynamics.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kenneth S Schweizer
- Department of Material Science, Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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4
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Rahmati M, Rajabzadeh S, Abdelrasoul A, Kawabata Y, Yoshioka T, Matsuyama H, Mohammadi T. Molecular dynamics simulation for investigating and assessing reaction conditions between carboxylated polyethersulfone and polyethyleneimine. J Appl Polym Sci 2021. [DOI: 10.1002/app.51304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mahmoud Rahmati
- Department of Chemical Engineering Graduate University of Advanced Technology Kerman Iran
| | - Saeid Rajabzadeh
- Research Center for Membrane and Film Technology, Department of Chemical Science and Engineering Kobe University Kobe Japan
| | - Amira Abdelrasoul
- Department of Chemical and Biological Engineering University of Saskatchewan Saskatoon Canada
| | - Yuki Kawabata
- Research Center for Membrane and Film Technology, Department of Chemical Science and Engineering Kobe University Kobe Japan
| | - Tomohisa Yoshioka
- Research Center for Membrane and Film Technology, Department of Chemical Science and Engineering Kobe University Kobe Japan
| | - Hideto Matsuyama
- Research Center for Membrane and Film Technology, Department of Chemical Science and Engineering Kobe University Kobe Japan
| | - Toraj Mohammadi
- Center of Excellence for Membrane Science and Technology, Department of Chemical, Petroleum and Gas Engineering Iran University of Science and Technology (IUST) Tehran Iran
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5
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Monet G, Bresme F, Kornyshev A, Berthoumieux H. Nonlocal Dielectric Response of Water in Nanoconfinement. PHYSICAL REVIEW LETTERS 2021; 126:216001. [PMID: 34114838 DOI: 10.1103/physrevlett.126.216001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Recent experiments reporting a very low dielectric permittivity for nanoconfined water have renewed the interest in the structure and dielectric properties of water in narrow gaps. Here, we describe such systems with a minimal Landau-Ginzburg field theory composed of a nonlocal bulk-determined term and a local water-surface interaction term. We show how the interplay between the boundary conditions and intrinsic bulk correlations encodes the dielectric properties of confined water. Our theoretical analysis is supported by molecular dynamics simulations and comparison with the experimental data.
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Affiliation(s)
- G Monet
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC, UMR 7600), F-75005 Paris, France
| | - F Bresme
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ 2AZ London, United Kingdom
| | - A Kornyshev
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ 2AZ London, United Kingdom
| | - H Berthoumieux
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC, UMR 7600), F-75005 Paris, France
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6
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Karnes JJ, Benjamin I. Deconstructing the Local Intermolecular Ordering and Dynamics of Liquid Chloroform and Bromoform. J Phys Chem B 2021; 125:3629-3637. [PMID: 33792320 DOI: 10.1021/acs.jpcb.0c10407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Local intermolecular structure and dynamics of the polar molecular liquids chloroform and bromoform are studied by molecular dynamics simulation. Structural distribution functions, including 1- and 2-D pair correlations and dipole contour plots allow direct comparison and show agreement with recent analyses of diffraction experiments. Studies of the haloforms' reorientational dynamics and longevity of structural features resulting from intermolecular interaction extend previous work toward deeper understanding of the factors controlling these features. Analyses of ensemble average structures and dynamical properties isolate mass, electrostatics, and steric packing as driving forces or contributing factors for the observed ordering and dynamics.
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Affiliation(s)
- John J Karnes
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, California 95064, United States
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7
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Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021; 154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander J. Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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8
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Zhou Y, Yamaguchi T, Ikeda K, Yoshida K, Otomo T, Fang C, Zhang W, Zhu F. Dihydrogen Bonds in Aqueous NaBD 4 Solution by Neutron and X-ray Diffraction. J Phys Chem Lett 2020; 11:1622-1628. [PMID: 32053379 DOI: 10.1021/acs.jpclett.9b03183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neutron diffraction, X-ray diffraction, and empirical potential structure refinement modeling were employed to study the structure of alkaline aqueous NaBD4 solutions at different NaBD4 concentrations and temperatures. In 1.0 mol·dm-3 NaBD4 aqueous solutions, about 5.6 ± 1.6 water molecules bond to BD4- via tetrahedral edges or tetrahedral corners without a very specific hydration geometry; that is, each hydrogen atom of BD4- bonds to 2.2 ± 1.0 water molecules through dihydrogen bonds with the D(B)···D(W) distance of 1.95 Å. The number of dihydrogen bonds decreases with increasing concentration and increases with temperature. Dihydrogen bonding is a predominantly electrostatic interaction which shows relatively lower directionality and saturability in comparison with the regular hydrogen bonds between water molecules. The water orientation around BD4- shows that the proportion of tetrahedral-edge dihydrogen bonds increases with temperature and decreases with concentration.
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Affiliation(s)
- Yongquan Zhou
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Xining 810008, China
| | - Toshio Yamaguchi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan, Fukuoka 814-0180, Japan
| | - Kazutaka Ikeda
- High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Koji Yoshida
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan, Fukuoka 814-0180, Japan
| | - Toshiya Otomo
- High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Chunhui Fang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Xining 810008, China
| | - Wenqian Zhang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Xining 810008, China
| | - Fayan Zhu
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Xining 810008, China
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9
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Priyadarshini A, Biswas A, Chakraborty D, Mallik BS. Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- and High-Density Regions. J Phys Chem B 2020; 124:1071-1081. [DOI: 10.1021/acs.jpcb.9b11596] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adyasa Priyadarshini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Debashree Chakraborty
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, 575025 Mangalore, Karnataka, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
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10
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11
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Shephard JJ, Evans JSO, Salzmann CG. Local structure and orientational ordering in liquid bromoform. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1648897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Structure of alkaline aqueous NaBH4 solutions by X-ray scattering and empirical potential structure refinement. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Kameda Y, Amo Y, Usuki T, Umebayashi Y, Ikeda K, Otomo T. Neutron Diffraction Study on Partial Pair Correlation Functions of Water at Ambient Temperature. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuo Kameda
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Yuko Amo
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Takeshi Usuki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Yasuhiro Umebayashi
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kazutaka Ikeda
- Institute of Material Structure Science, KEK, Tsukuba, Ibaraki 305-080, Japan
| | - Toshiya Otomo
- Institute of Material Structure Science, KEK, Tsukuba, Ibaraki 305-080, Japan
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14
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Gabovich AM, Voitenko AI. Electrostatic interaction near the interface between dielectric media taking into account the nonlocality of the Coulomb field screening. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.09.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Wade AD, Wang LP, Huggins DJ. Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties. J Chem Inf Model 2018; 58:1766-1778. [PMID: 30113842 DOI: 10.1021/acs.jcim.8b00166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural properties of three- and four-site water models are improved by extending the ForceBalance parametrization code to include a new methodology allowing for the targeting of any radial distribution function (RDF) during the parametrization of a force field. The mean squared difference (MSD) between the experimental and simulated RDFs contributes to an objective function, allowing for the systematic optimization of force field parameters to reach closer overall agreement with experiment. RDF fitting is applied to develop modified versions of the TIP3P and TIP4P/2005 water models in which the Lennard-Jones potential is replaced by a Buckingham potential. The optimized TIP3P-Buckingham and TIP4P-Buckingham potentials feature 93 and 98% lower MSDs in the OO RDF compared to the TIP3P and TIP4P/2005 models respectively, with marked decreases in the height of the first peak. Additionally, these Buckingham models predict the entropy of water more accurately, reducing the error in the entropy of TIP3P from 11 to 3% and the error in the entropy of TIP4P/2005 from 11 to 2%. These new Buckingham models have improved predictive power for many nonfitted properties particularly in the case of TIP3P. Our work directly demonstrates how the Buckingham potential can improve the description of water's structural properties beyond the Lennard-Jones potential. Moreover, adding a Buckingham potential is a favorable alternative to adding interaction sites in terms of computational speed on modern GPU hardware.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Lee-Ping Wang
- Department of Chemistry , University of California, Davis , Davis , California 95616 , United States
| | - David J Huggins
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.,Weill Cornell Medical College , Department of Physiology and Biophysics , 1300 York Avenue , New York , New York 10065 , United States
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16
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Biswas S, Chakraborty D, Mallik BS. Interstitial Voids and Resultant Density of Liquid Water: A First-Principles Molecular Dynamics Study. ACS OMEGA 2018; 3:2010-2017. [PMID: 31458509 PMCID: PMC6641304 DOI: 10.1021/acsomega.7b01996] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/07/2018] [Indexed: 05/31/2023]
Abstract
Many anomalous properties of water can be explained on the basis of the coexistence of more than one density states: high-density water (HDW) and low-density water (LDW). We investigated these two phases of water molecules through first-principles molecular dynamics simulations using density functional theory (DFT) in conjunction with various van der Waals-corrected exchange and correlation functionals. Different density regions were found to exist due to the difference in short-range and long-range forces present in DFT potentials. These density regions were identified and analyzed on the basis of the distribution of molecules and voids present. We defined a local structure index to distinguish and find the probability of occurrence of these different states. HDW and LDW arise due to the presence of "interstitial water" molecules in between the first and second coordination shells. The population of interstitial water molecules is found to affect the overall dynamics of the system as they change the hydrogen bond pattern.
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Affiliation(s)
- Sohag Biswas
- Department
of Chemistry, Indian Institute of Technology
Hyderabad, Kandi, 502285 Sangareddy, Telangana, India
| | - Debashree Chakraborty
- Department
of Chemistry, National Institute of Technology
Karnataka, Surathkal, Mangalore 575025, Karnataka, India
| | - Bhabani S. Mallik
- Department
of Chemistry, Indian Institute of Technology
Hyderabad, Kandi, 502285 Sangareddy, Telangana, India
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17
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Fiala T, Sleziakova K, Marsalek K, Salvadori K, Sindelar V. Thermodynamics of Halide Binding to a Neutral Bambusuril in Water and Organic Solvents. J Org Chem 2018; 83:1903-1912. [DOI: 10.1021/acs.joc.7b02846] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tomas Fiala
- Department of Chemistry and
RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kristina Sleziakova
- Department of Chemistry and
RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamil Marsalek
- Department of Chemistry and
RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karolina Salvadori
- Department of Chemistry and
RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vladimir Sindelar
- Department of Chemistry and
RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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18
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Shin S, Willard AP. Characterizing Hydration Properties Based on the Orientational Structure of Interfacial Water Molecules. J Chem Theory Comput 2018; 14:461-465. [PMID: 29266930 DOI: 10.1021/acs.jctc.7b00898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on the statistical analysis of the orientational configurations of interfacial water molecules. The method can be applied to generate position dependent maps of the hydration properties of heterogeneous surfaces. We present an application to the characterization of surface hydrophobicity, which we use to analyze simulations of a hydrated protein. We demonstrate that this approach is capable of revealing microscopic details of the collective dynamics of a protein hydration shell.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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19
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Zhou Y, Higa S, Fang C, Fang Y, Zhang W, Yamaguchi T. B(OH) 4- hydration and association in sodium metaborate solutions by X-ray diffraction and empirical potential structure refinement. Phys Chem Chem Phys 2017; 19:27878-27887. [PMID: 28991961 DOI: 10.1039/c7cp05107g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
X-ray diffraction is used to study the structure of aqueous sodium metaborate solutions at salt concentrations of 1, 3, and 5 (oversaturated) mol dm-3. The X-ray structure factors are subjected to empirical potential structure refinement (EPSR) modelling to extract the individual site-site pair correlation functions, the coordination numbers, and the spatial density functions (three-dimensional structure) of ion hydration and association as well as solvent water in the borate solutions. The sodium ion is surrounded on average by (5.4 ± 0.7), (4.6 ± 1.0), and (3.7 ± 1.2) water molecules at 1, 3, and 5 mol dm-3, respectively, with the Na-O (H2O) distance of 2.34 Å. The decrease in hydration number of the sodium ion is compensated by direct binding of the oxygen atom of the borate ion, B(OH)4-, with the average coordination number of (0.2 ± 0.5), (1.0 ± 0.8), and (2.1 ± 1.3) at the Na-O(B) distance of 2.34 Å to keep the octahedral hydration shell of the sodium ion. The average number of water molecules around the borate ion is (13.9 ± 1.8), (14.2 ± 1.8), and (16.1 ± 2.4) per borate ion with increasing salt concentration with the B-O(H2O) distance of 3.72 Å. The number of nearest-neighbour water molecules around a central water molecule in a solvent decreases as (4.8 ± 1.2), (3.8 ± 1.1), and (2.8 ± 1.1) with an increase in salt concentration with the O(H2O)-O(H2O) distance of 2.79 Å. The Na+-B(OH)4- ion association is characterized by the Na-O(B) and Na-B pair correlation functions. The Na-B interactions are observed at 3.00 Å as a shoulder and 3.57 Å as a main peak in the site-site pair correlation function, suggesting two occupancy sites of Na+ with one for the edge-shared bidentate bonding and the other for the corner-shared monodentate bonding. The total number of Na-B interactions at 3.00 and 3.57 Å is consistent with that of the Na-O(B) interactions. The detailed three-dimensional structure of the ion hydration and association is visualized as a function of salt concentration. The structure and stability of [NaB(OH)4(H2O)6]0 clusters are further investigated by DFT calculations, and the most likely structure is proposed and cross-checked.
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Affiliation(s)
- Yongquan Zhou
- Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
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20
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Matvija P, Rozbořil F, Sobotík P, Ošt'ádal I, Kocán P. Pair Correlation Function of a 2D Molecular Gas Directly Visualized by Scanning Tunneling Microscopy. J Phys Chem Lett 2017; 8:4268-4272. [PMID: 28830146 DOI: 10.1021/acs.jpclett.7b01965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The state of matter in fluid phases, determined by the interactions between particles, can be characterized by a pair correlation function (PCF). At the nanoscale, the PCF has been so far obtained experimentally only by means of reciprocal-space techniques. We use scanning tunneling microscopy (STM) at room temperature in combination with lattice-gas kinetic Monte Carlo (KMC) simulations to study a two-dimensional gas of highly mobile molecules of fluorinated copper phthalocyanine on a Si(111)/Tl-(1×1) surface. A relatively slow mechanism of STM image acquisition results in time-averaging of molecular occurrence under the STM tip. We prove by the KMC simulations that in the proximity of fixed molecules STM images represent the PCF. We demonstrate that STM is capable of visualizing directly the pair correlation function in real space.
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Affiliation(s)
- P Matvija
- Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles University , V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - F Rozbořil
- Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles University , V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - P Sobotík
- Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles University , V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - I Ošt'ádal
- Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles University , V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - P Kocán
- Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles University , V Holešovičkách 2, 180 00 Prague, Czech Republic
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21
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Dhabal D, Wikfeldt KT, Skinner LB, Chakravarty C, Kashyap HK. Probing the triplet correlation function in liquid water by experiments and molecular simulations. Phys Chem Chem Phys 2017; 19:3265-3278. [DOI: 10.1039/c6cp07599a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
| | | | | | | | - Hemant K. Kashyap
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
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22
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How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations. Biointerphases 2015. [DOI: 10.1116/1.4904339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Ploetz EA, Smith PE. Particle and Energy Pair and Triplet Correlations in Liquids and Liquid Mixtures from Experiment and Simulation. J Phys Chem B 2015; 119:7761-77. [DOI: 10.1021/acs.jpcb.5b00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
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24
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Li P, Song LF, Merz KM. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J Chem Theory Comput 2015; 11:1645-57. [PMID: 26574374 DOI: 10.1021/ct500918t] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
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25
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Ploetz EA, Karunaweera S, Smith PE. Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for pure liquids. J Chem Phys 2015; 142:044502. [PMID: 25637990 PMCID: PMC4312347 DOI: 10.1063/1.4905562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/22/2014] [Indexed: 11/14/2022] Open
Abstract
Fluctuation solution theory has provided an alternative view of many liquid mixture properties in terms of particle number fluctuations. The particle number fluctuations can also be related to integrals of the corresponding two body distribution functions between molecular pairs in order to provide a more physical picture of solution behavior and molecule affinities. Here, we extend this type of approach to provide expressions for higher order triplet and quadruplet fluctuations, and thereby integrals over the corresponding distribution functions, all of which can be obtained from available experimental thermodynamic data. The fluctuations and integrals are then determined using the International Association for the Properties of Water and Steam Formulation 1995 (IAPWS-95) equation of state for the liquid phase of pure water. The results indicate small, but significant, deviations from a Gaussian distribution for the molecules in this system. The pressure and temperature dependence of the fluctuations and integrals, as well as the limiting behavior as one approaches both the triple point and the critical point, are also examined.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
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26
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Shephard JJ, Soper AK, Callear SK, Imberti S, Evans JSO, Salzmann CG. Polar stacking of molecules in liquid chloroform. Chem Commun (Camb) 2015; 51:4770-3. [DOI: 10.1039/c4cc09235j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
‘Super-dipole’ aggregates in liquid chloroform may explain its outstanding solvent properties and highlight a route to designing new high-performance solvents.
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Affiliation(s)
- J. J. Shephard
- Department of Chemistry
- University College London
- WC1H 0AJ London
- UK
- Department of Chemistry
| | - A. K. Soper
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Harwell Oxford
- Didcot OX11 0QX
- UK
| | - S. K. Callear
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Harwell Oxford
- Didcot OX11 0QX
- UK
| | - S. Imberti
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Harwell Oxford
- Didcot OX11 0QX
- UK
| | - J. S. O. Evans
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
| | - C. G. Salzmann
- Department of Chemistry
- University College London
- WC1H 0AJ London
- UK
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27
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Bowron DT, Diaz Moreno S. Using synchrotron X-ray and neutron methods to investigate structural aspects of metal ion solvation and solution structure: An approach using empirical potential structure refinement. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.01.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Kuhn H, Rehage H. Solvation and Counterion-Distribution of Sodium Octanoate Micelles Studied by Molecular Dynamics Simulations. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/bbpc.199700012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Pardo LC, Henao A, Busch S, Guàrdia E, Tamarit JL. A continuous mixture of two different dimers in liquid water. Phys Chem Chem Phys 2014; 16:24479-83. [DOI: 10.1039/c4cp03664f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Liquid water is formed by a continuous mixture of two different dimers (cis and trans) with distinct energies related to different relative water molecule orientations.
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Affiliation(s)
- L. C. Pardo
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
| | - A. Henao
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
| | - S. Busch
- Laboratory of Molecular Biophysics
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU, UK
| | - E. Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física i Enginyeria Nuclear
- B4-B5 Campus Nord
- Universitat Politècnica de Catalunya
- E-08034 Barcelona, Spain
| | - J. Ll. Tamarit
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
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30
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Kameda Y, Usuki T, Uemura O. Diffraction Studies on Concentrated Aqueous Hydrochloric Acid Solutions. Isr J Chem 2013. [DOI: 10.1002/ijch.199900035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Price DL, Fu L, Bermejo FJ, Fernandez-Alonso F, Saboungi ML. Hydrogen/deuterium isotope effects in water and aqueous solutions of organic molecules and proteins. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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The Radial Distribution Functions of Water as Derived from Radiation Total Scattering Experiments: Is There Anything We Can Say for Sure? ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/279463] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present paper reviews the investigation of ambient water structure and focusses in particular on the determination of the radial distribution functions of water from total experimental radiation
scattering experiments. A novel method for removing the inelastic scattering from neutron data is introduced, and the effect of Compton scattering on X-ray data is discussed. In addition the extent to which quantum effects can be discerned between heavy and light water is analysed against these more recent data. It is concluded that, with the help of modern data analysis and computer simulation tools to interrogate the scattering data, a considerable degree of consistency can be obtained between recent and past scattering experiments on water. That consistency also gives a realistic estimate of the likely uncertainties in the extracted radial distribution functions, as well as offering a benchmark against which future experiments can be judged.
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33
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Meng S, Li W, Yin X, Xie J. A comprehensive theoretical study of the hydrogen bonding interactions and microscopic solvation structures of a pyridyl-urea-based hydrogelator in aqueous solution. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys 2013; 15:7450-65. [DOI: 10.1039/c3cp50247c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Meng S, Tang Y, Yin Y, Yin X, Xie J. A theoretical study of molecular conformations and gelation ability of N,N′-dipyridyl urea compounds in ethanol solution: DFT calculations and MD simulations. RSC Adv 2013. [DOI: 10.1039/c3ra43056a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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36
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Bowron DT, Amboage M, Boada R, Freeman A, Hayama S, Díaz-Moreno S. The hydration structure of Cu2+: more tetrahedral than octahedral? RSC Adv 2013. [DOI: 10.1039/c3ra42400f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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37
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Thaomola S, Tongraar A, Kerdcharoen T. Insights into the structure and dynamics of liquid water: A comparative study of conventional QM/MM and ONIOM-XS MD simulations. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Bankura A, Chandra A. A first principles molecular dynamics study of the solvation structure and migration kinetics of an excess proton and a hydroxide ion in binary water-ammonia mixtures. J Chem Phys 2012; 136:114509. [DOI: 10.1063/1.3691602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Meng S, Ma J. Solvent Effects on Isomerization and Spectral Properties of Photochromic-Switching Diarythene Derivatives in Polar and Apolar Solutions. J Phys Chem A 2012; 116:913-23. [DOI: 10.1021/jp210846b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suci Meng
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, People’s Republic of China
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, People’s Republic of China
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40
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Naidoo KJ. Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Phys Chem Chem Phys 2012; 14:9026-36. [DOI: 10.1039/c2cp23802k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Gallo P, Corradini D, Rovere M. Ion hydration and structural properties of water in aqueous solutions at normal and supercooled conditions: a test of the structure making and breaking concept. Phys Chem Chem Phys 2011; 13:19814-22. [DOI: 10.1039/c1cp22166c] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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43
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44
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Fogarty JC, Aktulga HM, Grama AY, van Duin ACT, Pandit SA. A reactive molecular dynamics simulation of the silica-water interface. J Chem Phys 2010; 132:174704. [DOI: 10.1063/1.3407433] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Strümpfer J, Naidoo KJ. Computing free energy hypersurfaces for anisotropic intermolecular associations. J Comput Chem 2010; 31:308-16. [PMID: 19462397 DOI: 10.1002/jcc.21317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We previously used an adaptive reaction coordinate force biasing method for calculating the free energy of conformation (Naidoo and Brady, J Am Chem Soc 1999, 121, 2244) and chemical reactions (Rajamani et al., J Comput Chem 2003, 24, 1775) amongst others. Here, we describe a generalized version able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces method. To illustrate it, we describe how we calculate a multidimensional intermolecular orientational free energy, which can be used to investigate complex systems such as protein conformation and liquids. This multidimensional intermolecular free energy W(r, theta(1), theta(2), phi) provides a measure of orientationally dependent interactions that are appropriate for applications in systems that inherently have molecular anisotropic features. It is a highly informative free energy volume, which can be used to parameterize key terms such as the Gay-Berne intermolecular potential in coarse grain simulations. To demonstrate the value of the information gained from the W(r, theta(1), theta(2), phi) hypersurfaces we calculated them for TIP3P, TIP4P, and TIP5P dimer water models in vacuum. A comparison with a commonly used one-dimensional distance free energy profile is made to illustrate the significant increase in configurational information. The W(r) plots show little difference between the three models while the W(r, theta(1), theta(2), phi) hypersurfaces reveal the underlying energetic reasons why these potentials reproduce tetrahedrality in the condensed phase so differently from each.
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Affiliation(s)
- Johan Strümpfer
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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46
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Lischner J, Arias TA. Classical Density-Functional Theory of Inhomogeneous Water Including Explicit Molecular Structure and Nonlinear Dielectric Response. J Phys Chem B 2010; 114:1946-53. [DOI: 10.1021/jp9012224] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Johannes Lischner
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853
| | - T. A. Arias
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853
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47
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Fu L, Bienenstock A, Brennan S. X-ray study of the structure of liquid water. J Chem Phys 2009; 131:234702. [DOI: 10.1063/1.3273874] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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KOLAFA JIŘÍ, NEZBEDA IVO. Effect of short and long range forces on the structure of water. II. Orientational ordering and the dielectric constant. Mol Phys 2009. [DOI: 10.1080/00268970009483356] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- JIŘÍ KOLAFA
- a E. Hála Laboratory of Thermodynamics , Institute of Chemical Process Fundamentals, Academy of Sciences , 165 02 Prague 6—Suchdol, Czech Republic
| | - IVO NEZBEDA
- a E. Hála Laboratory of Thermodynamics , Institute of Chemical Process Fundamentals, Academy of Sciences , 165 02 Prague 6—Suchdol, Czech Republic
- b Department of Physics , J. E. Purkyně University , 400 96 Ústí n. Lab., Czech Republic
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49
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Allen HC, Casillas-Ituarte NN, Sierra-Hernández MR, Chen X, Tang CY. Shedding light on water structure at air–aqueous interfaces: ions, lipids, and hydration. Phys Chem Chem Phys 2009; 11:5538-49. [DOI: 10.1039/b901209e] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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50
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Amrani M, Bendeddouch D, Bormann D, Krallafa A. Isothermal isobaric molecular dynamics simulation of water. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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