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Novakovskaya YV. Flexibility and Regularity of the Hydration Structures of Ions by an Example of Na +: Nonempirical Insight. J Phys Chem A 2022; 126:8434-8448. [DOI: 10.1021/acs.jpca.2c06690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yulia V. Novakovskaya
- Chemistry Department of the Lomonosov Moscow State University, Leninskie Gory, Moscow119991, Russia
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2
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Saunders M, Wineman-Fisher V, Jakobsson E, Varma S, Pandit SA. High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2840-2851. [PMID: 35192365 PMCID: PMC9801415 DOI: 10.1021/acs.langmuir.1c03105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing rules for Lennard-Jones (LJ) interactions. This, however, does not guarantee their reliability. In fact, compared to the quantum mechanical reference data, Lorentz-Berthelot mixing rules substantially underestimate the binding energies of Na+ ions with small-molecule analogues of lipid headgroups, yielding errors on the order of 80 and 130 kJ/mol, respectively, for methyl acetate and diethyl phosphate. Previously, errors associated with mixing force fields have been reduced using approaches such as "NB-fix" in which LJ interactions are computed using explicit cross terms rather than those from mixing rules. Building on this idea, we derive explicit lipid-ion cross terms that also may implicitly include many-body cooperativity effects. Additionally, to account for the interdependency between cross terms, we optimize all cross terms simultaneously by performing high-dimensional searches using our ParOpt software. The cross terms we obtain reduce the errors due to mixing rules to below 10 kJ/mol. MD simulation of the lipid bilayer conducted using these optimized cross terms resolves the structural discrepancies between our previous simulations and small-angle X-ray and neutron scattering experiments. These results demonstrate that simulations of lipid bilayers with ions that are accurate up to structural data from scattering experiments can be performed without explicit polarization terms. However, it is worth noting that such NB-fix cross terms are not based on any physical principle; a polarizable lipid model would be more realistic and is still desired. Our approach is generic and can be applied to improve the accuracies of simulations employing mixed force fields.
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Affiliation(s)
| | | | - Eric Jakobsson
- Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, and Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
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3
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Terban MW, Billinge SJL. Structural Analysis of Molecular Materials Using the Pair Distribution Function. Chem Rev 2022; 122:1208-1272. [PMID: 34788012 PMCID: PMC8759070 DOI: 10.1021/acs.chemrev.1c00237] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 12/16/2022]
Abstract
This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.
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Affiliation(s)
- Maxwell W. Terban
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Simon J. L. Billinge
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Condensed
Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, New York 11973, United States
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4
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Dočkal J, Svoboda M, Lísal M, Moučka F. A general hydrogen bonding definition based on three-dimensional spatial distribution functions and its extension to quantitative structural analysis of solutions and general intermolecular bonds. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Abstract
The sodium cation is ubiquitous in aqueous chemistry and biological systems. Yet, in spite of numerous studies, the (average) distance between the sodium cation and its water ligands, and the corresponding ionic radii, are still controversial. Recent experimental values in solution are notably smaller than those from previous X-ray studies and ab initio molecular dynamics. Here we adopt a "bottom-up" approach of obtaining these distances from quantum chemistry calculations [full MP2 with the 6-31++G(d,p) and cc-pVTZ basis-sets] of gas-phase Na+(H2O)n clusters, as a function of the sodium coordination number (CN = 2-6). The bulk limit is obtained by the polarizable continuum model, which acts to increase the interatomic distances at small CN, but has a diminishing effect as the CN increases. This extends the CN dependence of the sodium-water distances from crystal structures (CN = 4-12) to lower CN values, revealing a switch between two power laws, having a small exponent at small CNs and a larger one at large CNs. We utilize Bader's theory of atoms in molecules to bisect the Na+-O distances into Na+ and water radii. Contrary to common wisdom, the water radius is not constant, decreasing even more than that of Na+ as the CN decreases. We also find that the electron density at the bond critical point increases exponentially as the sodium radius decreases.
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Affiliation(s)
- Jean Jules Fifen
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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Galib M, Schenter GK, Mundy CJ, Govind N, Fulton JL. Unraveling the spectral signatures of solvent ordering in K-edge XANES of aqueous Na+. J Chem Phys 2018; 149:124503. [DOI: 10.1063/1.5024568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - G. K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - N. Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. L. Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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7
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Cota R, Ottosson N, Bakker HJ, Woutersen S. Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation. PHYSICAL REVIEW LETTERS 2018; 120:216001. [PMID: 29883173 DOI: 10.1103/physrevlett.120.216001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/08/2018] [Indexed: 06/08/2023]
Abstract
We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H_{2}O and D_{2}O. This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ∼1.6 for NaCl and ∼1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.
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Affiliation(s)
- Roberto Cota
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | | | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
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8
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Śmiechowski M. Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water. J Phys Chem B 2018. [PMID: 29513989 DOI: 10.1021/acs.jpcb.7b11334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques can extract important information from the computed IR spectra of aqueous solutions of BF4- and PF6-, interesting weakly coordinating anions that have been known for a long time to alter the IR spectrum of water in an unusual manner. The distance-dependent spectra of both ions are analyzed using the spectral similarity method that provides a quantitative picture of both the spectrum of the solute-affected solvent and the number of solvent molecules thus altered. We find, in accordance with previous experiments, a considerable blue shift of the νOH stretching band of liquid water by 264 cm-1 for BF4- and 306 cm-1 for PF6-, with the affected numbers being 3.7 and 4.2, respectively. Considering also the additional information on solute-solvent dipolar couplings delivered by radially and spatially resolved IR spectra, the computational IR spectroscopy based on AIMD simulations is shown to be a viable predictive tool with strong interpretative power.
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Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty , Gdańsk University of Technology , Narutowicza 11/12 , 80-233 Gdańsk , Poland
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9
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Duboué-Dijon E, Mason PE, Fischer HE, Jungwirth P. Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations. J Phys Chem B 2017; 122:3296-3306. [DOI: 10.1021/acs.jpcb.7b09612] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Henry E. Fischer
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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10
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Pal R. Viscosity-concentration relationships for nanodispersions based on glass transition point. CAN J CHEM ENG 2017. [DOI: 10.1002/cjce.22810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rajinder Pal
- Department of Chemical Engineering; University of Waterloo; Waterloo ON, N2L 3G1 Canada
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11
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Galib M, Baer MD, Skinner LB, Mundy CJ, Huthwelker T, Schenter GK, Benmore CJ, Govind N, Fulton JL. Revisiting the hydration structure of aqueous Na+. J Chem Phys 2017; 146:084504. [DOI: 10.1063/1.4975608] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- M. Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - M. D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - L. B. Skinner
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - C. J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T. Huthwelker
- Swiss Light Source, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland
| | - G. K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Benmore
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - N. Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. L. Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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12
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Riachy P, Roig F, García-Celma MJ, Stébé MJ, Pasc A, Esquena J, Solans C, Blin JL. Hybrid Hierarchical Porous Silica Templated in Nanoemulsions for Drug Release. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201501127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Barboiu M, Cazade PA, Le Duc Y, Legrand YM, van der Lee A, Coasne B. Polarized Water Wires under Confinement in Chiral Channels. J Phys Chem B 2015; 119:8707-17. [DOI: 10.1021/acs.jpcb.5b03322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Mihail Barboiu
- Adaptive
Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM-UM-UMR-CNRS5635, Place Eugène Bataillon CC047, 34095 Montpellier Cedex 5, France
| | - Pierre-André Cazade
- MultiScale
Materials Science for Energy and Environment, UMI 3466 CNRS-MIT and
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yann Le Duc
- Adaptive
Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM-UM-UMR-CNRS5635, Place Eugène Bataillon CC047, 34095 Montpellier Cedex 5, France
| | - Yves-Marie Legrand
- Adaptive
Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM-UM-UMR-CNRS5635, Place Eugène Bataillon CC047, 34095 Montpellier Cedex 5, France
| | - Arie van der Lee
- Adaptive
Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM-UM-UMR-CNRS5635, Place Eugène Bataillon CC047, 34095 Montpellier Cedex 5, France
| | - Benoit Coasne
- Institut Charles Gerhardt Montpellier (ICGM), UMR 5253 CNRS/ENSCM/Université Montpellier 2, 8 rue
de l’Ecole Normale, F-34296 Montpellier, France
- MultiScale
Materials Science for Energy and Environment, UMI 3466 CNRS-MIT and
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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15
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Smirnov PR. Structural parameters of the nearest surrounding of halide ions in the aqueous electrolyte solutions. RUSS J GEN CHEM+ 2013. [DOI: 10.1134/s107036321308001x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Mason PE, Neilson GW, Saboungi ML, Brady JW, Bush CA. The conformation of a ribose derivative in aqueous solution: a neutron-scattering and molecular dynamics study. Biopolymers 2013; 99:739-45. [PMID: 23828616 DOI: 10.1002/bip.22339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 06/19/2013] [Indexed: 11/10/2022]
Abstract
The structure of aqueous solutions of methyl β-D-ribofuranoside was investigated by coupling molecular dynamics (MD) simulations and neutron scattering measurements with isotopic substitution. Using a sample of the sugar isotopically-labeled at a single unique position, neutron scattering structure factors and radial distribution functions can be compared with MD simulations constrained to different conformations to determine which conformer best fits the experimental results. Three different simulations were performed with the methyl ether group of the sugar unconstrained and constrained in each of its staggered orientations. The results of the unconstrained simulation showed that the methyl ester group occupied predominantly the 300° position, which is in agreement with the diffraction experimental results. This result suggests that the molecular mechanics force field used in the simulation adequately describes the conformation of the 1-methyl ether group in the methyl β-D-ribofuranoside.
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Affiliation(s)
- Philip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY, 14853
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Mirza MA, Ahmad S, Mallick MN, Manzoor N, Talegaonkar S, Iqbal Z. Development of a novel synergistic thermosensitive gel for vaginal candidiasis: An in vitro, in vivo evaluation. Colloids Surf B Biointerfaces 2013. [DOI: 10.1016/j.colsurfb.2012.10.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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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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Sabo D, Jiao D, Varma S, Pratt LR, Rempe SB. Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule. ACTA ACUST UNITED AC 2013. [DOI: 10.1039/c3pc90009f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Mason PE, Neilson GW, Price DL, Saboungi ML, Brady JW. A new structural technique for examining ion-neutral association in aqueous solution. Faraday Discuss 2013; 160:161-70; discussion 207-24. [DOI: 10.1039/c2fd20081c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Ince HH, Dedeoglu B, Gul S, Aviyente V, Coldham I. Selectivity in the aggregates of the chiral organolithiumN-Boc-2-lithiopiperidine with a chiral ligand: a DFT study. Mol Phys 2012. [DOI: 10.1080/00268976.2011.647103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Sládek V, Lukeš V, Breza M, Ilčin M. Theoretical study of structural and optical properties of lithium cation complexes with dimethyl sulfoxide. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Te JA, Ichiye T. UNDERSTANDING STRUCTURAL EFFECTS OF MULTIPOLE MOMENTS ON AQUEOUS SOLVATION OF IONS USING THE SOFT-STICKY DIPOLE-QUADRUPOLE-OCTUPOLE WATER MODEL. Chem Phys Lett 2010; 499:219-225. [PMID: 21072252 DOI: 10.1016/j.cplett.2010.09.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The effects of water multipole moments on the aqueous solvation of ions were determined in Monte Carlo simulations using soft-sticky dipole-quadrupole-octupole (SSDQO) water. Water molecules formed linear hydrogen bonds to Cl(-) using the new SSDQO1 parameters, similar to multi-site models. However, the dipole vector was tilted rather than parallel to the oxygen-Na(+) internuclear vector as in most multi-site model, while experiment and ab initio molecular dynamics simulations generally indicate a range of values between tilted and parallel. By varying the multipoles in SSDQO, the octupole was found to determine the orientation around Na(+). Moreover, analysis of the multipoles of more conventional models is predictive of their performance as solvents.
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Affiliation(s)
- Jerez A Te
- Department of Chemistry, Georgetown University, Washington, DC, 20057
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25
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Asthagiri D, Dixit PD, Merchant S, Paulaitis ME, Pratt LR, Rempe SB, Varma S. Ion selectivity from local configurations of ligands in solutions and ion channels. Chem Phys Lett 2010; 485:1-7. [PMID: 23750043 DOI: 10.1016/j.cplett.2009.12.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Probabilities of numbers of ligands proximal to an ion lead to simple, general formulae for the free energy of ion selectivity between different media. That free energy does not depend on the definition of an inner shell for ligand-counting, but other quantities of mechanistic interest do. If analysis is restricted to a specific coordination number, then two distinct probabilities are required to obtain the free energy in addition. The normalizations of those distributions produce partition function formulae for the free energy. Quasi-chemical theory introduces concepts of chemical equilibrium, then seeks the probability that is simplest to estimate, that of the most probable coordination number. Quasi-chemical theory establishes the utility of distributions of ligand-number, and sharpens our understanding of quasi-chemical calculations based on electronic structure methods. This development identifies contributions with clear physical interpretations, and shows that evaluation of those contributions can establish a mechanistic understanding of the selectivity in ion channels.
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Affiliation(s)
- D Asthagiri
- Department of Chemical and Biomolecular Engineering and Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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26
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Mason PE, Ansell S, Neilson GW, Brady JW. Be2+ Hydration in Concentrated Aqueous Solutions of BeCl2. J Phys Chem B 2008; 112:1935-9. [DOI: 10.1021/jp710180v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philip E. Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, ISIS Department, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, U.K., and H.H.Wills Physics Laboratory, University of Bristol, BS8 1TL, U.K
| | - Stuart Ansell
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, ISIS Department, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, U.K., and H.H.Wills Physics Laboratory, University of Bristol, BS8 1TL, U.K
| | - George W. Neilson
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, ISIS Department, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, U.K., and H.H.Wills Physics Laboratory, University of Bristol, BS8 1TL, U.K
| | - John W. Brady
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, ISIS Department, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, U.K., and H.H.Wills Physics Laboratory, University of Bristol, BS8 1TL, U.K
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