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Huang B, Yun L, Yang Y, Han R, Chen K, Wang Z, Wang Y, Chen H, Du Y, Hao Y, Lv P, Ji P, Tan Y, Zheng L, Liu L, Li R, Yang J. Structural Study of Aqueous Electrolyte Solution by MeV Liquid Electron Scattering. J Phys Chem B 2024; 128:9197-9205. [PMID: 39268827 DOI: 10.1021/acs.jpcb.4c03681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
The impact of ions on water has long been a subject of great interest, as it is closely tied to the hydration structure, dynamics, and properties of electrolyte solutions. Over centuries of investigation, the influence of ions on water's structure remains highly debated. Prevailing techniques, such as neutron and X-ray scattering, primarily focus on the microscopic structure of salt solutions at very high concentrations, mostly above 1 mol/L. In this study, we measured the structure of aqueous potassium iodide (KI) and potassium chloride (KCl) solutions using MeV liquid electron scattering (MeV-LES) across a concentration range of 0.10 to 0.75 mol/L. The obtained results provide detailed insights into the variations in ion-oxygen and oxygen-oxygen correlations as a function of concentration. The observed structural differences between KI and KCl solutions are in line with the structure maker/breaker theory, which suggests that iodide ions exert a more pronounced effect than chloride ions on disrupting the water shell. This work demonstrates the potency of MeV-LES for investigating the atomic structure in liquids, augmenting the modern analytical toolbox.
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Affiliation(s)
- Bo Huang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Longteng Yun
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yining Yang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Ruinong Han
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Keke Chen
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhiyuan Wang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Yian Wang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Haowei Chen
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yingchao Du
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Yuxia Hao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Peng Lv
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Pengju Ji
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuemei Tan
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Lianmin Zheng
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Lihong Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Renkai Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing 100084, China
| | - Jie Yang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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2
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Chialvo AA. On the Elusive Links between Solution Microstructure, Dynamics, and Solvation Thermodynamics: Demystifying the Path through a Bridge over Troubled Conjectures and Misinterpretations. J Phys Chem B 2023; 127:10792-10813. [PMID: 38060479 DOI: 10.1021/acs.jpcb.3c04707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
We build a fundamentally based bridge between the solute-induced microstructural perturbation of the species environment and the dynamic as well as thermodynamic responses of the fluid system, regardless of the state conditions, composition, nature of the solvent, and either the magnitude or the type of solute-solvent intermolecular-interaction asymmetries. For that purpose, we advance a fluctuation-based solvation formalism of fluid mixtures to provide meaningful descriptors of solvation phenomena, the microstructural signatures of their solute-solvent intermolecular interaction asymmetry, and the thermodynamic manifestations linked to the solution nonideality. The rigorous foundations afford us to address some crucial issues frequently invoked in the literature including the microstructural perturbation domain, its proper identification and molecular-based meaning toward the interpretation of the solvation process, and the potential impact of the local differential behavior between anions and cations on the actual salt-induced perturbation of the solvent microstructure. Indeed, we link the precisely characterized species solvation behavior to fundamental thermodynamic residual-property relations, and the dynamics associated with either the viscous flow or diffusive behavior of the solvent, to finally illustrate their outcome with experimental data of aqueous electrolyte solutions from the available literature. Ultimately, this effort provides a highly desirable unambiguous identification of the cause-effect connections between the microstructurally perturbed domains and the experimentally measured macroscopic solvation properties, including their effect on the dynamics of the solvent environment. More importantly, it lends a well-established solvation framework to bridge rigorously the microstructural details of the mixture, its dynamics, and its solvation thermodynamics to enhance our understanding of well-defined ranked Hofmeister series, i.e., by avoiding ad hoc conjectures and unsupported microscopic interpretations of solvation phenomena.
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Affiliation(s)
- Ariel A Chialvo
- Retired Scientist, Knoxville, Tennessee 37922-3108, 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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Abstract
![]()
The
two sugar molecules sucrose and trehalose are both considered
as stabilizing molecules for the purpose of preserving biological
materials during, for example, lyophilization or cryo-preservation.
Although these molecules share a similar molecular structure, there
are several important differences in their properties when they interact
with water, such as differences in solubility, viscosity, and glass
transition temperature. In general, trehalose has been shown to be
more efficient than other sugar molecules in preserving different
biological molecules against stress, and thus by investigating how
these two disaccharides differ in their water interaction, it is possible
to further understand what makes trehalose special in its stabilizing
properties. For this purpose, the structure of aqueous solutions of
these disaccharides was studied by using neutron and X-ray diffraction
in combination with empirical potential structure refinement (EPSR)
modeling. The results show that there are surprisingly few differences
in the overall structure of the solutions, although there are indications
for that trehalose perturbs the water structure slightly more than
sucrose.
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Affiliation(s)
- Christoffer Olsson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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5
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Mason PE, Tavagnacco L, Saboungi ML, Hansen T, Fischer HE, Neilson GW, Ichiye T, Brady JW. Molecular Dynamics and Neutron Scattering Studies of Potassium Chloride in Aqueous Solution. J Phys Chem B 2019; 123:10807-10813. [PMID: 31769976 DOI: 10.1021/acs.jpcb.9b08422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Neutron diffraction with isotopic substitution (NDIS) experiments were done on both natural abundance potassium and isotopically labeled 41KCl heavy water solutions to characterize the solvent structuring around the potassium ion in water. Preliminary measurements suggested that the literature value for the coherent neutron scattering length (2.69 fm) for 41K was significantly in error. This value was remeasured using a neutron powder diffractometer and found to be 2.40 fm. This revision increases significantly the contrast between the natural abundance K and 41K by about 30% (from 1.0 to 1.3 fm). The experimentally determined structure factor of the potassium ion was then compared to that calculated from molecular dynamics (MD) simulations. Previous neutron scattering measurements of potassium gave a solvation number of 5.5 (see below). In this study, the NDIS and MD results are in good agreement and allowed us to derive a coordination number of 6.1 for water molecules and 0.8 for chloride ions around each K+ ion in 4 molal aqueous KCl solution.
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Affiliation(s)
- Philip E Mason
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic & Center for Biomolecules and Complex Molecular Systems , 16610 Prague 6 , Czech Republic
| | - Letizia Tavagnacco
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
| | - Marie-Louise Saboungi
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie , UMR 7590 CNRS - Sorbonne Université, Campus Pierre et Marie Curie , 4, Place Jussieu , 75005 Paris , France
| | - Thomas Hansen
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - Henry E Fischer
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - George W Neilson
- H.H. Wills Physics Laboratory , University of Bristol , BS8 1TL Bristol , U.K
| | - Toshiko Ichiye
- Department of Chemistry , Georgetown University , Box 571227, Washington , DC 20057 , United States
| | - John W Brady
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
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6
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Wang HW, Vlcek L, Neuefeind JC, Page K, Irle S, Simonson JM, Stack AG. Decoding Oxyanion Aqueous Solvation Structure: A Potassium Nitrate Example at Saturation. J Phys Chem B 2018; 122:7584-7589. [PMID: 29991255 DOI: 10.1021/acs.jpcb.8b05895] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to probe the structure of a salt solution at the atomic scale is fundamentally important for our understanding of many chemical reactions and their mechanisms. The capability of neutron diffraction to "see" hydrogen (or deuterium) and other light isotopes is exceptional for resolving the structural complexity around the dissolved solutes in aqueous electrolytes. We have made measurements using oxygen isotopes on aqueous nitrate to reveal a small hydrogen-bonded water coordination number (3.9 ± 1.2) around a nitrate oxyanion. This is compared to estimates made using the existing method of nitrogen isotope substitution and those of computational simulations (>5-6 water molecules). The low water coordination number, combined with a comparison to classical molecular dynamics simulations, suggests that ion-pair formation is significant. This insight demonstrates the utility of experimental diffraction data for benchmarking atomistic computer simulations, enabling the development of more accurate intermolecular potentials.
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7
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Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results. Int J Pharm 2018; 540:65-77. [PMID: 29412151 DOI: 10.1016/j.ijpharm.2018.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022]
Abstract
The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.
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8
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“Thought experiments” as dry-runs for “tough experiments”: novel approaches to the hydration behavior of oxyanions. PURE APPL CHEM 2016. [DOI: 10.1515/pac-2015-1002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWe explore the deconvolution of correlations for the interpretation of the microstructural behavior of aqueous electrolytes according to the neutron diffraction with isotopic substitution (NDIS) approach toward the experimental determination of ion coordination numbers of systems involving oxyanions, in particular, sulfate anions. We discuss the alluded interplay in the title of this presentation, emphasized the expectations, and highlight the significance of tackling the challenging NDIS experiments. Specifically, we focus on the potential occurrence of $N{i^{2 + }} \cdots SO_4^{2 - }$ pair formation, identify its signature, suggest novel ways either for the direct probe of the contact ion pair (CIP) strength and the subsequent correction of its effects on the measured coordination numbers, or for the determination of anion coordination numbers free of CIP contributions through the implementation of null-cation environments. For that purpose we perform simulations of NiSO4 aqueous solutions at ambient conditions to generate the distribution functions required in the analysis (a) to identify the individual partial contributions to the total neutron-weighted distribution function, (b) to isolate and assess the contribution of $N{i^{2 + }} \cdots SO_4^{2 - }$ pair formation, (c) to test the accuracy of the neutron diffraction with isotope substitution based coordination calculations and X-ray diffraction based assumptions, and (d) to describe the water coordination around both the sulfur and oxygen sites of the sulfate anion. We finally discuss the strength of this interplay on the basis of the inherent molecular simulation ability to provide all pair correlation functions that fully characterize the system microstructure and allows us to “reconstruct” the eventual NDIS output, i.e., to take an atomistic “peek” (e.g., see Figure 1) at the local environment around the isotopically-labeled species before any experiment is ever attempted, and ultimately, to test the accuracy of the “measured” NDIS-based coordination numbers against the actual values by the “direct” counting.
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9
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10
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Torabifard H, Starovoytov ON, Ren P, Cisneros GA. Development of an AMOEBA water model using GEM distributed multipoles. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1702-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Bakó I, Pálinkás G, Grósz T, Bálint S, Tóth G, Radnai T. A new approach to the determination of the uncertainty in neutron diffraction experiments with isotopic substitution method. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Allolio C, Salas-Illanes N, Desmukh YS, Hansen MR, Sebastiani D. H-Bonding Competition and Clustering in Aqueous LiI. J Phys Chem B 2013; 117:9939-46. [DOI: 10.1021/jp4033468] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Christoph Allolio
- Department of Chemistry, Martin-Luther Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle/Saale, Germany
| | - Nora Salas-Illanes
- Department of Chemistry, Martin-Luther Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle/Saale, Germany
| | - Yogesh S. Desmukh
- Department of Chemical
Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, Eindhoven, Netherlands
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600AX Eindhoven, The Netherlands
| | - Michael Ryan Hansen
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600AX Eindhoven, The Netherlands
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Daniel Sebastiani
- Department of Chemistry, Martin-Luther Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle/Saale, Germany
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13
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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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14
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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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15
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Collins KD. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions. Biophys Chem 2012; 167:43-59. [DOI: 10.1016/j.bpc.2012.04.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 01/13/2023]
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16
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Rega N, Brancato G, Petrone A, Caruso P, Barone V. Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: the Zn(II) ion in aqueous solution as a case study. J Chem Phys 2011; 134:074504. [PMID: 21341856 DOI: 10.1063/1.3549827] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye-Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion-solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.
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Affiliation(s)
- Nadia Rega
- Dipartimento di Chimica Paolo Corradini, Universita' Federico II Napoli, Napoli, Italy.
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17
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Abstract
Modern biophysics has benefited greatly from the use of X-ray and neutron diffraction from ordered single crystals of proteins and other macromolecules to give highly detailed pictures of these molecules in the solid state. However, the most biologically relevant environments for these molecules are liquid solutions, and their liquid state properties are sensitive to details of the liquid structuring. The best experimental method for studying such structuring is also neutron diffraction, but of course, the inherent disorder of the liquid state means that these experiments cannot hope to achieve the level of informational detail available from single crystal diffraction. Nonetheless, recent advances in neutron beam intensity, beam stability, and detector sensitivity mean that it should be possible, at least in principle, to use such measurements to extract information about structuring in much more complex systems than have previously been studied. We describe a series of neutron diffraction studies of isotopically labeled molecules in aqueous solution which, when combined with results from computer simulations, can be used to extract conformational information of the hydration of the molecules themselves, essentially opening up new avenues of investigation in structural biology.
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18
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Mason PE, Neilson GW, Dempsey CE, Price DL, Saboungi ML, Brady JW. Observation of pyridine aggregation in aqueous solution using neutron scattering experiments and MD simulations. J Phys Chem B 2010; 114:5412-9. [PMID: 20369858 DOI: 10.1021/jp9097827] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neutron diffraction with isotopic substitution (NDIS) experiments have been used to examine the structuring of aqueous solutions of pyridine. A new method is described for extracting the structure factors relating to intermolecular correlations from neutron scattering experiments on liquid solutions of complex molecular species. This approach performs experiments at different concentrations and exploits the intramolecular coordination number concentration invariance (ICNCI) to separate the internal and intermolecular contributions to the total intensities. The ability of this method to deconvolute molecular and intermolecular correlations is tested and demonstrated using simulated neutron scattering results predicted from molecular dynamics simulations of aqueous solutions of the polyatomic solute pyridine in which the inter- and intramolecular terms are known. The method is then implemented using neutron scattering measurements on solutions of pyridine. The results confirm that pyridine shows a significant propensity to aggregate in solution and demonstrate the prospects for the future application of the ICNCI approach to the study of large polyatomic solutes using next-generation neutron sources and detectors.
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Affiliation(s)
- Philip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
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19
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Lambert D, Leipply D, Shiman R, Draper DE. The influence of monovalent cation size on the stability of RNA tertiary structures. J Mol Biol 2009; 390:791-804. [PMID: 19427322 PMCID: PMC2712228 DOI: 10.1016/j.jmb.2009.04.083] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/29/2009] [Accepted: 04/30/2009] [Indexed: 01/03/2023]
Abstract
Many RNA tertiary structures are stable in the presence of monovalent ions alone. To evaluate the degree to which ions at or near the surfaces of such RNAs contribute to stability, the salt-dependent stability of a variety of RNA structures was measured with each of the five group I cations. The stability of hairpin secondary structures and a pseudoknot tertiary structure are insensitive to the ion identity, but the tertiary structures of two other RNAs, an adenine riboswitch and a kissing loop complex, become more stable by 2-3 kcal/mol as ion size decreases. This "default" trend is attributed to the ability of smaller ions to approach the RNA surface more closely. The degree of cation accumulation around the kissing loop complex was also inversely proportional to ion radius, perhaps because of the presence of sterically restricted pockets that can be accessed only by smaller ions. An RNA containing the tetraloop-receptor motif shows a strong (up to approximately 3 kcal/mol) preference for Na(+) or K(+) over other group I ions, consistent with the chelation of K(+) by this motif in some crystal structures. This RNA reverts to the default dependence on ion size when a base forming part of the chelation site is mutated. Lastly, an RNA aptamer for cobinamide, which was originally selected in the presence of high concentrations of LiCl, binds ligand more strongly in the presence of Li(+) than other monovalent ions. On the basis of these trends in RNA stability with group I ion size, it is argued that two features of RNA tertiary structures may promote strong interactions with ions at or near the RNA surface: negative charge densities that are higher than that in secondary structures, and the occasional presence of chelation sites, which are electronegative pockets that selectively bind ions of an optimum size.
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Affiliation(s)
- Dominic Lambert
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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20
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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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Thomas JL, Tobias DJ, Mackerell AD. Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation. J Phys Chem B 2007; 111:12941-4. [PMID: 17958354 PMCID: PMC2568990 DOI: 10.1021/jp076501p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present letter, we directly compare neutron structure factors calculated from force field (FF)-based molecular dynamics simulations with experimental structure factors for water, methanol, and tetrahydrofuran (THF). For water, the difference in the measured structure factors is more significant than differences between the FFs. It is shown that the inclusion of electronic polarization in the force field improves the agreement with experiment for the more-polar methanol, whereas the results are comparable for the additive and polarizable FF models of the less-polar THF. The data presented here confirm that comparing the calculated scattering profiles from FF-based MD simulations to measured neutron structure factors is a promising method for FF validation and development.
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Affiliation(s)
- Jennie L Thomas
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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22
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Adya AK, Kalugin ON, Howells WS. Dynamics and structure of nickel chloride-methanol solutions: quasi-elastic neutron scattering and molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:415120. [PMID: 28192332 DOI: 10.1088/0953-8984/19/41/415120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The high-resolution quasi-elastic neutron scattering (QENS) technique has been applied to study the translational diffusion of methanol protons in pure methanol (MeOH) at 223 and 297 K, and in 0.3 and 1.3 molal non-aqueous electrolyte solutions (NAESs) of NiCl2 in methanol at 297 K. Molecular dynamics (MD) simulations, in conjunction with the present QENS results and our previously published structural results obtained by neutron diffraction isotopic substitution (NDIS) experiments, have been carried out in the NVT ensemble to explore the particle dynamics and microscopic structures of the experimentally investigated systems. The simulated structure of the ∼1.35 molal NiCl2-MeOH NAES has been compared with the structures of Ni2+ and Cl- coordination shells in ∼1.4 molal NAES obtained earlier by the NDIS technique.
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Affiliation(s)
- Ashok K Adya
- Condensed Matter Group and BIONTHEBIO- and Nano-Technologies for Health and Environment. Centre, School of Contemporary Sciences, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
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23
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Collins KD, Neilson GW, Enderby JE. Ions in water: Characterizing the forces that control chemical processes and biological structure. Biophys Chem 2007; 128:95-104. [PMID: 17418479 DOI: 10.1016/j.bpc.2007.03.009] [Citation(s) in RCA: 441] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 03/09/2007] [Accepted: 03/10/2007] [Indexed: 11/29/2022]
Abstract
The continuum electrostatics model of Debye and Hückel [P. Debye and E. Hückel, On the theory of electrolytes. I. Freezing point depression and related phenomena., Phys. Z. 24 (1923) 185-206.] and its successors utilize a macroscopic dielectric constant and assume that all interactions involving ions are strictly electrostatic, implying that simple ions in water generate electric fields strong enough to orient water dipoles over long distances. However, solution neutron and X-ray diffraction indicate that even di- and tri-valent ions do not significantly alter the density or orientation of water more than two water molecules (5 A) away. Therefore the long range electric fields (generated by simple ions) which can be detected by various resonance techniques such as fluorescence resonance energy transfer over distances of 30 A (about 11 water diameters) or more must be weak relative to the strength of water-water interactions. Two different techniques indicate that the interaction of water with anions is by an approximately linear hydrogen bond, suggesting that the dominant forces on ions in water are short range forces of a chemical nature.
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Affiliation(s)
- Kim D Collins
- Center of Marine Biotechnology and Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201, USA.
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24
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Carrera F, Torrico F, Richens DT, Muñoz-Paez A, Martínez JM, Pappalardo RR, Marcos ES. Combined Experimental and Theoretical Approach to the Study of Structure and Dynamics of the Most Inert Aqua Ion [Ir(H2O)6]3+ in Aqueous Solution. J Phys Chem B 2007; 111:8223-33. [PMID: 17583938 DOI: 10.1021/jp0713716] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantitative determination of the hydration structure of hexaaquairidium(III), [Ir(H2O)6]3+, in aqueous solution, the most inert aqua ion known, has been achieved for the first time by a combined experimental-theoretical approach employing X-ray absorption spectroscopy and molecular dynamics (MD) simulations. The Ir LIII-edge extended X-ray absorption fine structure (EXAFS) spectrum and LI-, LII-, and LIII-edge X-ray absorption near-edge structure (XANES) spectra of three concentrations of [Ir(H2O)6]3+ in perchloric acid media were measured. To carry out classical MD simulations of the aqua ion in water, a new set of first-principles Ir-H2O intermolecular potentials, based on the hydrated ion concept, has been developed. Structural, dynamics, and energetic properties have been obtained from the analysis of the statistical trajectories generated. The Ir-O radial distribution function shows two well-defined peaks at 2.04 +/- 0.01 and 4.05 +/- 0.05 A corresponding to the first and second hydration shell, respectively; the fundamental frequencies for the aqua ion in water are well reproduced by the MD simulation, and its dynamic properties are similar to the experimental values corresponding to other hexahydrated trivalent ions. Particular attention has been devoted to the experimental determination of the second hydration shell. It has been found that contrarily to what expected on the basis of the inertness of the Ir3+ aquaion, the detection of the second hydration shell by EXAFS for this cation is more difficult than for others less inert aqua ions such as Cr3+ or Rh3+. But when combined with MD simulations it is possible to confirm the coordination distance for this shell at 4.1 +/- 0.1 A. In addition, the computation of LI, LII and LIII XANES spectra were carried out using the structural information obtained from MD. These computations allowed the assignment of special features of the spectra to the second hydration shell on a quantitative basis. Therefore, interestingly XANES spectra have given a stronger support to the second hydration shell than EXAFS. The fit of the LIII-edge EXAFS gives an accurate description of the first hydration shell structure in aqueous solution. The value for Ir-O first shell is 2.04 +/- 0.01 A. The statistical information available with the MD results has allowed the analysis of the standard deviation associated with the computation of the XANES spectrum. It is shown that the standard deviation increases with the number of hydration shells and this increase is nonuniform along the average spectrum.
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Affiliation(s)
- Flora Carrera
- Departamento de Química InorgAnica, ICMSE, CSIC, Universidad de Sevilla, 41012 Sevilla, Spain
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25
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Chialvo AA, Simonson JM. Ion pairing and counterion condensation in aqueous electrolyte and polyelectrolyte solutions: Insights from molecular simulation. J Mol Liq 2007. [DOI: 10.1016/j.molliq.2006.12.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Lu GW, Li YF, Sun W, Li CX. Molecular Dynamics Simulation of Hydration Structure of KNO3Electrolyte Solution. CHINESE J CHEM PHYS 2007. [DOI: 10.1360/cjcp2007.20(1).22.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Mason PE, Neilson GW, Enderby JE, Saboungi ML, Cuello G, Brady JW. Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose. J Chem Phys 2006; 125:224505. [PMID: 17176147 DOI: 10.1063/1.2393237] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The techniques of neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulations have been used to examine the rotational conformation of the exocyclic hydroxymethyl group of D-glucopyranose. First order H/D NDIS experiments were performed on the H6 position in 3m aqueous glucose solutions where the average coherent scattering length of the exchangeable hydrogen atoms was zero (i.e., all correlations between exchangeable hydrogen atoms and other atoms cancel and thus are not present in the scattering data). This H6 experimental result suggests that no single conformation for the C4-C5-C6-O6 dihedral reproduces the observed scattering data well, but that a mixture of the gg and gt conformations, which has been suggested by NMR experiments, gives a reasonable agreement between the MD and experimental data.
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Affiliation(s)
- Philip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
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28
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Ansell S, Barnes AC, Mason PE, Neilson GW, Ramos S. X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions. Biophys Chem 2006; 124:171-9. [PMID: 16815625 DOI: 10.1016/j.bpc.2006.04.018] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 04/28/2006] [Accepted: 04/29/2006] [Indexed: 11/23/2022]
Abstract
The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.
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Affiliation(s)
- S Ansell
- ISIS Division, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
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29
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Chialvo AA, Simonson JM. Ion association in aqueous LiCl solutions at high concentration: Predicted results via molecular simulation. J Chem Phys 2006; 124:154509. [PMID: 16674244 DOI: 10.1063/1.2186641] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We perform molecular dynamics simulations to study the ionic solvation and association behavior in concentrated aqueous LiCl solutions at ambient conditions, including consideration of expected signatures of ion pairing that might be found in neutron diffraction experiments with isotopic substitution. The ten possible pair radial distribution functions that define the microstructure of the systems are determined and used to assess the first-order difference of the neutron-weighted correlation functions for these solutions in heavy and null water. Then, both sets of correlation functions are applied to the interpretation of the ion's local environment in terms of the location of the relevant peaks and the penetration of ions into the counterion solvation shells as a signature of ion-pair formation. Finally, we illustrate how first-order difference experiments involving null and heavy water might be used to assess the magnitude of the M(v+) - X(v-) ion-pair formation for a salt M(v+)X(n) v- in an aqueous solution, provided the significant experimental challenges in these studies could be overcome.
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Affiliation(s)
- Ariel A Chialvo
- Chemical Sciences Division, Aqueous Chemistry and Geochemistry Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, USA.
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30
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Mudi A, Chakravarty C. Effect of Ionic Solutes on the Hydrogen Bond Network Dynamics of Water: Power Spectral Analysis of Aqueous NaCl Solutions. J Phys Chem B 2006; 110:8422-31. [PMID: 16623528 DOI: 10.1021/jp056003l] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To understand the modifications of the hydrogen bond network of water by ionic solutes, power spectra as well as static distributions of the potential energies of tagged solvent molecules and solute ions have been computed from molecular dynamics simulations of aqueous NaCl solutions. The key power spectral features of interest are the presence of high-frequency peaks due to localized vibrational modes, the existence of a multiple time scale or 1/falpha frequency regime characteristic of networked liquids, and the frequency of crossover from 1/falpha type behavior to white noise. Hydrophilic solutes, such as the sodium cation and the chloride anion, are shown to mirror the multiple time scale behavior of the hydrogen bond network fluctuations, unlike hydrophobic solutes which display essentially white noise spectra. While the power spectra associated with tagged H2O molecules are not very sensitive to concentration in the intermediate frequency 1/falpha regime, the crossover to white noise is shifted to lower frequencies on going from pure solvent to aqueous alkali halide solutions. This suggests that new and relatively slow time scales enter the picture, possibly associated with processes such as migration of water molecules from the hydration shell to the bulk or conversion of contact ion pairs into solvent-separated ion pairs which translate into variations in equilibrium transport properties of salt solutions with concentration. For anions, cations, and solvent molecules, the trends in the alpha exponents of the multiple time scale region and the self-diffusivities are found to be strongly correlated.
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Affiliation(s)
- Anirban Mudi
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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31
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Mason PE, Neilson GW, Enderby JE, Saboungi ML, Brady JW. Determination of a Hydroxyl Conformation in Aqueous Xylose Using Neutron Scattering and Molecular Dynamics. J Phys Chem B 2006; 110:2981-3. [PMID: 16494297 DOI: 10.1021/jp055658j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, it was shown using structural neutron diffraction with isotopic substitutions (NDIS) measurements, combined with molecular dynamics simulations, that in an aqueous solution of D-xylose the hydroxyl group on the C4 position does not significantly occupy the position trans to the H4 atom. Here, a similar combination of NDIS and MD studies is described which uses D-xylose deuterated at the C5 position to further characterize this hydroxyl conformation as being trans to the C5 atom, as predicted by constrained MD simulations, confirming the previous study.
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32
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Egorov AV, Komolkin AV, Lyubartsev AP, Laaksonen A. First and Second Hydration Shell of Ni2+ Studied by Molecular Dynamics Simulations. Theor Chem Acc 2006. [DOI: 10.1007/s00214-005-0050-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Lu GW, Li * CX, Wang WC, Wang ZH. A Monte Carlo simulation on structure and thermodynamics of potassium nitrate electrolyte solution. Mol Phys 2005. [DOI: 10.1080/00268970410001683834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Badyal YS, Barnes AC, Cuello GJ, Simonson JM. Understanding the Effects of Concentration on the Solvation Structure of Ca2+ in Aqueous Solution. II: Insights into Longer Range Order from Neutron Diffraction Isotope Substitution. J Phys Chem A 2004. [DOI: 10.1021/jp046476c] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yaspal S. Badyal
- Aqueous Chemistry and Geochemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, H.H. Wills Physical Laboratory, Bristol University, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Institut Laue-Langevin, 6, rue Jules Horowitz BP 156-38042 Grenoble Cedex 9, France
| | - Adrian C. Barnes
- Aqueous Chemistry and Geochemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, H.H. Wills Physical Laboratory, Bristol University, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Institut Laue-Langevin, 6, rue Jules Horowitz BP 156-38042 Grenoble Cedex 9, France
| | - Gabriel J. Cuello
- Aqueous Chemistry and Geochemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, H.H. Wills Physical Laboratory, Bristol University, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Institut Laue-Langevin, 6, rue Jules Horowitz BP 156-38042 Grenoble Cedex 9, France
| | - John M. Simonson
- Aqueous Chemistry and Geochemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, H.H. Wills Physical Laboratory, Bristol University, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Institut Laue-Langevin, 6, rue Jules Horowitz BP 156-38042 Grenoble Cedex 9, France
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35
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Mason PE, Neilson GW, Enderby JE, Saboungi ML, Dempsey CE, MacKerell AD, Brady JW. The Structure of Aqueous Guanidinium Chloride Solutions. J Am Chem Soc 2004; 126:11462-70. [PMID: 15366892 DOI: 10.1021/ja040034x] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described. The simulations and experiments were carried out at a concentration of 3 m at room temperature, allowing for an examination of any propensity for ion association in a realistic solution environment. The simulations satisfactorily reproduced the principal features of the neutron scattering and indicate a bimodal hydration of the guanidinium ions, with the N-H groups making well-ordered hydrogen bonds in the molecular plane, but with the planar faces relatively deficient in interactions with water. The most striking feature of these solutions is the rich ion-ion ordering observed around the guanidinium ion in the simulations. The marked tendency of the guanidinium ions to stack parallel to their water-deficient surfaces indicates that the efficiency of this ion as a denaturant is due to its ability to simultaneously interact favorably with both water and hydrophobic side chains of proteins.
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Affiliation(s)
- Philip E Mason
- Contribution from the Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
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36
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Chialvo A, Simonson J. The effect of salt concentration on the structure of water in CaCl2 aqueous solutions. J Mol Liq 2004. [DOI: 10.1016/j.molliq.2003.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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38
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Chialvo AA, Simonson JM. The structure of CaCl2 aqueous solutions over a wide range of concentration. Interpretation of diffraction experiments via molecular simulation. J Chem Phys 2003. [DOI: 10.1063/1.1610443] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [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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Mason PE, Neilson GW, Dempsey CE, Barnes AC, Cruickshank JM. The hydration structure of guanidinium and thiocyanate ions: implications for protein stability in aqueous solution. Proc Natl Acad Sci U S A 2003; 100:4557-61. [PMID: 12684536 PMCID: PMC404697 DOI: 10.1073/pnas.0735920100] [Citation(s) in RCA: 276] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neutron diffraction experiments were carried out on aqueous solutions containing either guanidinium or thiocyanate ions. The first-order difference method of neutron diffraction and isotopic substitution was applied, and the hydration structures of two of nature's strongest denaturant ions were determined. Each ion is shown to interact weakly with water: Guanidinium has no recognizable hydration shell and is one of the most weakly hydrated cations yet characterized. Hydration of thiocyanate is characterized by a low coordination number involving around one hydrogen-bonded water molecule and approximately two water molecules weakly interacting through "hydration bonds." The weak hydration of these denaturant ions strongly supports suggestions that a major contribution to the denaturant effect is the preferential interaction of the denaturant with the protein surface. By contrast, solute species such as many sugars and related polyols that stabilize proteins are strongly hydrated and are thus preferentially retained in the bulk solvent and excluded from the protein surface.
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Affiliation(s)
- P E Mason
- Department of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
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40
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Ramos S, Neilson GW, Barnes AC, Capitán MJ. Anomalous x-ray diffraction studies of Sr2+ hydration in aqueous solution. J Chem Phys 2003. [DOI: 10.1063/1.1555633] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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CHIALVO ARIELA, SIMONSON JMICHAEL. The structure of concentrated NiCl2aqueous solutions: what is molecular simulation revealing about the neutron scattering methodologies? Mol Phys 2002. [DOI: 10.1080/00268970110118231] [Citation(s) in RCA: 12] [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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42
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Eckert J, Draznieks CM, Cheetham AK. Direct observation of host-guest hydrogen bonding in the zeolite NaY/chloroform system by neutron scattering. J Am Chem Soc 2002; 124:170-1. [PMID: 11782158 DOI: 10.1021/ja011740q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The differential H pair distribution function obtained from neutron scattering contrast measurements on hydrogenous and deuterated chloroform adsorbed into zeolite NaY (two molecules per supercage) reveals direct evidence for hydrogen bonding between hydrogen atoms on the sorbate molecule and oxygen atoms of the zeolite framework. A vector between the hydrogen and framework Si/Al atoms is also observed. The results confirm the conclusions drawn from previous vibrational spectroscopy and computer modeling studies.
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Affiliation(s)
- Juergen Eckert
- Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
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43
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Mark P, Nilsson L. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K. J Phys Chem A 2001. [DOI: 10.1021/jp003020w] [Citation(s) in RCA: 1752] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Ramos S, Neilson GW, Barnes AC, Mazuelas A. An Anomalous X-ray Diffraction Study of Yttrium(III) Hydration. J Phys Chem B 2001. [DOI: 10.1021/jp003869c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. Ramos
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 4ED, United Kingdom and European Synchrotron Radiation Facility, Avenue des Martyrs, F-38043, Grenoble, France
| | - G. W. Neilson
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 4ED, United Kingdom and European Synchrotron Radiation Facility, Avenue des Martyrs, F-38043, Grenoble, France
| | - A. C. Barnes
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 4ED, United Kingdom and European Synchrotron Radiation Facility, Avenue des Martyrs, F-38043, Grenoble, France
| | - A. Mazuelas
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 4ED, United Kingdom and European Synchrotron Radiation Facility, Avenue des Martyrs, F-38043, Grenoble, France
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45
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Adya AK, Kalugin ON. Microscopic structure of Cl− coordination shell in NiCl2 methanol solution: A neutron diffraction study. J Chem Phys 2000. [DOI: 10.1063/1.1288689] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Danielewicz-Ferchmin I, Ferchmin AR. Hydration of ions at various temperatures: The role of electrostriction. J Chem Phys 1998. [DOI: 10.1063/1.476807] [Citation(s) in RCA: 14] [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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50
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Liu Q, Brady JW. Model Dependence of the Anisotropic Structuring of Solvent Water around Sugars in Molecular Dynamics Simulations. J Phys Chem B 1997. [DOI: 10.1021/jp962979+] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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