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Clavaguéra C, Thaunay F, Ohanessian G. Manifolds of low energy structures for a magic number of hydrated sulfate: SO 42-(H 2O) 24. Phys Chem Chem Phys 2021; 23:24428-24438. [PMID: 34693943 DOI: 10.1039/d1cp03123f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low energy structures of SO42-(H2O)24 have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO42-(H2O)24 does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.
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Affiliation(s)
- Carine Clavaguéra
- Institut de Chimie Physique, Université Paris-Saclay - CNRS, UMR 8000, 91405 Orsay, France.
| | - Florian Thaunay
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
| | - Gilles Ohanessian
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
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2
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Hydration of the pertechnetate anion. DFT study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abbott HE, Hey JC, Britton MM, Johnston RL. Effects of Hydration on the Conformational Behavior of Flexible Molecules with Two Charge Centers. J Phys Chem A 2020; 124:5323-5330. [PMID: 32501011 DOI: 10.1021/acs.jpca.0c02004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydration behavior of alkyl-diammonium di-cations and alkyl-dicarboxylate di-anions, of varying alkyl chain length, was examined using basin-hopping (BH) global optimization techniques. For every di-ion investigated, a conformational transition from linear to folded is observed at a critical hydration number, n*, specific to each di-ion. A stepwise hydration study has been undertaken for alkyl-dicarboxylate di-anions in finite water clusters containing 1-12 water molecules, and low-energy structures have been examined for larger water clusters. An even number of carbons in the alkyl chain gives rise to more stable conformations in unhydrated, implicitly solvated, and explicitly solvated conditions. This work provides valuable information on how the hydration of ammonium and carboxylate ions influence larger biomolecules' conformations.
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Affiliation(s)
- Helen E Abbott
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - John C Hey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Melanie M Britton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Roy L Johnston
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Karimova NV, Chen J, Gord JR, Staudt S, Bertram TH, Nathanson GM, Gerber RB. S N2 Reactions of N 2O 5 with Ions in Water: Microscopic Mechanisms, Intermediates, and Products. J Phys Chem A 2020; 124:711-720. [PMID: 31880456 DOI: 10.1021/acs.jpca.9b09095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Reactions of dinitrogen pentoxide (N2O5) greatly affect the concentrations of NO3, ozone, OH radicals, methane, and more. In this work, we employ ab initio molecular dynamics and other tools of computational chemistry to explore reactions of N2O5 with anions hydrated by 12 water molecules to shed light on this important class of reactions. The ions investigated are Cl-, SO42-, ClO4-, and RCOO- (R = H, CH3, C2H5). The following main results are obtained: (i) all the reactions take place by an SN2-type mechanism, with a transition state that involves a contact ion pair (NO2+NO3-) that interacts strongly with water molecules. (ii) Reactions of a solvent-separated nitronium ion (NO2+) are not observed in any of the cases. (iii) An explanation is provided for the suppression of ClNO2 formation from N2O5 reacting with salty water when sulfate or acetate ions are present, as found in recent experiments. (iv) Formation of novel intermediate species, such as (SO4NO2-) and RCOONO2, in these reactions is predicted. The results suggest atomistic-level mechanisms for the reactions studied and may be useful for the development of improved modeling of reaction kinetics in aerosol particles.
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Affiliation(s)
- Natalia V Karimova
- Department of Chemistry , University of California, Irvine , Irvine 92697 , California , United States
| | - James Chen
- Department of Chemistry , University of California, Irvine , Irvine 92697 , California , United States
| | - Joseph R Gord
- Department of Chemistry , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
| | - Sean Staudt
- Department of Chemistry , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
| | - Timothy H Bertram
- Department of Chemistry , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
| | - Gilbert M Nathanson
- Department of Chemistry , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
| | - R Benny Gerber
- Department of Chemistry , University of California, Irvine , Irvine 92697 , California , United States.,Institute of Chemistry and Fritz Haber Research Center , Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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Karimova N, McCaslin LM, Gerber RB. Ion reactions in atmospherically-relevant clusters: mechanisms, dynamics and spectroscopic signatures. Faraday Discuss 2019; 217:342-360. [DOI: 10.1039/c8fd00230d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Exploring models of reactions of N2O4 with ions in water in order to provide molecular-level understanding of these processes.
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Affiliation(s)
| | - Laura M. McCaslin
- Institute of Chemistry
- Fritz Haber Research Center
- Hebrew University of Jerusalem
- Jerusalem 91904
- Israel
| | - R. Benny Gerber
- Department of Chemistry
- University of California
- Irvine
- USA
- Institute of Chemistry
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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Kelly JT, Mayer M, Kennedy AC, Schemel C, Asmis KR. Probing the propensity of perchlorate anions for surface solvation by infrared photodissociation spectroscopy. J Chem Phys 2018; 148:222840. [DOI: 10.1063/1.5028416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- John T. Kelly
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, D-04103 Leipzig, Germany
| | - Martin Mayer
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, D-04103 Leipzig, Germany
| | - Adam C. Kennedy
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, D-04103 Leipzig, Germany
| | - Christian Schemel
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, D-04103 Leipzig, Germany
| | - Knut R. Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, D-04103 Leipzig, Germany
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Experimentally quantifying anion polarizability at the air/water interface. Nat Commun 2018; 9:1313. [PMID: 29615604 PMCID: PMC5882839 DOI: 10.1038/s41467-018-03598-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/19/2018] [Indexed: 12/22/2022] Open
Abstract
The adsorption of large, polarizable anions from aqueous solution on the air/water interface controls important atmospheric chemistry and is thought to resemble anion adsorption at hydrophobic interfaces generally. While the favourability of adsorption of such ions is clear, quantifying adsorption thermodynamics has proven challenging because it requires accurate description of the structure of the anion and its solvation shell at the interface. In principle anion polarizability offers a structural window, but to the best of our knowledge there has so far been no experimental technique that allowed its characterization with interfacial specificity. Here, we meet this challenge using interface-specific vibrational spectroscopy of Cl–O vibrations of the \documentclass[12pt]{minimal}
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\begin{document}$${\mathrm{ClO}}_4^ -$$\end{document}ClO4- anion at the air/water interface and report that the interface breaks the symmetry of the anion, the anisotropy of \documentclass[12pt]{minimal}
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\begin{document}$${\mathrm{ClO}}_4^ -$$\end{document}ClO4-’s polarizability tensor is more than two times larger than in bulk water and concentration dependent, and concentration-dependent polarizability changes are consistent with correlated changes in surface tension. Understanding anion-specific interactions with hydrophobic interfaces is challenging due to an absence of local structural probes. Here, the authors experimentally quantify the anisotropy of perchlorate’s polarizability at the air/water interface, a window into anion and solvation shell structure.
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Hey JC, Doyle EJ, Chen Y, Johnston RL. Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2018; 376:rsta.2017.0154. [PMID: 29431682 PMCID: PMC5805918 DOI: 10.1098/rsta.2017.0154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
We present putative global minima for the micro-hydrated sulfite SO32-(H2O) N and chlorate ClO3-(H2O) N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'.
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Affiliation(s)
- John C Hey
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Emily J Doyle
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Yuting Chen
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Roy L Johnston
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
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11
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Luo YH, Wang JW, Li YJ, Chen C, An PJ, Wang SL, You CQ, Sun BW. Selective separation of aqueous sulphate anions via crystallization of sulphate–water clusters. CrystEngComm 2017. [DOI: 10.1039/c7ce00693d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Korchagina KA, Simon A, Rapacioli M, Spiegelman F, Cuny J. Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach. J Phys Chem A 2016; 120:9089-9100. [DOI: 10.1021/acs.jpca.6b08251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kseniia A. Korchagina
- Laboratoire de Chimie et
Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Aude Simon
- Laboratoire de Chimie et
Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et
Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Fernand Spiegelman
- Laboratoire de Chimie et
Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et
Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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Bye JW, Baxter NJ, Hounslow AM, Falconer R, Williamson MP. Molecular Mechanism for the Hofmeister Effect Derived from NMR and DSC Measurements on Barnase. ACS OMEGA 2016; 1:669-679. [PMID: 31457155 PMCID: PMC6640789 DOI: 10.1021/acsomega.6b00223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/10/2016] [Indexed: 05/27/2023]
Abstract
The effects of sodium thiocyanate, sodium chloride, and sodium sulfate on the ribonuclease barnase were studied using differential scanning calorimetry (DSC) and NMR. Both measurements reveal specific and saturable binding at low anion concentrations (up to 250 mM), which produces localized conformational and energetic effects that are unrelated to the Hofmeister series. The binding of sulfate slows intramolecular motions, as revealed by peak broadening in 13C heteronuclear single quantum coherence spectroscopy. None of the anions shows significant binding to hydrophobic groups. Above 250 mM, the DSC results are consistent with the expected Hofmeister effects in that the chaotropic anion thiocyanate destabilizes barnase. In this higher concentration range, the anions have approximately linear effects on protein NMR chemical shifts, with no evidence for direct interaction of the anions with the protein surface. We conclude that the effects of the anions on barnase are mediated by solvent interactions. The results are not consistent with the predictions of the preferential interaction, preferential hydration, and excluded volume models commonly used to describe Hofmeister effects. Instead, they suggest that the Hofmeister anion effects on both stability and solubility of barnase are due to the way in which the protein interacts with water molecules, and in particular with water dipoles, which are more ordered around sulfate anions and less ordered around thiocyanate anions.
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Affiliation(s)
- Jordan W. Bye
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Robert
J. Falconer
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
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