1
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Fromsejer R, Jensen ML, Zacate MO, Karner VL, Pecoraro VL, Hemmingsen L. Molecular Rotational Correlation Times and Nanoviscosity Determined by 111m Cd Perturbed Angular Correlation (PAC) of γ-rays Spectroscopy. Chemistry 2023; 29:e202203084. [PMID: 36453728 PMCID: PMC10108235 DOI: 10.1002/chem.202203084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022]
Abstract
The nanoviscosity experienced by molecules in solution may be determined through measurement of the molecular rotational correlation time, τc , for example, by fluorescence and NMR spectroscopy. With this work, we apply PAC spectroscopy to determine the rate of rotational diffusion, λ=1/τc , of a de novo designed protein, TRIL12AL16C, in solutions with viscosities, ξ, from 1.7 to 88 mPa⋅s. TRIL12AL16C was selected as molecular probe because it exhibits minimal effects due to intramolecular dynamics and static line broadening, allowing for exclusive elucidation of molecular rotational diffusion. Diffusion rates determined by PAC data agree well with literature data from fluorescence and NMR spectroscopy, and scales linearly with 1/ξ in agreement with the Stokes-Einstein-Debye model. PAC experiments require only trace amounts (∼1011 ) of probe nuclei and can be conducted over a broad range of sample temperatures and pressures. Moreover, most materials are relatively transparent to γ-rays. Thus, PAC spectroscopy could find applications under circumstances where conventional techniques cannot be applied, spanning from the physics of liquids to in-vivo biochemistry.
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Affiliation(s)
- Rasmus Fromsejer
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100KøbenhavnDenmark
| | - Marianne L. Jensen
- Niels Bohr InstituteUniversity of CopenhagenBlegdamsvej 172100KøbenhavnDenmark
| | - Matthew O. Zacate
- Department of PhysicsGeology and Engineering TechnologyNorthern Kentucky UniversityHighland HeightsKY 41099-1900USA
| | | | - Vincent L. Pecoraro
- Department of ChemistryWillard H. Dow LaboratoriesUniversity of Michigan930N. University Ave.Ann ArborMI 48109-1055USA
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100KøbenhavnDenmark
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2
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Wang K. GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability. Brief Bioinform 2023; 24:6987821. [PMID: 36642411 DOI: 10.1093/bib/bbac620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 01/17/2023] Open
Abstract
Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a docking method for metalloproteins based on geometric probability (GPDOCK) with unprecedented accuracy. The docking tests of 10 common metal ions with 9360 metalloprotein-ligand complexes demonstrate that GPDOCK has an accuracy of 94.3% in predicting binding pose. What is more, it can accurately realize the docking of metalloproteins with ligand when one or two water molecules are engaged in the metal ion coordination. Since GPDOCK only depends on the three-dimensional structure of metalloprotein and ligand, structure-based machine learning model is employed for the scoring of binding poses, which significantly improves computational efficiency. The proposed docking strategy can be an effective and efficient tool for drug design and further study of binding mechanism of metalloproteins. The manual of GPDOCK and the code for the logistical regression model used to re-rank the docking results are available at https://github.com/wangkai-zhku/GPDOCK.git.
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Affiliation(s)
- Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China.,Abinitio Technology Company, Ltd, Guangzhou 510640, P. R. China
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3
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Grotz KK, Cruz-León S, Schwierz N. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties. J Chem Theory Comput 2021; 17:2530-2540. [PMID: 33720710 PMCID: PMC8047801 DOI: 10.1021/acs.jctc.0c01281] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 12/31/2022]
Abstract
Magnesium ions play an essential role in many vital processes. To correctly describe their interactions in molecular dynamics simulations, an accurate parametrization is crucial. Despite the importance and considerable scientific effort, current force fields based on the commonly used 12-6 Lennard-Jones interaction potential fail to reproduce a variety of experimental solution properties. In particular, no parametrization exists so far that simultaneously reproduces the solvation free energy and the distance to the water oxygens in the first hydration shell. Moreover, current Mg2+ force fields significantly underestimate the rate of water exchange leading to unrealistically slow exchange kinetics. In order to make progress in the development of improved models, we systematically optimize the Mg2+ parameters in combination with the TIP3P water model in a much larger parameter space than previously done. The results show that a long-ranged interaction potential and modified Lorentz-Berthelot combination rules allow us to accurately reproduce multiple experimental properties including the solvation free energy, the distances to the oxygens of the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, the self-diffusion coefficient, and the binding affinity to the phosphate oxygen of RNA. Matching this broad range of thermodynamic properties, we present two sets of optimal parameters: MicroMg yields water exchange on the microsecond timescale in agreement with experiments. NanoMg yields water exchange on the nanosecond timescale facilitating the direct observation of ion-binding events. As shown for the example of the add A-riboswitch, the optimized parameters correctly reproduce the structure of specifically bound ions and permit the de novo prediction of Mg2+-binding sites in biomolecular simulations.
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Affiliation(s)
- Kara K. Grotz
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Sergio Cruz-León
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
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4
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Schwierz N. Kinetic pathways of water exchange in the first hydration shell of magnesium. J Chem Phys 2020; 152:224106. [PMID: 32534547 DOI: 10.1063/1.5144258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg2+ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg2+, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations.
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Affiliation(s)
- Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt Am Main, Germany
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5
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Laureanti JA, Ginovska B, Buchko GW, Schenter GK, Hebert M, Zadvornyy OA, Peters JW, Shaw WJ. A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret Hebert
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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6
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Abstract
The highly toxic cadmium ion can cause destructive hazards to living systems by nonspecific and tight binding on functional macromolecules. However, most of the developed cadmium detoxification systems are not sufficient to recognize or detoxify cadmium ions, specifically due to the similar coordination behavior of heavy metal ions in thiolate-rich sites. Here we report that the ultraspecific cadmium regulator CadR has evolved 2 distinct types of functional recognition sites rather than a mono-type thiolate-rich site to achieve outstanding selectivity. The thiolate-rich site I and the adjacent histidine-rich recognition site II are highly associated with transcription activation. This cooperative binding mechanism could improve our understanding of the relationship between the structural dynamics and biological function of metalloregulators. Detoxification of the highly toxic cadmium element is essential for the survival of living organisms. Pseudomonas putida CadR, a MerR family transcriptional regulator, has been reported to exhibit an ultraspecific response to the cadmium ion. Our crystallographic and spectroscopic studies reveal that the extra cadmium selectivity of CadR is mediated by the unexpected cooperation of thiolate-rich site I and histidine-rich site II. Cadmium binding in site I mediates the reorientation of protein domains and facilitates the assembly of site II. Subsequently, site II bridge-links 2 DNA binding domains through ligands His140/His145 in the C-terminal histidine-rich tail. With dynamic transit between 2 conformational states, this bridge could stabilize the regulator into an optimal conformation that is critical for enhancing the transcriptional activity of the cadmium detoxification system. Our results provide dynamic insight into how nature utilizes the unique cooperative binding mechanism in multisite proteins to recognize cadmium ions specifically.
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Ruckthong L, Stuckey JA, Pecoraro VL. How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation. Chemistry 2019; 25:6773-6787. [PMID: 30861211 PMCID: PMC6510599 DOI: 10.1002/chem.201806040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 11/06/2022]
Abstract
A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as HgII , PbII , and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that CdII forms three-, four- or five-coordinate CdII S3 (OH2 )x (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating CdII S3 (OH2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdII S3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding CdII S3 , whereas d-Leu below opens more space, allowing for equal CdII S3 (OH2 ) and CdII S3 (OH2 )2 . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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8
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Remsing RC, Klein ML. Exponential Scaling of Water Exchange Rates with Ion Interaction Strength from the Perspective of Dynamic Facilitation Theory. J Phys Chem A 2019; 123:1077-1084. [PMID: 30609371 DOI: 10.1021/acs.jpca.8b09667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Richard C. Remsing
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Michael L. Klein
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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9
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Application of Heteronuclear NMR Spectroscopy to Bioinorganic and Medicinal Chemistry ☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2018. [PMCID: PMC7157447 DOI: 10.1016/b978-0-12-409547-2.10947-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Chakraborty S, Pallada S, Pedersen JT, Jancso A, Correia JG, Hemmingsen L. Nanosecond Dynamics at Protein Metal Sites: An Application of Perturbed Angular Correlation (PAC) of γ-Rays Spectroscopy. Acc Chem Res 2017; 50:2225-2232. [PMID: 28832106 DOI: 10.1021/acs.accounts.7b00219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloproteins are essential to numerous reactions in nature, and constitute approximately one-third of all known proteins. Molecular dynamics of proteins has been elucidated with great success both by experimental and theoretical methods, revealing atomic level details of function involving the organic constituents on a broad spectrum of time scales. However, the characterization of dynamics at biomolecular metal sites on nanosecond time scales is scarce in the literature. The aqua ions of many biologically relevant metal ions exhibit exchange of water molecules on the nanosecond time scale or faster, often defining their reactivity in aqueous solution, and this is presumably also a relevant time scale for the making and breaking of coordination bonds between metal ions and ligands at protein metal sites. Ligand exchange dynamics is critical for a variety of elementary steps of reactions in metallobiochemistry, for example, association and dissociation of metal bound water, association of substrate and dissociation of product in the catalytic cycle of metalloenzymes, at regulatory metal sites which require binding and dissociation of metal ions, as well as in the transport of metal ions across cell membranes or between proteins involved in metal ion homeostasis. In Perturbed Angular Correlation of γ-rays (PAC) spectroscopy, the correlation in time and space of two γ-rays emitted successively in a nuclear decay is recorded, reflecting the hyperfine interactions of the PAC probe nucleus with the surroundings. This allows for characterization of molecular and electronic structure as well as nanosecond dynamics at the PAC probe binding site. Herein, selected examples describing the application of PAC spectroscopy in probing the dynamics at protein metal sites are presented, including (1) exchange of Cd2+ bound water in de novo designed synthetic proteins, and the effect of remote mutations on metal site dynamics; (2) dynamics at the β-lactamase active site, where the metal ion appears to jump between the two adjacent sites; (3) structural relaxation in small blue copper proteins upon 111Ag+ to 111Cd2+ transformation in radioactive nuclear decay; (4) metal ion transfer between two HAH1 proteins with change in coordination number; and (5) metal ion sensor proteins with two coexisting metal site structures. With this Account, we hope to make our modest contribution to the field and perhaps spur additional interest in dynamics at protein metal sites, which we consider to be severely underexplored. Relatively little is known about detailed atomic motions at metal sites, for example, how ligand exchange processes affect protein function, and how the amino acid composition of the protein may control this facet of metal site characteristics. We also aim to provide the reader with a qualitative impression of the possibilities offered by PAC spectroscopy in bioinorganic chemistry, especially when elucidating dynamics at protein metal sites, and finally present data that may serve as benchmarks on a relevant time scale for development and tests of theoretical molecular dynamics methods applied to biomolecular metal sites.
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Affiliation(s)
- Saumen Chakraborty
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Stavroula Pallada
- ISOLDE/CERN, PH
Div, CH-1211 Geneve
23, Switzerland
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Jeppe T. Pedersen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Attila Jancso
- Department
of Inorganic and Analytical Chemistry, University of Szeged, Dóm
tér 7, H-6720 Szeged, Hungary
| | - Joao G. Correia
- ISOLDE/CERN, PH
Div, CH-1211 Geneve
23, Switzerland
- Centro
de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela, Portugal
| | - Lars Hemmingsen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
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11
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Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils. Chemistry 2017; 23:8232-8243. [PMID: 28384393 DOI: 10.1002/chem.201700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/31/2022]
Abstract
Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of ZnII Cl(CSL16D C)32- to the published structure of ZnII (H2 O)(GRAND-CSL12AL16L C)3- . Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand
| | - Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cherilyn E Pascoe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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Hellström M, Behler J. Proton-Transfer-Driven Water Exchange Mechanism in the Na+ Solvation Shell. J Phys Chem B 2017; 121:4184-4190. [DOI: 10.1021/acs.jpcb.7b01490] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matti Hellström
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jörg Behler
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
- Universität Göttingen, Institut für Physikalische
Chemie, Tammannstr. 6, 37077 Göttingen, Germany
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