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Li Y, Pan H, Liu Q, Ming X, Li Z. Ab initio mechanism revealing for tricalcium silicate dissolution. Nat Commun 2022; 13:1253. [PMID: 35273192 PMCID: PMC8913775 DOI: 10.1038/s41467-022-28932-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
Dissolution of minerals in water is ubiquitous in nature and industry, especially for the calcium silicate species. However, the behavior of such a complex chemical reaction is still unclear at atomic level. Here, we show that the ab initio molecular dynamics and metadynamics simulations enable quantitative analyses of reaction pathways, thermodynamics and kinetics of the calcium ion dissolution from the tricalcium silicate (Ca3SiO5) surface. The calcium sites with different coordination environments lead to different reaction pathways and free energy barriers. The low free energy barriers result in that the detachment of the calcium ion is a ligand exchange and auto-catalytic process. Moreover, the water adsorption, proton exchange and diffusion of water into the surface layer accelerate the leaching of the calcium ion from the surface step by step. The discovery in this work thus would be a landmark for revealing the mechanism of tricalcium silicate hydration.
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Affiliation(s)
- Yunjian Li
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao SAR, 999078, P. R. China
| | - Hui Pan
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao SAR, 999078, P. R. China.,Department of Physics and Chemistry, Faculty of Science and Technology, University of Macau, Macao SAR, 999078, P. R. China
| | - Qing Liu
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao SAR, 999078, P. R. China
| | - Xing Ming
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao SAR, 999078, P. R. China
| | - Zongjin Li
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao SAR, 999078, P. R. China.
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2
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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Chaudhari MI, Nair JR, Pratt LR, Soto FA, Balbuena PB, Rempe SB. Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion. J Chem Theory Comput 2016; 12:5709-5718. [DOI: 10.1021/acs.jctc.6b00824] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Jijeesh R. Nair
- Department
of Applied Science and Technology, Politecnico di Torino, Turin 10129, Italy
| | - Lawrence R. Pratt
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Fernando A. Soto
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Perla B. Balbuena
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Susan B. Rempe
- Center
for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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5
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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6
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Shen H, Hao T, Wen J, Tan RR, Zhang FS. Properties of pure water and sodium chloride solutions at high temperatures and pressures: a simulation study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.992019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Bankura A, Carnevale V, Klein ML. Hydration structure of salt solutions from ab initio molecular dynamics. J Chem Phys 2013; 138:014501. [PMID: 23298049 DOI: 10.1063/1.4772761] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
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Affiliation(s)
- Arindam Bankura
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Sabo D, Jiao D, Varma S, Pratt LR, Rempe SB. Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule. ACTA ACUST UNITED AC 2013. [DOI: 10.1039/c3pc90009f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Leung K, Nenoff TM. Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations. J Chem Phys 2012; 137:074502. [DOI: 10.1063/1.4742754] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Leung K, Criscenti LJ. Predicting the acidity constant of a goethite hydroxyl group from first principles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:124105. [PMID: 22395040 DOI: 10.1088/0953-8984/24/12/124105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Accurate predictions of the acid-base behavior of hydroxyl groups at mineral surfaces are critical for understanding the trapping of toxic and radioactive ions in soil samples. In this work, we apply ab initio molecular dynamics (AIMD) simulations and potential-of-mean-force techniques to calculate the pK(a) of a doubly protonated oxygen atom bonded to a single Fe atom (Fe(I)OH(2)) on the goethite (101) surface. Using formic acid as a reference system, pK(a) = 7.0 is predicted, suggesting that isolated, positively charged groups of this type are marginally stable at neutral pH. Similarities and differences between AIMD and the more empirical multi-site complexation methodology are highlighted, particularly with respect to the treatment of hydrogen bonding with water and proton sharing among surface hydroxyl groups. We also highlight the importance of an electronic structure method that can accurately predict transition metal ion properties for goethite pK(a) calculations.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 0754, Albuquerque, NM 87185, USA.
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11
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Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1146-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Møgelhøj A, Kelkkanen AK, Wikfeldt KT, Schiøtz J, Mortensen JJ, Pettersson LGM, Lundqvist BI, Jacobsen KW, Nilsson A, Nørskov JK. Ab Initio van der Waals Interactions in Simulations of Water Alter Structure from Mainly Tetrahedral to High-Density-Like. J Phys Chem B 2011; 115:14149-60. [DOI: 10.1021/jp2040345] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andreas Møgelhøj
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - André K. Kelkkanen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - K. Thor Wikfeldt
- Department of Physics, AlbaNova, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jakob Schiøtz
- Center for Individual Nanoparticle Functionality (CINF), Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jens Jørgen Mortensen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | - Bengt I. Lundqvist
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Karsten W. Jacobsen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Anders Nilsson
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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13
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Friedman R. Ions and the Protein Surface Revisited: Extensive Molecular Dynamics Simulations and Analysis of Protein Structures in Alkali-Chloride Solutions. J Phys Chem B 2011; 115:9213-23. [DOI: 10.1021/jp112155m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ran Friedman
- School of Natural Sciences, Linnæus University, 391 82 Kalmar, Sweden
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14
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Zhang C, Donadio D, Gygi F, Galli G. First Principles Simulations of the Infrared Spectrum of Liquid Water Using Hybrid Density Functionals. J Chem Theory Comput 2011; 7:1443-9. [DOI: 10.1021/ct2000952] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cui Zhang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Davide Donadio
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - François Gygi
- Department of Applied Science, University of California, Davis, California 95616, United States
- Department of Computer Science, University of California, Davis, California 95616, United States
| | - Giulia Galli
- Department of Chemistry, University of California, Davis, California 95616, United States
- Department of Physics, University of California, Davis, California 95616, United States
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15
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D’Angelo P, Migliorati V, Guidoni L. Hydration Properties of the Bromide Aqua Ion: the Interplay of First Principle and Classical Molecular Dynamics, and X-ray Absorption Spectroscopy. Inorg Chem 2010; 49:4224-31. [DOI: 10.1021/ic9025574] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Leonardo Guidoni
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli Studi dell’Aquila, via Campo di Pile, zona industriale di Pile, 67100, L’Aquila, Italy
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16
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Santra B, Michaelides A, Scheffler M. Coupled cluster benchmarks of water monomers and dimers extracted from density-functional theory liquid water: The importance of monomer deformations. J Chem Phys 2009; 131:124509. [DOI: 10.1063/1.3236840] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Yoo S, Zeng XC, Xantheas SS. On the phase diagram of water with density functional theory potentials: The melting temperature of ice I(h) with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals. J Chem Phys 2009; 130:221102. [PMID: 19530755 DOI: 10.1063/1.3153871] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The melting temperature (T(m)) of ice I(h) was determined from constant enthalpy and pressure (NPH) Born-Oppenheimer molecular dynamics simulations to be 417+/-3 K for the Perdew-Burke-Ernzerhof and 411+/-4 K for the Becke-Lee-Yang-Parr density functionals using a coexisting ice (I(h))-liquid phase at constant pressures of P=2500 and 10,000 bar and a density rho=1 g/cm(3), respectively. This suggests that ambient condition simulations at rho=1 g/cm(3) will rather describe a supercooled state that is overstructured when compared to liquid water.
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Affiliation(s)
- Soohaeng Yoo
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, MS K1-83, Richland, Washington 99352, USA
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18
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Leung K, Rempe SB, von Lilienfeld OA. Ab initio molecular dynamics calculations of ion hydration free energies. J Chem Phys 2009; 130:204507. [PMID: 19485457 PMCID: PMC2736677 DOI: 10.1063/1.3137054] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/25/2009] [Indexed: 11/14/2022] Open
Abstract
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
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Affiliation(s)
- Kevin Leung
- Department of Surface and Interface Sciences, MS 1415, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA.
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Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution. J Phys Chem A 2009; 113:2491-9. [DOI: 10.1021/jp805747f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | | | - Jeffrey W. Hudgens
- Computational Chemistry Group, Physical and Chemical Properties Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8380, Gaithersburg, Maryland 20899, Computational Materials Science Center, George Mason University, Research I, Fairfax, Virginia 22030, and Departamento de Química, Universidad de los Andes, Mérida-5101, Venezuela
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20
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Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. Glycosidic linkage conformation of methyl-α-mannopyranoside. J Chem Phys 2008; 129:045102. [DOI: 10.1063/1.2958916] [Citation(s) in RCA: 9] [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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21
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Pedroza LS, da Silva AJR. Adiabatic intramolecular movements for water systems. J Chem Phys 2008; 128:104311. [DOI: 10.1063/1.2889952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Allesch M, Lightstone FC, Schwegler E, Galli G. First principles and classical molecular dynamics simulations of solvated benzene. J Chem Phys 2008; 128:014501. [DOI: 10.1063/1.2806288] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rempe SB, Mattsson TR, Leung K. On “the complete basis set limit” and plane-wave methods in first-principles simulations of water. Phys Chem Chem Phys 2008; 10:4685-7. [DOI: 10.1039/b810017a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Leung K, Medforth CJ. Ab initio molecular dynamics study of manganese porphine hydration and interaction with nitric oxide. J Chem Phys 2007; 126:024501. [PMID: 17228957 DOI: 10.1063/1.2409702] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds strongly to a single H2O molecule in liquid water. The Mn in Mn(III)P is on average coplanar with the porphine plane and forms a stable complex with two H2O molecules. The residence times of these water molecules exceed 15 ps. The DFT+U method correctly predicts that water displaces NO from Mn(III)P-NO, but yields an ambiguous spin state for the MnP(II)-NO complex.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 1349 Albuquerque, New Mexico 87185, USA.
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Leung K. Ab initio molecular dynamics study of the hydration of the formohydroxamate anion. Biophys Chem 2006; 124:222-8. [PMID: 16678963 DOI: 10.1016/j.bpc.2006.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/29/2006] [Accepted: 04/01/2006] [Indexed: 11/19/2022]
Abstract
We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, NM 87185, United States.
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