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Listyarini R, Kriesche BM, Hofer TS. Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H 2O. J Chem Theory Comput 2024; 20:3028-3045. [PMID: 38595064 PMCID: PMC11044269 DOI: 10.1021/acs.jctc.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Bernhard M. Kriesche
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
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2
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Sassi P, Comez L, D'Amico F, Rossi B, Bartolini G, Fioretto D, Paolantoni M. Ultraviolet Resonant Raman Scattering of Electrolyte Solutions. APPLIED SPECTROSCOPY 2024:37028241245443. [PMID: 38632936 DOI: 10.1177/00037028241245443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Saltwater stands as the most prevalent liquid on Earth. Consequently, substantial interest has been directed toward its characterization, both as an independent system and as a solvent for complex structures such as biomacromolecules. In the last few decades, special emphasis was placed on the investigation of the hydration properties of ions for the fundamental role they play in numerous chemical processes. In this study, we employed multi-wavelength Raman spectroscopy to examine the hydration shell surrounding bromide ions in solutions of simple electrolytes, specifically lithium bromide, potassium bromide, and cesium bromide, at two different concentrations. Cation-induced differences among electrolytes were observed in connection to their tendency to form ion pairs. An increased sensitivity to reveal the structure of the first hydration shell was evidenced when employing ultraviolet excitation in the 228-266 nm range, under resonance conditions with the charge transfer transition to the solvent peaked at about 200 nm. Other than a significant increase in the Raman cross-section for the OH stretching band when shifting from pure water to the solution, a larger enhancement for the Raman signal of the H-O-H bending mode over the stretching vibration was observed. Thus, the bending band plays a crucial role in monitoring the H-bond structure of water around the anions related to the charge distribution within the first hydration shell of anions, being an effective probe of hydration phenomena.
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Affiliation(s)
- Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Lucia Comez
- CNR-Istituto Officina dei Materiali (IOM), Perugia, Italy
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S.C.p.A. di interesse nazionale, Trieste, Italy
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste S.C.p.A. di interesse nazionale, Trieste, Italy
| | - Gabriele Bartolini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
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3
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Jon JS, Ri WK, Sin KR, Son YC, Jo KW, Pak JS, Kim SJ, Ri YJ, An YC. Derivation of the solvation effect-incorporated Poisson-Boltzmann equation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Damyanov D, Nikolova V, Angelova S, Dudev T. Halide anion solvation and recognition by bambusurils: A DFT study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116160] [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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5
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Wang L, Ceriotti M, Markland TE. Quantum kinetic energy and isotope fractionation in aqueous ionic solutions. Phys Chem Chem Phys 2020; 22:10490-10499. [PMID: 31942581 DOI: 10.1039/c9cp06483d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
At room temperature, the quantum contribution to the kinetic energy of a water molecule exceeds the classical contribution by an order of magnitude. The quantum kinetic energy (QKE) of a water molecule is modulated by its local chemical environment and leads to uneven partitioning of isotopes between different phases in thermal equilibrium, which would not occur if the nuclei behaved classically. In this work, we use ab initio path integral simulations to show that QKEs of the water molecules and the equilibrium isotope fractionation ratios of the oxygen and hydrogen isotopes are sensitive probes of the hydrogen bonding structures in aqueous ionic solutions. In particular, we demonstrate how the QKE of water molecules in path integral simulations can be decomposed into translational, rotational and vibrational degrees of freedom, and use them to determine the impact of solvation on different molecular motions. By analyzing the QKEs and isotope fractionation ratios, we show how the addition of the Na+, Cl- and HPO42- ions perturbs the competition between quantum effects in liquid water and impacts their local solvation structures.
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Affiliation(s)
- Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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6
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Dischinger SM, Gupta S, Carter BM, Miller DJ. Transport of Neutral and Charged Solutes in Imidazolium-Functionalized Poly(phenylene oxide) Membranes for Artificial Photosynthesis. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b05628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sarah M. Dischinger
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Shubham Gupta
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Blaine M. Carter
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel J. Miller
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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8
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Formation of HONO from the NH 3-promoted hydrolysis of NO 2 dimers in the atmosphere. Proc Natl Acad Sci U S A 2018; 115:7236-7241. [PMID: 29941594 DOI: 10.1073/pnas.1807719115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One challenging issue in atmospheric chemistry is identifying the source of nitrous acid (HONO), which is believed to be a primary source of atmospheric "detergent" OH radicals. Herein, we show a reaction route for the formation of HONO species from the NH3-promoted hydrolysis of a NO2 dimer (ONONO2), which entails a low free-energy barrier of 0.5 kcal/mol at room temperature. Our systematic study of HONO formation based on NH3 + ONONO2 + nH2O and water droplet systems with the metadynamics simulation method and a reaction pathway searching method reveals two distinct mechanisms: (i) In monohydrates (n = 1), tetrahydrates (n = 4), and water droplets, only one water molecule is directly involved in the reaction (denoted the single-water mechanism); and (ii) the splitting of two neighboring water molecules is seen in the dihydrates (n = 2) and trihydrates (n = 3) (denoted the dual-water mechanism). A comparison of the computed free-energy surface for NH3-free and NH3-containing systems indicates that gaseous NH3 can markedly lower the free-energy barrier to HONO formation while stabilizing the product state, producing a more exergonic reaction, in contrast to the endergonic reaction for the NH3-free system. More importantly, the water droplet reduces the free-energy barrier for HONO formation to 0.5 kcal/mol, which is negligible at room temperature. We show that the entropic contribution is important in the mechanism by which NH3 promotes HONO formation. This study provides insight into the importance of fundamental HONO chemistry and its broader implication to aerosol and cloud processing chemistry at the air-water interface.
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9
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Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations. Proc Natl Acad Sci U S A 2016; 113:4629-33. [PMID: 27071120 DOI: 10.1073/pnas.1601651113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation.
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10
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Choudhary A, Chandra A. Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:6132-45. [DOI: 10.1039/c5cp07352a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke–Lee–Yang–Parr) and dispersion corrected BLYP-D functionals.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
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11
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Karmakar A, Chandra A. Ab initio molecular dynamics studies of hydrogen bonded structure, molecular motion, and frequency fluctuations of water in the vicinity of azide ions. J Chem Phys 2015; 142:164505. [DOI: 10.1063/1.4918579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Anwesa Karmakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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12
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Karmakar A, Chandra A. Effects of dispersion interaction on vibrational spectral diffusion in aqueous NaBr solutions: An ab initio molecular dynamics study. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Hassanali AA, Cuny J, Verdolino V, Parrinello M. Aqueous solutions: state of the art in ab initio molecular dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20120482. [PMID: 24516179 DOI: 10.1098/rsta.2012.0482] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
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Affiliation(s)
- Ali A Hassanali
- Department of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, , via G. Buffi 13, 6900 Lugano, Switzerland
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14
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A first principles simulation study of vibrational spectral diffusion in aqueous NaBr solutions: Dynamics of water in ion hydration shells. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Baer MD, Mundy CJ. An ab initio approach to understanding the specific ion effect. Faraday Discuss 2013; 160:89-101; discussion 103-20. [DOI: 10.1039/c2fd20113e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Ferreira JAB, Sánchez-Coronilla A, Togashi DM, Ferreira H, Ascenso JR, Costa SMB. Electrophilic reactivity of tetrabromorhodamine 123 is bromine induced: convergent interpretation through complementary molecular descriptors. J Phys Chem A 2012; 116:11938-45. [PMID: 23134615 DOI: 10.1021/jp307461m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleophilic addition of water and of methanol to 3,6-diamino-2,4,5,7-tetrabromo-9-[2-(methoxycarbonyl) phenyl]-9H-xanthen-9-ylium, 4BrR123, yields respectively 2-(3,6-diamino-2,4,5,7-tetrabromo-9-hydroxy-9H-xanthen-9-yl)xanthyl benzoate, HO4BrR123 and 2-(3,6-diamino-2,4,5,7-tetrabromo-9-methoxy-9H-xanthen-9-yl)xanthyl benzoate, MeO4BrR123. The novel experimental results are addressed theoretically. The linear free energy relationship, LFER, second-order perturbation theory analysis of the natural bond orbital, NBO, and quantum theory of atoms in molecules, QTAIM, lead to the same conclusion: the electron-withdrawing effect of bonded Br atoms in 4BrR123 extremely enhances the molecular electrophilicity, as compared to 3,6-diamino-9-[2-(methoxycarbonyl) phenyl]-9H-xanthen-9-ylium, R123. The reactivity of these diaminoxanthylium cations is discussed in the context of local and global softness in extended conjugated systems.
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Affiliation(s)
- José A B Ferreira
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade Técnica de Lisboa, Portugal.
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17
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Computational investigation on the new high energy density material of aluminum enriched 1, 1-diamino-2, 2-dinitroethylene. J Mol Model 2012; 19:131-8. [DOI: 10.1007/s00894-012-1533-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/08/2012] [Indexed: 10/28/2022]
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18
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Galib M, Hanna G. Mechanistic Insights into the Dissociation and Decomposition of Carbonic Acid in Water via the Hydroxide Route: An Ab Initio Metadynamics Study. J Phys Chem B 2011; 115:15024-35. [DOI: 10.1021/jp207752m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirza Galib
- Department of Chemistry, University of Alberta, Alberta, Canada
| | - Gabriel Hanna
- Department of Chemistry, University of Alberta, Alberta, Canada
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19
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Mallik BS, Chandra A. An ab initio molecular dynamics study of supercritical aqueous ionic solutions: Hydrogen bonding, rotational dynamics and vibrational spectral diffusion. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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A Comparison of the Performance of the Semiempirical PM6 Method Versus DFT Methods in Ru-Catalyzed Olefin Metathesis. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-90-481-3433-5_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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21
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Carnevale V, Raugei S. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car–Parrinello and classical molecular dynamics investigation. J Chem Phys 2009; 131:225103. [DOI: 10.1063/1.3268703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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22
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Lin YS, Auer BM, Skinner JL. Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions. J Chem Phys 2009; 131:144511. [DOI: 10.1063/1.3242083] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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23
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Tian GC, Li J, Hua YX. Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water. CHINESE J CHEM PHYS 2009. [DOI: 10.1088/1674-0068/22/05/460-466] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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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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25
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Mallik BS, Semparithi A, Chandra A. A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions: D2O in hydration shells of Cl(-) ions. J Chem Phys 2009; 129:194512. [PMID: 19026071 DOI: 10.1063/1.3006032] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions is presented from first principles without employing any empirical potential models. The present calculations are based on ab initio molecular dynamics for trajectory generation and wavelet analysis of the simulated trajectories for time dependent frequency calculations. Results are obtained for two different deuterated aqueous solutions: the first one is a relatively dilute solution of a single Cl(-) ion and the second one is a concentrated solution of NaCl ( approximately 3M) dissolved in liquid D(2)O. It is found that the frequencies of OD bonds in the anion hydration shell, i.e., those which are hydrogen bonded to the chloride ion, have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the anion-water hydrogen bond distance. On the dynamical side, when the vibrational spectral diffusion is calculated exclusively for the hydration shell water molecules in the first solution, the dynamics reveals three time scales: a short-time relaxation ( approximately 200 fs) corresponding to the dynamics of intact ion-water hydrogen bonds, a slower relaxation ( approximately 3 ps) corresponding to the lifetimes of chloride ion-water hydrogen bonds, and another longer-time constant ( approximately 20 ps) corresponding to the escape dynamics of water from the anion hydration shell. Existence of such three time scales for hydration shell water molecules was also reported earlier for water containing a single iodide ion using classical molecular dynamics [B. Nigro et al., J. Phys. Chem. A 110, 11237 (2006)]. Hence, the present study confirms the basic results of this earlier work using a different methodology. However, when the vibrational spectral diffusion is calculated over all the OD modes, only two time scales of approximately 150 fs and approximately 2.7 ps are found without the slowest component of approximately 20 ps. This is likely because of the very small weight that the hydration shell water molecules carry to the overall spectral diffusion in the solution containing a single ion. For the concentrated solution also, the slowest component of approximately 20 ps is not found in the spectral diffusion of all water molecules because a distinct separation between the hydration shell and bulk water in terms of their stretch frequencies does not hold at this high concentration regime. The present first principles results are compared with those of the available experiments and classical simulations.
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Affiliation(s)
- Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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26
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Rowley CN, Woo TK. Reaction Dynamics of β-Hydrogen Transfer in the Zirconocene Olefin Polymerization Catalyst: A DFT Path Sampling Study. Organometallics 2008. [DOI: 10.1021/om800891w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher N. Rowley
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Tom K. Woo
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
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Petit L, Vuilleumier R, Maldivi P, Adamo C. Ab Initio Molecular Dynamics Study of a Highly Concentrated LiCl Aqueous Solution. J Chem Theory Comput 2008; 4:1040-8. [DOI: 10.1021/ct800007v] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Petit
- Laboratoire de Reconnaissance Ionique et de Chimie de Coordination, CEA - INAC/LCIB (UMRE 3 CEA-UJF), 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France, Laboratoire de Physique Théorique de la Matiere Condensée, UMR7600, Université Pierre et Marie Curie, Paris, Tour 24 Boite 121, 4 place Jussieu, F-75252 Paris CEDEX 05, France, and Laboratoire d’Electrochimie et de Chimie Analytique, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
| | - R. Vuilleumier
- Laboratoire de Reconnaissance Ionique et de Chimie de Coordination, CEA - INAC/LCIB (UMRE 3 CEA-UJF), 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France, Laboratoire de Physique Théorique de la Matiere Condensée, UMR7600, Université Pierre et Marie Curie, Paris, Tour 24 Boite 121, 4 place Jussieu, F-75252 Paris CEDEX 05, France, and Laboratoire d’Electrochimie et de Chimie Analytique, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
| | - P. Maldivi
- Laboratoire de Reconnaissance Ionique et de Chimie de Coordination, CEA - INAC/LCIB (UMRE 3 CEA-UJF), 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France, Laboratoire de Physique Théorique de la Matiere Condensée, UMR7600, Université Pierre et Marie Curie, Paris, Tour 24 Boite 121, 4 place Jussieu, F-75252 Paris CEDEX 05, France, and Laboratoire d’Electrochimie et de Chimie Analytique, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
| | - C. Adamo
- Laboratoire de Reconnaissance Ionique et de Chimie de Coordination, CEA - INAC/LCIB (UMRE 3 CEA-UJF), 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France, Laboratoire de Physique Théorique de la Matiere Condensée, UMR7600, Université Pierre et Marie Curie, Paris, Tour 24 Boite 121, 4 place Jussieu, F-75252 Paris CEDEX 05, France, and Laboratoire d’Electrochimie et de Chimie Analytique, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
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28
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Mallik BS, Semparithi A, Chandra A. Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles. J Phys Chem A 2008; 112:5104-12. [PMID: 18491881 DOI: 10.1021/jp801405a] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.
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Affiliation(s)
- Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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29
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Stuart CM, Tauber MJ, Mathies RA. Structure and Dynamics of the Solvated Electron in Alcohols from Resonance Raman Spectroscopy. J Phys Chem A 2007; 111:8390-400. [PMID: 17676822 DOI: 10.1021/jp068283q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Resonance Raman (RR) spectroscopy is used to probe the structure and excited-state dynamics of the solvated electron in the primary liquid alcohols methanol (MeOH), ethanol (EtOH), n-propanol (n-PrOH), and n-butanol (n-BuOH). The strong resonance enhancements (>or=10(4) relative to pure solvent) of the libration, CO stretch, COH bend, CH3 bend, CH2 bend, and OH stretch reveal significant Franck-Condon coupling of the intermolecular and intramolecular vibrational modes of the solvent to the electronic excitation of the solvated electron. All enhanced bands are fully accounted for by a model of the solvated electron that is comprised of several nearby solvent molecules that are only perturbed by the presence of the electron; no new molecular species are required to explain our data. The 340 cm(-1) downshift observed for the OH stretch frequency of e-(MeOH), relative to pure solvent, strongly suggests that the methanol molecules in the first solvent shell have the hydroxyl group directed linearly toward the excess electron density. The smaller downshifts observed for e-(EtOH), e-(n-PrOH), and e-(n-BuOH) are explained in terms of a OH group that is bent 28-40 degrees from linear. The Raman cross sections and absorption spectra are modeled, lending quantitative support for the inhomogeneous origin of the broad absorption spectra, the necessity of OH local motion in all enhanced Raman modes of the alcohols, and the dominant librational response of the solvent upon photoexcitation of the electron.
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Affiliation(s)
- Christina M Stuart
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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30
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Chowdhuri S, Chandra A. Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature. J Phys Chem B 2007; 110:9674-80. [PMID: 16686518 DOI: 10.1021/jp057544d] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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31
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Lamoureux G, Roux B. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J Phys Chem B 2007; 110:3308-22. [PMID: 16494345 DOI: 10.1021/jp056043p] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model [Lamoureux, G.; MacKerell, A. D., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185]. Induced polarization is incorporated using classical Drude oscillators that are treated as auxiliary dynamical degrees of freedom. The ions are represented as polarizable Lennard-Jones centers, whose parameters are optimized to reproduce the binding energies of gas-phase monohydrates and the hydration free energies in the bulk liquid. Systematic exploration of the parameters shows that the monohydrate binding energies can be consistent with a unique hydration free energy scale if the computed hydration free energies incorporate the contribution from the air/water interfacial electrostatic potential (-540 mV for SWM4-DP). The final model, which can satisfyingly reproduce both gas and bulk-phase properties, corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol.
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Affiliation(s)
- Guillaume Lamoureux
- Département de physique, Université de Montréal, C.P. 6128, succ. centre-ville, Montréal, Québec H3C 3J7, Canada
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32
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Dal Peraro M, Raugei S, Carloni P, Klein ML. Solute-solvent charge transfer in aqueous solution. Chemphyschem 2007; 6:1715-8. [PMID: 16080223 DOI: 10.1002/cphc.200500039] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Matteo Dal Peraro
- Center for Molecular Modeling, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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33
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Lee JG, Asciutto E, Babin V, Sagui C, Darden T, Roland C. Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations. J Phys Chem B 2006; 110:2325-31. [PMID: 16471820 DOI: 10.1021/jp055809i] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.
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Affiliation(s)
- Jung-Goo Lee
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
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34
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Faralli C, Pagliai M, Cardini G, Schettino V. Structure and Dynamics of Br- Ion in Liquid Methanol. J Phys Chem B 2006; 110:14923-8. [PMID: 16869605 DOI: 10.1021/jp061230o] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A Car-Parrinello molecular dynamics simulation has been performed on a solution of Br- in liquid methanol analyzing with particular attention charge transfer and polarization effects. The first solvation shell has been characterized in terms of H-bonds, and it has been found that the high polarization of the bromide gives rise to a stable solvent cage. The differences in the coordination number with the chloride can be ascribed to the ionic radius and to the stronger perturbations brought by the solvent to the bromide ion.
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Affiliation(s)
- Cristian Faralli
- Laboratorio di Spettroscopia Molecolare, Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italia
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35
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Gourlaouen C, Gérard H, Parisel O. Exploring the Hydration of Pb2+: Ab Initio Studies and First-Principles Molecular Dynamics. Chemistry 2006; 12:5024-32. [PMID: 16642524 DOI: 10.1002/chem.200600045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.
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Affiliation(s)
- Christophe Gourlaouen
- Université Pierre et Marie Curie - Paris 6, Laboratoire de Chimie Théorique, UMR 7616, CC 137, 4 place Jussieu, 75252 Paris Cedex 05, France
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36
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Leung K, Rempe SB. Ab initio rigid water: Effect on water structure, ion hydration, and thermodynamics. Phys Chem Chem Phys 2006; 8:2153-62. [PMID: 16751873 DOI: 10.1039/b515126k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 & 0310, Albuquerque, NM 87185, USA
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37
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Thompson AL, Parker D, Fulton DA, Howard JAK, Pandya SU, Puschmann H, Senanayake K, Stenson PA, Badari A, Botta M, Avedano S, Aime S. On the role of the counter-ion in defining water structure and dynamics: order, structure and dynamics in hydrophilic and hydrophobic gadolinium salt complexes. Dalton Trans 2006:5605-16. [PMID: 17225897 DOI: 10.1039/b606206g] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of the hydrated salts of [Gd.DOTAM]3+ and its more hydrophobic derivative [Gd.]3+, bearing 4 alpha-phenylethyl groups, (both Gd and Yb salts) are reported and compared. The nature of the anion determines the degree of ordering in the lattice and the extent of hydration. These effects are correlated with the results of 17O and 1H NMR measurements of water exchange dynamics in solution. With [Gd.DOTAM]3+, structural ordering or the extent of hydration in the hydrated lattice follows the sequence Cl->Br->I- and this order also defines the water exchange rate in solution: 7.3, 19.5, 33.3x10(4) s-1 (298 K), respectively. For [Gd.]3+ salts, the measured relaxivity is determined purely by the outer sphere term and the water exchange rate at 298 K is very similar (typically 1x10(4) s-1) for chloride, bromide, iodide, acetate, triflate and nitrate salts, notwithstanding the different nature and extent of hydration found in the crystalline lattice.
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Affiliation(s)
- Amber L Thompson
- Department of Chemistry, University of Durham, South Road, Durham, DH13LE, UK
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38
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39
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Yang ZZ, Li X. Ion Solvation in Water from Molecular Dynamics Simulation with the ABEEM/MM Force Field. J Phys Chem A 2005; 109:3517-20. [PMID: 16839014 DOI: 10.1021/jp051106p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic study on monovalent ions in water clusters and in aqueous solution is presented for providing insight into their solvation structures, charge distributions, binding energies, as well as dynamic and thermodynamic properties in terms of the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges into the Coulomb term in MM. For hydrated systems of M+(H2O)n, M+ being Li+, Na+, and K+, as well as X-(H2O)n, X- being F-, Cl-, and Br-, with n = 1-6, parameters for the effective interaction between the ion and the water molecules were determined, so as to reproduce the experimental or ab initio results. The corresponding parameters were tested with molecular dynamics (MD) simulations of these ions in liquid water and with solvation free energy calculations using the perturbation technique. The results of aqueous ionic solution simulations with the ABEEM/MM force field provide a reasonable description of many important properties, which are in good agreement with the experimental measurements. This work demonstrates that the combination of ABEEM/MM-MD provides a powerful tool in analyzing solvation processes of monovalent ions in water.
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Affiliation(s)
- Zhong-Zhi Yang
- Department of Chemistry, Liaoning Normal University, Dalian 116029, PR China
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40
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Pagliai M, Cardini G, Schettino V. Solvation Dynamics of Li+ and Cl- Ions in Liquid Methanol. J Phys Chem B 2005; 109:7475-81. [PMID: 16851858 DOI: 10.1021/jp050428q] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Car-Parrinello molecular dynamics simulations have been performed on Li(+) and Cl(-) in fully deuterated liquid methanol. The results have been compared with available experimental and theoretical data. It has been found that the lithium cation has a stable tetrahedral coordination, whereas the chloride anion presents an average coordination number of 3.56. The polarization effects induced by the ion on the solvent have been analyzed in terms of Wannier function centers. Particular attention has been devoted to the charge transfer, which is particularly important in these types of systems. Evidence for the stability of the lithium cation solvent cage also has been found in the vibrational spectra.
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Affiliation(s)
- Marco Pagliai
- Laboratorio di Spettroscopia Molecolare, Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
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41
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Tongraar A, Rode BM. Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.01.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Leung K, Rempe SB. Ab initio molecular dynamics study of formate ion hydration. J Am Chem Soc 2004; 126:344-51. [PMID: 14709101 DOI: 10.1021/ja036267q] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We perform ab initio molecular dynamics simulations of the aqueous formate ion. The mean number of water molecules in the first solvation shell, or the hydration number, of each formate oxygen is found to be consistent with recent experiments. Our ab initio pair correlation functions, however, differ significantly from many classical force field results and hybrid quantum mechanics/molecular mechanics predictions. They yield roughly one less hydrogen bond between each formate oxygen and water than force field or hybrid methods predict. Both the BLYP and PW91 exchange correlation functionals give qualitatively similar results. The time dependence of the hydration numbers are examined, and Wannier function techniques are used to analyze electronic configurations along the molecular dynamics trajectory.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 0316, Albuquerque, New Mexico 87185, USA.
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43
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44
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Chandra A. Dynamical Behavior of Anion−Water and Water−Water Hydrogen Bonds in Aqueous Electrolyte Solutions: A Molecular Dynamics Study. J Phys Chem B 2003. [DOI: 10.1021/jp022147d] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Marlow GE, Pettitt BM. Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride. Biopolymers 2003; 68:192-209. [PMID: 12548623 DOI: 10.1002/bip.10292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In order to quantify specific ion effects, a simulation study of bis(penicllamine) enkephalin, also known as DPDPE, has been performed in aqueous ammonium chloride solution and has been compared to a previous simulation of DPDPE in aqueous sodium chloride solution. Global thermodynamics have been calculated for a model system and the solution environment around DPDPE has been characterized. Associations of ions with DPDPE have been investigated. The observed differences between sodium chloride solution and ammonium chloride solution suggest that individual cations affect the solvation and peptide binding properties of a given anion.
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Affiliation(s)
- Gail E Marlow
- Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
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46
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Ayala R, Martı́nez JM, Pappalardo RR, Saint-Martı́n H, Ortega-Blake I, Sánchez Marcos E. Development of first-principles interaction model potentials. An application to the study of the bromide hydration. J Chem Phys 2002. [DOI: 10.1063/1.1519843] [Citation(s) in RCA: 40] [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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47
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Sillanpää AJ, Simon C, Klein ML, Laasonen K. Structural and Spectral Properties of Aqueous Hydrogen Fluoride Studied Using ab Initio Molecular Dynamics. J Phys Chem B 2002. [DOI: 10.1021/jp0260088] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Atte J. Sillanpää
- Department of Chemistry, University of Oulu, PO Box 3000, FIN-90014 Oulun Yliopisto, Finland, and Department of Chemistry and Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Christian Simon
- Department of Chemistry, University of Oulu, PO Box 3000, FIN-90014 Oulun Yliopisto, Finland, and Department of Chemistry and Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Michael L. Klein
- Department of Chemistry, University of Oulu, PO Box 3000, FIN-90014 Oulun Yliopisto, Finland, and Department of Chemistry and Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Kari Laasonen
- Department of Chemistry, University of Oulu, PO Box 3000, FIN-90014 Oulun Yliopisto, Finland, and Department of Chemistry and Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
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48
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Balasubramanian S, Pal S, Bagchi B. Hydrogen-bond dynamics near a micellar surface: origin of the universal slow relaxation at complex aqueous interfaces. PHYSICAL REVIEW LETTERS 2002; 89:115505. [PMID: 12225151 DOI: 10.1103/physrevlett.89.115505] [Citation(s) in RCA: 294] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2002] [Indexed: 05/21/2023]
Abstract
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.
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Affiliation(s)
- Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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49
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Boero M, Terakura K, Tateno M. Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme. J Am Chem Soc 2002; 124:8949-57. [PMID: 12137550 DOI: 10.1021/ja017843q] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By using finite temperature first principles molecular dynamics, the mechanism of the enzymatic reaction of ribozyme was investigated for both the anionic and the radical charge states of the modeled RNA fragment. In the case of the anionic system, a pseudorotation and the subsequent 3' --> 2' migration occur in a vacuum, rather than the self-cleavage of the phosphodiester. On the other hand, when either a divalent metal ion (Mg(2+)) catalyst or the continuous hydrogen bond network of the solvent is present, the reaction path of the anionic species changes dramatically, going toward the transesterification channel. In a radical system, the transesterification can occur without a metal catalyst, as a consequence of the displacement of a hole (empty electronic state) along the reaction path. Thus, the present analysis suggests that a metal ion might be essential not only in lowering the activation barrier but also in selecting the reaction path among those corresponding to possible different charge states of the intermediate structure in vivo. Furthermore, simulation of the anionic species in solution shows that, in the absence of a metal catalyst, water molecules cooperate with the proton transfer via a proton wire mechanism and the hydrogen bond network plays a crucial role in preventing pseudorotations. On the other hand, when a metal cation is present in the vicinity of the site where the nucleophilic attack occurs, the hydrogen bond network is interrupted and detachment of the proton, enhanced by the catalyst, does not give rise to any proton-transfer process.
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Affiliation(s)
- Mauro Boero
- Angstrom Technology Partnership, Joint Research Center for Atom Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-0046, Japan.
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Raugei S, Klein ML. An ab initio study of water molecules in the bromide ion solvation shell. J Chem Phys 2002. [DOI: 10.1063/1.1421366] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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