1
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Huo J, Chen J, Liu P, Hong B, Zhang J, Dong H, Li S. Microscopic Mechanism of Proton Transfer in Pure Water under Ambient Conditions. J Chem Theory Comput 2023. [PMID: 37365994 DOI: 10.1021/acs.jctc.3c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Water molecules and the associated proton transfer (PT) are prevalent in chemical and biological systems and have been a hot research topic. Spectroscopic characterization and ab initio molecular dynamics (AIMD) simulations have previously revealed insights into acidic and basic liquids. Presumably, the situation in the acidic/basic solution is not necessarily the same as in pure water; in addition, the autoionization constant for water is only 10-14 under ambient conditions, making the study of PT in pure water challenging. To overcome this issue, we modeled periodic water box systems containing 1000 molecules for tens of nanoseconds based on a neural network potential (NNP) with quantum mechanical accuracy. The NNP was generated by training a dataset containing the energies and atomic forces of 17 075 configurations of periodic water box systems, and these data points were calculated at the MP2 level that considers electron correlation effects. We found that the size of the system and the duration of the simulation have a significant impact on the convergence of the results. With these factors considered, our simulations showed that hydronium (H3O+) and hydroxide (OH-) ions in water have distinct hydration structures, thermodynamic and kinetic properties, e.g., the longer-lasting and more stable hydrated structure of OH- ions than that of H3O+, as well as a significantly higher free energy barrier for the OH--associated PT than that of H3O+, leading the two to exhibit completely different PT behaviors. Given these characteristics, we further found that PT via OH- ions tends not to occur multiple times or between many molecules. In contrast, PT via H3O+ can synergistically occur among multiple molecules and prefers to adopt a cyclic pattern among three water molecules, while it occurs mostly in a chain pattern when more water molecules are involved. Therefore, our studies provide a detailed and solid microscopic explanation for the PT process in pure water.
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Affiliation(s)
- Jun Huo
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Jianghao Chen
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Pei Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Benkun Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Jian Zhang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
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2
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Garofalini SH, Lentz J. Subpicosecond Molecular Rearrangements Affect Local Electric Fields and Auto-Dissociation in Water. J Phys Chem B 2023; 127:3392-3401. [PMID: 37036747 DOI: 10.1021/acs.jpcb.2c06490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Molecular simulations of auto-dissociation of water molecules in an 81,000 atom bulk water system show that the electric field variations caused by local bond length and angle variations enhance proton transfer within ∼600 fs prior to auto-dissociation. In this paper, auto-dissociation relates to the initial separation of a proton from a water molecule to another, forming the H33O+ and OH- ions. Only transfers for which a proton's initial nearest covalently bonded oxygen remained the same for at least 1 ps prior to the transfer and for which that proton's new nearest acceptor oxygen remained the same for at least 1 ps after the transfer were evaluated. Electric fields from solvent atoms within 6 Å of a transferring proton (H*) are dominant, with little contribution from farther molecules. However, exclusion of the accepting oxygen in such electric field calculations shows that the field on H* from the other solvent atoms weakens as the time to transfer becomes less than 600 fs, indicating the primary importance of the accepting oxygen on enabling auto-dissociation. All resultant OH- and H3O+ ion pairs recombined at times greater than 1 ps after auto-dissociation. A concentration of 8.01 × 1017 cm-3 for these ion pairs was observed. The simulations indicate that transient auto-dissociation in water is more common than that inferred from dc-conductivity experiments (10-5 vs 10-7) and is consistent with the results of calculations that include nuclear quantum effects. The conductivity experiments require the rearrangement of farther water molecules to form hydrogen-bonded "water wires" that afford long-range and measurable proton transport away from the reaction site. Nonetheless, the relatively large number of picosecond-lived auto-dissociation products might be engineered within 2D layers and oriented external fields to offer new energy-related systems.
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Affiliation(s)
- Stephen H Garofalini
- Department of Matserials Science and Engineering, Rutgers University, 607 Taylor Road, Piscataway, New Jersey 08855, United States
| | - Jesse Lentz
- Department of Matserials Science and Engineering, Rutgers University, 607 Taylor Road, Piscataway, New Jersey 08855, United States
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3
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Vibrational dynamics of the OD stretch in an atomistic simulation of HDO in H2O. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Mabuchi T. Revealing the Anticorrelation Behavior Mechanism between the Grotthuss and Vehicular Diffusions for Proton Transport in Concentrated Acid Solutions. J Phys Chem B 2022; 126:3319-3326. [PMID: 35468285 DOI: 10.1021/acs.jpcb.1c09742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we performed reactive molecular dynamics simulations to characterize proton solvation and transport in concentrated hydrochloric acid solutions. The correlation contribution to the total proton mean square displacement is found to be negative for all acid concentrations, indicating the anticorrelation between the Grotthuss and vehicular diffusions. For the vehicular diffusion, the hydronium ions tend to move freely toward the lone pair side independent of acid concentrations, whereas for the Grotthuss diffusion, the proton hopping direction is limited to one of the hydrogen-bonded water molecules on the opposite side of the lone pair region, which are specifically oriented with respect to the neighboring hydronium ion at higher acid concentrations. This result is justified by our findings of the higher fraction of proton rattling with the single hopping event and longer hydrogen bond lifetimes at higher acid concentrations. However, the angular distribution for both the vehicular and Grotthuss diffusions is found to be rather broad and comparable for all acid concentrations, and thus, the anticorrelation shows a minimal dependence on the acid concentration. Our results reveal that the anticorrelation behavior between the vehicle and Grotthuss diffusions is attributed to the amphiphilic nature of hydronium ions and thus is independent of the acid concentrations in solutions.
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Affiliation(s)
- Takuya Mabuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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5
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Cha J. Morphological effect of side chain on H 3O + transfer inside polymer electrolyte membranes across polymeric chain via molecular dynamics simulation. Sci Rep 2020; 10:22014. [PMID: 33328487 PMCID: PMC7745029 DOI: 10.1038/s41598-020-77971-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/12/2020] [Indexed: 11/25/2022] Open
Abstract
Performance and durability of polymer electrolyte membrane are critical to fuel cell quality. As fuel cell vehicles become increasingly popular, membrane fundamentals must be understood in detail. Here, this study used molecular dynamic simulations to explore the morphological effects of perfluorosulfonic acid (PFSA)-based membranes on ionic conductivity. In particular, I developed an intuitive quantitative approach focusing principally on hydronium adsorbing to, and desorbing from, negatively charged sulfonate groups, while conventional ionic conductivity calculations featured the use of mean square displacements that included natural atomic vibrations. The results revealed that shorter side-chains caused more hydroniums to enter the conductive state, associated with higher ion conductivity. In addition, the hydronium path tracking showed that shorter side-chains allowed hydroniums to move among host groups, facilitating chain adsorption, in agreement with a mechanism suggested in earlier studies.
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Affiliation(s)
- JinHyeok Cha
- Institute of Fundamentals and Advanced Technology, Hyundai Motor Company, 37 Cheoldobangmulgwan-ro, Uiwang-si, Gyeonggi-do, 16082, Republic of Korea.
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6
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Turi L, Rodriguez J, Laria D. Combined Effects from Solvation and Nuclear Quantum Fluctuations on Autoionization Mechanisms in Aqueous Clusters. J Phys Chem B 2020; 124:2198-2208. [PMID: 32075372 DOI: 10.1021/acs.jpcb.9b11087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using path-integral molecular dynamics simulations, we examine isomerization paths involving collective proton transfers in [H2O]5 and [H2O]8 clusters under cryogenic conditions. We focused attention on combined effects derived from solvation and nuclear quantum fluctuations on the characteristics of free energy barriers and relative stabilities of reactants and products. In particular, we analyzed two different processes: the first one involves the exchange of donor-acceptor hydrogen bond roles along cyclic moieties, whereas the second one corresponds to charge separation leading to stable [H3O]+[OH]- ion pairs. In the first case, the explicit incorporation of quantum tunneling introduces important modifications in the classical free energy profile. The resulting quantum profile presents two main contributions, one corresponding to compressions of O-O distances and a second one ascribed to nuclear tunneling of the light protons. Solvation effects promote a moderate polarization of the cyclic structures and a partial loss of concertedness in the collective modes, most notably, at the onset of tunneling. Still, the latter effects are also sufficiently strong to promote the stabilization of ion pairs along the classical trajectories. In contrast, the explicit incorporation of nuclear quantum fluctuations leads to charge separated configurations that are marginally stable. As such, the latter states could also be regarded as short-lived intermediate states along the reactive exchange path.
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Affiliation(s)
- László Turi
- Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, Budapest, 112 H-1518, Hungary
| | - Javier Rodriguez
- Departamento de Fı́sica de la Materia Condensada, Comisión Nacional de Energı́a Atómica, Avenida Libertador 8250, 1429 Buenos Aires, Argentina.,ECyT, UNSAM, Martı́n de Irigoyen 3100, 1650 San Martı́n, Provincia de Buenos Aires, Argentina
| | - Daniel Laria
- Departamento de Fı́sica de la Materia Condensada, Comisión Nacional de Energı́a Atómica, Avenida Libertador 8250, 1429 Buenos Aires, Argentina.,Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica-Fı́sica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Pabellón II, 1428 Buenos Aires, Argentina
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7
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Lentz J, Garofalini SH. Formation and migration of H3O+ and OH− ions at the water/silica and water/vapor interfaces under the influence of a static electric field: a molecular dynamics study. Phys Chem Chem Phys 2020; 22:22537-22548. [DOI: 10.1039/d0cp03656k] [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
Water ‘layers’ 1 and 2 in pink; ‘layer’ 3 in blue and green over portion of glass surface (grey). +90° field causes water migration and clustering.
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Affiliation(s)
- Jesse Lentz
- Interfacial Molecular Science Laboratory
- Department of Materials Science and Engineering, Rutgers University
- USA
| | - Stephen H. Garofalini
- Interfacial Molecular Science Laboratory
- Department of Materials Science and Engineering, Rutgers University
- USA
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8
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Sakti AW, Nishimura Y, Nakai H. Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aditya W. Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
| | - Hiromi Nakai
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering Waseda University Tokyo Japan
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9
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Hofer TS, Kilchert FM, Tanjung BA. An effective partial charge model for bulk and surface properties of cubic ZrO 2, Y 2O 3 and yttrium-stabilised zirconia. Phys Chem Chem Phys 2019; 21:25635-25648. [PMID: 31720638 DOI: 10.1039/c9cp04307a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO2, Y2O3 and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO2 and Y2O3 under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO2 and Y2O3, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO2 case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.
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Affiliation(s)
- Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
| | - Franziska M Kilchert
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
| | - Bagas A Tanjung
- Theoretical Chemistry Division, 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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10
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Lentz J, Garofalini SH. Role of the hydrogen bond lifetimes and rotations at the water/amorphous silica interface on proton transport. Phys Chem Chem Phys 2019; 21:12265-12278. [PMID: 31139793 DOI: 10.1039/c9cp01994d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a highly robust and reactive all-atom potential, molecular dynamics computer simulations have been used to provide detailed analysis of the behavior of water and protons at a large-scale amorphous silica surface that offers the heterogeneity of surface sites and water/silica interactions. Structural data of the H-O distances as a function of distance from the glass surface showed variation in hydrogen bond (H-bond) lengths to second and third nearest oxygen neighbors that play an important role in H-bond lifetimes, rotations, and proton transfer, especially at the glass surface. The higher density and inherently closer average spacing between oxygens in the glass surface (2.6 Å) in comparison to that in water (2.8 Å) create a significantly different environment for H-bond lifetimes and proton transfers. Continuous H-bond lifetime autocorrelation functions for water H-bonded to the surface are considerably shorter than those of bulk water, whereas the intermittent lifetime autocorrelation functions are longer. Such results affect proton transfers that are over an order of magnitude higher at the surface than farther from the surface or in bulk water. However, most of these transfers are rattling events between the participating oxygens, one of which is the newly formed H3O+ ion adjacent to the interface. Such a H3O+ ion has an extremely low barrier to proton transfer back to the surface site in comparison to a H3O+ ion in bulk water. Nonetheless, the simulations showed that rotation of the H3O+ ion away from the initial transfer site allowed for structural diffusion of an excess proton away from the surface. Proton conduction from such rotations could be enhanced by external forces.
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Affiliation(s)
- Jesse Lentz
- Interfacial Molecular Science Laboratory, Department of Materials Science and Engineering, Rutgers University, USA.
| | - Stephen H Garofalini
- Interfacial Molecular Science Laboratory, Department of Materials Science and Engineering, Rutgers University, USA.
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11
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Hofer TS, Wiedemair MJ. Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces. Phys Chem Chem Phys 2018; 20:28523-28534. [DOI: 10.1039/c8cp04957b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.
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Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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12
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Lentz J, Garofalini SH. Structural aspects of the topological model of the hydrogen bond in water on auto-dissociation via proton transfer. Phys Chem Chem Phys 2018; 20:16414-16427. [DOI: 10.1039/c8cp02592d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different H-bond structures of donor and acceptor water molecules significantly affect structure, H-bond lifetimes, and autodissociation via proton transfer.
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Affiliation(s)
- Jesse Lentz
- Department of Materials Science and Engineering
- Rutgers University
- Piscataway
- USA
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13
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Wiedemair MJ, Hofer TS. Towards a dissociative SPC-like water model – probing the impact of intramolecular Coulombic contributions. Phys Chem Chem Phys 2017; 19:31910-31920. [DOI: 10.1039/c7cp06191a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modification of the dissociative Garofalini water model towards an SPC-like Coulombic formulation proved to enhance accuracy and transferability of this successful force field approach.
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Affiliation(s)
- Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
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14
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Martí J. Potentials of mean force in acidic proton transfer reactions in constrained geometries. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1239824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, Barcelona, Spain
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15
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Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
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16
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Wiedemair MJ, Hitzenberger M, Hofer TS. Tuning the reactivity of a dissociative force field: proton transfer properties of aqueous H3O+ and their dependence on the three-body interaction. Phys Chem Chem Phys 2015; 17:10934-43. [DOI: 10.1039/c4cp05607h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective adjustment of the three-body interaction of a dissociative water potential results in a significant improvement in the description of proton transport properties.
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Affiliation(s)
- Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- Innrain 80-82
| | - Manuel Hitzenberger
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- Innrain 80-82
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- Innrain 80-82
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17
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Hofer TS. Probing Proton Transfer Reactions in Molecular Dynamics—A Crucial Prerequisite for QM/MM Simulations Using Dissociative Models. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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18
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Canaval LR, Lutz OMD, Weiss AKH, Huck CW, Hofer TS. A Dissociative Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation and Infrared Experiments Reveal Characteristics of the Strongly Hydrolytic Arsenic(III). Inorg Chem 2014; 53:11861-70. [DOI: 10.1021/ic4031156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Lorenz R. Canaval
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Oliver M. D. Lutz
- Institute for Analytical Chemistry and
Radiochemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Christian W. Huck
- Institute for Analytical Chemistry and
Radiochemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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19
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Wolf MG, Groenhof G. Explicit proton transfer in classical molecular dynamics simulations. J Comput Chem 2014; 35:657-71. [DOI: 10.1002/jcc.23536] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Maarten G. Wolf
- Computational Biomolecular Chemistry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11; Göttingen D-37077, Germany
| | - Gerrit Groenhof
- Computational Biomolecular Chemistry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11; Göttingen D-37077, Germany
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20
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Hofer TS. Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined.
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Kagan M, Lockwood GK, Garofalini SH. Reactive simulations of the activation barrier to dissolution of amorphous silica in water. Phys Chem Chem Phys 2014; 16:9294-301. [DOI: 10.1039/c4cp00030g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Free energy barriers for hydrolyzation of different Si sites on amorphous silica surfaces from the Qi (i = the number of bridging oxygen atoms) to Q(j) (j = (i − 1)) reaction during dissolution to form the labeled Qij reaction; the distribution indicates the importance of including structural heterogeneity of amorphous silica surfaces in computations.
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Affiliation(s)
- Michael Kagan
- Interfacial Molecular Science Laboratory
- Department of Materials Science and Engineering
- Rutgers University
- Piscataway, USA
| | - Glenn K. Lockwood
- Interfacial Molecular Science Laboratory
- Department of Materials Science and Engineering
- Rutgers University
- Piscataway, USA
| | - Stephen H. Garofalini
- Interfacial Molecular Science Laboratory
- Department of Materials Science and Engineering
- Rutgers University
- Piscataway, USA
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Abstract
The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.
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Affiliation(s)
- Terrence M Chang
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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