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Masłowski T, Drzewiński A, Ulner J, Wojtkiewicz J, Zdanowska-Frączek M, Nordlund K, Kuronen A. Kinetic Monte Carlo simulations of proton conductivity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:012135. [PMID: 25122279 DOI: 10.1103/physreve.90.012135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Indexed: 06/03/2023]
Abstract
The kinetic Monte Carlo method is used to model the dynamic properties of proton diffusion in anhydrous proton conductors. The results have been discussed with reference to a two-step process called the Grotthuss mechanism. There is a widespread belief that this mechanism is responsible for fast proton mobility. We showed in detail that the relative frequency of reorientation and diffusion processes is crucial for the conductivity. Moreover, the current dependence on proton concentration has been analyzed. In order to test our microscopic model the proton transport in polymer electrolyte membranes based on benzimidazole C(7)H(6)N(2) molecules is studied.
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Affiliation(s)
- T Masłowski
- Institute of Physics, University of Zielona Góra, ul. Prof. Szafrana 4a, 65-516 Zielona Góra, Poland
| | - A Drzewiński
- Institute of Physics, University of Zielona Góra, ul. Prof. Szafrana 4a, 65-516 Zielona Góra, Poland
| | - J Ulner
- Institute of Low Temperature and Structure Research PAN, ul. Okólna 2, 50-422 Wrocław, Poland
| | - J Wojtkiewicz
- Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, ul. Hoża 74, 00-682 Warszawa, Poland
| | - M Zdanowska-Frączek
- Institute of Molecular Physics, Polish Academy of Sciences, ul. M. Smoluchowskiego 17, 60-179 Poznań, Poland
| | - K Nordlund
- Division of Materials Physics, Department of Physics, P.O. Box 43, FI-00014, University of Helsinki, Finland
| | - A Kuronen
- Division of Materials Physics, Department of Physics, P.O. Box 43, FI-00014, University of Helsinki, Finland
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2
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Decornez H, Hammes-Schiffer S. Effects of Model Protein Environments on the Dynamics of Proton Wires. Isr J Chem 2013. [DOI: 10.1002/ijch.199900045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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3
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Conductivity by Electron Pairs. Chem Phys 2012. [DOI: 10.1201/b11524-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Solimannejad M, Shahbazi F, Alkorta I. A Computational Study of the Potential Energy Surface of Peroxyformic Acid Dimers. J Phys Chem A 2010; 114:9388-93. [DOI: 10.1021/jp1056539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammad Solimannejad
- Quantum Chemistry Group, Department of Chemistry, Faculty of Sciences, Arak University, Arak 38156-8-8349, Iran
| | - Fatemeh Shahbazi
- Quantum Chemistry Group, Department of Chemistry, Faculty of Sciences, Arak University, Arak 38156-8-8349, Iran
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3; 28006-Madrid, Spain
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5
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Cooperativity of multiple H-bonds in influencing structural and spectroscopic features of the peptide unit of proteins. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Decornez H, Drukker K, Hurley MM, Hammes-Schiffer S. Proton transport along water chains and NADH hydride transfer in solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19981020337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sagarik K, Phonyiem M, Lao-ngam C, Chaiwongwattana S. Mechanisms of proton transfer in Nafion®: elementary reactions at the sulfonic acid groups. Phys Chem Chem Phys 2008; 10:2098-112. [DOI: 10.1039/b718480h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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9
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Solimannejad M, Shirazi SG, Scheiner S. Analysis of Complexes Pairing Hydroperoxyl Radical with Peroxyformic Acid. J Phys Chem A 2007; 111:10717-21. [PMID: 17914777 DOI: 10.1021/jp074663f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ab initio quantum calculations are used to analyze the binding of complexes pairing OOH with HOOCHO. Six minima are located on the potential energy surface, all of cyclic geometry. Of particular interest are the OH...O and CH...O H-bonds that arise in the complexes and the manner in which these interactions influence the internal properties of the subunits. The analysis is complicated by the presence of an intramolecular H-bond in the unperturbed HOOCHO molecule, which must be broken in order to form the pair of intermolecular H-bonds that are responsible for the binding in the most stable complex. The CH bond of HOOCHO is contracted, and its stretching frequency undergoes a blue shift, when this group participates in a H-bond.
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Affiliation(s)
- Mohammad Solimannejad
- Quantum Chemistry Group, Department of Chemistry, Arak University, 38156-879 Arak, Iran
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Herzog E, Frigato T, Helms V, Lancaster CRD. Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations. J Comput Chem 2007; 27:1534-47. [PMID: 16847935 DOI: 10.1002/jcc.20442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proton transfer reactions were studied in all titratable pairs of amino acid side chains where, under physiologically reasonable conditions, one amino acid may function as a donor and the other one as an acceptor. Energy barriers for shifting the proton from donor to acceptor atom were calculated by electronic structure methods at the MP2/6-31++G(d,p) level, and the well-known double-well potentials were characterized. The energy difference between both minima can be expressed by a parabola using as argument the donor-acceptor distance R(DA). In this work, the fit parameters of the quadratic expression are determined for each donor-acceptor pair. Moreover, it was found previously that the energy barriers of the reactions can be expressed by an analytical expression depending on the distance between donor and acceptor and the energy difference between donor and acceptor bound states. The validity of this approach is supported by the extensive new data set. This new parameterization of proton transfer barriers between titratable amino acid side chains allows us to very efficiently estimate proton transfer probabilities in molecular modelling studies or during classical molecular dynamics simulation of biomolecular systems.
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Affiliation(s)
- Elena Herzog
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics,Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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Solimannejad M, Scheiner S. Theoretical Evidence for a NH···XC Blue-Shifting Hydrogen Bond: Complexes Pairing Monohalomethanes with HNO. J Phys Chem A 2007; 111:4431-5. [PMID: 17474730 DOI: 10.1021/jp071695u] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Correlated ab initio calculations are used to analyze the interaction between nitrosyl hydride (HNO) and CH3X (X = F, Cl, Br). Three minima are located on the potential energy surface of each complex. The more strongly bound contains a NH...X bond, along with CH...O; CH...O and CH...N bonds occur in the less stable minimum. Binding energies of the global minimum lie in the range of 11-13 kJ/mol, and there is little sensitivity to the identity of the halogen atom. Unlike most other such hydrogen bonds, the NH covalent bond in this set of complexes becomes shorter, and its stretching frequency shifts to the blue, upon forming the NH...X hydrogen bond. The amount of this blue shift varies in the order F > Cl > Br.
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Affiliation(s)
- Mohammad Solimannejad
- Quantum Chemistry Group, Department of Chemistry, Arak University, 38156-879 Arak, Iran.
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Karpan VM, Zolotaryuk Y, Christiansen PL, Zolotaryuk AV. Discrete kink dynamics in hydrogen-bonded chains: the two-component model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:056602. [PMID: 15600774 DOI: 10.1103/physreve.70.056602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2003] [Revised: 04/06/2004] [Indexed: 05/24/2023]
Abstract
We study discrete topological solitary waves (kinks and antikinks) in two nonlinear diatomic chain models that describe the collective dynamics of proton transfers in one-dimensional hydrogen-bonded networks. The essential ingredients of the models are (i) a realistic (anharmonic) ion-proton interaction in the hydrogen bond, (ii) a harmonic coupling between the protons in adjacent hydrogen bonds, and (iii) a harmonic coupling between the nearest-neighbor heavy ions (an isolated diatomic chain with the lowest acoustic band) or instead a harmonic on-site potential for the heavy ions (a diatomic chain subject to a substrate with two optical bands), both providing a bistability of the hydrogen-bonded proton. Exact two-component (kink and antikink) discrete solutions for these models are found numerically. We compare the soliton solutions and their properties in both the one- (when the heavy ions are fixed) and two-component models. The effect of stability switchings, discovered previously for a class of one-component kink-bearing models, is shown to exist in these two-component models as well. However, the presence of the second component, i.e., the softness of the heavy-ion sublattice, brings principal differences, like a significant difference in the stability switchings behavior for the kinks and the antikinks. Water-filled carbon nanotubes are briefly discussed as possible realistic systems, where topological discrete (anti)kink states might exist.
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Affiliation(s)
- V M Karpan
- Section of Mathematical Physics, IMM, Technical University of Denmark, DK-2800 Lyngby, Denmark
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13
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Cukier R. A temperature-dependent Hartree approach for excess proton transport in hydrogen-bonded chains. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2004.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Coussan S, Manca C, Tanner C, Bach A, Leutwyler S. Ammonia-chain clusters: Vibronic spectra of 7-hydroxyquinoline⋅(NH3)2. J Chem Phys 2003. [DOI: 10.1063/1.1589482] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Karpan VM, Zolotaryuk Y, Christiansen PL, Zolotaryuk AV. Discrete kink dynamics in hydrogen-bonded chains: the one-component model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 66:066603. [PMID: 12513425 DOI: 10.1103/physreve.66.066603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2002] [Indexed: 05/24/2023]
Abstract
We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on-site potential plays the role of the proton potential in the hydrogen bond. The system supports a rich variety of stationary kink solutions with different symmetry properties. We study the stability and bifurcation structure of all these stationary kink states. An exactly solvable model with a piecewise "parabola-constant" approximation of the double-Morse potential is suggested and studied analytically. The dependence of the Peierls-Nabarro potential on the system parameters is studied. Discrete traveling-wave solutions of a narrow permanent profile are shown to exist, depending on the anharmonicity of the Morse potential and the cooperativity of the hydrogen bond (the coupling constant of the interaction between nearest-neighbor protons).
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Affiliation(s)
- V M Karpan
- Section of Mathematical Physics, IMM, Technical University of Denmark, DK-2800 Lyngby, Denmark
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Zolotaryuk AV, Peyrard M, Spatschek KH. Collective proton transport with weak proton-proton coupling. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:5706-10. [PMID: 11089129 DOI: 10.1103/physreve.62.5706] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2000] [Indexed: 11/07/2022]
Abstract
A mechanism based on the peculiar dynamical properties of the hydrogen bond is suggested to describe fast proton transfers in hydrogen-bonded chains with realistic (weak) intersite proton-proton interactions. For this purpose, a two-sublattice model is suggested and studied analytically that admits an exact soliton solution. The solitons, which are topological objects (kinks and antikinks) on the one hand, but dynamical entities (like Boussinesq solitons) on the other hand, are shown to have a sufficiently large width to allow free propagation along the chain.
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Affiliation(s)
- AV Zolotaryuk
- Bogolyubov Institute for Theoretical Physics, 03143 Kiev, Ukraine
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Bach A, Coussan S, Müller A, Leutwyler S. Water-chain clusters: Vibronic spectra of 7-hydroxyquinoline⋅(H2O)2. J Chem Phys 2000. [DOI: 10.1063/1.480672] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Fabian WMF, Schweiger K, Weis R. Effect of substituents on the formation of isomeric isoxazolo heterocycles: rationalization by semi-empirical PM3 molecular orbital calculations. J PHYS ORG CHEM 1999. [DOI: 10.1002/(sici)1099-1395(199908)12:8<635::aid-poc166>3.0.co;2-q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Decornez H, Drukker K, Hammes-Schiffer S. Solvation and Hydrogen-Bonding Effects on Proton Wires. J Phys Chem A 1999. [DOI: 10.1021/jp984775u] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hélène Decornez
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Karen Drukker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Sharon Hammes-Schiffer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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Hammes-Schiffer S. Mixed Quantum/Classical Dynamics of Hydrogen Transfer Reactions. J Phys Chem A 1998. [DOI: 10.1021/jp983246n] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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Drukker K, de Leeuw SW, Hammes-Schiffer S. Proton transport along water chains in an electric field. J Chem Phys 1998. [DOI: 10.1063/1.476095] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Drukker K, Hammes-Schiffer S. An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains. J Chem Phys 1997. [DOI: 10.1063/1.474397] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Cukier RI. Proton-Coupled Electron Transfer Reactions: Evaluation of Rate Constants. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961025g] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
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Vener M. Intensity distribution in the fluorescence low-frequency mode progressions of the “slightly” asymmetric hydrogen bonded AHB fragment. Chem Phys 1994. [DOI: 10.1016/0301-0104(94)00271-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Vener MV, Scheiner S, Sokolov ND. Theoretical study of hydrogen bonding and proton transfer in the ground and lowest excited singlet states of tropolone. J Chem Phys 1994. [DOI: 10.1063/1.467941] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zolotaryuk AV, Savin AV, Economou EN. Nonlinear collective proton dynamics in ice crystal: Square lattice model for ionic defects. PHYSICAL REVIEW LETTERS 1994; 73:2871-2874. [PMID: 10057217 DOI: 10.1103/physrevlett.73.2871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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27
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Cappadonia M, Kornyshev AA, Krause S, Kuznetsov AM, Stimming U. Low‐temperature proton transport in clathrates. J Chem Phys 1994. [DOI: 10.1063/1.468260] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Karpfen A, Yanovitskii O. Structure and vibrational spectra of neutral, protonated and deprotonated hydrogen bonded polymers: an ab initio SCF study on chain-like hydrogen fluoride clusters. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0166-1280(94)80120-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yanovitskii O, Vlastou-Tsinganos G, Flytzanis N. Self-consistent-phonon-approximation study of a double Morse hydrogen-bonded chain. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:12645-12654. [PMID: 10007634 DOI: 10.1103/physrevb.48.12645] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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