201
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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202
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Fifen JJ, Agmon N. Structure and Spectroscopy of Hydrated Sodium Ions at Different Temperatures and the Cluster Stability Rules. J Chem Theory Comput 2016; 12:1656-73. [DOI: 10.1021/acs.jctc.6b00038] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean Jules Fifen
- The
Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department
of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Noam Agmon
- The
Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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203
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Mandal A, Tokmakoff A. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy. J Chem Phys 2016; 143:194501. [PMID: 26590536 DOI: 10.1063/1.4935174] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O-H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm(-1). We observe rapid vibrational relaxation processes on 150-250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1-2 ps time scales. Furthermore, the O-H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.
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Affiliation(s)
- Aritra Mandal
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
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204
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Ge X, Gunner MR. Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Proteins 2016; 84:639-54. [DOI: 10.1002/prot.25013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/24/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaoxia Ge
- Physics Department; City College of New York; New York NY 10031
| | - M. R. Gunner
- Physics Department; City College of New York; New York NY 10031
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205
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Gasparotto P, Hassanali AA, Ceriotti M. Probing Defects and Correlations in the Hydrogen-Bond Network of ab Initio Water. J Chem Theory Comput 2016; 12:1953-64. [DOI: 10.1021/acs.jctc.5b01138] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piero Gasparotto
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ali A. Hassanali
- Condensed
Matter Physics Section, The Abdus Salaam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste Italy
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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206
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Willow SY, Zeng XC, Xantheas SS, Kim KS, Hirata S. Why Is MP2-Water "Cooler" and "Denser" than DFT-Water? J Phys Chem Lett 2016; 7:680-684. [PMID: 26821830 DOI: 10.1021/acs.jpclett.5b02430] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water require lower temperature and pressure than DFT/GGA to keep water liquid. Here we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the different temperatures and pressures between DFT/GGA and MP2 at which the simulated water displays the experimentally observed liquid structure under the ambient conditions can be largely explained by their differences in polarizability and dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for DFT-water to be liquid. MP2 gives a stronger dispersion interaction and thus shorter intermolecular distances than dispersionless DFT/GGA, which is why MP2-water is denser than DFT-water under the same external pressure.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska at Lincoln , 536 Hamilton Hall, Lincoln, Nebraska 68588, United States
| | - Sotiris S Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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207
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Xi E, Remsing RC, Patel AJ. Sparse Sampling of Water Density Fluctuations in Interfacial Environments. J Chem Theory Comput 2016; 12:706-13. [DOI: 10.1021/acs.jctc.5b01037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erte Xi
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard C. Remsing
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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208
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Bhatt H, Murli C, Mishra AK, Verma AK, Garg N, Deo MN, Chitra R, Sharma SM. Hydrogen Bond Symmetrization in Glycinium Oxalate under Pressure. J Phys Chem B 2016; 120:851-9. [DOI: 10.1021/acs.jpcb.5b11507] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himal Bhatt
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Chitra Murli
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - A. K. Mishra
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Ashok K. Verma
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Nandini Garg
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - M. N. Deo
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - R. Chitra
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Surinder M. Sharma
- High Pressure and Synchrotron Radiation Physics Division, ‡Solid State Physics
Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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209
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Rossini E, Knapp EW. Proton solvation in protic and aprotic solvents. J Comput Chem 2016; 37:1082-91. [DOI: 10.1002/jcc.24297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emanuele Rossini
- Institute of Chemistry and Biochemistry, Freie Universität Berlin; Fabeckstr. 36a Berlin D-14195 Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Freie Universität Berlin; Fabeckstr. 36a Berlin D-14195 Germany
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210
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Murdachaew G, Nathanson GM, Benny Gerber R, Halonen L. Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations. Phys Chem Chem Phys 2016; 18:29756-29770. [DOI: 10.1039/c6cp06071d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.
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Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| | | | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
- Institute of Chemistry and the Fritz Haber Research Center
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
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211
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Cassone G, Creazzo F, Giaquinta PV, Saija F, Marco Saitta A. Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field. Phys Chem Chem Phys 2016; 18:23164-73. [DOI: 10.1039/c6cp03926j] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of salty water under an electric field reveal two regimes of the relative mobilities of chlorine and sodium ions. When water dissociation and proton transfer are actived at strong field intensities, the presence of the ions hinders the efficiency of the proton transfer mechanism.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics – Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Fabrizio Creazzo
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environment
- UMR8587 (CHARMMMAT)
- Université d'Evry val d'Essone
- 91025 Evry
- France
| | - Paolo V. Giaquinta
- Università degli Studi di Messina
- Dipartimento di Scienze Matematiche e Informatiche
- Scienze Fisiche e Scienze della Terra
- 98166 Messina
- Italy
| | | | - A. Marco Saitta
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie
- 75005 Paris
- France
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212
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Fuchs EC, Bitschnau B, Wexler AD, Woisetschläger J, Freund FT. A Quasi-Elastic Neutron Scattering Study of the Dynamics of Electrically Constrained Water. J Phys Chem B 2015; 119:15892-900. [DOI: 10.1021/acs.jpcb.5b10751] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elmar C. Fuchs
- Wetsus European
Centre of Excellence for Sustainable Water Technology, Agora 1, 8900 CC Leeuwarden, The Netherlands
| | | | - Adam D. Wexler
- Wetsus European
Centre of Excellence for Sustainable Water Technology, Agora 1, 8900 CC Leeuwarden, The Netherlands
| | | | - Friedemann T. Freund
- NASA
Ames Research Center, NASA Program and Projects Division PX, Moffett
Field, CA, and Department of Physics, San Jose State University, San Jose, California 95192, United States
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213
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Nir O, Bishop NF, Lahav O, Freger V. Modeling pH variation in reverse osmosis. WATER RESEARCH 2015; 87:328-335. [PMID: 26447944 DOI: 10.1016/j.watres.2015.09.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/17/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
The transport of hydronium and hydroxide ions through reverse osmosis membranes constitutes a unique case of ionic species characterized by uncommonly high permeabilities. Combined with electromigration, this leads to complex behavior of permeate pH, e.g., negative rejection, as often observed for monovalent ions in nanofiltration of salt mixtures. In this work we employed a rigorous phenomenological approach combined with chemical equilibrium to describe the trans-membrane transport of hydronium and hydroxide ions along with salt transport and calculate the resulting permeate pH. Starting from the Nernst-Planck equation, a full non-linear transport equation was derived, for which an approximate solution was proposed based on the analytical solution previously developed for trace ions in a dominant salt. Using the developed approximate equation, transport coefficients were deduced from experimental results obtained using a spiral wound reverse osmosis module operated under varying permeate flux (2-11 μm/s), NaCl feed concentrations (0.04-0.18 M) and feed pH values (5.5-9.0). The approximate equation agreed well with the experimental results, corroborating the finding that diffusion and electromigration, rather than a priori neglected convection, were the major contributors to the transport of hydronium and hydroxide. The approach presented here has the potential to improve the predictive capacity of reverse osmosis transport models for acid-base species, thereby improving process design/control.
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Affiliation(s)
- Oded Nir
- Faculty of Civil and Environmental Engineering, Technion - IIT, Haifa, 32000, Israel
| | | | - Ori Lahav
- Faculty of Civil and Environmental Engineering, Technion - IIT, Haifa, 32000, Israel
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214
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Biswas R, Tse YLS, Tokmakoff A, Voth GA. Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. J Phys Chem B 2015; 120:1793-804. [PMID: 26575795 DOI: 10.1021/acs.jpcb.5b09466] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium is transiently solvated by four water molecules, similar to the typical solvation structure of water, by accepting a weak hydrogen bond from the fourth water molecule. A new version 3.2 multistate empirical valence bond (MS-EVB 3.2) model for the hydrated excess proton incorporating this presolvation behavior is therefore developed. The classical MS-EVB simulations show similar structural properties as those of the previous model but with significantly improved diffusive behavior. The inclusion of nuclear quantum effects in the MS-EVB also provides an even better description of the proton diffusion rate. To quantify the influence of anharmonicity, a second model (aMS-EVB 3.2) is developed using the anharmonic aSPC/Fw water model, which provides similar structural properties but improved spectroscopic responses at high frequencies.
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Affiliation(s)
- Rajib Biswas
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ying-Lung Steve Tse
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
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215
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Thämer M, De Marco L, Ramasesha K, Mandal A, Tokmakoff A. Ultrafast 2D IR spectroscopy of the excess proton in liquid water. Science 2015; 350:78-82. [DOI: 10.1126/science.aab3908] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite decades of study, the structures adopted to accommodate an excess proton in water and the mechanism by which they interconvert remain elusive. We used ultrafast two-dimensional infrared (2D IR) spectroscopy to investigate protons in aqueous hydrochloric acid solutions. By exciting O–H stretching vibrations and detecting the spectral response throughout the mid-IR region, we observed the interaction between the stretching and bending vibrations characteristic of the flanking waters of the Zundel complex, [H(H2O)2]+, at 3200 and 1760 cm−1, respectively. From time-dependent shifts of the stretch-bend cross peak, we determined a lower limit on the lifetime of this complex of 480 femtoseconds. These results suggest a key role for the Zundel complex in aqueous proton transfer.
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216
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Lounasvuori MM, Rosillo-Lopez M, Salzmann CG, Caruana DJ, Holt KB. The influence of acidic edge groups on the electrochemical performance of graphene nanoflakes. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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217
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Ho MH, Rousseau R, Roberts JAS, Wiedner ES, Dupuis M, DuBois DL, Bullock RM, Raugei S. Ab Initio-Based Kinetic Modeling for the Design of Molecular Catalysts: The Case of H2 Production Electrocatalysts. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01152] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming-Hsun Ho
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - Roger Rousseau
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - John A. S. Roberts
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - Eric S. Wiedner
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - Michel Dupuis
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - Daniel L. DuBois
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - R. Morris Bullock
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
| | - Simone Raugei
- Center
for Molecular Electrocatalysis, Pacific Northwest National Laboratory, P.O. Box 999, K1-83, Richland, Washington 99352, United States
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218
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Fournier JA, Wolke CT, Johnson MA, Odbadrakh TT, Jordan KD, Kathmann SM, Xantheas SS. Snapshots of Proton Accommodation at a Microscopic Water Surface: Understanding the Vibrational Spectral Signatures of the Charge Defect in Cryogenically Cooled H+(H2O)n=2–28 Clusters. J Phys Chem A 2015; 119:9425-40. [DOI: 10.1021/acs.jpca.5b04355] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Joseph A. Fournier
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Conrad T. Wolke
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Tuguldur T. Odbadrakh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15620, United States
| | - Kenneth D. Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15620, United States
| | - Shawn M. Kathmann
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Sotiris S. Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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219
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Abstract
Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.
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220
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Pylaeva S, Allolio C, Koeppe B, Denisov GS, Limbach HH, Sebastiani D, Tolstoy PM. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system. Phys Chem Chem Phys 2015; 17:4634-44. [PMID: 25586486 DOI: 10.1039/c4cp04727c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.
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Affiliation(s)
- Svetlana Pylaeva
- Department of Physics, St. Petersburg State University, Ulianovskaya st. 3, 198504 St. Petersburg, Russia.
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221
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Jezierska A, Panek JJ. “Zwitterionic Proton Sponge” Hydrogen Bonding Investigations on the Basis of Car–Parrinello Molecular Dynamics. J Chem Inf Model 2015; 55:1148-57. [DOI: 10.1021/ci500560g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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222
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Clark JK, Habenicht BF, Paddison SJ. Ab initio molecular dynamics simulations of aqueous triflic acid confined in carbon nanotubes. Phys Chem Chem Phys 2015; 16:16465-79. [PMID: 24983213 DOI: 10.1039/c4cp01066c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ab initio molecular dynamics simulations were performed to investigate the effects of nanoscale confinement on the structural and dynamical properties of aqueous triflic acid (CF3SO3H). Single-walled carbon nanotubes (CNTs) with diameters ranging from ∼11 to 14 Å were used as confinement vessels, and the inner surface of the CNT were either left bare or fluorinated to probe the influence of the confined environment on structural and dynamical properties of the water and triflic acidic. The systems were simulated at hydration levels of n = 1-3 H2O/CF3SO3H. Proton dissociation expectedly increased with increasing hydration. Along with the level of hydration, hydrogen bond connectivity between the triflic acid molecules, both directly and via a single water molecule, played a role on proton dissociation. Direct hydrogen bonding between the CF3SO3H molecules, most commonly found in the larger bare CNT, also promoted interactions between water molecules allowing for greater separation of the dissociated protons from the CF3SO3(-) as the hydration level was increased. However, this also resulted in a decrease in the overall proportion of dissociated protons. The confinement dimensions altered both the hydrogen bond network and the distribution of water molecules where the H2O in the fluorinated CNTs tended to form small clusters with less proton dissociation at n = 1 and 2 but the highest at n = 3. In the absence of nearby hydrogen bond accepting sites from H2O or triflic acid SO3H groups, the water molecules formed weak hydrogen bonds with the fluorine atoms. In the bare CNT systems, these involved the CF3 groups of triflic acid and were more frequently observed when direct hydrogen bonding between CF3SO3H hindered potential hydrogen bonding sites. In the fluorinated tubes, interactions with the covalently bound fluorine atoms of the CNT wall dominated which appear to stabilize the hydrogen bond network. Increasing the hydration level increased the frequency of the OH···F (CNT) hydrogen bonding which was highly pronounced in the smaller fluorinated CNT indicating an influence on the confinement dimensions on these interactions.
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Affiliation(s)
- Jeffrey K Clark
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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223
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De Wispelaere K, Ensing B, Ghysels A, Meijer EJ, Van Speybroeck V. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics. Chemistry 2015; 21:9385-96. [DOI: 10.1002/chem.201500473] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Indexed: 11/05/2022]
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224
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225
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Mandal A, Ramasesha K, De Marco L, Tokmakoff A. Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy. J Chem Phys 2015; 140:204508. [PMID: 24880302 DOI: 10.1063/1.4878490] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The infrared spectra of aqueous solutions of NaOH and other strong bases exhibit a broad continuum absorption for frequencies between 800 and 3500 cm(-1), which is attributed to the strong interactions of the OH(-) ion with its solvating water molecules. To provide molecular insight into the origin of the broad continuum absorption feature, we have performed ultrafast transient absorption and 2DIR experiments on aqueous NaOH by exciting the O-H stretch vibrations and probing the response from 1350 to 3800 cm(-1) using a newly developed sub-70 fs broadband mid-infrared source. These experiments, in conjunction with harmonic vibrational analysis of OH(-)(H2O)n (n = 17) clusters, reveal that O-H stretch vibrations of aqueous hydroxides arise from coupled vibrations of multiple water molecules solvating the ion. We classify the vibrations of the hydroxide complex by symmetry defined by the relative phase of vibrations of the O-H bonds hydrogen bonded to the ion. Although broad and overlapping spectral features are observed for 3- and 4-coordinate ion complexes, we find a resolvable splitting between asymmetric and symmetric stretch vibrations, and assign the 2850 cm(-1) peak infrared spectra of aqueous hydroxides to asymmetric stretch vibrations.
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Affiliation(s)
- Aritra Mandal
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Krupa Ramasesha
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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226
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Zarzycki P, Smith DM, Rosso KM. Proton Dynamics on Goethite Nanoparticles and Coupling to Electron Transport. J Chem Theory Comput 2015; 11:1715-24. [DOI: 10.1021/ct500891a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Piotr Zarzycki
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Dayle M. Smith
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin M. Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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227
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Nag TN, Das T, Mondal S, Maity A, Purkayastha P. Promoting the "water-wire" mechanism of double proton transfer in [2,2'-bipyridyl]-3,3'-diol by porous gold nanoparticles. Phys Chem Chem Phys 2015; 17:6572-6. [PMID: 25662192 DOI: 10.1039/c4cp03968h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of nanopores in porous gold nanoparticles (Au NPs) on excited-state double proton transfer (DPT) in [2,2'-bipyridyl]-3,3'-diol (BP(OH)2) in an aqueous environment is the main focus of the present work. DPT in BP(OH)2 is known to take place through two mechanisms. In a bulk environment, an open solvated molecule facilitates the process and emits at 460 nm whereas, in a confined situation, formation of a "water wire" between the prototropic centers leads to the transfer of protons. It has been shown spectroscopically in the present study that in the nanovessels provided by nanoporous Au NPs, the unconventional mechanism of DPT through the formation of a "water wire" is promoted due to the presence of a limited number of water molecules around the probe. Experiments in the presence of solid pure Au, Ag and Au/Ag NPs were performed to support our proposition. Time-resolved fluorescence spectral changes confirm our findings.
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Affiliation(s)
- Tarak Nath Nag
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India.
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228
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Bekçioğlu G, Allolio C, Sebastiani D. Water Wires in Aqueous Solutions from First-Principles Calculations. J Phys Chem B 2015; 119:4053-60. [DOI: 10.1021/jp5121417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gül Bekçioğlu
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Christoph Allolio
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, CZ-16610 Prague 6, Czech Republic
| | - Daniel Sebastiani
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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229
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Donaldson SH, Røyne A, Kristiansen K, Rapp MV, Das S, Gebbie MA, Lee DW, Stock P, Valtiner M, Israelachvili J. Developing a general interaction potential for hydrophobic and hydrophilic interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2051-64. [PMID: 25072835 DOI: 10.1021/la502115g] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We review direct force measurements on a broad class of hydrophobic and hydrophilic surfaces. These measurements have enabled the development of a general interaction potential per unit area, W(D) = -2γ(i)Hy exp(-D/D(H)) in terms of a nondimensional Hydra parameter, Hy, that applies to both hydrophobic and hydrophilic interactions between extended surfaces. This potential allows one to quantitatively account for additional attractions and repulsions not included in the well-known combination of electrostatic double layer and van der Waals theories, the so-called Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The interaction energy is exponentially decaying with decay length D(H) ≈ 0.3-2 nm for both hydrophobic and hydrophilic interactions, with the exact value of D(H) depending on the precise system and conditions. The pre-exponential factor depends on the interfacial tension, γ(i), of the interacting surfaces and Hy. For Hy > 0, the interaction potential describes interactions between partially hydrophobic surfaces, with the maximum hydrophobic interaction (i.e., two fully hydrophobic surfaces) corresponding to Hy = 1. Hydrophobic interactions between hydrophobic monolayer surfaces measured with the surface forces apparatus (SFA) are shown to be well described by the proposed interaction potential. The potential becomes repulsive for Hy < 0, corresponding to partially hydrophilic (hydrated) interfaces. Hydrated surfaces such as mica, silica, and lipid bilayers are discussed and reviewed in the context of the values of Hy appropriate for each system.
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Affiliation(s)
- Stephen H Donaldson
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106-5080, United States
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230
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Bankura A, Chandra A. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations. J Chem Phys 2015; 142:044701. [DOI: 10.1063/1.4905495] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arindam Bankura
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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231
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Abstract
Using ab initio simulations, we explore the glassy landscape of the OH(-)(H2O)20 cluster and its infrared spectrum. We show that the OH(-) has an amphiphilic Janus-type behavior like the hydronium ion induced by the ability of its O-H bond to be buried inside of the cluster or exposed at the surface with different coordination numbers. Recent infrared experiments of aqueous NaOH have found two pronounced peaks at 2000 and 2850 cm(-1) [Mandal, A.; J. Chem. Phys. 2014, 140, 1-12]. The microscopic origins of these spectral features remain elusive. Herein, we disentangle the contribution of the spectra between 1700 and 3000 cm(-1) in terms of the microscopic solvation structure of OH(-) and dub this as the amphiphilic band. The delocalized nature of OH(-) results in a red shift to the O-H stretch, which mixes with bend-vibrations, the extent to which is tuned by the local coordination number. These results have important bearing on understanding the spectroscopic signatures of OH(-) in environments like the air-water interface.
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Affiliation(s)
- Yanier Crespo
- The Abdus Salam ICTP, Strada Costiera 11, I-34151 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam ICTP, Strada Costiera 11, I-34151 Trieste, Italy
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232
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Tse YLS, Knight C, Voth GA. An analysis of hydrated proton diffusion in ab initio molecular dynamics. J Chem Phys 2015; 142:014104. [DOI: 10.1063/1.4905077] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying-Lung Steve Tse
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA
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233
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Decka D, Schwaab G, Havenith M. A THz/FTIR fingerprint of the solvated proton: evidence for Eigen structure and Zundel dynamics. Phys Chem Chem Phys 2015; 17:11898-907. [DOI: 10.1039/c5cp01035g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Zundel (orange), Eigen (red) and hydration water (light blue) contributions to the THz/FIR extinction of the solvated proton.
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Affiliation(s)
- Dominique Decka
- Department of Physical Chemistry II
- Ruhr-University Bochum
- Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II
- Ruhr-University Bochum
- Germany
| | - Martina Havenith
- Department of Physical Chemistry II
- Ruhr-University Bochum
- Germany
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234
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Méndez-Hurtado J, Menéndez MI, López R, Ruiz-López MF. Unraveling the intramolecular cyclization mechanism of oxidized tryptophan in aqueous solution as a function of pH. Org Biomol Chem 2015; 13:8695-702. [DOI: 10.1039/c5ob01193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
pH tunes the mechanism of the intramolecular cyclization of 3a-substituted tryptophan derivatives.
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Affiliation(s)
| | - M. Isabel Menéndez
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | - Ramón López
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | - Manuel F. Ruiz-López
- Theoretical Chemistry and Biochemistry Group
- SRSMC
- Nancy-University CNRS
- 54506 Vandoeuvre-lès-Nancy Cedex
- France
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235
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Jiang T, Boereboom JM, Michel C, Fleurat-Lessard P, Bulo RE. Proton Transfer in Aqueous Solution: Exploring the Boundaries of Adaptive QM/MM. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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236
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Hammerich AD, Finlayson-Pitts BJ, Gerber RB. Mechanism for formation of atmospheric Cl atom precursors in the reaction of dinitrogen oxides with HCl/Cl− on aqueous films. Phys Chem Chem Phys 2015; 17:19360-70. [DOI: 10.1039/c5cp02664d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of atmospheric chlorine atom precursors ClNO2 and ClNO in the reaction of HCl with oxides of nitrogen on a water film: left – formation of N–Cl bond as N–O bond breaks; right – concurrent changes in Mulliken charges.
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Affiliation(s)
| | | | - R. Benny Gerber
- Department of Chemistry
- University of California Irvine
- Irvine
- USA
- Institute of Chemistry and the Fritz Haber Research Center
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237
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Cuny J, Hassanali AA. Ab Initio Molecular Dynamics Study of the Mechanism of Proton Recombination with a Weak Base. J Phys Chem B 2014; 118:13903-12. [DOI: 10.1021/jp507246e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jérôme Cuny
- Laboratoire
de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
- Department
of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich and Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Ali A. Hassanali
- Condensed
Matter Physics Section, The Abdus Salaam International Center for Theoretical Physics, Strada Costiera 11, Trieste I-34151, Italy
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238
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Spura T, John C, Habershon S, Kühne TD. Nuclear quantum effects in liquid water from path-integral simulations using anab initioforce-matching approach. Mol Phys 2014. [DOI: 10.1080/00268976.2014.981231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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239
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Xie Y, Luk HL, Yang X, Glusac KD. Excited-State Hydroxide Ion Transfer from a Model Xanthenol Photobase. J Phys Chem B 2014; 119:2498-506. [DOI: 10.1021/jp5080169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yun Xie
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Hoi Ling Luk
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Xin Yang
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Ksenija D. Glusac
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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240
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Giberti F, Hassanali AA, Ceriotti M, Parrinello M. The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water. J Phys Chem B 2014; 118:13226-35. [DOI: 10.1021/jp507752e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Federico Giberti
- Department
of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Ali A. Hassanali
- The Abdus Salaam International Center for Theoretical Physics, Condensed Matter Physics Section, Strada Costiera 11, I-34151 Trieste, Italy
| | - Michele Ceriotti
- Laboratory of Computational
Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Parrinello
- Department
of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano, Switzerland
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241
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Cassone G, Giaquinta PV, Saija F, Saitta AM. Effect of Electric Field Orientation on the Mechanical and Electrical Properties of Water Ices: An Ab-initio Study. J Phys Chem B 2014; 118:12717-24. [DOI: 10.1021/jp507376v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Giuseppe Cassone
- Dipartimento
di Fisica e di Scienze della Terra, Università degli Studi di Messina, Contrada Papardo, 98166 Messina, Italy
- CNR-IPCF, Viale Ferdinando Stagno d’Alcontres
37, 98158 Messina, Italy
- UMR 7590, IMPMC,
UPMC Univ Paris 06, Sorbonne Universités, F-75005 Paris, France
- UMR 7590, IMPMC, CNRS, F-75005 Paris, France
| | - Paolo V. Giaquinta
- Dipartimento
di Fisica e di Scienze della Terra, Università degli Studi di Messina, Contrada Papardo, 98166 Messina, Italy
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d’Alcontres
37, 98158 Messina, Italy
| | - A. Marco Saitta
- UMR 7590, IMPMC,
UPMC Univ Paris 06, Sorbonne Universités, F-75005 Paris, France
- UMR 7590, IMPMC, CNRS, F-75005 Paris, France
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242
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Tadokoro M, Ohata Y, Shimazaki Y, Ishimaru S, Yamada T, Nagao Y, Sugaya T, Isoda K, Suzuki Y, Kitagawa H, Matsui H. Anomalous Enhancement of Proton Conductivity for Water Molecular Clusters Stabilized in Interstitial Spaces of Porous Molecular Crystals. Chemistry 2014; 20:13698-709. [DOI: 10.1002/chem.201402900] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Makoto Tadokoro
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1‐3, Shinjuku‐ku, Tokyo 162‐8601 (Japan), Fax: (+81) 3 3620 3858
| | - Yuki Ohata
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1‐3, Shinjuku‐ku, Tokyo 162‐8601 (Japan), Fax: (+81) 3 3620 3858
| | - Yuriko Shimazaki
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1‐3, Shinjuku‐ku, Tokyo 162‐8601 (Japan), Fax: (+81) 3 3620 3858
| | - Shin'ichi Ishimaru
- Department of Environmental Materials Science, School of Engineering, Tokyo Denki University, Senjuasahimachi 5, Adachi‐ku, Tokyo 120‐8551 (Japan)
| | - Teppei Yamada
- Department of Materials Science: New Materials Design and Synthesis (Japan), Advanced Institute of Science and Technology School of Materials Science, 1–1 Asahidai, Nomi, Ishikawa 923‐1292 (Japan)
| | - Yuki Nagao
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto‐oka, Nishi‐ku, Fukuoka 819‐0395 (Japan)
| | - Tomoaki Sugaya
- Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Waseda University, 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 (Japan)
| | - Kyosuke Isoda
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1‐3, Shinjuku‐ku, Tokyo 162‐8601 (Japan), Fax: (+81) 3 3620 3858
| | - Yuta Suzuki
- Department of Physics, Graduate School of Science, Tohoku University, 6–3 Aoba, Aramakiaza, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hiroshi Kitagawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitasirakawaoiwake‐cho, Sakyo‐ku, Kyoto 606‐8502 (Japan)
| | - Hiroshi Matsui
- Department of Physics, Graduate School of Science, Tohoku University, 6–3 Aoba, Aramakiaza, Aoba‐ku, Sendai 980‐8578 (Japan)
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243
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Kühne TD. Second generation Car-Parrinello molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1176] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas D. Kühne
- Institute of Physical Chemistry and Center for Computational Sciences; Johannes Gutenberg University Mainz; Mainz Germany
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244
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Cassone G, Giaquinta PV, Saija F, Saitta AM. Proton Conduction in Water Ices under an Electric Field. J Phys Chem B 2014; 118:4419-24. [DOI: 10.1021/jp5021356] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Giuseppe Cassone
- Dipartimento
di Fisica e di Scienze della Terra, Università degli Studi di Messina, Contrada Papardo, 98166 Messina, Italy
- CNR-IPCF, Viale
Ferdinando Stagno d’Alcontres 37, 98158 Messina, Italy
- UPMC Univ
Paris
06, UMR 7590, IMPMC, F-75005 Paris, France
- CNRS, UMR 7590,
IMPMC, F-75005 Paris, France
| | - Paolo V. Giaquinta
- Dipartimento
di Fisica e di Scienze della Terra, Università degli Studi di Messina, Contrada Papardo, 98166 Messina, Italy
| | - Franz Saija
- CNR-IPCF, Viale
Ferdinando Stagno d’Alcontres 37, 98158 Messina, Italy
| | - A. Marco Saitta
- UPMC Univ
Paris
06, UMR 7590, IMPMC, F-75005 Paris, France
- CNRS, UMR 7590,
IMPMC, F-75005 Paris, France
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245
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Dagrada M, Casula M, Saitta AM, Sorella S, Mauri F. Quantum Monte Carlo Study of the Protonated Water Dimer. J Chem Theory Comput 2014; 10:1980-93. [DOI: 10.1021/ct401077x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Dagrada
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Michele Casula
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Antonino M. Saitta
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Sandro Sorella
- International School for Advanced Studies (SISSA) Via Beirut 2,4 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste, Italy
| | - Francesco Mauri
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
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246
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Roberts ST, Mandal A, Tokmakoff A. Local and collective reaction coordinates in the transport of the aqueous hydroxide ion. J Phys Chem B 2014; 118:8062-9. [PMID: 24666116 DOI: 10.1021/jp501145p] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We investigate local and collective reaction coordinates for the structural diffusion of the hydroxide ion in dilute aqueous NaOH solution using a multistate empirical valence bond (MS-EVB) simulation. We characterize a 15 fs time scale associated with shifting of the equally shared proton within a Zundel-like H3O2(-) ion to form a water molecule, a 550 fs relaxation from this transition state largely guided by electrostatic fluctuations of the surrounding environment, and a 9.6 ps time scale that corresponds to the solvation of the water molecule formed by the proton transfer event. When individual proton transfer events are examined, we are unable to identify a unique transition state solely on the basis of a decrease in the hydroxide ion's coordination number. Instead, we find that the collective electric field along the proton transfer direction is better suited to describe the creation and relaxation of Zundel-like transition states that allow structural diffusion of the hydroxide ion.
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Affiliation(s)
- Sean T Roberts
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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247
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DeCoursey TE, Hosler J. Philosophy of voltage-gated proton channels. J R Soc Interface 2014; 11:20130799. [PMID: 24352668 PMCID: PMC3899857 DOI: 10.1098/rsif.2013.0799] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 02/02/2023] Open
Abstract
In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.
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Affiliation(s)
- Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, 1750 West Harrison, Chicago, IL 60612, USA
| | - Jonathan Hosler
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
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248
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Abstract
The dynamics of water exhibits anomalous behavior in the presence of different electrolytes. Recent experiments [Kim JS, Wu Z, Morrow AR, Yethiraj A, Yethiraj A (2012) J Phys Chem B 116(39):12007-12013] have found that the self-diffusion of water (Dw) can either be enhanced or suppressed around CsI and NaCl, respectively, relative to that of neat water. Here we show that unlike classical empirical potentials, ab initio molecular dynamics simulations successfully reproduce the qualitative trends observed experimentally. These types of phenomena have often been rationalized in terms of the "structure-making" or "structure-breaking" effects of different ions on the solvent, although the microscopic origins of these features have remained elusive. Rather than disrupting the network in a significant manner, the electrolytes studied here cause rather subtle changes in both structural and dynamical properties of water. In particular, we show that water in the ab initio molecular dynamics simulations is characterized by dynamic heterogeneity, which turns out to be critical in reproducing the experimental trends.
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249
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Angulo-Sherman A, Mercado-Uribe H. Water under inner pressure: a dielectric spectroscopy study. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022406. [PMID: 25353481 DOI: 10.1103/physreve.89.022406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 06/04/2023]
Abstract
Water is the most studied substance on Earth. However, it is not completely understood why its structural and dynamical properties give rise to some anomalous behaviors. Some of them emerge when experiments at low temperatures and/or high pressures are performed. Here we report dielectric measurements on cold water under macroscopically constrained conditions, i.e., water in a large container at constant volume that cannot freeze below the melting point. The inner pressure in these conditions shifts the α relaxation peak to similar frequencies as seen in ice Ih. At 267 K we observe a peculiar response possibly due to the Grotthuss mechanism. At 251 K (the triple point) ice III forms.
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250
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Bekçioğlu G, Allolio C, Ekimova M, Nibbering ETJ, Sebastiani D. Competition between excited state proton and OH− transport via a short water wire: solvent effects open the gate. Phys Chem Chem Phys 2014; 16:13047-51. [DOI: 10.1039/c4cp00970c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the acid–base proton exchange reaction in a microsolvated bifunctional chromophore by means of quantum chemical calculations.
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Affiliation(s)
- Gül Bekçioğlu
- Physics Department
- Freie Universität Berlin
- 14195 Berlin, Germany
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
| | - Christoph Allolio
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale), Germany
| | - Maria Ekimova
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin, Germany
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin, Germany
| | - Daniel Sebastiani
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale), Germany
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