1
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Jurado Romero A, Calero C, Sibert EL, Rey R. High energy vibrational excitations of nitromethane in liquid water. J Chem Phys 2023; 158:2890474. [PMID: 37184013 DOI: 10.1063/5.0147459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
The pathways and timescales of vibrational energy flow in nitromethane are investigated in both gas and condensed phases using classical molecular mechanics, with a particular focus on relaxation in liquid water. We monitor the flow of excess energy deposited in vibrational modes of nitromethane into the surrounding solvent. A marked energy flux anisotropy is found when nitromethane is immersed in liquid water, with a preferential flow to those water molecules in contact to the nitro group. The factors that permit such anisotropic energy relaxation are discussed, along with the potential implications on the molecule's non-equilibrium dynamics. In addition, the energy flux analysis allows us to identify the solvent motions responsible for the uptake of solute energy, confirming the crucial role of water librations. Finally, we also show that no anisotropic vibrational energy relaxation occurs when nitromethane is surrounded by argon gas.
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Affiliation(s)
- Arnau Jurado Romero
- Departament de Física, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
| | - Carles Calero
- Departament de Física de la Matèria Condensada and Institut de Nanociència i Nanotecnologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Edwin L Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
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2
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Singh A, Doan LC, Lou D, Wen C, Vinh NQ. Interfacial Layers between Ion and Water Detected by Terahertz Spectroscopy. J Chem Phys 2022; 157:054501. [DOI: 10.1063/5.0095932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic fluctuations in hydrogen-bond network of water occur from femto- to nano-second timescale and provides insights into structural/dynamical aspects of water at ion-water interfaces. Employing terahertz spectroscopy assisted with molecular dynamics simulations, we study aqueous chloride solutions of five monovalent cations, namely, Li, Na, K, Rb and Cs. We show that ions modify the behavior of surrounding water molecules and form interfacial layers of water around them with physical properties distinct from that of bulk water. Small cations with high charge densities influence the kinetics of water well beyond the first solvation shell. At terahertz frequencies, we observe an emergence of fast relaxation processes of water with their magnitude following the ionic order Cs>Rb>K>Na>Li, revealing an enhanced population density of weakly coordinated water at ion-water interface. The results shed light on the structure breaking tendency of monovalent cations and provide insights into the properties of ionic solutions at the molecular level.
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Affiliation(s)
- Abhishek Singh
- Physics, Virginia Polytechnic Institute and State University, United States of America
| | - Luan C Doan
- Virginia Polytechnic Institute and State University, United States of America
| | - Djamila Lou
- Virginia Polytechnic Institute and State University, United States of America
| | - Chengyuan Wen
- Virginia Polytechnic Institute and State University - National Capital Region, United States of America
| | - Nguyen Q Vinh
- Department of Physics, Virginia Polytechnic Institute and State University, United States of America
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3
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Petersen J, Møller KB, Hynes JT, Rey R. Ultrafast Rotational and Translational Energy Relaxation in Neat Liquids. J Phys Chem B 2021; 125:12806-12819. [PMID: 34762424 DOI: 10.1021/acs.jpcb.1c08014] [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
The excess energy flow pathways during rotational and translational relaxation induced by rotational or translational excitation of a single molecule of and within each of four different neat liquids (H2O, MeOH, CCl4, and CH4) are studied using classical molecular dynamics simulations and energy flux analysis. For all four liquids, the relaxation processes for both types of excitation are ultrafast, but the energy flow is significantly faster for the polar, hydrogen-bonded (H-bonded) liquids H2O and MeOH. Whereas the majority of the initial excess energy is transferred into hindered rotations (librations) for rotational excitation in the H-bonded liquids, an almost equal efficiency for transfer to translational and rotational motions is observed in the nonpolar, non-H-bonded liquids CCl4 and CH4. For translational excitation, transfer to translational motions dominates for all liquids. In general, the energy flows are quite local; i.e., more than 70% of the energy flows directly to the first solvent shell molecules, reaching almost 100% for CCl4 and CH4. Finally, the determined validity of linear response theory for these nonequilibrium relaxation processes is quite solvent-dependent, with the deviation from linear response most marked for rotational excitation and for the nonpolar liquids.
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Affiliation(s)
- Jakob Petersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - James T Hynes
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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4
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Rey R, Hynes JT. Solvation Dynamics in Water. 4. On the Initial Regime of Solvation Relaxation. J Phys Chem B 2020; 124:7668-7681. [PMID: 32790403 DOI: 10.1021/acs.jpcb.0c05706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is shown, by means of numerical and analytic work, that initial molecular momenta play little significant role in the initial fast solvation relaxation that follows electronic excitation of, and charge creation for, a standard model system of a solute in water. Instead, the nonequilibrium dynamics are predominantly described by noninertial "steering" by the torques directly generated by the newly created charge distribution. It is this process that largely overcomes inertia and drives the relaxation dynamics on a time scale of a few tens of femtoseconds in the key initial regime of the dynamics. These results are discussed in the context of commonly employed descriptions such as inertial, Gaussian, and underdamped dynamical behavior.
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Affiliation(s)
- Rossend Rey
- Departament de Fı́sica, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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5
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Novelli F, Ruiz Pestana L, Bennett KC, Sebastiani F, Adams EM, Stavrias N, Ockelmann T, Colchero A, Hoberg C, Schwaab G, Head-Gordon T, Havenith M. Strong Anisotropy in Liquid Water upon Librational Excitation Using Terahertz Laser Fields. J Phys Chem B 2020; 124:4989-5001. [DOI: 10.1021/acs.jpcb.0c02448] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabio Novelli
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Luis Ruiz Pestana
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Miami, Coral Gables, Florida, United States
| | - Kochise C. Bennett
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Federico Sebastiani
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Ellen M. Adams
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Nikolas Stavrias
- Radboud University, FELIX Laboratory, Toernooiveld 7, Nijmegen, The Netherlands
| | - Thorsten Ockelmann
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Alejandro Colchero
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Claudius Hoberg
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
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6
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Krueger TD, Boulanger SA, Zhu L, Tang L, Fang C. Discovering a rotational barrier within a charge-transfer state of a photoexcited chromophore in solution. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024901. [PMID: 32161777 PMCID: PMC7056454 DOI: 10.1063/1.5143441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/18/2020] [Indexed: 05/15/2023]
Abstract
Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS), and fluorescence quantum yield measurements via steady-state electronic spectroscopy reveal the energy dissipation pathways of MPTS following photoexcitation. Various solvents enable a systematic characterization of the H-bonding interaction, viscosity, and dynamic solvation that influence the ensuing relaxation pathways. The formation of a charge-transfer state out of the Franck-Condon region occurs on the femtosecond-to-picosecond solvation timescale before encountering a rotational barrier. The rotational relaxation correlates with the H-bond donating strength of solvent, while the rotational time constant lengthens as solvent viscosity increases. Time-resolved excited-state FSRS, aided by quantum calculations, provides crucial structural dynamics knowledge and reveals the sulfonate groups playing a dominant role during solvation. Several prominent vibrational motions of the pyrene ring backbone help maneuver the population toward the more fluorescent state. These ultrafast correlated electronic and nuclear motions ultimately govern the fate of the photoexcited chromophore in solution. Overall, MPTS in water displays the highest probability to fluoresce, while the aprotic and more viscous dimethyl sulfoxide enhances the nonradiative pathways. These mechanistic insights may apply robustly to other photoexcited chromophores that do not undergo excited-state proton transfer or remain trapped in a broad electronic state and also provide design principles to control molecular optical responses with site-specific atomic substitution.
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Affiliation(s)
- Taylor D. Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Sean A. Boulanger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
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7
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8
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Madhavi WAM, Weerasinghe S, Momot KI. Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations. Aust J Chem 2020. [DOI: 10.1071/ch19537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.
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9
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Carpenter WB, Lewis NHC, Fournier JA, Tokmakoff A. Entropic barriers in the kinetics of aqueous proton transfer. J Chem Phys 2019; 151:034501. [PMID: 31325917 DOI: 10.1063/1.5108907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aqueous proton transport is uniquely rapid among aqueous processes, mediated by fluctuating hydrogen bond reorganization in liquid water. In a process known as Grotthuss diffusion, the excess charge diffuses primarily by sequential proton transfers between water molecules rather than standard Brownian motion, which explains the anomalously high electrical conductivity of acidic solutions. Employing ultrafast IR spectroscopy, we use the orientational anisotropy decay of the bending vibrations of the hydrated proton complex to study the picosecond aqueous proton transfer kinetics as a function of temperature, concentration, and counterion. We find that the orientational anisotropy decay exhibits Arrhenius behavior, with an apparent activation energy of 2.4 kcal/mol in 1M and 2M HCl. Interestingly, acidic solutions at high concentration with longer proton transfer time scales display corresponding decreases in activation energy. We interpret this counterintuitive trend by considering the entropic and enthalpic contributions to the activation free energy for proton transfer. Halide counteranions at high concentrations impose entropic barriers to proton transfer in the form of constraints on the solution's collective H-bond fluctuations and obstruction of potential proton transfer pathways. The corresponding proton transfer barrier decreases due to weaker water-halide H-bonds in close proximity to the excess proton, but the entropic effects dominate and result in a net reduction in the proton transfer rate. We estimate the activation free energy for proton transfer as ∼1.0 kcal/mol at 280 K.
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Affiliation(s)
- William B Carpenter
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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10
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Kundu A, Dahms F, Fingerhut BP, Nibbering ET, Pines E, Elsaesser T. Ultrafast vibrational relaxation and energy dissipation of hydrated excess protons in polar solvents. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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12
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Mishra PK, Bettaque V, Vendrell O, Santra R, Welsch R. Prospects of Using High-Intensity THz Pulses To Induce Ultrafast Temperature-Jumps in Liquid Water. J Phys Chem A 2018; 122:5211-5222. [DOI: 10.1021/acs.jpca.8b00828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pankaj Kr. Mishra
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Vincent Bettaque
- Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
| | - Oriol Vendrell
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
| | - Ralph Welsch
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany
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13
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Cerezo J, Liu Y, Lin N, Zhao X, Improta R, Santoro F. Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case. J Chem Theory Comput 2018; 14:820-832. [PMID: 29207245 DOI: 10.1021/acs.jctc.7b01015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.
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Affiliation(s)
- Javier Cerezo
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Yanli Liu
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,School of Physics and Optoelectronics Engineering, Ludong University , 264025 Yantai, P. R. China
| | - Na Lin
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR) , via Mezzocannone 16, I-80136 Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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14
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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15
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Fischer MP, Bühler J, Fitzky G, Kurihara T, Eggert S, Leitenstorfer A, Brida D. Coherent field transients below 15 THz from phase-matched difference frequency generation in 4H-SiC. OPTICS LETTERS 2017; 42:2687-2690. [PMID: 28708144 DOI: 10.1364/ol.42.002687] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
We experimentally demonstrate tunable, phase-matched difference frequency generation covering the spectral region below 15 THz using 4H-SiC as a nonlinear crystal. This material combines a non-centrosymmetric lattice and strong birefringence with broadband transparency at low optical frequencies. Thorough refractive index measurements in the terahertz spectral range allow us to calculate phase-matching conditions for any near-infrared pump laser source. 4H-SiC is also exploited as a detector crystal for electro-optic sampling. The results allow us to estimate the effective second-order nonlinear coefficient.
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16
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Kolář MH, Kubař T. Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer. J Phys Chem B 2017; 121:1520-1532. [PMID: 28121443 DOI: 10.1021/acs.jpcb.6b12109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
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Affiliation(s)
- Michal H Kolář
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich , 52428 Jülich, Germany.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , 16610 Praha, Czech Republic
| | - Tomáš Kubař
- Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
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17
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Rey R, Hynes JT. Solvation Dynamics in Liquid Water. III. Energy Fluxes and Structural Changes. J Phys Chem B 2017; 121:1377-1385. [PMID: 28095693 DOI: 10.1021/acs.jpcb.6b11805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation-and in particular, hydration- relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent's spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible "inverse snowball" effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors' principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor.
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Affiliation(s)
- Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya , Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Chemistry Department, Ecole Normale Supérieure-PSL Research University , Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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18
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Rey R, Hynes JT. Solvation Dynamics in Water: 2. Energy Fluxes on Excited- and Ground-State Surfaces. J Phys Chem B 2016; 120:11287-11297. [DOI: 10.1021/acs.jpcb.6b08965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rossend Rey
- Departament
de Física, Universitat Politècnica de Catalunya, Campus
Nord B4-B5, Barcelona 08034, Spain
| | - James T. Hynes
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Ecole Normale Supérieure-PSL
Research
University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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19
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Tong Y, Kampfrath T, Campen RK. Experimentally probing the libration of interfacial water: the rotational potential of water is stiffer at the air/water interface than in bulk liquid. Phys Chem Chem Phys 2016; 18:18424-30. [PMID: 27339861 DOI: 10.1039/c6cp01004k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Most properties of liquid water are determined by its hydrogen-bond network. Because forming an aqueous interface requires termination of this network, one might expect the molecular level properties of interfacial water to markedly differ from water in bulk. Intriguingly, much prior experimental and theoretical work has found that, from the perspective of their time-averaged structure and picosecond structural dynamics, hydrogen-bonded OH groups at an air/water interface behave the same as hydrogen-bonded OH groups in bulk liquid water. Here we report the first experimental observation of interfacial water's libration (i.e. frustrated rotation) using the laser-based technique vibrational sum frequency spectroscopy. We find this mode has a frequency of 834 cm(-1), ≈165 cm(-1) higher than in bulk liquid water at the same temperature and similar to bulk ice. Because libration frequency is proportional to the stiffness of water's rotational potential, this increase suggests that one effect of terminating bulk water's hydrogen bonding network at the air/water interface is retarding rotation of water around intact hydrogen bonds. Because in bulk liquid water the libration plays a key role in stabilizing reaction intermediates and dissipating excess vibrational energy, we expect the ability to probe this mode in interfacial water to open new perspectives on the kinetics of heterogeneous reactions at aqueous interfaces.
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Affiliation(s)
- Yujin Tong
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
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20
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Mishra PK, Vendrell O, Santra R. Subpicosecond energy transfer from a highly intense THz pulse to water: A computational study based on the TIP4P/2005 rigid-water-molecule model. Phys Rev E 2016; 93:032124. [PMID: 27078309 DOI: 10.1103/physreve.93.032124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Indexed: 11/07/2022]
Abstract
The dynamics of ultrafast energy transfer to water clusters and to bulk water by a highly intense, subcycle THz pulse of duration ≈150 fs is investigated in the context of force-field molecular dynamics simulations. We focus our attention on the mechanisms by which rotational and translational degrees of freedom of the water monomers gain energy from these subcycle pulses with an electric field amplitude of up to about 0.6 V/Å. It has been recently shown that pulses with these characteristics can be generated in the laboratory [C. Vicario, B. Monoszlai, and C. P. Hauri, Phys. Rev. Lett. 112, 213901 (2014)]. Through their permanent dipole moment, water molecules are acted upon by the electric field and forced off their preferred hydrogen-bond network conformation. This immediately sets them in motion with respect to one another as energy quickly transfers to their relative center of mass displacements. We find that, in the bulk, the operation of these mechanisms is strongly dependent on the initial temperature and density of the system. In low density systems, the equilibration between rotational and translational modes is slow due to the lack of collisions between monomers. As the initial density of the system approaches 1 g/cm(3), equilibration between rotational and translational modes after the pulse becomes more efficient. In turn, low temperatures hinder the direct energy transfer from the pulse to rotational motion owing to the resulting stiffness of the hydrogen bond network. For small clusters of just a few water molecules we find that fragmentation due to the interaction with the pulse is faster than equilibration between rotations and translations, meaning that the latter remain colder than the former after the pulse. In contrast, clusters with more than a few tens of water molecules already display energy gain dynamics similar to water in condensed phases owing to inertial confinement of the internal water molecules by the outer shells. In these cases, a complete equilibration becomes possible.
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Affiliation(s)
- Pankaj Kr Mishra
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, D-22761 Hamburg, Germany.,Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
| | - Oriol Vendrell
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, D-22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, D-22761 Hamburg, Germany.,Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
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Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path. J Phys Chem B 2016; 120:2281-90. [PMID: 26876428 DOI: 10.1021/acs.jpcb.5b12744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an ∼100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base ΔpKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale ∼120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3(+).
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Affiliation(s)
- Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics. J Phys Chem B 2016; 120:2271-80. [PMID: 26879554 DOI: 10.1021/acs.jpcb.5b12742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton.
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Affiliation(s)
- Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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23
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Takae K, Onuki A. Fluctuations of local electric field and dipole moments in water between metal walls. J Chem Phys 2015; 143:154503. [PMID: 26493911 DOI: 10.1063/1.4932972] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We examine the thermal fluctuations of the local electric field Ek (loc) and the dipole moment μk in liquid water at T = 298 K between metal walls in electric field applied in the perpendicular direction. We use analytic theory and molecular dynamics simulation. In this situation, there is a global electrostatic coupling between the surface charges on the walls and the polarization in the bulk. Then, the correlation function of the polarization density pz(r) along the applied field contains a homogeneous part inversely proportional to the cell volume V. Accounting for the long-range dipolar interaction, we derive the Kirkwood-Fröhlich formula for the polarization fluctuations when the specimen volume v is much smaller than V. However, for not small v/V, the homogeneous part comes into play in dielectric relations. We also calculate the distribution of Ek (loc) in applied field. As a unique feature of water, its magnitude |Ek (loc)| obeys a Gaussian distribution with a large mean value E0 ≅ 17 V/nm, which arises mainly from the surrounding hydrogen-bonded molecules. Since |μk|E0 ∼ 30kBT, μk becomes mostly parallel to Ek (loc). As a result, the orientation distributions of these two vectors nearly coincide, assuming the classical exponential form. In dynamics, the component of μk(t) parallel to Ek (loc)(t) changes on the time scale of the hydrogen bonds ∼5 ps, while its smaller perpendicular component undergoes librational motions on time scales of 0.01 ps.
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Affiliation(s)
- Kyohei Takae
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Akira Onuki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
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Czurlok D, Torres-Alacan J, Vöhringer P. Ultrafast 2DIR spectroscopy of ferric azide precursors for high-valent iron. Vibrational relaxation, spectral diffusion, and dynamic symmetry breaking. J Chem Phys 2015; 142:212402. [DOI: 10.1063/1.4914154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Denis Czurlok
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Joel Torres-Alacan
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Peter Vöhringer
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
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25
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Hynes JT. Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere. Annu Rev Phys Chem 2015; 66:1-20. [DOI: 10.1146/annurev-physchem-040214-121833] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James T. Hynes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309;
- Department of Chemistry, UMR ENS-CNRS-UPMC-8640, Ecole Normale Supérieure, Paris, France 75005
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26
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Rey R, Hynes JT. Solvation Dynamics in Liquid Water. 1. Ultrafast Energy Fluxes. J Phys Chem B 2015; 119:7558-70. [DOI: 10.1021/jp5113922] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rossend Rey
- Departament de Física
i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus
Nord B4-B5, Barcelona 08034, Spain
| | - James T. Hynes
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Chemistry Department, Ecole Normale
Supérieure,
UMR ENS-CNRS-UPMC 8640, 24 Rue Lhomond, 75005 Paris, France
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27
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Wang L, Liu W, Fang C. Elucidating low-frequency vibrational dynamics in calcite and water with time-resolved third-harmonic generation spectroscopy. Phys Chem Chem Phys 2015; 17:17034-40. [DOI: 10.1039/c5cp01813g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Coherent low-frequency vibrational dynamics in condensed phase from crystal, water, to aqueous electrolyte are elucidated by time-resolved third-harmonic-generation (TRTHG) spectroscopy.
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Affiliation(s)
- Liang Wang
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Center (lab)
- Corvallis
- USA
| | - Weimin Liu
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Center (lab)
- Corvallis
- USA
| | - Chong Fang
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Center (lab)
- Corvallis
- USA
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28
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Ahmed M, Namboodiri V, Singh AK, Mondal JA. On the intermolecular vibrational coupling, hydrogen bonding, and librational freedom of water in the hydration shell of mono- and bivalent anions. J Chem Phys 2014; 141:164708. [DOI: 10.1063/1.4899070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Costard R, Elsaesser T. Femtosecond OH Bending Dynamics of Water Nanopools Confined In Reverse Micelles. J Phys Chem B 2013; 117:15338-45. [DOI: 10.1021/jp403559d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 a,
D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 a,
D-12489 Berlin, Germany
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