1
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Shen H, Shen X, Wu Z. Simulating the isotropic Raman spectra of O-H stretching mode in liquid H 2O based on a machine learning potential: the influence of vibrational couplings. Phys Chem Chem Phys 2023; 25:28180-28188. [PMID: 37819214 DOI: 10.1039/d3cp03035k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that the DP model exhibits DFT-level accuracy, and the DeePMD simulation is a promising approach for modeling the structural properties of liquid water. Based on the DeePMD simulation trajectories, we calculated the isotropic Raman spectra of the O-H stretching mode using the surface-specific velocity-velocity correlation function (ssVVCF), showing that the DeePMD/ssVVCF approach can correctly capture the bimodal characteristics of the experimental Raman spectra, with one peak located near 3400 cm-1 and the other near 3250 cm-1. The success of the DeePMD/ssVVCF approach should be credited to (1) the DFT-level accuracy of the DP model for H2O, (2) the ssVVCF formulation considering the coupling between vibrational modes, and (3) non-Condon effects. Furthermore, the DeePMD simulations revealed that the anharmonic interactions between the coupled water molecules in the first and second hydration shells should play an essential role in the strong mixing of the H-O-H bending mode and the O-H stretching mode, leading to the delocalization of the O-H stretching band. In particular, increasing the strength of hydrogen bonds would enhance the bend-stretch coupling, leading to the red-shifting of the O-H vibrational spectra and the increase in the intensity of the shoulder around 3250 cm-1.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang 550018, China.
| | - Xu Shen
- National Center of Technology Innovation for Intelligent Design and Numerical Control, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhenhua Wu
- Department of Big Data and Artificial Intelligence, Guizhou Vocational Technology College of Electronics & Information, Kaili, 556000, China
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2
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Kwac K, Freedman H, Cho M. Machine Learning Approach for Describing Water OH Stretch Vibrations. J Chem Theory Comput 2021; 17:6353-6365. [PMID: 34498885 DOI: 10.1021/acs.jctc.1c00540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A machine learning approach employing neural networks is developed to calculate the vibrational frequency shifts and transition dipole moments of the symmetric and antisymmetric OH stretch vibrations of a water molecule surrounded by water molecules. We employed the atom-centered symmetry functions (ACSFs), polynomial functions, and Gaussian-type orbital-based density vectors as descriptor functions and compared their performances in predicting vibrational frequency shifts using the trained neural networks. The ACSFs perform best in modeling the frequency shifts of the OH stretch vibration of water among the types of descriptor functions considered in this paper. However, the differences in performance among these three descriptors are not significant. We also tried a feature selection method called CUR matrix decomposition to assess the importance and leverage of the individual functions in the set of selected descriptor functions. We found that a significant number of those functions included in the set of descriptor functions give redundant information in describing the configuration of the water system. We here show that the predicted vibrational frequency shifts by trained neural networks successfully describe the solvent-solute interaction-induced fluctuations of OH stretch frequencies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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3
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Torii H, Ukawa R. Role of Intermolecular Charge Fluxes in the Hydrogen-Bond-Induced Frequency Shifts of the OH Stretching Mode of Water. J Phys Chem B 2021; 125:1468-1475. [PMID: 33506673 DOI: 10.1021/acs.jpcb.0c11461] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relation between the vibrational properties and the electrostatic situations of the vibrating functional group is useful to predict vibrational spectroscopic features based on, for example, classical molecular dynamics of liquids or biomolecular systems, but to pursue its generality or the extent of applicability, it is required to understand the mechanisms giving rise to it. Here such an analysis is carried out for the OH stretching mode of water. By examining the correlations among various (structural, vibrational, and electrostatic) properties and by analyzing the spatial characteristics of the behavior of electrons occurring upon the vibration, it is shown that the dependence of the vibrational frequency and the dipole derivative of the OH stretching mode on the electric field is not of purely electrostatic origin, and the delocalized electronic motions occurring with this mode, called intermolecular charge fluxes, related to both the dipole first and second derivatives play important roles.
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Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Ryota Ukawa
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
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4
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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5
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Ojha D, Chandra A. Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations. J Comput Chem 2019; 40:2086-2095. [PMID: 31099905 DOI: 10.1002/jcc.25860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/27/2019] [Accepted: 04/29/2019] [Indexed: 11/06/2022]
Abstract
A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
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6
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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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7
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Ojha D, Chandra A. Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations. J Phys Chem B 2019; 123:3325-3336. [DOI: 10.1021/acs.jpcb.9b01904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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8
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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9
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Biswas S, Mallik BS. Vibration Spectral Dynamics of Weakly Coordinating Water Molecules near an Anion: FPMD Simulations of an Aqueous Solution of Tetrafluoroborate. J Phys Chem B 2019; 123:2135-2146. [PMID: 30759344 DOI: 10.1021/acs.jpcb.9b00069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent to which the ions affect the nearby water molecules will decide the structure-making or breaking nature of those ions in aqueous solutions. The effects of a weakly coordinating anion on the structure, dynamics, and vibrational properties of water molecules are not so significant as compared to an anion capable of making strong ion-water hydrogen bonds. The present work deals with the first-principles molecular dynamics study of an aqueous solution of such a weakly coordinating anion, tetrafluoroborate (BF4-), using dispersion-corrected DFT-based first-principles molecular dynamics (FPMD) simulations. Various structural, dynamical, and spectral properties, such as radial distribution functions (RDFs), rotational dynamics, vibrational density of states (VDOS), hydrogen bond as well as dangling OH autocorrelation functions, and residence dynamics, were calculated to investigate the effects of the anion on nearby water molecules. The process of spectral diffusion was assessed through a time series wavelet transformation of trajectories obtained from FPMD simulations. The first ion-water solvation shell extends up to 5.5 Å, containing around 20 water molecules. The lifetime of the ion-water hydrogen bond is found to be 1.19 ps, whereas the water-water hydrogen bond lifetime is found to be 1.13 ps. Inside the solvation shell, the persistence time of dangling OH chromophores and the average frequency of OH modes inside the solvation shell are found to be more compared to bulk. Three time scales are found for solvation shell OH modes from the frequency-frequency correlation function. A very short time scale is found for the intact ion-water interaction; the short time scale is for the ion-water hydrogen bond, and the long time scale is for escape dynamics of water molecules from the ion solvation shell. From the mean squared displacement, it is found that solvation water molecules diffuse slower than the bulk. However, solvation shell water molecules show faster relaxation from the analysis of rotational anisotropy. Within the longer time scale of spectral diffusion, this process (which is related to various dynamics of the molecules) is not yet complete, as compared to fast anisotropic decay. This fact is similar to the experimental finding of spectral diffusion and anisotropy time scales in the aqueous solution of borohydride anion. The calculated results are also compared with available experimental data wherever possible.
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Affiliation(s)
- Sohag Biswas
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi, Sangareddy , 502 285 Telangana , India
| | - Bhabani S Mallik
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi, Sangareddy , 502 285 Telangana , India
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10
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Ojha D, Chandra A. Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations. Phys Chem Chem Phys 2019; 21:6485-6498. [DOI: 10.1039/c8cp07121g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The temperature dependence of the vibrational spectral diffusion of OD modes in liquid water is investigated through calculations of vibrational echo spectral observables from first principles molecular dynamics.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
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11
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De Marco L, Fournier JA, Thämer M, Carpenter W, Tokmakoff A. Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy. J Chem Phys 2016; 145:094501. [DOI: 10.1063/1.4961752] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Joseph A. Fournier
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Martin Thämer
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - William Carpenter
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
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12
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De Marco L, Carpenter W, Liu H, Biswas R, Bowman JM, Tokmakoff A. Differences in the Vibrational Dynamics of H(2)O and D(2)O: Observation of Symmetric and Antisymmetric Stretching Vibrations in Heavy Water. J Phys Chem Lett 2016; 7:1769-1774. [PMID: 27115316 DOI: 10.1021/acs.jpclett.6b00668] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Water's ability to donate and accept hydrogen bonds leads to unique and complex collective dynamical phenomena associated with its hydrogen-bond network. It is appreciated that the vibrations governing liquid water's molecular dynamics are delocalized, with nuclear motion evolving coherently over the span of several molecules. Using two-dimensional infrared spectroscopy, we have found that the nuclear motions of heavy water, D2O, are qualitatively different than those of H2O. The nonlinear spectrum of liquid D2O reveals distinct O-D stretching resonances, in contrast to H2O. Furthermore, our data indicates that condensed-phase O-D vibrations have a different character than those in the gas phase, which we understand in terms of weakly delocalized symmetric and antisymmetric stretching vibrations. This difference in molecular dynamics reflects the shift in the balance between intra- and intermolecular couplings upon deuteration, an effect which can be understood in terms of the anharmonicity of the nuclear potential energy surface.
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Affiliation(s)
- Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - William Carpenter
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Hanchao Liu
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Rajib Biswas
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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13
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Ito H, Tanimura Y. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water. J Chem Phys 2016; 144:074201. [DOI: 10.1063/1.4941842] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Hironobu Ito
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
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14
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Yang M. Validity of Förster Theory for Vibrational Energy Transfer in Low-Dimensional Water. J Phys Chem B 2015; 119:15516-21. [DOI: 10.1021/acs.jpcb.5b10371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
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15
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van der Post ST, Hsieh CS, Okuno M, Nagata Y, Bakker HJ, Bonn M, Hunger J. Strong frequency dependence of vibrational relaxation in bulk and surface water reveals sub-picosecond structural heterogeneity. Nat Commun 2015; 6:8384. [PMID: 26382651 PMCID: PMC4595750 DOI: 10.1038/ncomms9384] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
Because of strong hydrogen bonding in liquid water, intermolecular interactions between water molecules are highly delocalized. Previous two-dimensional infrared spectroscopy experiments have indicated that this delocalization smears out the structural heterogeneity of neat H2O. Here we report on a systematic investigation of the ultrafast vibrational relaxation of bulk and interfacial water using time-resolved infrared and sum-frequency generation spectroscopies. These experiments reveal a remarkably strong dependence of the vibrational relaxation time on the frequency of the OH stretching vibration of liquid water in the bulk and at the air/water interface. For bulk water, the vibrational relaxation time increases continuously from 250 to 550 fs when the frequency is increased from 3,100 to 3,700 cm(-1). For hydrogen-bonded water at the air/water interface, the frequency dependence is even stronger. These results directly demonstrate that liquid water possesses substantial structural heterogeneity, both in the bulk and at the surface.
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Affiliation(s)
| | - Cho-Shuen Hsieh
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.,Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Masanari Okuno
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Huib J Bakker
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Mischa Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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16
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Ojha D, Chandra A. Ultrafast Vibrational Echo Spectroscopy of Liquid Water from First-Principles Simulations. J Phys Chem B 2015; 119:11215-28. [PMID: 26161933 DOI: 10.1021/acs.jpcb.5b03109] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational echo spectroscopy has become a powerful technique to study vibrational spectral diffusion in water and aqueous solutions. The dynamics of vibrational spectral diffusion is intimately related to the hydrogen bond fluctuations in liquid water and other hydrogen bonded liquids. Earlier theoretical calculations of vibrational echo spectroscopy of aqueous systems were based on classical molecular dynamics simulations involving empirical force fields of water. In the current work, we have employed the method of ab initio molecular dynamics simulation to calculate the spectral observables of vibrational echo and two-dimensional infrared (2D-IR) spectroscopy of liquid water at room temperature under Condon and cumulant approximations. The time scales extracted from the temporal decay of the frequency-time correlation function (FTCF), short-time slope of three pulse photon echo (SP3E), dynamic line width (DLW), and the slope of nodal line of 2D-IR spectra are found to be in reasonably close agreement with each other which reinforces the assertion that signatures of FTCF can be captured using three pulse photon echo and 2D-IR spectroscopy.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
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17
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Noriega R, Finley DT, Haberstroh J, Geissler PL, Francis MB, Ginsberg NS. Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity. J Phys Chem B 2015; 119:6963-73. [PMID: 26035585 DOI: 10.1021/acs.jpcb.5b03784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.
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Affiliation(s)
| | | | | | | | | | - Naomi S Ginsberg
- ∇Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
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18
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Zhang C, Guidoni L, Kühne TD. Competing factors on the frequency separation between the OH stretching modes in water. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2014.09.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Kruiger JF, van der Vegte CP, Jansen TLC. Suppressing sampling noise in linear and two-dimensional spectral simulations. J Chem Phys 2015; 142:054201. [DOI: 10.1063/1.4907277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Johannes F. Kruiger
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Cornelis P. van der Vegte
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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20
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Gruenbaum SM, Skinner JL. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. III. Water clustering and vibrational energy transfer. J Chem Phys 2014; 139:175103. [PMID: 24206336 DOI: 10.1063/1.4827018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Water clustering and connectivity around lipid bilayers strongly influences the properties of membranes and is important for functions such as proton and ion transport. Vibrational anisotropic pump-probe spectroscopy is a powerful tool for understanding such clustering, as the measured anisotropy depends upon the time-scale and degree of intra- and intermolecular vibrational energy transfer. In this article, we use molecular dynamics simulations and theoretical vibrational spectroscopy to help interpret recent experimental measurements of the anisotropy of water in lipid multi-bilayers as a function of both lipid hydration level and isotopic substitution. Our calculations are in satisfactory agreement with the experiments of Piatkowski, Heij, and Bakker, and from our simulations we can directly probe water clustering and connectivity. We find that at low hydration levels, many water molecules are in fact isolated, although up to 70% of hydration water forms small water clusters or chains. At intermediate hydration levels, water forms a wide range of cluster sizes, while at higher hydration levels, the majority of water molecules are part of a large, percolating water cluster. Therefore, the size, number, and nature of water clusters are strongly dependent on lipid hydration level, and the measured anisotropy reflects this through its dependence on intermolecular energy transfer.
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Affiliation(s)
- S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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21
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Imoto S, Xantheas SS, Saito S. Ultrafast dynamics of liquid water: frequency fluctuations of the OH stretch and the HOH bend. J Chem Phys 2014; 139:044503. [PMID: 23901989 DOI: 10.1063/1.4813071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Frequency fluctuations of the OH stretch and the HOH bend in liquid water are reported from the third-order response function evaluated using the TTM3-F potential for water. The simulated two-dimensional infrared spectra of the OH stretch are similar to previously reported theoretical results. The present study suggests that the frequency fluctuation of the HOH bend is faster than that of the OH stretch. The ultrafast loss of the frequency correlation of the HOH bend is due to the strong couplings with the OH stretch as well as the intermolecular hydrogen bond bend.
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Affiliation(s)
- Sho Imoto
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
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22
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Otto KE, Xue Z, Zielke P, Suhm MA. The Raman spectrum of isolated water clusters. Phys Chem Chem Phys 2014; 16:9849-58. [DOI: 10.1039/c3cp54272f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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24
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Olschewski M, Knop S, Lindner J, Vöhringer P. From Single Hydrogen Bonds to Extended Hydrogen-Bond Wires: Low-Dimensional Model Systems for Vibrational Spectroscopy of Associated Liquids. Angew Chem Int Ed Engl 2013; 52:9634-54. [DOI: 10.1002/anie.201210009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 11/06/2022]
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25
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Olschewski M, Knop S, Lindner J, Vöhringer P. Von einzelnen H-Brücken zu ausgedehnten H-verbrückten Drähten: niederdimensionale Modellsysteme für die Schwingungsspektroskopie vernetzter Flüssigkeiten. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Gruenbaum SM, Tainter CJ, Shi L, Ni Y, Skinner JL. Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy. J Chem Theory Comput 2013; 9:3109-17. [DOI: 10.1021/ct400292q] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. M. Gruenbaum
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - C. J. Tainter
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - L. Shi
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - Y. Ni
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - J. L. Skinner
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
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27
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Choi JH, Cho M. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants. J Chem Phys 2013; 138:174108. [DOI: 10.1063/1.4802991] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Yagasaki T, Saito S. Fluctuations and Relaxation Dynamics of Liquid Water Revealed by Linear and Nonlinear Spectroscopy. Annu Rev Phys Chem 2013; 64:55-75. [DOI: 10.1146/annurev-physchem-040412-110150] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.
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Affiliation(s)
- Takuma Yagasaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
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29
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Kim K, Saito S. Multiple length and time scales of dynamic heterogeneities in model glass-forming liquids: A systematic analysis of multi-point and multi-time correlations. J Chem Phys 2013; 138:12A506. [DOI: 10.1063/1.4769256] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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30
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Ni Y, Gruenbaum SM, Skinner JL. Slow hydrogen-bond switching dynamics at the water surface revealed by theoretical two-dimensional sum-frequency spectroscopy. Proc Natl Acad Sci U S A 2013; 110:1992-8. [PMID: 23329327 PMCID: PMC3568345 DOI: 10.1073/pnas.1222017110] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using our newly developed explicit three-body (E3B) water model, we simulate the surface of liquid water. We find that the timescale for hydrogen-bond switching dynamics at the surface is about three times slower than that in the bulk. In contrast, with this model rotational dynamics are slightly faster at the surface than in the bulk. We consider vibrational two-dimensional (2D) sum-frequency generation (2DSFG) spectroscopy as a technique for observing hydrogen-bond rearrangement dynamics at the water surface. We calculate the nonlinear susceptibility for this spectroscopy for two different polarization conditions, and in each case we see the appearance of cross-peaks on the timescale of a few picoseconds, signaling hydrogen-bond rearrangement on this timescale. We thus conclude that this 2D spectroscopy will be an excellent experimental technique for observing slow hydrogen-bond switching dynamics at the water surface.
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Affiliation(s)
- Yicun Ni
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - Scott M. Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - James L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
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31
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Piatkowski L, de Heij J, Bakker HJ. Probing the distribution of water molecules hydrating lipid membranes with ultrafast Förster vibrational energy transfer. J Phys Chem B 2013; 117:1367-77. [PMID: 23360328 DOI: 10.1021/jp310602v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We determine the relative positioning of water molecules in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membranes by measuring the rate of vibrational resonant (Förster) energy transfer between the water hydroxyl stretch vibrations. The rate of Förster energy transfer is strongly distance dependent and thus gives detailed information on the relative positioning of the water molecules. We determine the rate of intermolecular Förster energy by measuring the anisotropy dynamics of excited O-D stretch vibrations of HDO and D(2)O molecules with polarization-resolved femtosecond mid-infrared spectroscopy. We study the dynamics for deuterium fractions between 0.1 and 1 and for hydration levels between 2 and 12 water molecules per DOPC lipid molecule. We find that most of the water molecules hydrating the membrane are contained in nanoclusters and have an average intermolecular distance of 3.4 Å. The density of these nanoclusters increases with increasing hydration level of the DOPC membranes.
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Affiliation(s)
- L Piatkowski
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
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32
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Yang M, Szyc Ł, Elsaesser T. Vibrational dynamics of the water shell of DNA studied by femtosecond two-dimensional infrared spectroscopy. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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34
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Falvo C, Zhuang W, Kim YS, Axelsen PH, Hochstrasser RM, Mukamel S. Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations. J Phys Chem B 2012; 116:3322-30. [PMID: 22338639 DOI: 10.1021/jp2096423] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils.
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Affiliation(s)
- Cyril Falvo
- Institut des Sciences Moléculaires d'Orsay, UMR CNRS 8214, Université Paris-Sud 11, 91405 Orsay, France.
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35
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Muniz-Miranda F, Pagliai M, Cardini G, Righini R. Bifurcated Hydrogen Bond in Lithium Nitrate Trihydrate Probed by ab Initio Molecular Dynamics. J Phys Chem A 2012; 116:2147-53. [DOI: 10.1021/jp2120115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Francesco Muniz-Miranda
- European Laboratory for Nonlinear Spectroscopy (LENS), via Nello Carrara
1, 50019 Sesto Fiorentino (Firenze), Italy
| | - Marco Pagliai
- Dipartimento di Chimica “Ugo
Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
| | - Gianni Cardini
- European Laboratory for Nonlinear Spectroscopy (LENS), via Nello Carrara
1, 50019 Sesto Fiorentino (Firenze), Italy
- Dipartimento di Chimica “Ugo
Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
| | - Roberto Righini
- European Laboratory for Nonlinear Spectroscopy (LENS), via Nello Carrara
1, 50019 Sesto Fiorentino (Firenze), Italy
- Dipartimento di Chimica “Ugo
Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
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36
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Ye S, Ma S, Wei F, Li H. Intramolecular vibrational coupling in water molecules revealed by compatible multiple nonlinear vibrational spectroscopic measurements. Analyst 2012; 137:4981-7. [DOI: 10.1039/c2an35684h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Yagasaki T, Saito S. Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study. J Chem Phys 2011; 135:244511. [DOI: 10.1063/1.3671993] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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38
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Torii H, Giorgini MG, Musso M. Merged- and Separate-Band Behavior of the C═O Stretching Band in N,N-Dimethylformamide Isotopic Liquid Mixtures: DMF/DMF-d1, DMF/DMF-d6, and DMF/DMF-13C═O. J Phys Chem B 2011; 116:353-66. [DOI: 10.1021/jp209119e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Torii
- Department of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
| | - Maria Grazia Giorgini
- Dipartimento di Chimica Fisica ed Inorganica, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Maurizio Musso
- Fachbereich Materialforschung und Physik, Abteilung Physik und Biophysik, Universität Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
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39
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Yang M, Li F, Skinner JL. Vibrational energy transfer and anisotropy decay in liquid water: Is the Förster model valid? J Chem Phys 2011; 135:164505. [DOI: 10.1063/1.3655894] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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40
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Yang M, Szyc Ł, Elsaesser T. Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy. J Phys Chem B 2011; 115:13093-100. [PMID: 21972952 DOI: 10.1021/jp208166w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.
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Affiliation(s)
- Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany
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41
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Bakulin AA, Pshenichnikov MS. Reduced coupling of water molecules near the surface of reverse micelles. Phys Chem Chem Phys 2011; 13:19355-61. [PMID: 21959913 DOI: 10.1039/c1cp22235j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on vibrational dynamics of water near the surface of AOT reverse micelles studied by narrow-band excitation, mid-IR pump-probe spectroscopy. Evidence of OH-stretch frequency splitting into the symmetric and asymmetric modes is clearly observed for the interfacial H(2)O molecules. The polarization memory of interfacial waters is preserved over an exceptionally extended >10 ps timescale which is a factor of 100 longer than in bulk water. These observations point towards negligibly small intermolecular vibrational coupling between the water molecules as well as strongly reduced water rotational mobility within the interfacial water layer.
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Affiliation(s)
- Artem A Bakulin
- Department of Physical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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42
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Yagasaki T, Saito S. A novel method for analyzing energy relaxation in condensed phases using nonequilibrium molecular dynamics simulations: Application to the energy relaxation of intermolecular motions in liquid water. J Chem Phys 2011; 134:184503. [DOI: 10.1063/1.3587105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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43
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Hasegawa T, Tanimura Y. A Polarizable Water Model for Intramolecular and Intermolecular Vibrational Spectroscopies. J Phys Chem B 2011; 115:5545-53. [DOI: 10.1021/jp111308f] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Taisuke Hasegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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44
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Marcotte G, Ayotte P. Strong intermolecular coupling between the HF stretching and H2O bending vibrations in HF:H2O binary amorphous solids: breakdown of the electrostatic description of the hydrogen bond. J Chem Phys 2011; 134:114522. [PMID: 21428647 DOI: 10.1063/1.3562368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coupling mechanism between the HF stretching and H(2)O bending vibrations observed in the infrared spectra of HF:H(2)O binary amorphous solids is analyzed using a simple cluster model. The intermolecular vibrational coupling derived from electrostatic potentials is one order of magnitude smaller, and of the opposite sign, than that obtained from electronic structure-based potentials. This highlights the distinctively covalent character of strong H-bonds and unveils fundamental weaknesses of electrostatic descriptions of vibrational energy transfer in liquid water and aqueous solutions.
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Affiliation(s)
- Guillaume Marcotte
- Département de chimie, Université de Sherbrooke, 2500 boulevard université, Sherbrooke, Québec J1K 2R1, Canada.
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45
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Torii H. Intra- and intermolecular charge fluxes induced by the OH stretching mode of water and their effects on the infrared intensities and intermolecular vibrational coupling. J Phys Chem B 2011; 114:13403-9. [PMID: 20886869 DOI: 10.1021/jp106952q] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intra- and intermolecular charge fluxes induced by the OH stretching mode of water and their effects on the infrared (IR) intensities and intermolecular vibrational coupling are analyzed theoretically. Density functional theoretical (DFT) calculations are carried out for the clusters consisting of 28 and 30 water molecules, and the change in the electron density induced by the OH stretching mode, i.e., the electron density derivative ∂ρ((el))(r)/∂Q(OH), is calculated and its effect is analyzed. It is shown that the electron density derivative extends to the spatial region of the water molecule that accepts the hydrogen bond donated by the vibrating OH bond, indicating that intermolecular charge flux is induced. Both the amount of vibration-induced change in the electric charge (the charge derivative) and the distance between charge centers are large for the intermolecular charge flux, giving rise to a significant enhancement of the dipole derivative, and hence the IR intensity. After showing quantitatively that it is possible to understand the intermolecular vibrational coupling between the OH stretching oscillators with the picture of the "electric field modulation by one vibration" and the "response by the other vibration to the electric field modulation", the effect of the intermolecular charge flux on the intermolecular vibrational coupling is analyzed. It is shown that the intermolecular charge flux plays an important role also in this relation, but the two factors determining the dipole derivative (the charge derivative and the distance between charge centers) should be carefully taken into account.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan.
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46
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King JT, Baiz CR, Kubarych KJ. Solvent-dependent spectral diffusion in a hydrogen bonded "vibrational aggregate". J Phys Chem A 2011; 114:10590-604. [PMID: 20831231 DOI: 10.1021/jp106142u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) is used to measure the viscosity-dependent spectral diffusion of a model vibrational probe, Mn(2)(CO)(10) (dimanganese decacarbonyl, DMDC), in a series of alcohols with time scales ranging from 2.67 ps in methanol to 5.33 ps in 1-hexanol. Alcohol-alkane solvent mixtures were found to produce indistinguishable linear IR spectra, while still demonstrating viscosity-dependent spectral diffusion. Using a vibrational exciton model to characterize the inhomogeneous energy landscape, several analogies emerge with multichromophoric electronic systems, such as J-aggregates and light-harvesting protein complexes. An excitonic, local vibrational mode Hamiltonian parametrized to reproduce the vibrational structure of DMDC serves as a starting point from which site energies (i.e., local carbonyl frequencies) are given Gaussian distributed disorder. The model gives excellent agreement with both the linear IR spectrum and the inhomogeneous widths extracted from 2DIR, indicating the system can be considered to be a "vibrational aggregate." This model naturally leads to exchange narrowing due to disorder-induced exciton localization, producing line widths consistent with our 1D and 2D measurements. Further, the diagonal disorder alone effectively reduces the molecular symmetry, leading to the appearance of Raman bands in the IR spectrum in accord with the measurements. Here, we show that the static inhomogeneity of the excitonic model with disorder successfully captures the essential details of the 1D spectrum while predicting the degree of IR activity of forbidden modes as well as the inhomogeneous widths and relative magnitudes of the transition moments.
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Affiliation(s)
- John T King
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
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Knop S, Jansen TLC, Lindner J, Vöhringer P. On the nature of OH-stretching vibrations in hydrogen-bonded chains: Pump frequency dependent vibrational lifetime. Phys Chem Chem Phys 2011; 13:4641-50. [DOI: 10.1039/c0cp02143a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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48
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Paarmann A, Lima M, Chelli R, Volkov VV, Righini R, Miller RJD. Excitonic effects in two-dimensional vibrational spectra of liquid formamide. Phys Chem Chem Phys 2011; 13:11351-8. [PMID: 21573300 DOI: 10.1039/c0cp02961k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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49
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Kuehn W, Reimann K, Woerner M, Elsaesser T, Hey R. Two-dimensional terahertz correlation spectra of electronic excitations in semiconductor quantum wells. J Phys Chem B 2010; 115:5448-55. [PMID: 21171588 DOI: 10.1021/jp1099046] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We discuss a novel approach for nonlinear two-dimensional (2D) spectroscopy in the terahertz (THz) frequency range which is based on a collinear interaction geometry of a sequence of THz pulses with the sample. The nonlinear polarization is determined by a phase-resolved measurement of the electric field transmitted through the sample as a function of the delay τ between two phase-locked pulses and the "real" time t. The information provided by a single 2D scan along the τ and t axes is equivalent to that from a noncollinear photon-echo setup equipped with four local oscillators, each interacting with a different diffracted order. We address basic concepts of collinear 2D THz spectroscopy, in particular data analysis and phasing issues. Different rephasing and nonrephasing contributions to the third-order response are separated and 2D correlation spectra derived. As a prototype application, 2D correlation spectra of intersubband excitations of electrons in semiconductor quantum wells are presented.
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Affiliation(s)
- W Kuehn
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
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Yagasaki T, Saito S, Ohmine I. Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study. J Phys Chem A 2010; 114:12573-84. [PMID: 21077653 DOI: 10.1021/jp1084795] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.
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Affiliation(s)
- Takuma Yagasaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
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