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Zhong K, Nguyen HL, Do TN, Tan HS, Knoester J, Jansen TLC. Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems. J Chem Theory Comput 2024; 20:6111-6124. [PMID: 38996082 PMCID: PMC11270824 DOI: 10.1021/acs.jctc.4c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
Two-dimensional electronic spectroscopy (2DES) has proven to be a highly effective technique in studying the properties of excited states and the process of excitation energy transfer in complex molecular assemblies, particularly in biological light-harvesting systems. However, the accurate simulation of 2DES for large systems still poses a challenge because of the heavy computational demands it entails. In an effort to overcome this limitation, we devised a coarse-grained 2DES method. This method encompasses the treatment of the entire system by dividing it into distinct weakly coupled segments, which are assumed to communicate predominantly through incoherent exciton transfer. We first demonstrate the efficiency of this method through simulation on a model dimer system, which demonstrates a marked improvement in calculation efficiency, with results that exhibit good concordance with reference spectra calculated with less approximate methods. Additionally, the application of this method to the light-harvesting antenna 2 (LH2) complex of purple bacteria showcases its advantages, accuracy, and limitations. Furthermore, simulating the anisotropy decay in LH2 induced by energy transfer and its comparison with experiments confirm that the method is capable of accurately describing dynamical processes in a biologically relevant system. This method presented lends itself to an extension that accounts for the effect of intrasegment relaxation processes on the 2DES spectra, which for computational efficiency are ignored in the implementation reported here. It is envisioned that the method will be employed in the future to accurately and efficiently calculate 2D spectra of more extensive systems, such as photosynthetic supercomplexes.
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Affiliation(s)
- Kai Zhong
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Hoang Long Nguyen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Thanh Nhut Do
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Howe-Siang Tan
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Jasper Knoester
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- Faculty
of Science, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
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2
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Malik R, Das B, Chandra A. Theoretical Two Dimensional Infrared Spectroscopy of Aqueous Solutions of tert-Butyl Alcohol: Variation of the Dynamics of Spectral Diffusion along the Percolation Transition. J Phys Chem B 2023; 127:4099-4111. [PMID: 37126459 DOI: 10.1021/acs.jpcb.2c08916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Binary mixtures of water and tert-butyl alcohol (TBA) are known to exhibit the so-called percolation transition where small clusters of TBA molecules span into large aggregates beyond a threshold concentration of the alcohol. In the present study, we have investigated the linear and two-dimensional infrared spectral features of aqueous solutions of TBA for varying concentration of the alcohol along the percolation transition. The percolation transition is characterized through calculations of intermolecular radial distribution functions and average size of the largest cluster of TBA molecules. It is found that, with variation of alcohol concentration, the radial distribution functions of the central carbon atoms of TBA molecules show a nonmonotonic change in the height of the first peak and also the size of the largest cluster of TBA molecules show a jump in the increase of its size for TBA mole fraction between 0.04 and 0.06 corresponding to a transition from smaller clusters to larger spanning aggregates. However, it is found that the linear infrared spectrum of water does not exhibit any noticeable changes on variation of TBA concentration along the percolation transition. Subsequently, two-dimensional infrared (2DIR) spectra and vibrational frequency time correlation function of water are calculated for all the TBA-water solutions considered in this study. The spectral diffusion of water calculated from 2DIR is found to slow down with increase of the TBA concentration. The time scales of spectral diffusion of water, as characterized by the relaxation of frequency time correlation function, 2DIR metric of central line slope, and also the hydrogen bond time correlation functions, are found to exhibit a noticeable jump along the percolation transition. The hydrophilic group of TBA is found to retard the water dynamics more effectively than the hydrophobic groups. Also, the jump in the dynamical slowdown along the percolation transition is found to be more significant for water molecules at the hydrophilic sites.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Banshi Das
- 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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3
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van Hengel CDN, van Adrichem KE, Jansen TLC. Simulation of two-dimensional infrared Raman spectroscopy with application to proteins. J Chem Phys 2023; 158:064106. [PMID: 36792507 DOI: 10.1063/5.0138958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.
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Affiliation(s)
- Carleen D N van Hengel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim E van Adrichem
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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4
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Abstract
Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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5
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Ishiyama T. Ab initio molecular dynamics study on energy relaxation path of hydrogen-bonded OH vibration in bulk water. J Chem Phys 2021; 154:204502. [PMID: 34241149 DOI: 10.1063/5.0050078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational energy relaxation paths of hydrogen-bonded (H-bonded) OH excited in pure water and in isotopically diluted (deuterated) water are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The present study extends the previous NE-AIMD simulation for the energy relaxation of an excited free OH vibration at an air/water interface [T. Ishiyama, J. Chem. Phys. 154, 104708 (2021)] to the energy relaxation of an excited H-bonded OH vibration in bulk water. The present simulation shows that the excited OH vibration in pure water dissipates its energy on a timescale of 0.1 ps, whereas that in deuterated water relaxes on a timescale of 0.7 ps, consistent with the experimental observations. To decompose these relaxation energies into the components due to intramolecular and intermolecular couplings, constraints are introduced on the vibrational modes except for the target path in the NE-AIMD simulation. In the case of pure water, 80% of the total relaxation is attributed to the pathway due to the resonant intermolecular OH⋯OH stretch coupling, and the remaining 17% and 3% are attributed to intramolecular couplings with the bend overtone and with the conjugate OH stretch, respectively. This result strongly supports a significant role for the Förster transfer mechanism of pure water due to the intermolecular dipole-dipole interactions. In the case of deuterated water, on the other hand, 36% of the total relaxation is due to the intermolecular stretch coupling, and all the remaining 64% arises from coupling with the intramolecular bend overtone.
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Affiliation(s)
- Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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6
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Zhang X, Chen X, Kuroda DG. Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks. J Chem Phys 2021; 154:164514. [PMID: 33940799 DOI: 10.1063/5.0044911] [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
The description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.
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Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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7
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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: 173] [Impact Index Per Article: 43.3] [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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8
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Karković Marković A, Jakobušić Brala C, Pilepić V, Uršić S. Kinetic Isotope Effects and Hydrogen Tunnelling in PCET Oxidations of Ascorbate: New Insights into Aqueous Chemistry? Molecules 2020; 25:molecules25061443. [PMID: 32210039 PMCID: PMC7144389 DOI: 10.3390/molecules25061443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 01/12/2023] Open
Abstract
Recent experimental studies of kinetic isotope effects (KIE-s) and hydrogen tunnelling comprising three proton-coupled electron transfer (PCET) oxidations of ascorbate monoanion, (a) in aqueous reaction solutions, (b) in the mixed water-organic cosolvent systems, (c) in aqueous solutions of various salts and (d) in fairly diluted aqueous solutions of the various partial hydrophobes are reviewed. A number of new insights into the wealth of the kinetic isotope phenomena in the PCET reactions have been obtained. The modulation of KIE-s and hydrogen tunnelling observed when partially hydrophobic solutes are added into water reaction solution, in the case of fairly diluted solutions is revealed as the strong linear correlation of the isotopic ratios of the Arrhenius prefactors Ah/Ad and the isotopic differences in activation energies ΔEa (D,H). The observation has been proposed to be a signature of the involvement of the collective intermolecular excitonic vibrational dynamics of water in activation processes and aqueous chemistry.
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Affiliation(s)
| | | | | | - Stanko Uršić
- Correspondence: (C.J.B.); (S.U.); Tel.: +385-01-4870-267 (C.J.B.)
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9
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Karković Marković A, Jakobušić Brala C, Pilepić V, Uršić S. Hydrogen Tunnelling as a Probe of the Involvement of Water Vibrational Dynamics in Aqueous Chemistry? Molecules 2019; 25:E172. [PMID: 31906197 PMCID: PMC6983115 DOI: 10.3390/molecules25010172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/14/2019] [Accepted: 12/28/2019] [Indexed: 11/17/2022] Open
Abstract
Our study of tunnelling in proton-coupled electron transfer (PCET) oxidation of ascorbate with hexacyanoferrate(III) follows the insights obtained from ultrafast 2D IR spectroscopy and theoretical studies of the vibrational water dynamics that led to the proposal of the involvement of collective intermolecular excitonic vibrational water dynamics in aqueous chemistry. To test the proposal, the hydrogen tunnelling modulation observed in the PCET reaction studied in the presence of low concentrations of various partial hydrophobic solutes in the water reaction system has been analyzed in terms of the proposed involvement of the collective intermolecular vibrational water dynamics in activation process in the case. The strongly linear correlation between common tunnelling signatures, isotopic values of Arrhenius prefactor ratios ln AH/AD and isotopic differences in activation enthalpies ΔΔH‡ (H,D) observed in the process in fairly diluted water solutions containing various partial hydrophobic solutes (such as dioxane, acetonitrile, ethanol, and quaternary ammonium ions) points to the common physical origin of the phenomenon in all the cases. It is suggested that the phenomenon can be rooted in an interplay of delocalized collective intermolecular vibrational dynamics of water correlated with vibrations of the coupled transition configuration, where the donor-acceptor oscillations, the motions being to some degree along the reaction coordinate, lead to modulation of hydrogen tunnelling in the reaction.
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Affiliation(s)
| | - Cvijeta Jakobušić Brala
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia; (A.K.M.); (V.P.)
| | | | - Stanko Uršić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia; (A.K.M.); (V.P.)
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10
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Kananenka AA, Yao K, Corcelli SA, Skinner JL. Machine Learning for Vibrational Spectroscopic Maps. J Chem Theory Comput 2019; 15:6850-6858. [DOI: 10.1021/acs.jctc.9b00698] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alexei A. Kananenka
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - J. L. Skinner
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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11
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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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12
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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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13
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Stefanutti E, Bove LE, Alabarse FG, Lelong G, Bruni F, Ricci MA. Vibrational dynamics of confined supercooled water. J Chem Phys 2019; 150:224504. [PMID: 31202218 DOI: 10.1063/1.5094147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quest for a possible liquid-liquid coexistence line in supercooled water below its homogeneous nucleation temperature is faced by confining water within a porous silica substrate (MCM-41). This system is investigated by synchrotron radiation infrared spectroscopy, exploring both the intramolecular and the intermolecular vibrational dynamics, in the temperature range from ambient down to ∼120 K, along several isobaric paths between 0.7 kbar and 3.0 kbar. Upon lowering the temperature, the OH-stretching band shows that the intramolecular vibrational dynamics continuously evolves from predominantly liquidlike to predominantly icelike. An abrupt change in the line shape of the intermolecular vibrational band between 220 K and 240 K, depending on the pressure, is the signature of nucleation of ice within the MCM-41 pores. These findings do not support the presence of two liquid phases and provide evidence for the coexistence of liquid water and ice in water confined in MCM-41.
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Affiliation(s)
- E Stefanutti
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - L E Bove
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F G Alabarse
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - G Lelong
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F Bruni
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - M A Ricci
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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14
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Kananenka AA, Hestand NJ, Skinner JL. OH-Stretch Raman Multivariate Curve Resolution Spectroscopy of HOD/H2O Mixtures. J Phys Chem B 2019; 123:5139-5146. [DOI: 10.1021/acs.jpcb.9b02686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexei A. Kananenka
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas J. Hestand
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - J. L. Skinner
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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15
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Yang N, Duong CH, Kelleher PJ, McCoy AB, Johnson MA. Deconstructing water's diffuse OH stretching vibrational spectrum with cold clusters. Science 2019; 364:275-278. [PMID: 31000660 DOI: 10.1126/science.aaw4086] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
The diffuse vibrational envelope displayed by water precludes direct observation of how different hydrogen-bond topologies dictate the spectral response of individual hydroxy group (OH) oscillators. Using cold, isotopically labeled cluster ions, we report the spectral signatures of a single, intact water (H2O) molecule embedded at various sites in the clathrate-like cage structure adopted by the Cs+·(D2O)20 ion. These patterns reveal the site-dependent correlation between the frequencies of the two OH groups on the same water molecule and establish that the bound OH companion of the free OH group exclusively accounts for bands in the lower-energy region of the spectrum. The observed multiplet structures reveal the homogeneous linewidths of the fundamentals and quantify the anharmonic contributions arising from coupling to both the intramolecular bending and intermolecular soft modes.
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Affiliation(s)
- Nan Yang
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Chinh H Duong
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Patrick J Kelleher
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA.
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16
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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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17
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Rubtsov IV, Burin AL. Ballistic and diffusive vibrational energy transport in molecules. J Chem Phys 2019; 150:020901. [PMID: 30646721 DOI: 10.1063/1.5055670] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Energy transport in molecules is essential for many areas of science and technology. Strong covalent bonds of a molecular backbone can facilitate the involvement of the molecule's high-frequency modes in energy transport, which, under certain conditions, makes the transport fast and efficient. We discuss such conditions and describe various transport regimes in molecules, including ballistic, diffusive, directed diffusion, and intermediate regime cases, in light of recently developed experimental and theoretical approaches.
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Affiliation(s)
- Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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18
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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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19
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Carpenter WB, Fournier JA, Biswas R, Voth GA, Tokmakoff A. Delocalization and stretch-bend mixing of the HOH bend in liquid water. J Chem Phys 2018; 147:084503. [PMID: 28863511 DOI: 10.1063/1.4987153] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H2O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H2O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm-1 to beyond 1900 cm-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δHOH on 2-7 water molecules.
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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
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rajib Biswas
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Gregory A Voth
- 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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20
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Sanders SE, Vanselous H, Petersen PB. Water at surfaces with tunable surface chemistries. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:113001. [PMID: 29393860 DOI: 10.1088/1361-648x/aaacb5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aqueous interfaces are ubiquitous in natural environments, spanning atmospheric, geological, oceanographic, and biological systems, as well as in technical applications, such as fuel cells and membrane filtration. Where liquid water terminates at a surface, an interfacial region is formed, which exhibits distinct properties from the bulk aqueous phase. The unique properties of water are governed by the hydrogen-bonded network. The chemical and physical properties of the surface dictate the boundary conditions of the bulk hydrogen-bonded network and thus the interfacial properties of the water and any molecules in that region. Understanding the properties of interfacial water requires systematically characterizing the structure and dynamics of interfacial water as a function of the surface chemistry. In this review, we focus on the use of experimental surface-specific spectroscopic methods to understand the properties of interfacial water as a function of surface chemistry. Investigations of the air-water interface, as well as efforts in tuning the properties of the air-water interface by adding solutes or surfactants, are briefly discussed. Buried aqueous interfaces can be accessed with careful selection of spectroscopic technique and sample configuration, further expanding the range of chemical environments that can be probed, including solid inorganic materials, polymers, and water immiscible liquids. Solid substrates can be finely tuned by functionalization with self-assembled monolayers, polymers, or biomolecules. These variables provide a platform for systematically tuning the chemical nature of the interface and examining the resulting water structure. Finally, time-resolved methods to probe the dynamics of interfacial water are briefly summarized before discussing the current status and future directions in studying the structure and dynamics of interfacial water.
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Affiliation(s)
- Stephanie E Sanders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
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21
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Carpenter WB, Fournier JA, Lewis NHC, Tokmakoff A. Picosecond Proton Transfer Kinetics in Water Revealed with Ultrafast IR Spectroscopy. J Phys Chem B 2018; 122:2792-2802. [PMID: 29452488 DOI: 10.1021/acs.jpcb.8b00118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aqueous proton transport involves the ultrafast interconversion of hydrated proton species that are closely linked to the hydrogen bond dynamics of water, which has been a long-standing challenge to experiments. In this study, we use ultrafast IR spectroscopy to investigate the distinct vibrational transition centered at 1750 cm-1 in strong acid solutions, which arises from bending vibrations of the hydrated proton complex. Broadband ultrafast two-dimensional IR spectroscopy and transient absorption are used to measure vibrational relaxation, spectral diffusion, and orientational relaxation dynamics. The hydrated proton bend displays fast vibrational relaxation and spectral diffusion timescales of 200-300 fs; however, the transient absorption anisotropy decays on a remarkably long 2.5 ps timescale, which matches the timescale for hydrogen bond reorganization in liquid water. These observations are indications that the bending vibration of the aqueous proton complex is relatively localized, with an orientation that is insensitive to fast hydrogen bonding fluctuations and dependent on collective structural relaxation of the liquid to reorient. We conclude that the orientational relaxation is a result of proton transfer between configurations that are well described by a Zundel-like proton shared between two flanking water molecules.
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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 , United States
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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22
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Grechko M, Hasegawa T, D'Angelo F, Ito H, Turchinovich D, Nagata Y, Bonn M. Coupling between intra- and intermolecular motions in liquid water revealed by two-dimensional terahertz-infrared-visible spectroscopy. Nat Commun 2018; 9:885. [PMID: 29491413 PMCID: PMC5830436 DOI: 10.1038/s41467-018-03303-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
The interaction between intramolecular and intermolecular degrees of freedom in liquid water underlies fundamental chemical and physical phenomena such as energy dissipation and proton transfer. Yet, it has been challenging to elucidate the coupling between these different types of modes. Here, we report on the direct observation and quantification of the coupling between intermolecular and intramolecular coordinates using two-dimensional, ultra-broadband, terahertz-infrared-visible (2D TIRV) spectroscopy and molecular dynamics calculations. Our study reveals strong coupling of the O-H stretch vibration, independent of the degree of delocalization of this high-frequency mode, to low-frequency intermolecular motions over a wide frequency range from 50 to 250 cm-1, corresponding to both the intermolecular hydrogen bond bending (≈ 60 cm-1) and stretching (≈ 180 cm-1) modes. Our results provide mechanistic insights into the coupling of the O-H stretch vibration to collective, delocalized intermolecular modes.
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Affiliation(s)
- Maksim Grechko
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany.
| | - Taisuke Hasegawa
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Francesco D'Angelo
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Hironobu Ito
- Department of Chemistry, Faculty of Education, Shizuoka University, 836 Ohya, 422-8529, Shizuoka, Japan
| | - Dmitry Turchinovich
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
- Fakultät für Physik, Universität Duisburg-Essen, Lotharstr. 1, 47057, Duisburg, Germany
| | - Yuki Nagata
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
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23
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Jansen TLC. Simple Quantum Dynamics with Thermalization. J Phys Chem A 2018; 122:172-183. [PMID: 29199829 PMCID: PMC5770886 DOI: 10.1021/acs.jpca.7b10380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/04/2017] [Indexed: 02/05/2023]
Abstract
In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.
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Affiliation(s)
- Thomas L. C. Jansen
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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24
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Jeon K, Yang M. Dimension of discrete variable representation for mixed quantum/classical computation of three lowest vibrational states of OH stretching in liquid water. J Chem Phys 2017; 146:054107. [PMID: 28178837 DOI: 10.1063/1.4974934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three low-lying vibrational states of molecular systems are responsible for the signals of linear and third-order nonlinear vibrational spectroscopies. Theoretical studies based on mixed quantum/classical calculations provide a powerful way to analyze those experiments. A statistically meaningful result can be obtained from the calculations by solving the vibrational Schrödinger equation over many numbers of molecular configurations. The discrete variable representation (DVR) method is a useful technique to calculate vibrational eigenstates subject to an arbitrary anharmonic potential surface. Considering the large number of molecular configurations over which the DVR calculations are repeated, the calculations are desired to be optimized in balance between the cost and accuracy. We determine a dimension of the DVR method which appears to be optimum for the calculations of the three states of molecular vibrations with anharmonic strengths often found in realistic molecular systems. We apply the numerical technique to calculate the local OH stretching frequencies of liquid water, which are well known to be widely distributed due to the inhomogeneity in molecular configuration, and found that the frequencies of the 0-1 and 1-2 transitions are highly correlated. An empirical relation between the two frequencies is suggested and compared with the experimental data of nonlinear IR spectroscopies.
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Affiliation(s)
- Kiyoung Jeon
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
| | - Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
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25
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Daly CA, Berquist EJ, Brinzer T, Garrett-Roe S, Lambrecht DS, Corcelli SA. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: II. Spectroscopic Map. J Phys Chem B 2016; 120:12633-12642. [DOI: 10.1021/acs.jpcb.6b09509] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clyde A. Daly
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
| | - Eric J. Berquist
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Thomas Brinzer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel S. Lambrecht
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Steven A. Corcelli
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
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26
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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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27
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Fournier JA, Carpenter W, De Marco L, Tokmakoff A. Interplay of Ion–Water and Water–Water Interactions within the Hydration Shells of Nitrate and Carbonate Directly Probed with 2D IR Spectroscopy. J Am Chem Soc 2016; 138:9634-45. [DOI: 10.1021/jacs.6b05122] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joseph A. Fournier
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - William Carpenter
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Luigi De Marco
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, Chicago, Illinois 60637, United States
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28
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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29
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Shi L, Skinner JL, Jansen TLC. Two-dimensional infrared spectroscopy of neat ice Ih. Phys Chem Chem Phys 2016; 18:3772-9. [PMID: 26765972 DOI: 10.1039/c5cp07264f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assignment of the distinct peaks observed in the OH stretch lineshape of ice Ih is controversial. Recent two-dimensional infrared spectroscopic measurements provided new data. The spectra are, however, challenging to interpret and here we provide simulations that help overcome experimental issues as thermal signals and finite pulse duration. We find good agreement with experiment and the difference between H2O and D2O ices is well accounted for. The overall dynamics is demonstrated to be faster than observed for the corresponding liquid water. We find that excitonic cross peaks exist between the dominant exciton peaks. This leads us to conclude that the cross peaks arise due to the formation of delocalized exciton states, which have essentially no directional correlation between their transition dipoles as opposed to what is commonly seen, for example, in isolated water, where the transition dipoles of the eigenstates are perpendicular to each other.
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Affiliation(s)
- Liang Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA 02139, USA
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30
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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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31
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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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32
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Mandal A, Ramasesha K, De Marco L, Tokmakoff A. Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy. J Chem Phys 2015; 140:204508. [PMID: 24880302 DOI: 10.1063/1.4878490] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The infrared spectra of aqueous solutions of NaOH and other strong bases exhibit a broad continuum absorption for frequencies between 800 and 3500 cm(-1), which is attributed to the strong interactions of the OH(-) ion with its solvating water molecules. To provide molecular insight into the origin of the broad continuum absorption feature, we have performed ultrafast transient absorption and 2DIR experiments on aqueous NaOH by exciting the O-H stretch vibrations and probing the response from 1350 to 3800 cm(-1) using a newly developed sub-70 fs broadband mid-infrared source. These experiments, in conjunction with harmonic vibrational analysis of OH(-)(H2O)n (n = 17) clusters, reveal that O-H stretch vibrations of aqueous hydroxides arise from coupled vibrations of multiple water molecules solvating the ion. We classify the vibrations of the hydroxide complex by symmetry defined by the relative phase of vibrations of the O-H bonds hydrogen bonded to the ion. Although broad and overlapping spectral features are observed for 3- and 4-coordinate ion complexes, we find a resolvable splitting between asymmetric and symmetric stretch vibrations, and assign the 2850 cm(-1) peak infrared spectra of aqueous hydroxides to asymmetric stretch vibrations.
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Affiliation(s)
- Aritra Mandal
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Krupa Ramasesha
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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33
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Panman MR, Shaw DJ, Ensing B, Woutersen S. Local orientational order in liquids revealed by resonant vibrational energy transfer. PHYSICAL REVIEW LETTERS 2014; 113:207801. [PMID: 25432055 DOI: 10.1103/physrevlett.113.207801] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Indexed: 06/04/2023]
Abstract
We demonstrate that local orientational ordering in a liquid can be observed in the decay of the vibrational anisotropy caused by resonant transfer of vibrational excitations between its constituent molecules. We show that the functional form of this decay is determined by the (distribution of) angles between the vibrating bonds of the molecules between which energy transfer occurs, and that the initial drop in the decay reflects the average angle between nearest neighbors. We use this effect to observe the difference in local orientational ordering in the two hydrogen-bonded liquids ethanol and N-methylacetamide.
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Affiliation(s)
- M R Panman
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - D J Shaw
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B Ensing
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S Woutersen
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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34
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van der Vegte CP, Knop S, Vöhringer P, Knoester J, Jansen TLC. OH-stretching in synthetic hydrogen-bonded chains. J Phys Chem B 2014; 118:6256-64. [PMID: 24820546 DOI: 10.1021/jp504267h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study hydrogen bond dynamics in stereoselectively synthesized polyalcohols by combining linear and two-dimensional (2D) infrared spectroscopy experiments with simulations. We consider two variants of the polyalcohols: the all-syn and all-anti tetrol, which because of their different stereochemistry of the hydroxyl groups form a linear hydrogen-bonded chain that is stable for tens of picoseconds or a system where hydrogen bonds are formed and broken on a picosecond timescale, respectively. The differences in structure and hydrogen bond dynamics gives rise to significant differences in the linear spectra for the two compounds. Furthermore, we show that the stronger hydrogen bonding for the all-syn variant leads to faster fluctuations of the site frequencies than for the all-anti one, which is reflected in the higher degree of homogeneous broadening in the 2D spectra. Because of the different stereochemistry, the coupling in the all-syn molecule is stronger than for the all-anti one, which leads to a faster delocalization of a local excitation. This explains the previously observed pump-frequency independent vibrational lifetime for the all-syn variant, since the excitation loses the memory of the pump frequency before relaxation. For the all-anti form, the coupling is weak and the excitation remains in the initially excited state, maintaining the memory of the pump frequency.
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Affiliation(s)
- C P van der Vegte
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Yang M. Effects of excluded volume and correlated molecular orientations on Förster resonance energy transfer in liquid water. J Chem Phys 2014; 140:144508. [PMID: 24735306 DOI: 10.1063/1.4870937] [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
Förster theory for the survival probability of excited chromophores is generalized to include the effects of excluded volume and orientation correlation in the molecular distribution. An analytical expression for survival probability was derived and written in terms of a few simple elementary functions. Because of the excluded volume, the survival probability exhibits exponential decay at early times and stretched exponential decay at later times. Experimental schemes to determine the size of the molecular excluded volume are suggested. With the present generalization of theory, we analyzed vibrational resonance energy transfer kinetics in neat water. Excluded volume effects prove to be important and slow down the kinetics at early times. The majority of intermolecular resonance energy transfer was found to occur with exponential kinetics, as opposed to the stretched exponential behavior predicted by Förster theory. Quantum yields of intra-molecular vibrational relaxation, intra-, and intermolecular energy transfer were calculated to be 0.413, 0.167, and 0.420, respectively.
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Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
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36
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Bai S, Xie W, Zhu L, Shi Q. Calculation of absorption spectra involving multiple excited states: Approximate methods based on the mixed quantum classical Liouville equation. J Chem Phys 2014; 140:084105. [DOI: 10.1063/1.4866367] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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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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38
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Ramasesha K, De Marco L, Mandal A, Tokmakoff A. Water vibrations have strongly mixed intra- and intermolecular character. Nat Chem 2013; 5:935-40. [DOI: 10.1038/nchem.1757] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 08/14/2013] [Indexed: 11/09/2022]
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39
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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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40
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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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41
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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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42
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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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43
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Affiliation(s)
- Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich , Zürich, Switzerland
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, Germany
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44
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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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45
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Tesar SL, Kasyanenko VM, Rubtsov IV, Rubtsov GI, Burin AL. Theoretical Study of Internal Vibrational Relaxation and Energy Transport in Polyatomic Molecules. J Phys Chem A 2013; 117:315-23. [DOI: 10.1021/jp309481u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah L. Tesar
- Department
of Chemistry, Tulane University, New Orleans
Louisiana 70118, United
States
| | - Valeriy M. Kasyanenko
- Department
of Chemistry, Tulane University, New Orleans
Louisiana 70118, United
States
| | - Igor V. Rubtsov
- Department
of Chemistry, Tulane University, New Orleans
Louisiana 70118, United
States
| | - Grigory I. Rubtsov
- Institute for Nuclear Research of RAS, 60th October Anniversary st. 7a, Moscow,
Russia 117312
| | - Alexander L. Burin
- Department
of Chemistry, Tulane University, New Orleans
Louisiana 70118, United
States
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46
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Baiz CR, Reppert M, Tokmakoff A. Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins. J Phys Chem A 2012; 117:5955-61. [DOI: 10.1021/jp310689a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Mike Reppert
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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47
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Nihonyanagi S, Singh PC, Yamaguchi S, Tahara T. Ultrafast Vibrational Dynamics of a Charged Aqueous Interface by Femtosecond Time-Resolved Heterodyne-Detected Vibrational Sum Frequency Generation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120051] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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48
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Liang C, Knoester J, Jansen TLC. Proton Transport in a Membrane Protein Channel: Two-Dimensional Infrared Spectrum Modeling. J Phys Chem B 2012; 116:6336-45. [DOI: 10.1021/jp3019827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chungwen Liang
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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49
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Liang C, Jansen TLC. An Efficient N(3)-Scaling Propagation Scheme for Simulating Two-Dimensional Infrared and Visible Spectra. J Chem Theory Comput 2012; 8:1706-13. [PMID: 26593664 DOI: 10.1021/ct300045c] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system. This is needed for calculating the third-order response functions governing the two-dimensional infrared and visible spectra. The method is tested on a model dimer system, the amide I spectrum of the Gramicidin A antimicrobial peptide, the spectrum of the OH stretching vibration of bulk water, and a homogeneous J-aggregate. Errors due to the approximation are hardly observable in the calculated spectra. Scaling simulations with different system sizes are used to demonstrate that the new scheme is indeed scaling with the system size to the third power, one order faster than the existing methods.
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Affiliation(s)
- Chungwen Liang
- 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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50
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Sun Y, Zheng R, Shi Q. Theoretical Study of Raman Spectra of Methanol in Aqueous Solutions: Non-Coincident Effect of the CO Stretch. J Phys Chem B 2012; 116:4543-51. [DOI: 10.1021/jp300178v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanyuan Sun
- Beijing National
Laboratory for Molecular Sciences,
State Key Laboratory for Structural Chemistry of Unstable and Stable
Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Renhui Zheng
- Beijing National
Laboratory for Molecular Sciences,
State Key Laboratory for Structural Chemistry of Unstable and Stable
Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National
Laboratory for Molecular Sciences,
State Key Laboratory for Structural Chemistry of Unstable and Stable
Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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