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Giubertoni G, Caporaletti F, Roeters SJ, Chatterley AS, Weidner T, Laity P, Holland C, Woutersen S. In Situ Identification of Secondary Structures in Unpurified Bombyx mori Silk Fibrils Using Polarized Two-Dimensional Infrared Spectroscopy. Biomacromolecules 2022; 23:5340-5349. [PMID: 36437734 DOI: 10.1021/acs.biomac.2c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behavior of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the noninvasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools because the absorption bands of amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk films cast from Bombyx mori silk feedstock. Without any additional peak fitting, we find that the initial effect of hydration is an increase of the random coil content at the expense of the helical content, while the β-sheet content is unchanged and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.
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Affiliation(s)
- Giulia Giubertoni
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Federico Caporaletti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Steven J Roeters
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands
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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: 165] [Impact Index Per Article: 41.3] [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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Lee H, Cheon S, Cho M. Chiroptical nature of two-exciton states of light-harvesting complex: Doubly resonant three-wave-mixing spectroscopy. J Chem Phys 2010; 132:225102. [PMID: 20550421 DOI: 10.1063/1.3432624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Photosynthetic light-harvesting complex is a coupled multichromophore system. Due to electronic couplings between neighboring chlorophylls in the complex, the one- and two-exciton states are delocalized and they can be written as linear combinations of singly and doubly excited configurations, respectively. Despite that the chiroptical properties of one-exciton states in such a multichromophore system have been investigated by using linear optical activity measurement techniques; those of two-exciton states have not been studied before due to a lack of appropriate measurement methods. Here, we present a theoretical description on chiroptical chi((2)) spectroscopy and show that it can be used to investigate such properties of a photosynthetic light-harvesting system, which is the Fenna-Matthews-Olson complex, consisting of seven bacteriochlorophylls in its protein subunit. To simulate the doubly resonant sum- and difference-frequency-generation spectra of the complex, one- and two-exciton transition dipoles were calculated. Carrying out quantum chemistry calculations of electronically excited states of a model bacteriochlorophyll system and taking into account the dipole-induced dipole electronic transition processes between the ground state and two-exciton states, we could calculate the two-dimensional sum-frequency-generation spectra revealing dominant second-order chiroptical transition pathways and involved one- and two-exciton states. It is believed that the present computational scheme and the theoretically proposed doubly resonant two-dimensional three-wave-mixing spectroscopy would be of use to shed light on the chiroptical natures of two-exciton states of arbitrary coupled multichromophore systems.
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Affiliation(s)
- Hochan Lee
- Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
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Li C, Cheng S, Tjahjono M, Schreyer M, Garland M. Concurrent Synergism and Inhibition in Bimetallic Catalysis: Catalytic Binuclear Elimination, Solute−Solute Interactions and a Hetero-Bimetallic Hydrogen-Bonded Complex in Rh−Mo Hydroformylations. J Am Chem Soc 2010; 132:4589-99. [DOI: 10.1021/ja909696b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanzhao Li
- Institute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore, 627833
| | - Shuying Cheng
- Institute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore, 627833
| | - Martin Tjahjono
- Institute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore, 627833
| | - Martin Schreyer
- Institute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore, 627833
| | - Marc Garland
- Institute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore, 627833
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Fournier F, Guo R, Gardner EM, Donaldson PM, Loeffeld C, Gould IR, Willison KR, Klug DR. Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis. Acc Chem Res 2009; 42:1322-31. [PMID: 19548660 DOI: 10.1021/ar900074p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.
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Affiliation(s)
- Frederic Fournier
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Rui Guo
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Elizabeth M. Gardner
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Paul M. Donaldson
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Christian Loeffeld
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Ian R. Gould
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Keith R. Willison
- Institute of Cancer Research, Chester Beatty Laboratories, Cancer Research U.K., Centre of Cellular and Molecular Biology, London SW3 6JB, U.K
| | - David R. Klug
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
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Guo R, Fournier F, Donaldson PM, Gardner EM, Gould IR, Klug DR. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration–vibration two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2009; 11:8417-21. [DOI: 10.1039/b910804a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Suzuki Y, Tanimura Y. Exploring a free energy landscape by means of multidimensional infrared and terahertz spectroscopies. J Chem Phys 2008; 128:164501. [PMID: 18447453 DOI: 10.1063/1.2897982] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A model for the dipolar crystal system is employed to explore a role of free energy landscape (FEL), in which dipolar molecules are posted on two-dimensional lattice sites with two-state libratinal dynamics. All dipole-dipole interactions are included to have frustrated interactions among the dipoles. For the regular and distorted lattice cases, the FEL is calculated from the interaction energies and the total polarizations for all possible dipolar states at various temperatures. At high temperatures, the shape of the calculated FEL is smooth and parabolic, while it becomes bumpy at low temperatures exhibiting multiple local minima. To study dynamical aspects of the system, the single flip dynamics and the single-double mixed flips dynamics of dipoles are examined from a master equation approach. As the observables of linear absorption and two-dimensional (2D) infrared, far infrared, and terahertz spectroscopies, the first- and third-order response functions of polarization are calculated for different physical conditions characterized by the FEL. While the linear absorption signals decay in time in a similar manner regardless of the FEL profiles, the 2D signals exhibit prominent differences for those profiles. This indicates that we may differentiate the FEL profiles by changing two-time valuables in 2D spectroscopy. As illustrated in the single-double flips case, the FEL study by means of 2D spectroscopy, however, relies on the dynamics which is set independently from the FEL. The Smoluchowski equation is applied to examine the description of the collective dynamics on the microscopically calculated FEL. We found that the one-dimensional and 2D signals calculated from the Smoluchowski equation agree with those from master equation only at temperatures where the FEL becomes parabolic shape.
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Affiliation(s)
- Yohichi Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan.
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Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
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Choi JH, Cheon S, Lee H, Cho M. Two-dimensional nonlinear optical activity spectroscopy of coupled multi-chromophore system. Phys Chem Chem Phys 2008; 10:3839-56. [DOI: 10.1039/b719263k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Choi JH, Cheon S, Cho M. Doubly resonant two-dimensional three-wave-mixing spectroscopy of polypeptides: Structure–spectrum relationships. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cheon S, Lee H, Choi JH, Cho M. Doubly resonant three-wave-mixing spectroscopy of a chiral coupled-chromophore system in solution: coherent two-dimensional optical activity spectroscopy. J Chem Phys 2007; 126:054505. [PMID: 17302483 DOI: 10.1063/1.2431806] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Theoretical descriptions of doubly resonant two-dimensional (2D) sum-frequency-generation (SFG) and difference-frequency-generation (DFG) spectroscopies of coupled-chromophore systems are presented. Despite that each electronic or vibrational chromophore is achiral, the interaction-induced chirality of a coupled multichromophore system in solution can be measured by using the doubly resonant 2D three-wave-mixing (3WM) spectroscopic method. An electronically coupled dimer, where each monomer is modeled as a simple two-level system, can have nonvanishing SFG (or DFG) properties, e.g., susceptibility in frequency domain or nonlinear response function in time domain, if the induced dipole vector of the dimer is not orthogonal to the vector product of the two monomer electronic transition dipole vectors. In order to demonstrate that these 2D 3WM spectroscopic methods can be used to determine the solution structure of a polypeptide, the authors carried out quantum chemistry calculations for an alanine dipeptide and obtained first- and second-order dipole derivatives associated with the amide I vibrational transitions of the dipeptide. It is shown that the numerically simulated 2D IR-IR SFG spectrum is highly sensitive to the dipeptide secondary structure and provides rich information on the one- and two-exciton states. It is believed that the theoretically proposed doubly resonant 2D 3WM spectroscopy, which can be considered to be an optical activity spectroscopy, will be of use in studying both structural and dynamical aspects of coupled multichromophore systems, such as proteins, nucleic acids, nanoparticle aggregates etc.
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Affiliation(s)
- Sangheon Cheon
- Department of Chemistry, Korea University, Seoul 136-701, Korea and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea
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Kötting C, Blessenohl M, Suveyzdis Y, Goody RS, Wittinghofer A, Gerwert K. A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein. Proc Natl Acad Sci U S A 2006; 103:13911-6. [PMID: 16968776 PMCID: PMC1599887 DOI: 10.1073/pnas.0604128103] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Indexed: 11/18/2022] Open
Abstract
The hydrolysis of nucleoside triphosphates by enzymes is used as a regulation mechanism in key biological processes. Here, the GTP hydrolysis of the protein complex of Ras with its GTPase-activating protein is monitored at atomic resolution in a noncrystalline state by time-resolved FTIR spectroscopy. At 900 ms, after the attack of water at the gamma-phosphate, there appears a H2PO4- intermediate that is shown to be hydrogen-bonded in an eclipsed conformation to the beta-phosphate of GDP. The H2PO4- intermediate is in a position where it can either reform GTP or be released from the protein in 7 s in the rate-limiting step of the GTPase reaction. We propose that such an intermediate also occurs in other GTPases and ATPases.
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Affiliation(s)
| | | | | | - Roger S. Goody
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; and
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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Nagata Y, Tanimura Y. Two-dimensional Raman spectra of atomic solids and liquids. J Chem Phys 2006; 124:024508. [PMID: 16422612 DOI: 10.1063/1.2131053] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We calculate third- and fifth-order Raman spectra of simple atoms interacting through a soft-core potential by means of molecular-dynamics (MD) simulations. The total polarizability of molecules is treated by the dipole-induced dipole model. Two- and three-body correlation functions of the polarizability at various temperatures are evaluated from equilibrium MD simulations based on a stability matrix formulation. To analyze the processes involved in the spectroscopic measurements, we divide the fifth-order response functions into symmetric and antisymmetric integrated response functions; the symmetric one is written as a simple three-body correlation function, while the antisymmetric one depends on a stability matrix. This analysis leads to a better understanding of the time scales and molecular motions that govern the two-dimensional (2D) signal. The 2D Raman spectra show novel differences between the solid and liquid phases, which are associated with the decay rates of coherent motions. On the other hand, these differences are not observed in the linear Raman spectra.
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Affiliation(s)
- Yuki Nagata
- Department of Chemistry, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan.
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Hyeon-Deuk K, Hyeon-Deuk K, Tanimura Y. Multidimensional infrared spectroscopy for molecular vibrational modes with dipolar interactions, anharmonicity, and nonlinearity of dipole moments and polarizability. J Chem Phys 2005; 123:224310. [PMID: 16375479 DOI: 10.1063/1.2134702] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We present an analytical expression for the linear and nonlinear infrared spectra of interacting molecular vibrational motions. Each of the molecular modes is explicitly represented by a classical damped oscillator on an anharmonic multidimensional potential-energy surface. The two essential interactions, the dipole-dipole (DD) and the dipole-induced-dipole (DID) interactions, are taken into account, and each dipole moment and polarizability are expanded to nonlinear order with respect to the nuclear vibrational coordinate. Our analytical treatment leads to expressions for the contributions of anharmonicity, DD and DID interactions, and the nonlinearity of dipole moments and polarizability elements to the one-, two-, and three-dimensional spectra as separated terms, which allows us to discuss the relative importance of these respective contributions. We can calculate multidimensional signals for various configurations of molecules interacting through DD and DID interactions for different material parameters over the whole range of frequencies. We demonstrate that contributions from the DD and DID interactions and anharmonicity are separately detectable through the third-order three-dimensional IR spectroscopy, whereas they cannot be distinguished from each other in either the linear or the second-order IR spectroscopies. The possibility of obtaining the intra- or intermolecular structural information from multidimensional spectra is also discussed.
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Affiliation(s)
- Kim Hyeon-Deuk
- Department of Chemistry, Kyoto University, Kyoto 606-8502, Japan.
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Ding F, Fulmer EC, Zanni MT. Heterodyned fifth-order two-dimensional IR spectroscopy: Third-quantum states and polarization selectivity. J Chem Phys 2005; 123:94502. [PMID: 16164348 DOI: 10.1063/1.1998829] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A heterodyned fifth-order two-dimensional (2D) IR spectrum of a model coupled oscillator system, Ir(CO)(2)(C(5)H(7)O(2)), is reported. The spectrum is generated by a pulse sequence that probes the eigenstate energies up to the second overtone and combination bands, providing a more rigorous potential-energy surface of the coupled carbonyl local modes than can be obtained with third-order spectroscopy. Furthermore, the pulse sequence is designed to generate and then rephase a two-quantum coherence so that the spectrum is line narrowed and the resolution improved for inhomogeneously broadened systems. Features arising from coherence transfer processes are identified, which are more pronounced than in third-order 2D IR spectroscopy because the transition dipoles of the second overtone and combination states are not rigorously orthogonal, relaxing the polarization constraints on the signal intensity for these features. The spectrum provides a stringent test of cascading signals caused by third-order emitted fields and no cascading is observed. In the Appendix, formulas for calculating the signal intensities for resonant fifth-order spectroscopies with arbitrarily polarized pulses and transition dipoles are reported. These relationships are useful for interpreting and designing polarization conditions to enhance specific spectral features.
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Affiliation(s)
- Feng Ding
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Interplay of the Intramolecular Water Vibrations and Hydrogen Bond in N-Methylacetamide-Water Complexes: Ab Initio Calculation Studies. B KOREAN CHEM SOC 2003. [DOI: 10.5012/bkcs.2003.24.8.1061] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Linear optical spectroscopies have long been used to study the behavior of liquids. Laser technology has progressed to the point that it has become possible to perform nonlinear optical experiments that probe higher-order correlation functions in liquids, opening a new window into our understanding of the microscopic details of solution-phase processes. Here we review advances that have been made in recent years in employing higher-order electronic and vibrational spectroscopies to study liquid-state dynamics and structure.
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Affiliation(s)
- John T Fourkas
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA.
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Golonzka O, Khalil M, Demirdöven N, Tokmakoff A. Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibrational echo spectroscopy. J Chem Phys 2001. [DOI: 10.1063/1.1417504] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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21
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Zanni MT, Hochstrasser RM. Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures. Curr Opin Struct Biol 2001; 11:516-22. [PMID: 11785750 DOI: 10.1016/s0959-440x(00)00243-8] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recently, new methods for determining time-evolving structures using infrared analogs of NMR spectroscopy have been introduced that have outstanding potential in structural biology. Already, within the past two years, structures of dipeptides, tripeptides and pentapeptides have been determined on much faster timescales than the conformational dynamics. Also, two-dimensional infrared correlation spectra of some proteins and isotopically edited alanine-rich helices have been examined.
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Affiliation(s)
- M T Zanni
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.
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Suzuki Y, Tanimura Y. Nonequilibrium initial conditions of a Brownian oscillator system observed by two-dimensional spectroscopy. J Chem Phys 2001. [DOI: 10.1063/1.1379768] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shuang F, Yang C, Yan Y. Dynamical semigroup Fokker–Planck equation approach to transient absorption and fluorescence upconversion spectroscopies. J Chem Phys 2001. [DOI: 10.1063/1.1344608] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cho M. Two-dimensional vibrational spectroscopy. VII. Investigation of the vibronic and vibrational couplings by using novel triply resonant two-dimensional vibrational spectroscopies. J Chem Phys 2000. [DOI: 10.1063/1.1314351] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sung J, Cho M. Calculation of the two-dimensional vibrational response function. J Chem Phys 2000. [DOI: 10.1063/1.1312276] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Park K, Cho M. Two-dimensional vibrational spectroscopy. VI. Higher-order contributions to the two-dimensional vibrational response functions. J Chem Phys 2000. [DOI: 10.1063/1.481684] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cho M. Two-dimensional vibrational spectroscopy. V. Novel 2-dimensional surface vibrational spectroscopies of adsorbed molecules on surfaces or at interfaces. J Chem Phys 2000. [DOI: 10.1063/1.481634] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Cho M. Triply resonant infrared-infrared-visible sum frequency generation: Three-dimensional vibronic spectroscopy for the investigation of vibrational and vibronic couplings. J Chem Phys 2000. [DOI: 10.1063/1.481512] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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