51
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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52
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Do TN, Gelin MF, Tan HS. Simplified expressions that incorporate finite pulse effects into coherent two-dimensional optical spectra. J Chem Phys 2017; 147:144103. [DOI: 10.1063/1.4985888] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Maxim F. Gelin
- Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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53
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He X, Yu P, Zhao J, Wang J. Efficient Vibrational Energy Transfer through Covalent Bond in Indigo Carmine Revealed by Nonlinear IR Spectroscopy. J Phys Chem B 2017; 121:9411-9421. [DOI: 10.1021/acs.jpcb.7b06766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xuemei He
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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54
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Markmann S, Nong H, Pal S, Fobbe T, Hekmat N, Mohandas RA, Dean P, Li L, Linfield EH, Davies AG, Wieck AD, Jukam N. Two-dimensional coherent spectroscopy of a THz quantum cascade laser: observation of multiple harmonics. OPTICS EXPRESS 2017; 25:21753-21761. [PMID: 29041469 DOI: 10.1364/oe.25.021753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Two-dimensional spectroscopy is performed on a terahertz (THz) frequency quantum cascade laser (QCL) with two broadband THz pulses. Gain switching is used to amplify the first THz pulse and the second THz pulse is used to probe the system. Fourier transforms are taken with respect to the delay time between the two THz pulses and the sampling time of the THz probe pulse. The two-dimensional spectrum consists of three peaks at (ωτ = 0, ωt = ω0), (ωτ = ω0, ωt = ω0), and (ωτ = 2ω0, ωt = ω0) where ω0 denotes the lasing frequency. The peak at ωτ = 0 represents the response of the probe to the zero-frequency (rectified) component of the instantaneous intensity and can be used to measure the gain recovery.
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55
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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56
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Hoffman DJ, Sokolowsky KP, Fayer MD. Direct observation of dynamic crossover in fragile molecular glass formers with 2D IR vibrational echo spectroscopy. J Chem Phys 2017; 146:124505. [DOI: 10.1063/1.4978852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- David J. Hoffman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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57
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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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58
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Jin GY, Kim YS. Phase-Resolved Heterodyne-Detected Transient Grating Enhances the Capabilities of 2D IR Echo Spectroscopy. J Phys Chem A 2017; 121:1007-1011. [DOI: 10.1021/acs.jpca.6b12713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
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59
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Kwon Y, Lee J, Park S. Effect of ion–ligand binding on ion pairing dynamics studied by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2017; 19:10889-10897. [DOI: 10.1039/c6cp08852j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-specific ion pairing dynamics between M+ (M = Ag or Cu) and SCN− in N,N-dimethylthioformamide (DMTF) are studied by probing the nitrile (CN) stretching vibration.
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Affiliation(s)
- YoungAh Kwon
- Department of Chemistry
- Korea University
- Seoul
- Korea
| | - Junho Lee
- Department of Chemistry
- Korea University
- Seoul
- Korea
| | - Sungnam Park
- Department of Chemistry
- Korea University
- Seoul
- Korea
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60
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Kraack JP, Hamm P. Surface-Sensitive and Surface-Specific Ultrafast Two-Dimensional Vibrational Spectroscopy. Chem Rev 2016; 117:10623-10664. [DOI: 10.1021/acs.chemrev.6b00437] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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61
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Ranieri U, Giura P, Gorelli FA, Santoro M, Klotz S, Gillet P, Paolasini L, Koza MM, Bove LE. Dynamical Crossover in Hot Dense Water: The Hydrogen Bond Role. J Phys Chem B 2016; 120:9051-9. [DOI: 10.1021/acs.jpcb.6b04142] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Umbertoluca Ranieri
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
- Institut Laue Langevin, 71, avenue
des Martyrs, B.P. 156, 38042 Grenoble, Cedex 9, France
| | - Paola Giura
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
| | - Federico A. Gorelli
- Istituto Nazionale di Ottica, CNR-INO, via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory
for Non Linear Optics, LENS, via N.
Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Mario Santoro
- Istituto Nazionale di Ottica, CNR-INO, via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory
for Non Linear Optics, LENS, via N.
Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Stefan Klotz
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
| | - Philippe Gillet
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
| | - Luigi Paolasini
- ESRF - The European Synchrotron, 71, avenue des Martyrs, CS 40220 38043 Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue Langevin, 71, avenue
des Martyrs, B.P. 156, 38042 Grenoble, Cedex 9, France
| | - Livia E. Bove
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
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62
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Sokolowsky KP, Bailey HE, Hoffman DJ, Andersen HC, Fayer MD. Critical Slowing of Density Fluctuations Approaching the Isotropic–Nematic Transition in Liquid Crystals: 2D IR Measurements and Mode Coupling Theory. J Phys Chem B 2016; 120:7003-15. [DOI: 10.1021/acs.jpcb.6b04997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Heather E. Bailey
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - David J. Hoffman
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Hans C. Andersen
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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63
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Courtney TL, Fox ZW, Slenkamp KM, Khalil M. Two-dimensional vibrational-electronic spectroscopy. J Chem Phys 2016; 143:154201. [PMID: 26493900 DOI: 10.1063/1.4932983] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two-dimensional vibrational-electronic (2D VE) spectroscopy is a femtosecond Fourier transform (FT) third-order nonlinear technique that creates a link between existing 2D FT spectroscopies in the vibrational and electronic regions of the spectrum. 2D VE spectroscopy enables a direct measurement of infrared (IR) and electronic dipole moment cross terms by utilizing mid-IR pump and optical probe fields that are resonant with vibrational and electronic transitions, respectively, in a sample of interest. We detail this newly developed 2D VE spectroscopy experiment and outline the information contained in a 2D VE spectrum. We then use this technique and its single-pump counterpart (1D VE) to probe the vibrational-electronic couplings between high frequency cyanide stretching vibrations (νCN) and either a ligand-to-metal charge transfer transition ([Fe(III)(CN)6](3-) dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN)5Fe(II)CNRu(III)(NH3)5](-) dissolved in formamide). The 2D VE spectra of both molecules reveal peaks resulting from coupled high- and low-frequency vibrational modes to the charge transfer transition. The time-evolving amplitudes and positions of the peaks in the 2D VE spectra report on coherent and incoherent vibrational energy transfer dynamics among the coupled vibrational modes and the charge transfer transition. The selectivity of 2D VE spectroscopy to vibronic processes is evidenced from the selective coupling of specific νCN modes to the MMCT transition in the mixed valence complex. The lineshapes in 2D VE spectra report on the correlation of the frequency fluctuations between the coupled vibrational and electronic frequencies in the mixed valence complex which has a time scale of 1 ps. The details and results of this study confirm the versatility of 2D VE spectroscopy and its applicability to probe how vibrations modulate charge and energy transfer in a wide range of complex molecular, material, and biological systems.
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Affiliation(s)
- Trevor L Courtney
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Zachary W Fox
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Karla M Slenkamp
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Munira Khalil
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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64
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Xu B, Wu Y, Sun D, Dai HL, Rao Y. Stabilized phase detection of heterodyne sum frequency generation for interfacial studies. OPTICS LETTERS 2015; 40:4472-5. [PMID: 26421559 DOI: 10.1364/ol.40.004472] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present a collinear-geometry heterodyne sum frequency generation (HD-SFG) method for interfacial studies. The HD detection is based on a collinear SFG configuration, in which picosecond visible and femtosecond IR beams are used to first produce a strong local oscillator and then to generate weak SFG signals from an interface. A time-delay compensator, consisting of an MgF2 window, is placed before the sample to introduce the time delay between the local oscillator and the interfacial SFG signals for spectral interferometry. Our HD-SFG method exhibits advantages of long-time phase stability. It is not sensitive to sample heights, does not require reflection correction, and is easy to implement.
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65
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Bakulin AA, Selig O, Bakker HJ, Rezus YLA, Müller C, Glaser T, Lovrincic R, Sun Z, Chen Z, Walsh A, Frost JM, Jansen TLC. Real-Time Observation of Organic Cation Reorientation in Methylammonium Lead Iodide Perovskites. J Phys Chem Lett 2015; 6:3663-9. [PMID: 26722739 DOI: 10.1021/acs.jpclett.5b01555] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The introduction of a mobile and polarized organic moiety as a cation in 3D lead-iodide perovskites brings fascinating optoelectronic properties to these materials. The extent and the time scales of the orientational mobility of the organic cation and the molecular mechanism behind its motion remain unclear, with different experimental and computational approaches providing very different qualitative and quantitative description of the molecular dynamics. Here we use ultrafast 2D vibrational spectroscopy of methylammonium (MA) lead iodide to directly resolve the rotation of the organic cations within the MAPbI3 lattice. Our results reveal two characteristic time constants of motion. Using ab initio molecular dynamics simulations, we identify these as a fast (∼300 fs) "wobbling-in-a-cone" motion around the crystal axis and a relatively slow (∼3 ps) jump-like reorientation of the molecular dipole with respect to the iodide lattice. The observed dynamics are essential for understanding the electronic properties of perovskite materials.
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Affiliation(s)
- Artem A Bakulin
- FOM Institute AMOLF , Science Park 104, Amsterdam, 1098 XG, The Netherlands
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB30HE, United Kingdom
| | - Oleg Selig
- FOM Institute AMOLF , Science Park 104, Amsterdam, 1098 XG, The Netherlands
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, Amsterdam, 1098 XG, The Netherlands
| | - Yves L A Rezus
- FOM Institute AMOLF , Science Park 104, Amsterdam, 1098 XG, The Netherlands
| | - Christian Müller
- Institute for High-Frequency Technology, TU Braunschweig , Schleinitzstr. 22, 38106 Braunschweig, Germany
- InnovationLab GmbH , Speyerer Str. 4, 69115 Heidelberg, Germany
- Kirchhoff-Institute for Physics, Heidelberg University , Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | - Tobias Glaser
- InnovationLab GmbH , Speyerer Str. 4, 69115 Heidelberg, Germany
- Kirchhoff-Institute for Physics, Heidelberg University , Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | - Robert Lovrincic
- Institute for High-Frequency Technology, TU Braunschweig , Schleinitzstr. 22, 38106 Braunschweig, Germany
- InnovationLab GmbH , Speyerer Str. 4, 69115 Heidelberg, Germany
| | - Zhenhua Sun
- LPEM-UMR 8213, ESPCI-ParisTech/CNRS/Université Pierre et Marie Curie , 10 Rue Vauquelin, 75005 Paris, France
| | - Zhuoying Chen
- LPEM-UMR 8213, ESPCI-ParisTech/CNRS/Université Pierre et Marie Curie , 10 Rue Vauquelin, 75005 Paris, France
| | - Aron Walsh
- Department of Chemistry, University of Bath , Claverton Down, Bath BA2 7AY, United Kingdom
| | - Jarvist M Frost
- Department of Chemistry, University of Bath , Claverton Down, Bath BA2 7AY, United Kingdom
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenbough 4, 9747 AG, Groningen, The Netherlands
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66
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Ultrafast Structural Fluctuations of Myoglobin-Bound Thiocyanate and Selenocyanate Ions Measured with Two-Dimensional Infrared Photon Echo Spectroscopy. Chemphyschem 2015; 16:3468-76. [DOI: 10.1002/cphc.201500606] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/27/2015] [Indexed: 11/07/2022]
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67
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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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68
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van Wilderen LJGW, Bredenbeck J. Von ultraschnellen Strukturbestimmungen bis zum Steuern von Reaktionen: mehrdimensionale gemischte IR/nicht-IR-Schwingungsspektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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69
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van Wilderen LJGW, Bredenbeck J. From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies. Angew Chem Int Ed Engl 2015; 54:11624-40. [PMID: 26394274 DOI: 10.1002/anie.201503155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/27/2022]
Abstract
Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.
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Affiliation(s)
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main (Germany).
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70
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71
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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72
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Nilsen IA, Osborne DG, White AM, Anna JM, Kubarych KJ. Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes. J Chem Phys 2015; 141:134313. [PMID: 25296812 DOI: 10.1063/1.4896536] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.
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Affiliation(s)
- Ian A Nilsen
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Derek G Osborne
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Aaron M White
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Jessica M Anna
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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73
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Calladine JA, Horvath R, Davies AJ, Wriglesworth A, Sun XZ, George MW. Probing organometallic reactions by time-resolved infrared spectroscopy in solution and in the solid state using quantum cascade lasers. APPLIED SPECTROSCOPY 2015; 69:519-524. [PMID: 25811673 DOI: 10.1366/14-07708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The photochemistry and photophysics of metal carbonyl compounds (W(CO)6, Cp*Rh(CO)2 (Cp* = η(5)-C5Me5), and fac-[Re(CO)3(4,4'-bpy)2Br] [bpy = bipyridine]) have been examined on the nanosecond timescale using a time-resolved infrared spectrometer with an external cavity quantum cascade laser (QCL) as the infrared source. We show the photochemistry of W(CO)6 in alkane solution is easily monitored, and very sensitive measurements are possible with this approach, meaning it can monitor small transients with absorbance changes less than 10(-6) ΔOD. The C-H activation of Cp*Rh(CO)(C6H12) to form Cp*Rh(CO)(C6H11)H occurs within the first few tens of nanoseconds following photolysis, and we demonstrate that kinetics obtained following deconvolution are in excellent agreement with those measured using an ultrafast laser-based spectrometer. We also show that the high flux and tunability of QCLs makes them suited for solid-state and time-resolved measurements.
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74
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Ghosh R, Samanta T, Banaerjee S, Biswas R, Bagchi B. Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy. Faraday Discuss 2015; 177:313-28. [PMID: 25692942 DOI: 10.1039/c4fd00201f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface). The altered dynamics of water in the presence of such diverse surfaces has attracted considerable attention in recent years. As these interfaces are quite narrow, only a few molecular layers thick, they are hard to study by conventional methods. The recent development of two dimensional infra-red (2D-IR) spectroscopy allows us to estimate length and time scales of such dynamics fairly accurately. In this work, we present a series of interesting studies employing two dimensional infra-red spectroscopy (2D-IR) to investigate (i) the heterogeneous dynamics of water inside reverse micelles of varying sizes, (ii) supercritical water near the Widom line that is known to exhibit pronounced density fluctuations and also study (iii) the collective and local polarization fluctuation of water molecules in the presence of several different proteins. The spatio-temporal correlation of confined water molecules inside reverse micelles of varying sizes is well captured through the spectral diffusion of corresponding 2D-IR spectra. In the case of supercritical water also, we observe a strong signature of dynamic heterogeneity from the elongated nature of the 2D-IR spectra. In this case the relaxation is ultrafast. We find remarkable agreement between the different tools employed to study the relaxation of density heterogeneity. For aqueous protein solutions, we find that the calculated dielectric constant of the respective systems unanimously shows a noticeable increment compared to that of neat water. However, the 'effective' dielectric constant for successive layers shows significant variation, with the layer adjacent to the protein having a much lower value. Relaxation is also slowest at the surface. We find that the dielectric constant achieves the bulk value at distances more than 3 nm from the surface of the protein.
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Affiliation(s)
- Rikhia Ghosh
- SSCU, Indian Institute of Science, Bangalore 560012, India.
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75
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Verma PK, Steinbacher A, Koch F, Nuernberger P, Brixner T. Monitoring ultrafast intramolecular proton transfer processes in an unsymmetric β-diketone. Phys Chem Chem Phys 2015; 17:8459-66. [DOI: 10.1039/c4cp05811a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Electronic excitation of a UV-absorbing unsymmetric β-diketone discloses intramolecular proton transfer among electronic ground as well as excited states.
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Affiliation(s)
- Pramod Kumar Verma
- Institut für Physikalische und Theoretische Chemie
- Universität Würzburg
- Am Hubland
- Germany
| | - Andreas Steinbacher
- Institut für Physikalische und Theoretische Chemie
- Universität Würzburg
- Am Hubland
- Germany
| | - Federico Koch
- Institut für Physikalische und Theoretische Chemie
- Universität Würzburg
- Am Hubland
- Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie
- Universität Würzburg
- Am Hubland
- Germany
- Physikalische Chemie II
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie
- Universität Würzburg
- Am Hubland
- Germany
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76
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Tookmanian EM, Fenlon EE, Brewer SH. Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids. RSC Adv 2014; 5:1274-1281. [PMID: 26478813 PMCID: PMC4603873 DOI: 10.1039/c4ra14244f] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.
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Affiliation(s)
- Elise M. Tookmanian
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Edward E. Fenlon
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Scott H. Brewer
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
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77
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Sokolowsky KP, Bailey HE, Fayer MD. New divergent dynamics in the isotropic to nematic phase transition of liquid crystals measured with 2D IR vibrational echo spectroscopy. J Chem Phys 2014; 141:194502. [DOI: 10.1063/1.4901081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | - Heather E. Bailey
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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78
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Kraack JP, Lotti D, Hamm P. Ultrafast, Multidimensional Attenuated Total Reflectance Spectroscopy of Adsorbates at Metal Surfaces. J Phys Chem Lett 2014; 5:2325-9. [PMID: 26279554 DOI: 10.1021/jz500978z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ultrafast dynamics of molecules at solid-liquid interfaces are of outstanding importance in chemistry and physics due to their involvement in processes of heterogeneous catalysis. We present a new spectroscopic approach to resolve coherent, time-resolved, 2D vibrational spectra as well as ultrafast vibrational relaxation dynamics of molecules adsorbed on metallic thin films in contact with liquids. The setup is based on the technique of attenuated total reflectance (ATR) spectroscopy, which is used at interfaces between materials that exhibit different refractive indices. As a sample molecule, we consider carbon monoxide adsorbed in different binding configurations on different metals and resolve its femtosecond vibrational dynamics. It is presented that mid-infrared, multidimensional ATR spectroscopy allows for obtaining a surface-sensitive characterization of adsorbates' vibrational relaxation, spectral diffusion dynamics, and sample inhomogeneity on the femtosecond time scale.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Davide Lotti
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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79
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Alberding BG, Lear BJ. Concentration-dependent dynamics of hydrogen bonding between acetonitrile and methanol as determined by 1D vibrational spectroscopy. J Phys Chem A 2014; 118:4363-71. [PMID: 24911870 DOI: 10.1021/jp4110147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solutions of acetonitrile (MeCN) in methanol (MeOH) at various concentrations have been investigated by variable temperature Raman spectroscopy. In the ν(CN) region of the spectrum, the variable temperature spectra at each concentration show two overlapping bands from hydrogen bound and free MeCN. These two species undergo dynamic exchange that gives rise to increasing coalescence of the two bands with increasing temperature. By simulation of the band shape, the rate of exchange was determined at each temperature. Arrhenius plots yielded values for the activation energy, Ea, and the natural log of the pre-exponential factor, ln[A/s(-1)], for the hydrogen bond formation/cleavage. Both of these dynamic parameters were found to depend on the relative amounts of MeCN and MeOH in the solutions. In particular, two different concentration regimes of dynamic hydrogen bonding were observed. First, at low MeCN concentration, the dynamics are largely independent of changes in MeCN concentration. Second, at higher MeCN concentration (above ∼0.2 MeCN mole fraction) the dynamics are strongly dependent on further increases of MeCN content. Over the range of MeCN mole fractions that we studied (0.03-0.5), the ln[A/s(-1)] changes from 32.5 ± 0.1 to 30.1 ± 0.2 and Ea changes from 3.73 ± 0.08 to 2.7 ± 0.1 kcal/mol. We suggest the observed changes in dynamics arise from changes in the local solvent microstructure that occur above a critical mole fraction of MeCN.
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Affiliation(s)
- Brian G Alberding
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16801, United States
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80
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Kel O, Tamimi A, Fayer MD. The Influence of Cholesterol on Fast Dynamics Inside of Vesicle and Planar Phospholipid Bilayers Measured with 2D IR Spectroscopy. J Phys Chem B 2014; 119:8852-62. [DOI: 10.1021/jp503940k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oksana Kel
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Amr Tamimi
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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81
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Ghosh A, Tucker MJ, Gai F. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations. J Phys Chem B 2014; 118:7799-805. [PMID: 24712671 PMCID: PMC4317052 DOI: 10.1021/jp411901m] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrational transition. Specifically, for the histidine dipeptide studied, the amide unit of the histidine gives rise to three spectrally resolvable amide I features at approximately 1630, 1644, and 1656 cm(-1), respectively, which, based on measurements at different pH values and frequency calculations, are assigned to a τ tautomer (1630 cm(-1) component) and a π tautomer with a hydrated (1644 cm(-1) component) or dehydrated (1656 cm(-1) component) amide. Because of the intrinsic ultrafast time resolution of 2D IR spectroscopy, we believe that the current approach, when combined with the isotope editing techniques, will be useful in revealing the structural dynamics of key histidine residues in proteins that are important for function.
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Affiliation(s)
- Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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82
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Terranova ZL, Corcelli SA. Molecular dynamics investigation of the vibrational spectroscopy of isolated water in an ionic liquid. J Phys Chem B 2014; 118:8264-72. [PMID: 24650158 DOI: 10.1021/jp501631m] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental studies examining the structure and dynamics of water in ionic liquids (ILs) have revealed local ion rearrangements that occur an order of magnitude faster than complete randomization of the liquid structure. Simulations of an isolated water molecule embedded in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6], were performed to shed insight into the nature of these coupled water-ion dynamics. The theoretical calculations of the spectral diffusion dynamics and the infrared absorption spectra of the OD stretch of isolated HOD in [bmim][PF6] agree well with experiment. The infrared absorption line shape of the OD stretch is narrower and blue-shifted in the IL compared to those in aqueous solution. Decomposition of the OD frequency time correlation function revealed that translational motions of the anions dominate the spectral diffusion dynamics.
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Affiliation(s)
- Z L Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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83
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Jeon J, Cho M. An Accurate Classical Simulation of a Two-Dimensional Vibrational Spectrum: OD Stretch Spectrum of a Hydrated HOD Molecule. J Phys Chem B 2014; 118:8148-61. [DOI: 10.1021/jp501182d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonggu Jeon
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
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84
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Sokolowsky KP, Bailey HE, Fayer MD. Length Scales and Structural Dynamics in Nematogen Pseudonematic Domains Measured with 2D IR Vibrational Echoes and Optical Kerr Effect Experiments. J Phys Chem B 2014; 118:7856-68. [DOI: 10.1021/jp500144p] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Heather E. Bailey
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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85
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Wu T, Zhang R, Li H, Yang L, Zhuang W. Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study. J Chem Phys 2014; 140:055101. [PMID: 24511982 DOI: 10.1063/1.4863562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.
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Affiliation(s)
- Tianmin Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Huanhuan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
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86
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Chen H, Wen X, Guo X, Zheng J. Intermolecular vibrational energy transfers in liquids and solids. Phys Chem Chem Phys 2014; 16:13995-4014. [DOI: 10.1039/c4cp01300j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resonant and nonresonant intermolecular vibrational energy transfers in liquids and solids are measured and elucidated using two competing mechanisms.
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Affiliation(s)
- Hailong Chen
- Department of Chemistry
- Rice University
- Houston, USA
| | - Xiewen Wen
- Department of Chemistry
- Rice University
- Houston, USA
| | - Xunmin Guo
- Department of Chemistry
- Rice University
- Houston, USA
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87
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Sokolowsky KP, Fayer MD. Dynamics in the isotropic phase of nematogens using 2D IR vibrational echo measurements on natural-abundance 13CN and extended lifetime probes. J Phys Chem B 2013; 117:15060-71. [PMID: 24156524 DOI: 10.1021/jp4071955] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The long time scale orientational relaxation of nematogens in the isotropic phase is associated with the randomization of pseudonematic domains, which have a correlation length that grows as the isotropic-to-nematic phase transition temperature is approached from above. Here we begin to address the fast dynamics of the nematogen molecules within the domains using two-dimensional infrared (2D IR) vibrational echo experiments. The problems of performing ultrafast IR experiments in pure liquids are discussed, and solutions are presented. In addition, the issue of short vibrational lifetimes, which limit the ability of 2D IR experiments to examine dynamics over a wide range of times, is addressed. The experiments were performed on the nematogen 4-cyano-4'-pentylbiphenyl (5CB), with the CN stretch initially used as the vibrational probe. Although the CN stretch has a small transition dipole, because the sample is a pure liquid it is necessary to use an exceedingly thin sample to perform the experiments. The small sample volume leads to massive heating effects that distort the results. In addition, the high concentration in the pure liquid can result in vibrational excitation transfer that interferes with the measurements of structural dynamics, and the CN vibrational lifetime is very short (3.6 ps). These problems were overcome by performing the experiments on the natural-abundance (13)CN stretch (5(13)CB), which greatly reduced the absorbance, eliminating the heating problems; also, this stretch has a longer lifetime (7.9 ps). Experiments were also performed on benzonitrile, which showed that the heating problems associated with pure liquids are not unique to 5CB. Again, the problems were eliminated by conducting measurements on the (13)CN stretch, which has an even longer lifetime (20.2 ps) compared with the (12)CN stretch (5.6 ps). Finally, to extend the range of the dynamical measurements, 4-pentyl-4'-thiocyanobiphenyl (5SCB) was synthesized and studied as a dilute solute in 5CB. The CN stretch of 5SCB has a vibrational lifetime of 103 ps, which permits dynamical measurements to 200 ps, revealing the full range of fast structural dynamics in the isotropic phase of 5CB. It is shown that the 5SCB probe reports essentially the same dynamics as 5(13)CB on the short time scale that is observable with the 5(13)CB vibrational probe.
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Affiliation(s)
- Kathleen P Sokolowsky
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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88
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Tomkins J, Hanna G. Signatures of nanoconfinement on the linear and nonlinear vibrational spectroscopy of a model hydrogen-bonded complex dissolved in a polar solvent. J Phys Chem B 2013; 117:13619-30. [PMID: 24079369 DOI: 10.1021/jp407469f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one-dimensional IR (1D-IR) absorption and IR pump-probe spectra of a hydrogen stretch in a model hydrogen-bonded complex dissolved in a polar solvent confined in spherical hydrophobic cavities of different sizes were simulated using ground-state mixed quantum-classical dynamics. Due to a thorough analysis of key properties of the complex and solvent from equilibrium trajectory data, we were able to gain insight into the microscopic details underlying the spectra. Both the 1D-IR and IR pump-probe spectra manifested the effects of confinement on the relative stabilities of the covalent and ionic forms of the complex through pronounced changes in their peak intensities and numbers. However, in contrast to the 1D-IR spectra, the time-resolved pump-probe spectra were found to be uniquely sensitive to the changes in the molecular dynamics as the cavity size is varied. In particular, it was found that the variations in the time evolutions of the peak intensities in the pump-probe spectra reflect the differences in the solvation dynamics associated with the various forms of the complex in different locations within the cavities. The ability to detect these differences underscores the advantage of using pump-probe spectroscopy for studying nanoconfined systems.
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Affiliation(s)
- Joseph Tomkins
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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89
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Singh PC. Communication: Ultrafast vibrational dynamics of hydrogen bond network terminated at the air/water interface: A two-dimensional heterodyne-detected vibrational sum frequency generation study. J Chem Phys 2013; 139:161101. [DOI: 10.1063/1.4826095] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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90
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Son H, Nam D, Park S. Real-Time Probing of Hydrogen-Bond Exchange Dynamics in Aqueous NaPF6 Solutions by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2013; 117:13604-13. [DOI: 10.1021/jp406805c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyewon Son
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
| | - Dayoung Nam
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
| | - Sungnam Park
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
- Multidimensional
Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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91
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Sow CS, Tomkins J, Hanna G. Computational study of the one- and two-dimensional infrared spectra of a proton-transfer mode in a hydrogen-bonded complex dissolved in a polar nanocluster. Chemphyschem 2013; 14:3309-18. [PMID: 23946271 DOI: 10.1002/cphc.201300610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/07/2022]
Abstract
The signatures of nanosolvation on the one- and two-dimensional (1D and 2D) IR spectra of a proton-transfer mode in a hydrogen-bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum-classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk-like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time-resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster-to-bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off-diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off-diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk-like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off-diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.
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Affiliation(s)
- Chia Shen Sow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 (Canada)
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92
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93
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Kim H, Cho M. Infrared Probes for Studying the Structure and Dynamics of Biomolecules. Chem Rev 2013; 113:5817-47. [DOI: 10.1021/cr3005185] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute,
Seoul 136-713, Korea
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94
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Wu H, Berg MA. Multiple population-period transient spectroscopy (MUPPETS) in excitonic systems. J Chem Phys 2013; 138:034201. [DOI: 10.1063/1.4773982] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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95
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Kubiak CP. Inorganic Electron Transfer: Sharpening a Fuzzy Border in Mixed Valency and Extending Mixed Valency across Supramolecular Systems. Inorg Chem 2013; 52:5663-76. [DOI: 10.1021/ic302331s] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Clifford P. Kubiak
- Department
of Chemistry and Biochemistry, University of California, San Diego (UCSD), 9500 Gilman Drive,
MC 0358, La Jolla, California 92093, United States
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96
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Chen H, Bian H, Li J, Wen X, Zheng J. Ultrafast multiple-mode multiple-dimensional vibrational spectroscopy. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.733116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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97
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Réhault J, Helbing J. Angle determination and scattering suppression in polarization-enhanced two-dimensional infrared spectroscopy in the pump-probe geometry. OPTICS EXPRESS 2012; 20:21665-21677. [PMID: 23037285 DOI: 10.1364/oe.20.021665] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The signal to noise in two-dimensional spectra recorded in the pump-probe geometry can be significantly improved with a quasi-crossed polarizer configuration, often employed in linear dichroism measurements. Here we examine this method in detail and demonstrate how to analyse and interpret the amplified signals. The angle between transition dipole moments can be determined with better accuracy than in conventional anisotropy measurements, and the method can be used to selectively suppress individual peaks and to efficiently remove scattering contributions. We present spectra of the coupled CO-stretch modes of a Ruthenium-carbonyl complex in DMSO for experimental illustration.
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Affiliation(s)
- Julien Réhault
- Physikalisch-chemisches Institut, Universitat Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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98
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Chung JK, Thielges MC, Lynch SR, Fayer MD. Fast dynamics of HP35 for folded and urea-unfolded conditions. J Phys Chem B 2012; 116:11024-31. [PMID: 22909017 DOI: 10.1021/jp304058x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The changes in fast dynamics of HP35 with a double CN vibrational dynamics label (HP35-P(2)) as a function of the extent of denaturation by urea were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy. Cyanophenylalanine (PheCN) replaces the native phenylalanine at two residues in the hydrophobic core of HP35, providing vibrational probes. NMR data show that HP35-P(2) maintains the native folded structure similar to wild type and that both PheCN residues share essentially the same environment within the peptide. A series of time-dependent 2D IR vibrational echo spectra were obtained for the folded peptide and the increasingly unfolded peptide. Analysis of the time dependence of the 2D spectra yields the system's spectral diffusion, which is caused by the sampling of accessible structures of the peptide under thermal equilibrium conditions. The structural dynamics become faster as the degree of unfolding is increased.
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Affiliation(s)
- Jean K Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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99
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Rosenfeld DE, Fayer MD. Excitation transfer induced spectral diffusion and the influence of structural spectral diffusion. J Chem Phys 2012; 137:064109. [DOI: 10.1063/1.4742762] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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100
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Hayes D, Engel GS. Peak shape analysis of diagonal and off-diagonal features in the two-dimensional electronic spectra of the Fenna-Matthews-Olson complex. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:3692-708. [PMID: 22753821 DOI: 10.1098/rsta.2011.0201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have recorded a series of two-dimensional electronic spectra of the Fenna-Matthews-Olson (FMO) complex from Prosthecochloris aestuarii, with several crosspeaks sufficiently resolved to permit a quantitative analysis of both the amplitude and the two-dimensional peak shape. The exponential growth and/or decay of peaks on and off the main diagonal provides information on population transfer rates between pairs of excitons. Quantum beats observed in the amplitudes and shapes of these peaks persist throughout the relaxation process, indicating that energy transfer in FMO involves both incoherent and coherent dynamics. By comparing the oscillations in the amplitude and shape of crosspeaks, we confirm theoretical predictions regarding their correlation and identify previously indistinguishable combinations of nonlinear response pathways that contribute to the signal at particular positions in the spectra. Such analysis is crucial to understanding the enormous amount of information contained in two-dimensional electronic spectra and offers a new route to uncovering a complete description of the energy transfer kinetics in photosynthetic antennae.
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Affiliation(s)
- Dugan Hayes
- Department of Chemistry and The James Franck Institute, University of Chicago, 929 East 57th St., Chicago, IL 60637, USA
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