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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: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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2
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Kananenka AA, Yao K, Corcelli SA, Skinner JL. Machine Learning for Vibrational Spectroscopic Maps. J Chem Theory Comput 2019; 15:6850-6858. [DOI: 10.1021/acs.jctc.9b00698] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alexei A. Kananenka
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - J. L. Skinner
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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3
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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4
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Yu Y, Fan W, Wang Y, Zhou X, Sun J, Liu S. Probe of Alcohol Structures in the Gas and Liquid States Using C⁻H Stretching Raman Spectroscopy. SENSORS (BASEL, SWITZERLAND) 2018; 18:E2061. [PMID: 29958405 PMCID: PMC6068699 DOI: 10.3390/s18072061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 01/16/2023]
Abstract
Vibrational spectroscopy is a powerful tool for probing molecular structures and dynamics since it offers a unique fingerprint that allows molecular identification. One of important aspects of applying vibrational spectroscopy is to develop the probes that can characterize the related properties of molecules such as the conformation and intermolecular interaction. Many examples of vibrational probes have appeared in the literature, including the azide group (⁻N₃), amide group (⁻CONH₂), nitrile groups (⁻CN), hydroxyl group (⁻OH), ⁻CH group and so on. Among these probes, the ⁻CH group is an excellent one since it is ubiquitous in organic and biological molecules and the C⁻H stretching vibrational spectrum is extraordinarily sensitive to the local molecular environment. However, one challenge encountered in the application of C⁻H probes arises from the difficulty in the accurate assignment due to spectral congestion in the C⁻H stretching region. In this paper, recent advances in the complete assignment of C⁻H stretching spectra of aliphatic alcohols and the utility of C⁻H vibration as a probe of the conformation and weak intermolecular interaction are outlined. These results fully demonstrated the potential of the ⁻CH chemical group as a molecular probe.
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Affiliation(s)
- Yuanqin Yu
- Department of Physics, Anhui University, Hefei 230601, China.
| | - Wei Fan
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Yuxi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Jin Sun
- Department of Physics, Anhui University, Hefei 230601, China.
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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6
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Daly CA, Berquist EJ, Brinzer T, Garrett-Roe S, Lambrecht DS, Corcelli SA. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: II. Spectroscopic Map. J Phys Chem B 2016; 120:12633-12642. [DOI: 10.1021/acs.jpcb.6b09509] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clyde A. Daly
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
| | - Eric J. Berquist
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Thomas Brinzer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel S. Lambrecht
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Steven A. Corcelli
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
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7
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Yu Y, Wang Y, Hu N, Lin K, Zhou X, Liu S. Cβ–H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states. Phys Chem Chem Phys 2016; 18:10563-72. [DOI: 10.1039/c6cp00244g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The CH2 symmetric stretching mode at the β-carbon position can be used as a new probe for the five conformations of n-propanol.
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Affiliation(s)
- Yuanqin Yu
- School of Physics and Material Science
- Anhui University
- Hefei
- China
| | - Yuxi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
| | - Naiyin Hu
- Hefei National Laboratory for Physical Sciences at the Microscale
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
| | - Ke Lin
- Hefei National Laboratory for Physical Sciences at the Microscale
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
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8
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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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9
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Buchanan EG, Dean JC, Zwier TS, Sibert EL. Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane. J Chem Phys 2013; 138:064308. [DOI: 10.1063/1.4790163] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Lee H, Choi JH, Cho M. Vibrational solvatochromism and electrochromism. II. Multipole analysis. J Chem Phys 2013; 137:114307. [PMID: 22998262 DOI: 10.1063/1.4751477] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.
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Affiliation(s)
- Hochan Lee
- Department of Chemistry and Research Institute for Basic Sciences, Korea University, Seoul 136-713, South Korea
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11
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Terranova ZL, Corcelli SA. Monitoring Intramolecular Proton Transfer with Two-Dimensional Infrared Spectroscopy: A Computational Prediction. J Phys Chem Lett 2012; 3:1842-1846. [PMID: 26291870 DOI: 10.1021/jz300714t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proton transfer processes are ubiquitous and play a vital role in a broad range of chemical and biochemical phenomena. The ability of two-dimensional infrared (2D IR) spectroscopy with a carbon-deuterium (C-D) reporter to monitor the kinetics of proton transfer in the model compound malonaldehyde was demonstrated computationally. One of the two carbonyl/enol carbon atoms in malonaldehyde was labeled with a C-D bond. The C-D stretch vibrational frequency provides ∼150 cm(-1) of sensitivity to the two tautomers of malonaldehyde. Mixed quantum mechanics/molecular mechanics simulations employing the self-consistent-charge density functional tight binding (SCC-DFTB) method were used to compute 2D IR line shapes for the C-D stretch of labeled malonaldehyde in aqueous solution. The 2D IR spectra reveal cross peaks from the chemical exchange of the proton. The kinetics for the growth of the cross-peaks (and the decay of the diagonal peaks) precisely match the proton transfer rate observed in the SCC-DFTB simulations.
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Affiliation(s)
- Z L Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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12
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Hua W, Ai YJ, Gao B, Li H, Ågren H, Luo Y. X-ray spectroscopy of blocked alanine in water solution from supermolecular and supermolecular-continuum solvation models: a first-principles study. Phys Chem Chem Phys 2012; 14:9666-75. [DOI: 10.1039/c2cp40732a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Hickert AS, Durgan AC, Patton DA, Blake SA, Cremeens ME. A B3LYP investigation of the conformational and environmental sensitivity of carbon–deuterium frequencies of aryl-perdeuterated phenylalanine and tryptophan. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1050-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Waegele MM, Culik RM, Gai F. Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. J Phys Chem Lett 2011; 2:2598-2609. [PMID: 22003429 PMCID: PMC3192500 DOI: 10.1021/jz201161b] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Elucidating the underlying molecular mechanisms of protein folding and function is a very exciting and active research area, but poses significant challenges. This is due in part to the fact that existing experimental techniques are incapable of capturing snapshots along the 'reaction coordinate' in question with both sufficient spatial and temporal resolutions. In this regard, recent years have seen increased interests and efforts in development and employment of site-specific probes to enhance the structural sensitivity of spectroscopic techniques in conformational and dynamical studies of biological molecules. In particular, the spectroscopic and chemical properties of nitriles, thiocyanates, and azides render these groups attractive for the interrogation of complex biochemical constructs and processes. Here, we review their signatures in vibrational, fluorescence and NMR spectra and their utility in the context of elucidating chemical structure and dynamics of protein and DNA molecules.
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Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
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15
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Nydegger MW, Rock W, Cheatum CM. 2D IR Spectroscopy of the C–D stretching vibration of the deuterated formic acid dimer. Phys Chem Chem Phys 2011; 13:6098-104. [DOI: 10.1039/c0cp01087a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Mirkin NG, Krimm S. Conformation dependence of the CαDα stretch mode in peptides: Side-chain influence in dipeptide structures. Biopolymers 2010; 93:1065-71. [DOI: 10.1002/bip.21523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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17
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Miller CS, Corcelli SA. Carbon−Deuterium Vibrational Probes of Amino Acid Protonation State. J Phys Chem B 2009; 113:8218-21. [DOI: 10.1021/jp903520s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C. S. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - S. A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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18
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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