1
|
McDonnell RP, Oram K, Boyer MA, Kohler DD, Meyer KA, Sibert Iii EL, Wright JC. Direct Probe of Vibrational Fingerprint and Combination Band Coupling. J Phys Chem Lett 2024; 15:3975-3981. [PMID: 38569133 DOI: 10.1021/acs.jpclett.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Vibrational fingerprints and combination bands are a direct measure of couplings that control molecular properties. However, most combination bands possess small transition dipoles. Here we use multiple, ultrafast coherent infrared pulses to resolve vibrational coupling between CH3CN fingerprint modes at 918 and 1039 cm-1 and combination bands in the 2750-6100 cm-1 region via doubly vibrationally enhanced (DOVE) coherent multidimensional spectroscopy (CMDS). This approach provides a direct probe of vibrational coupling between fingerprint modes and near-infrared combination bands of large and small transition dipoles in a molecular system over a large frequency range.
Collapse
Affiliation(s)
- Ryan P McDonnell
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kelson Oram
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Mark A Boyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Daniel D Kohler
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kent A Meyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Edwin L Sibert Iii
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - John C Wright
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
2
|
Seliya P, Bonn M, Grechko M. On selection rules in two-dimensional terahertz-infrared-visible spectroscopy. J Chem Phys 2024; 160:034201. [PMID: 38230809 DOI: 10.1063/5.0179041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Two-dimensional terahertz-infrared-visible (2D TIRV) spectroscopy directly measures the coupling between quantum high-frequency vibrations and classical low-frequency modes of molecular motion. In addition to coupling strength, the signal intensity in 2D TIRV spectroscopy can also depend on the selection rules of the excited transitions. Here, we explore the selection rules in 2D TIRV spectroscopy by studying the coupling between the high-frequency CH3 stretching and low-frequency vibrations of liquid dimethyl sulfoxide (DMSO). Different excitation pathways are addressed using variations in laser pulse timing and different polarizations of exciting pulses and detected signals. The DMSO signals generated via different excitation pathways can be readily distinguished in the spectrum. The intensities of different excitation pathways vary unequally with changes in polarization. We explain how this difference stems from the intensities of polarized and depolarized Raman and hyper-Raman spectra of high-frequency modes. These results apply to various systems and will help design and interpret new 2D TIRV spectroscopy experiments.
Collapse
Affiliation(s)
- Pankaj Seliya
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Maksim Grechko
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| |
Collapse
|
3
|
Soenarjo AL, Lan Z, Sazanovich IV, Chan YS, Ringholm M, Jha A, Klug DR. The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy. J Am Chem Soc 2023; 145:19622-19632. [PMID: 37647128 PMCID: PMC10510320 DOI: 10.1021/jacs.3c04044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 09/01/2023]
Abstract
A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the regulation of gene transcription and telomerase-mediated telomere maintenance and, therefore, is a target for drugs. The details of the molecular interactions that cause stacking of the guanine-tetrads are not well-understood, which limits a rational approach to the drugability of G4 sequences. To explore these interactions, we employed electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectroscopy to measure extended vibrational coupling spectra for a parallel-stranded G4-DNA formed by the Myc2345 nucleotide sequence. We also tracked the structural changes associated with G4-folding as a function of K+-ion concentration. To classify the structural elements that the folding process generates in terms of vibrational coupling characteristics, we used quantum-chemical calculations utilizing density functional theory to predict the coupling spectra associated with given structures, which are compared against the experimental data. Overall, 102 coupling peaks are experimentally identified and followed during the folding process. Several phenomena are noted and associated with formation of the folded form. This includes frequency shifting, changes in cross-peak intensity, and the appearance of new coupling peaks. We used these observations to propose a folding sequence for this particular type of G4 under our experimental conditions. Overall, the combination of experimental 2DIR data and DFT calculations suggests that guanine-quartets may already be present before the addition of K+-ions, but that these quartets are unstacked until K+-ions are added, at which point the full G4 structure is formed.
Collapse
Affiliation(s)
- A. Larasati Soenarjo
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Zhihao Lan
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton
Laboratory, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Yee San Chan
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - David R. Klug
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| |
Collapse
|
4
|
Wright JC, Kohler DD, Bergmann U. X-ray/Extreme Ultraviolet Floquet State Multidimensional Spectroscopy, an Analogue of Multiple Quantum Nuclear Magnetic Resonance. J Phys Chem Lett 2023:4908-4913. [PMID: 37201210 DOI: 10.1021/acs.jpclett.3c00778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
There is great interest in developing fully coherent multidimensional X-ray/extreme ultraviolet (XUV) spectroscopic techniques because of their capability for achieving atomic spectral selectivity. Current proposals rest on using sequentially and coherently driven core excitations with multiple X-ray/XUV excitation pulses and measuring the output using time domain Fourier transform methods. In this paper, we propose an alternative method that creates an entanglement of core and optical transitions to form a Floquet state that creates directional and coherent output beams. Multidimensional spectra are obtained by measuring the intensity of output beams while tuning the optical frequencies across resonances. This approach expands on previous optical pump-XUV probe spectroscopy of MoTe2 by theoretically demonstrating its multidimensional capabilities. Both parametric and non-parametric pathways are proposed to optimize the resolution of inhomogeneous broadening and k-selective features.
Collapse
Affiliation(s)
- John C Wright
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Daniel D Kohler
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
5
|
Begušić T, Blake GA. Two-dimensional infrared-Raman spectroscopy as a probe of water's tetrahedrality. Nat Commun 2023; 14:1950. [PMID: 37029146 PMCID: PMC10082090 DOI: 10.1038/s41467-023-37667-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Two-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.
Collapse
Affiliation(s)
- Tomislav Begušić
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Geoffrey A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| |
Collapse
|
6
|
Long F, Xie H, Zhuang W. Identification of Trans- and Cis-2-Methylcyclopropanecarboxylic acid using EVV 2DIR spectroscopy: A theoretical study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
7
|
Pinakov DV, Makotchenko VG, Semushkina GI, Chekhova GN, Prosvirin IP, Asanov IP, Fedoseeva YV, Makarova AA, Shubin YV, Okotrub AV, Bulusheva LG. Redox reactions between acetonitrile and nitrogen dioxide in the interlayer space of fluorinated graphite matrices. Phys Chem Chem Phys 2021; 23:10580-10590. [PMID: 33903859 DOI: 10.1039/d0cp06412b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The interlayer space of 2D materials can be a slit reactor where transformations not typical for the gas phase occur. We report redox reactions involving acetonitrile and nitrogen oxide guests in galleries of fluorinated graphite. Fluorinated graphite intercalation compounds with acetonitrile are treated with dinitrogen tetraoxide and the synthesis products are studied by a set of experimental methods. Data analysis reveals that N2O4 dissociates in fluorinated graphite matrices to form nitrogen-containing species NO3, NO2, NO, and N2. The interaction of NO3 with acetonitrile yields HNO3, which predominates as a guest in the synthesis products independently of the fluorination degree of the matrix. This reaction is accompanied by the removal of fluorine atoms weakly bonded to the graphite layers, leading to partial defluorination of the matrices. Our work demonstrates the possibility of using fluorinated graphite as a test nanoreactor whose dimension can be controlled by fluorination of the layers.
Collapse
Affiliation(s)
- D V Pinakov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - V G Makotchenko
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - G I Semushkina
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - G N Chekhova
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - I P Prosvirin
- Boreskov Institute of Catalysis SB RAS, 5 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - I P Asanov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - Yu V Fedoseeva
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - A A Makarova
- Physikalische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yu V Shubin
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - A V Okotrub
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| | - L G Bulusheva
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Acad. Lavrentiev Ave., 630090 Novosibirsk, Russia.
| |
Collapse
|
8
|
Donaldson PM. Photon echoes and two dimensional spectra of the amide I band of proteins measured by femtosecond IR - Raman spectroscopy. Chem Sci 2020; 11:8862-8874. [PMID: 34123140 PMCID: PMC8163424 DOI: 10.1039/d0sc02978e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infrared (IR) and Raman spectroscopy are fundamental techniques in chemistry, allowing the convenient determination of bond specific chemical composition and structure. Over the last decades, ultrafast multidimensional IR approaches using sequences of femtosecond IR pulses have begun to provide a new means of gaining additional information on molecular vibrational couplings, distributions of molecular structures and ultrafast molecular structural dynamics. In this contribution, new approaches to measuring multidimensional spectra involving IR and Raman processes are presented and applied to the study of the amide I band of proteins. Rephasing of the amide I band is observed using dispersed IR-Raman photon echoes and frequency domain 2D-IR-Raman spectra are measured by use of a mid-IR pulse shaper or over a broader spectral range using a tuneable picosecond laser. A simple pulse shaping approach to performing heterodyned time-domain Fourier Transform 2D-IR-Raman spectroscopy is introduced, revealing that the 2D-IR-Raman spectra distinguish homogeneous and inhomogeneous broadening in the same way as the well-established methods of 2D-IR spectroscopy. Across all datasets, the unique dependence of the amide I data on the IR and Raman strengths, vibrational anharmonicities and inhomogeneous broadening provides a fascinating spectroscopic view of the amide I band. New ultrafast 2D-IR-Raman photon echo spectroscopy techniques are introduced and applied to the structural analysis of proteins.![]()
Collapse
Affiliation(s)
- Paul M Donaldson
- Central Laser Facility, RCaH, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus Didcot OX11 0QX UK
| |
Collapse
|
9
|
Sowley H, Liu Z, Davies J, Peach R, Guo R, Sim S, Long F, Holdgate G, Willison K, Zhuang W, Klug DR. Detection of Drug Binding to a Target Protein Using EVV 2DIR Spectroscopy. J Phys Chem B 2019; 123:3598-3606. [PMID: 30848913 DOI: 10.1021/acs.jpcb.9b00501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We demonstrate that electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) can be used to detect the binding of a drug to a target protein-active site. The EVV 2DIR spectrum of the FGFR1 kinase target protein is found to have ∼200 detectable cross-peaks in the spectral region 1250-1750 cm-1/2600-3400 cm-1, with additional 63 peaks caused by the addition of a drug, SU5402. Of these 63 new peaks, it is shown that only six are due to protein-drug interactions, with the other 57 being due to vibrational coupling within the drug itself. Quantum mechanical calculations employing density functional theory are used to support assignment of the six binding-dependent peaks, with one being assigned to a known interaction between the drug and a backbone carbonyl group which forms part of the binding site. None of the 57 intramolecular coupling peaks associated with the drug molecule change substantially in either intensity or frequency when the drug binds to the target protein. This strongly suggests that the structure of the drug in the target binding site is essentially identical to that when it is not bound.
Collapse
Affiliation(s)
| | - ZhiQiang Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
| | | | | | | | | | - FengQin Long
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
| | - Geoffrey Holdgate
- Hit Discovery, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Macclesfield SK10 2NA , U.K
| | | | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
| | | |
Collapse
|
10
|
Long F, Chen Z, Han K, Zhang L, Zhuang W. Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy. Molecules 2019; 24:molecules24050869. [PMID: 30823671 PMCID: PMC6429144 DOI: 10.3390/molecules24050869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 11/16/2022] Open
Abstract
Intermediates lie at the center of chemical reaction mechanisms. However, detecting intermediates in an organic reaction and understanding its role in reaction mechanisms remains a big challenge. In this paper, we used the theoretical calculations to explore the potential of the electron-vibration-vibration two-dimensional infrared (EVV-2DIR) spectroscopy in detecting the intermediates in the oxidation reactions of enamines and tautomerizable imines with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). We show that while it is difficult to identify the intermediates from their infrared and Raman signals, the simulated EVV-2DIR spectra of these intermediates have well resolved spectral features, which are absent in the signals of reactants and products. These characteristic spectral signatures can, therefore, be used to reveal the reaction mechanism as well as monitor the reaction progress. Our work suggests the potential strength of EVV-2DIR technique in studying the molecular mechanism of organic reactions in general.
Collapse
Affiliation(s)
- Fengqin Long
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Zheng Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
| |
Collapse
|
11
|
Vietze L, Bonn M, Grechko M. Two-Dimensional Terahertz-Infrared-Visible Spectroscopy Elucidates Coupling Between Low- and High-Frequency Modes. SPRINGER SERIES IN OPTICAL SCIENCES 2019. [DOI: 10.1007/978-981-13-9753-0_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Grechko M, Hasegawa T, D'Angelo F, Ito H, Turchinovich D, Nagata Y, Bonn M. Coupling between intra- and intermolecular motions in liquid water revealed by two-dimensional terahertz-infrared-visible spectroscopy. Nat Commun 2018; 9:885. [PMID: 29491413 PMCID: PMC5830436 DOI: 10.1038/s41467-018-03303-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
The interaction between intramolecular and intermolecular degrees of freedom in liquid water underlies fundamental chemical and physical phenomena such as energy dissipation and proton transfer. Yet, it has been challenging to elucidate the coupling between these different types of modes. Here, we report on the direct observation and quantification of the coupling between intermolecular and intramolecular coordinates using two-dimensional, ultra-broadband, terahertz-infrared-visible (2D TIRV) spectroscopy and molecular dynamics calculations. Our study reveals strong coupling of the O-H stretch vibration, independent of the degree of delocalization of this high-frequency mode, to low-frequency intermolecular motions over a wide frequency range from 50 to 250 cm-1, corresponding to both the intermolecular hydrogen bond bending (≈ 60 cm-1) and stretching (≈ 180 cm-1) modes. Our results provide mechanistic insights into the coupling of the O-H stretch vibration to collective, delocalized intermolecular modes.
Collapse
Affiliation(s)
- Maksim Grechko
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany.
| | - Taisuke Hasegawa
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Francesco D'Angelo
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Hironobu Ito
- Department of Chemistry, Faculty of Education, Shizuoka University, 836 Ohya, 422-8529, Shizuoka, Japan
| | - Dmitry Turchinovich
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
- Fakultät für Physik, Universität Duisburg-Essen, Lotharstr. 1, 47057, Duisburg, Germany
| | - Yuki Nagata
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| |
Collapse
|
13
|
Neff-Mallon NA, Wright JC. Multidimensional Spectral Fingerprints of a New Family of Coherent Analytical Spectroscopies. Anal Chem 2017; 89:13182-13189. [PMID: 29135230 DOI: 10.1021/acs.analchem.7b02917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triply resonant sum frequency (TRSF) and doubly vibrationally enhanced (DOVE) spectroscopies are examples of a recently developed family of coherent multidimensional spectroscopies (CMDS) that are analogous to multidimensional NMR and current analytical spectroscopies. CMDS methods are particularly promising for analytical applications because their inherent selectivity makes them applicable to complex samples. Like NMR, they are based on creating quantum mechanical superposition states that are fully coherent and lack intermediate quantum state populations that cause quenching or other relaxation effects. Instead of the nuclear spin states of NMR, their multidimensional spectral fingerprints result from creating quantum mechanical mixtures of vibrational and electronic states. Vibrational states provide spectral selectivity, and electronic states provide large signal enhancements. This paper presents the first electronically resonant DOVE spectra and demonstrates the capabilities for analytical chemistry applications by comparing electronically resonant TRSF and DOVE spectra with each other and with infrared absorption and resonance Raman spectra using a Styryl 9 M dye as a model system. The methods each use two infrared absorption transitions and a resonant Raman transition to create a coherent output beam, but they differ in how they access the vibrational and electronic states and the frequency of their output signal. Just as FTIR, UV-vis, Raman, and resonance Raman are complementary methods, TRSF and DOVE methods are complementary to coherent Raman methods such as coherent anti-Stokes Raman spectroscopy (CARS).
Collapse
Affiliation(s)
- Nathan A Neff-Mallon
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - John C Wright
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| |
Collapse
|
14
|
Wright JC. Applications of the New Family of Coherent Multidimensional Spectroscopies for Analytical Chemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:45-70. [PMID: 28375700 DOI: 10.1146/annurev-anchem-061516-045349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new family of vibrational and electronic spectroscopies has emerged, comprising the coherent analogs of traditional analytical methods. These methods are also analogs of coherent multidimensional nuclear magnetic resonance (NMR) spectroscopy. This new family is based on creating the same quantum mechanical superposition states called multiple quantum coherences (MQCs). NMR MQCs are mixtures of nuclear spin states that retain their quantum mechanical phase information for milliseconds. The MQCs in this new family are mixtures of vibrational and electronic states that retain their phases for picoseconds or shorter times. Ultrafast, high-intensity coherent beams rapidly excite multiple states. The excited MQCs then emit bright beams while they retain their phases. Time-domain methods measure the frequencies of the MQCs by resolving their phase oscillations, whereas frequency-domain methods measure the resonance enhancements of the output beam while scanning the excitation frequencies. The resulting spectra provide multidimensional spectral signatures that increase the spectroscopic selectivity required for analyzing complex samples.
Collapse
Affiliation(s)
- John C Wright
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706;
| |
Collapse
|
15
|
Wright JC. Analytical chemistry, multidimensional spectral signatures, and the future of coherent multidimensional spectroscopy. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
16
|
Rezende Valim L, Davies JA, Tveen Jensen K, Guo R, Willison KR, Spickett CM, Pitt AR, Klug DR. Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy. J Phys Chem B 2014; 118:12855-64. [PMID: 25347525 DOI: 10.1021/jp509053q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy.
Collapse
|
17
|
Ringholm M, Jonsson D, Bast R, Gao B, Thorvaldsen AJ, Ekström U, Helgaker T, Ruud K. Analytic cubic and quartic force fields using density-functional theory. J Chem Phys 2014; 140:034103. [DOI: 10.1063/1.4861003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
18
|
Zhao W, He A, Xu Y. Second hyperpolarizability of C-H, C-D, and C≡N stretch vibrations determined from computational Raman activities and a comparison with experiments. J Phys Chem B 2013; 117:15812-8. [PMID: 24020330 DOI: 10.1021/jp4073119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have recently demonstrated that the second hyperpolarizability γ of a selected vibrational mode of a molecule can be determined by using the computational Raman activity against an internal standard with a known Raman γ value. This approach provides a convenient way for prediction of the γ magnitude of DOVE four wave mixing spectroscopy, an optical analogue to two-dimensional (2D) NMR. Here, by using the Hartree-Fock (HF) method, the density functional theory (DFT) method, and the second-order Møller-Plesset perturbation theory (MP2) method, we extend our early work from the less anharmonic region <2000 cm(-1) into the more anharmonic region >2000 cm(-1) covering C-H, C-D, and C≡N stretching modes of benzene, deuterated benzene, acetonitrile, deuterated acetonitrile, and tetrahydrofuran. The computed Raman γ values of these vibrational modes have been determined by using either the 992 cm(-1) Raman band of benzene or the compound's own Raman band (C-C stretch) around 800-1000 cm(-1) as an internal standard. In this more anharmonic region, the HF method with a larger basis set provides the best outputs and the predicted Raman γ values agree well with experimental values for most of the vibrational modes studied. By choosing a suitable method and basis set, this facile approach could be applied to a broader spectral range for Raman γ estimation of various materials.
Collapse
Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock , 2801 South University Avenue, Little Rock, Arkansas 72204, United States
| | | | | |
Collapse
|
19
|
Zhao W, He A, Xu Y. Raman second hyperpolarizability determination using computational Raman activities and a comparison with experiments. J Phys Chem A 2013; 117:6217-23. [PMID: 23683174 DOI: 10.1021/jp400447a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Doubly vibrationally enhanced (DOVE) four-wave mixing spectroscopy, an optical analogue to 2D NMR, involves two infrared transitions and a Raman transition. The magnitude of the DOVE second hyperpolarizability γ (or third-order susceptibility χ((3))) can be theoretically estimated if the values of the dipolar moments of the two infrared transitions and the γ of the Raman transition are known. The Raman γ can be measured by using the four-wave mixing interferometric method or conventional Raman spectroscopy in the presence of an internal standard. In this work, we examine if one can use the Raman activity computed from density functional theory calculation to determine the Raman γ of selected vibrational modes of several samples including deuterated benzene, acetonitrile, tetrahydrofuran, and sodium benzoate aqueous solution. The 992 cm(-1) Raman band of benzene serves as an internal standard for organic solvents, and the 880 cm(-1) Raman band of hydrogen peroxide is for the aqueous solution sample with known γ values. We have found that the predicted Raman γ values from the computational Raman activities match experimental data reasonably well, suggesting a facile approach to predict the Raman γ of interested systems.
Collapse
Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock, 2801 South University Avenue, Little Rock, Arkansas 72204, USA.
| | | | | |
Collapse
|
20
|
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
| |
Collapse
|
21
|
Nishida J, Shigeto S, Yabumoto S, Hamaguchi HO. Anharmonic coupling of the CH-stretch and CH-bend vibrations of chloroform as studied by near-infrared electroabsorption spectroscopy. J Chem Phys 2012; 137:234501. [DOI: 10.1063/1.4770264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
22
|
Liu S, Fourkas JT. Orientational Time Correlation Functions for Vibrational Sum-Frequency Generation. 1. Acetonitrile. J Phys Chem A 2012; 117:5853-64. [DOI: 10.1021/jp306296s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shule Liu
- Department of Chemistry & Biochemistry, ‡Institute for Physical Science and Technology, §Maryland NanoCenter, and ∥Center for Nanophysics and Advanced Materials, University of Maryland, College Park, Maryland 20742, United States
| | - John T. Fourkas
- Department of Chemistry & Biochemistry, ‡Institute for Physical Science and Technology, §Maryland NanoCenter, and ∥Center for Nanophysics and Advanced Materials, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
23
|
Han C, Wang J. Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides. Chemphyschem 2012; 13:1522-34. [DOI: 10.1002/cphc.201100995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/09/2022]
|
24
|
Zhao W. Measurement of Raman χ(3) and theoretical estimation of DOVE four wave mixing of hydrogen peroxide. J Phys Chem A 2011; 115:6525-30. [PMID: 21591714 DOI: 10.1021/jp202977v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydrogen peroxide has strong infrared (IR) transitions ν(6) and its combination band ν(2)+ν(6), which may provide a unique opportunity to implement doubly vibrationally enhanced (DOVE) four wave mixing (FWM) for directly measuring hydrogen peroxide in spectrally overcrowded mixtures. In this work, the magnitude of the DOVE third-order susceptibility χ(3) was theoretically estimated. By using a FWM interferometric method, one of the strongest Raman bands, O-O stretch ν(3) Raman χ(3) of 30 wt % H(2)O(2), was first measured to be 1.2 × 10(-14) esu. The Raman χ(3) of ν(2) was then determined to be 5.3 × 10(-15) esu based on their relative Raman intensities. The resulting Raman χ(3) of ν(2) was used to calculate the DOVE χ(3) of (ν(6), ν(2)+ν(6)), together with the dipolar moments of the two IR transitions determined from IR absorption measurement. The calculated value of DOVE-IR χ(3) was 1.1 × 10(-13) esu for pure H(2)O(2), about 1.5 times larger than that of the strong ring breathing Raman band of benzene. The large DOVE χ(3) suggests the feasibility of direct measurement of hydrogen peroxide in an aqueous environment using DOVE four wave mixing.
Collapse
Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock, 2801 South University Avenue, Little Rock, Arkansas 72204, United States.
| |
Collapse
|
25
|
Affiliation(s)
- John C. Wright
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706;
| |
Collapse
|
26
|
Guo R, Miele M, Gardner EM, Fournier F, Kornau KM, Gould IR, Klug DR. Potential for the detection of molecular complexes and determination of interaction geometry by 2DIR: Application to protein sciences. Faraday Discuss 2011; 150:161-74; discussion 257-92. [PMID: 22457947 DOI: 10.1039/c1fd00007a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Rui Guo
- Institute of Chemical Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
27
|
Lee H, Cheon S, Cho M. Chiroptical nature of two-exciton states of light-harvesting complex: Doubly resonant three-wave-mixing spectroscopy. J Chem Phys 2010; 132:225102. [PMID: 20550421 DOI: 10.1063/1.3432624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Photosynthetic light-harvesting complex is a coupled multichromophore system. Due to electronic couplings between neighboring chlorophylls in the complex, the one- and two-exciton states are delocalized and they can be written as linear combinations of singly and doubly excited configurations, respectively. Despite that the chiroptical properties of one-exciton states in such a multichromophore system have been investigated by using linear optical activity measurement techniques; those of two-exciton states have not been studied before due to a lack of appropriate measurement methods. Here, we present a theoretical description on chiroptical chi((2)) spectroscopy and show that it can be used to investigate such properties of a photosynthetic light-harvesting system, which is the Fenna-Matthews-Olson complex, consisting of seven bacteriochlorophylls in its protein subunit. To simulate the doubly resonant sum- and difference-frequency-generation spectra of the complex, one- and two-exciton transition dipoles were calculated. Carrying out quantum chemistry calculations of electronically excited states of a model bacteriochlorophyll system and taking into account the dipole-induced dipole electronic transition processes between the ground state and two-exciton states, we could calculate the two-dimensional sum-frequency-generation spectra revealing dominant second-order chiroptical transition pathways and involved one- and two-exciton states. It is believed that the present computational scheme and the theoretically proposed doubly resonant two-dimensional three-wave-mixing spectroscopy would be of use to shed light on the chiroptical natures of two-exciton states of arbitrary coupled multichromophore systems.
Collapse
Affiliation(s)
- Hochan Lee
- Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | | | | |
Collapse
|
28
|
Wilson KC, Lyons B, Mehlenbacher R, Sabatini R, McCamant DW. Two-dimensional femtosecond stimulated Raman spectroscopy: Observation of cascading Raman signals in acetonitrile. J Chem Phys 2009; 131:214502. [DOI: 10.1063/1.3263909] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
29
|
Fournier F, Guo R, Gardner EM, Donaldson PM, Loeffeld C, Gould IR, Willison KR, Klug DR. Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis. Acc Chem Res 2009; 42:1322-31. [PMID: 19548660 DOI: 10.1021/ar900074p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.
Collapse
Affiliation(s)
- Frederic Fournier
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Rui Guo
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Elizabeth M. Gardner
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Paul M. Donaldson
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Christian Loeffeld
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Ian R. Gould
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Keith R. Willison
- Institute of Cancer Research, Chester Beatty Laboratories, Cancer Research U.K., Centre of Cellular and Molecular Biology, London SW3 6JB, U.K
| | - David R. Klug
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| |
Collapse
|
30
|
Baiz CR, McRobbie PL, Preketes NK, Kubarych KJ, Geva E. Two-Dimensional Infrared Spectroscopy of Dimanganese Decacarbonyl and Its Photoproducts: An Ab Initio Study. J Phys Chem A 2009; 113:9617-23. [DOI: 10.1021/jp9054654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
31
|
Infrared-induced coherent vibration of a hydrogen-bonded system: Effects of mechanical and electrical anharmonic couplings. J Chem Phys 2009; 131:044512. [DOI: 10.1063/1.3181777] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
32
|
Guo R, Fournier F, Donaldson PM, Gardner EM, Gould IR, Klug DR. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration–vibration two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2009; 11:8417-21. [DOI: 10.1039/b910804a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Thorvaldsen AJ, Ferrighi L, Ruud K, Ågren H, Coriani S, Jørgensen P. Analytic ab initio calculations of coherent anti-Stokes Raman scattering (CARS). Phys Chem Chem Phys 2009; 11:2293-304. [DOI: 10.1039/b812045e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Protein identification and quantification by two-dimensional infrared spectroscopy: implications for an all-optical proteomic platform. Proc Natl Acad Sci U S A 2008; 105:15352-7. [PMID: 18832166 DOI: 10.1073/pnas.0805127105] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.
Collapse
|
35
|
Oh KI, Lee JH, Joo C, Han H, Cho M. β-Azidoalanine as an IR Probe: Application to Amyloid Aβ(16-22) Aggregation. J Phys Chem B 2008; 112:10352-7. [DOI: 10.1021/jp801558k] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea, and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Joo-Hyun Lee
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea, and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Cheonik Joo
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea, and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea, and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea, and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| |
Collapse
|
36
|
Donaldson PM, Guo R, Fournier F, Gardner EM, Gould IR, Klug DR. Decongestion of methylene spectra in biological and non-biological systems using picosecond 2DIR spectroscopy measuring electron-vibration–vibration coupling. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.02.050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
| |
Collapse
|
38
|
Fournier F, Gardner EM, Guo R, Donaldson PM, Barter LM, Palmer DJ, Barnett CJ, Willison KR, Gould IR, Klug DR. Optical fingerprinting of peptides using two-dimensional infrared spectroscopy: Proof of principle. Anal Biochem 2008; 374:358-65. [DOI: 10.1016/j.ab.2007.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 10/29/2007] [Accepted: 11/01/2007] [Indexed: 11/30/2022]
|
39
|
Donaldson PM, Guo R, Fournier F, Gardner EM, Barter LMC, Barnett CJ, Gould IR, Klug DR, Palmer DJ, Willison KR. Direct identification and decongestion of Fermi resonances by control of pulse time ordering in two-dimensional IR spectroscopy. J Chem Phys 2007; 127:114513. [PMID: 17887863 DOI: 10.1063/1.2771176] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We show that it is possible to both directly measure and directly calculate Fermi resonance couplings in benzene. The measurement method used was a particular form of two-dimensional infrared spectroscopy (2D-IR) known as doubly vibrationally enhanced four wave mixing. By using different pulse orderings, vibrational cross peaks could be measured either purely at the frequencies of the base vibrational states or split by the coupling energy. This capability is a feature currently unique to this particular form of 2D-IR and can be helpful in the decongestion of complex spectra. Five cross peaks of the ring breathing mode nu13 with a range of combination bands were observed spanning a region of 1500-4550 cm(-1). The coupling energy was measured for two dominant states of the nu13+nu16 Fermi resonance tetrad. Dephasing rates were measured in the time domain for nu13 and the two (nu13+nu16) Fermi resonance states. The electronic and mechanical vibrational anharmonic coefficients were calculated to second and third orders, respectively, giving information on relative intensities of the cross peaks and enabling the Fermi resonance states of the combination band nu13+nu16 at 3050-3100 cm(-1) to be calculated. The excellent agreement between calculated and measured spectral intensities and line shapes suggests that assignment of spectral features from ab initio calculations is both viable and practicable for this form of spectroscopy.
Collapse
Affiliation(s)
- Paul M Donaldson
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Naraharisetty SRG, Kurochkin DV, Rubtsov IV. C–D Modes as structural reporters via dual-frequency 2DIR spectroscopy. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
41
|
Quinet O, Champagne B, Rodriguez V. Experimental and theoretical investigation of the Raman and hyper-Raman spectra of acetonitrile and its derivatives. J Chem Phys 2006; 124:244312. [PMID: 16821982 DOI: 10.1063/1.2208350] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Raman and hyper-Raman spectra of acetonitrile and its deuterated analog have been investigated by combining experimental analysis and theoretical interpretation. It has been observed that the Raman spectra can easily be reproduced at both the Hartree-Fock and Moller-Plesset second-order levels of approximation and that for these fundamental transitions, inclusion of anharmonicity effects is not essential. On the other hand, the hyper-Raman spectra are more difficult to simulate and interpret. In particular, electron correlation has to be included in order to describe properly the intensity of the CN stretching mode. Then, a pseudo-C(infinity v) symmetry was assumed to better fit the experimental observations. This accounts for the fact that the a1- and e-symmetry modes correspond to time-decoupled vibrations. The e-symmetry modes, associated with nuclear motions perpendicular to the molecular axis are indeed subject to relaxation processes and, except the CCN bending mode, not visible in the hyper-Raman spectra of acetonitrile or of its deuterated analog. This assumption is supported by the gradual decrease of the phenomenon when going from acetonitrile to trichloroacetonitrile, where the presence of the heavier chlorine atoms in the latter reduces the relaxation processes.
Collapse
Affiliation(s)
- Olivier Quinet
- Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | | | | |
Collapse
|
42
|
Condon NJ, Wright JC. Doubly Vibrationally Enhanced Four-Wave Mixing in Crotononitrile. J Phys Chem A 2005; 109:721-9. [PMID: 16838939 DOI: 10.1021/jp045963p] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Doubly vibrationally enhanced (DOVE) resonances have been observed in the infrared four-wave mixing (IRFWM) spectra of crotononitrile. The 2D DOVE-FWM spectra of the cis and trans isomers of crotononitrile showed cross peaks between the CN stretching fundamental and the CN + C=C stretch and the CN + C-C stretch combination bands for each of the two isomers that were observed, demonstrating the isomer selectivity of DOVE-IRFWM. Frequency-domain simulations were able to reproduce the features of the observed spectra, so the values for the nonlinearity and dephasing rates of all of the nonlinear processes could be measured. The results are compared to the calculations of the third-order susceptibility based on the transition moments, line positions, and line widths observed in the infrared absorption and the Raman spectra of crotononitrile.
Collapse
Affiliation(s)
- Nicholas J Condon
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | |
Collapse
|
43
|
Meyer KA, Wright JC. Interference, Dephasing, and Coherent Control in Time-Resolved Frequency Domain Two-Dimensional Vibrational Spectra. J Phys Chem A 2003. [DOI: 10.1021/jp035146+] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
44
|
|
45
|
Wright JC, Condon NJ, Murdoch KM, Besemann DM, Meyer KA. Quantitative Modeling of Nonlinear Processes in Coherent Two-Dimensional Vibrational Spectroscopy. J Phys Chem A 2003. [DOI: 10.1021/jp034018i] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John C. Wright
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706
| | - Nicholas J. Condon
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706
| | - Keith M. Murdoch
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706
| | - Daniel M. Besemann
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706
| | - Kent A. Meyer
- Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|