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Hutchison CM, Perrett S, van Thor JJ. XFEL Beamline Optical Instrumentation for Ultrafast Science. J Phys Chem B 2024; 128:8855-8868. [PMID: 39087627 PMCID: PMC11421085 DOI: 10.1021/acs.jpcb.4c01492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Free electron lasers operating in the soft and hard X-ray regime provide capabilities for ultrafast science in many areas, including X-ray spectroscopy, diffractive imaging, solution and material scattering, and X-ray crystallography. Ultrafast time-resolved applications in the picosecond, femtosecond, and attosecond regimes are often possible using single-shot experimental configurations. Aside from X-ray pump and X-ray probe measurements, all other types of ultrafast experiments require the synchronized operation of pulsed laser excitation for resonant or nonresonant pumping. This Perspective focuses on the opportunities for the optical control of structural dynamics by applying techniques from nonlinear spectroscopy to ultrafast X-ray experiments. This typically requires the synthesis of two or more optical pulses with full control of pulse and interpulse parameters. To this end, full characterization of the femtosecond optical pulses is also highly desirable. It has recently been shown that two-color and two-pulse femtosecond excitation of fluorescent protein crystals allowed a Tannor-Rice coherent control experiment, performed under characterized conditions. Pulse shaping and the ability to synthesize multicolor and multipulse conditions are highly desirable and would enable XFEL facilities to offer capabilities for structural dynamics. This Perspective will give a summary of examples of the types of experiments that could be achieved, and it will additionally summarize the laser, pulse shaping, and characterization that would be recommended as standard equipment for time-resolved XFEL beamlines, with an emphasis on ultrafast time-resolved serial femtosecond crystallography.
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Affiliation(s)
- Christopher
D. M. Hutchison
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Samuel Perrett
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Jasper J. van Thor
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
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2
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Rode AJ, Arpin PC, Turner DB. Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates. J Chem Phys 2024; 160:164101. [PMID: 38647298 DOI: 10.1063/5.0200570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
When used as pump pulses in transient absorption spectroscopy measurements, femtosecond laser pulses can produce oscillatory signals known as quantum beats. The quantum beats arise from coherent superpositions of the states of the sample and are best studied in the Fourier domain using Femtosecond Coherence Spectroscopy (FCS), which consists of one-dimensional amplitude and phase plots of a specified oscillation frequency as a function of the detection frequency. Prior works have shown ubiquitous amplitude nodes and π phase shifts in FCS from excited-state vibrational wavepackets in monomer samples. However, the FCS arising from vibronic-exciton states in molecular aggregates have not been studied theoretically. Here, we use a model of vibronic-exciton states in molecular dimers based on displaced harmonic oscillators to simulate FCS for dimers in two important cases. Simulations reveal distinct spectral signatures of excited-state vibronic-exciton coherences in molecular dimers that may be used to distinguish them from monomer vibrational coherences. A salient result is that, for certain relative orientations of the transition dipoles, the key resonance condition between the electronic coupling and the frequency of the vibrational mode may yield strong enhancement of the quantum-beat amplitude and, perhaps, also cause a significant decrease of the oscillation frequency to a value far lower than the vibrational frequency. Future studies using these results will lead to new insights into the excited-state coherences generated in photosynthetic pigment-protein complexes.
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Affiliation(s)
- Alexander J Rode
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul C Arpin
- Department of Physics, California State University, Chico, Chico, California 95929, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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3
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Barclay M, Huff JS, Pensack RD, Davis PH, Knowlton WB, Yurke B, Dean JC, Arpin PC, Turner DB. Characterizing Mode Anharmonicity and Huang-Rhys Factors Using Models of Femtosecond Coherence Spectra. J Phys Chem Lett 2022; 13:5413-5423. [PMID: 35679146 PMCID: PMC9234982 DOI: 10.1021/acs.jpclett.1c04162] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Femtosecond laser pulses readily produce coherent quantum beats in transient-absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck-Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang-Rhys factors and anharmonicity values. We discuss the extracted Huang-Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from molecular vibrations, which will aid studies of molecular aggregates and photosynthetic proteins.
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Affiliation(s)
- Matthew
S. Barclay
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jonathan S. Huff
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan D. Pensack
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jacob C. Dean
- Department
of Physical Science, Southern Utah University, Cedar City, Utah 84720, United States
| | - Paul C. Arpin
- Department
of Physics, California State University,
Chico, Chico, California 95929, United States
| | - Daniel B. Turner
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
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4
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Arpin PC, Turner DB. Signatures of Vibrational and Electronic Quantum Beats in Femtosecond Coherence Spectra. J Phys Chem A 2021; 125:2425-2435. [PMID: 33724844 PMCID: PMC8023717 DOI: 10.1021/acs.jpca.0c10807] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Indexed: 11/29/2022]
Abstract
Femtosecond laser pulses can produce oscillatory signals in transient-absorption spectroscopy measurements. The quantum beats are often studied using femtosecond coherence spectra (FCS), the Fourier domain amplitude, and phase profiles at individual oscillation frequencies. In principle, one can identify the mechanism that gives rise to each quantum-beat signal by comparing its measured FCS to those arising from microscopic models. To date, however, most measured FCS deviate from the ubiquitous harmonic oscillator model. Here, we expand the inventory of models to which the measured spectra can be compared. We develop quantum-mechanical models of the fundamental, overtone, and combination-band FCS arising from harmonic potentials, the FCS of anharmonic potentials, and the FCS of a purely electronic dimer. This work solidifies the use of FCS for identifying electronic coherences that can arise in measurements of molecular aggregates including photosynthetic proteins. Furthermore, future studies can use the derived expressions to fit the measured FCS and thereby extract microscopic parameters of molecular potential-energy surfaces.
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Affiliation(s)
- Paul C. Arpin
- Department
of Physics, California State University,
Chico, Chico, California 95929, United States
| | - Daniel B. Turner
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
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6
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Ferrante C, Batignani G, Pontecorvo E, Montemiglio LC, Vos MH, Scopigno T. Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:2285-2292. [PMID: 31917551 PMCID: PMC7735705 DOI: 10.1021/jacs.9b10560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Identifying
the structural rearrangements during photoinduced reactions is a fundamental
challenge for understanding from a microscopic perspective the dynamics
underlying the functional mechanisms of heme proteins. Here, femtosecond
stimulated Raman spectroscopy is applied to follow the ultrafast evolution
of two different proteins, each bearing a six-coordinate heme with
two amino acid axial ligands. By exploiting the sensitivity of Raman
spectra to the structural configuration, we investigate the effects
of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for
different time delays and Raman pump resonances, we show how detailed
properties of atomic motions and energy redistribution can be unveiled.
In particular, we demonstrate substantially faster energy flow from
the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme–protein
bonds.
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Affiliation(s)
- Carino Ferrante
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| | | | | | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Tullio Scopigno
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
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7
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NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy. Proc Natl Acad Sci U S A 2015; 112:12922-7. [PMID: 26438842 DOI: 10.1073/pnas.1424446112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein's function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼ 200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump-probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.
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9
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Hu C, Barabanschikov A, Ellison MK, Zhao J, Alp EE, Sturhahn W, Zgierski MZ, Sage JT, Scheidt WR. Nuclear resonance vibrational spectra of five-coordinate imidazole-ligated iron(II) porphyrinates. Inorg Chem 2012; 51:1359-70. [PMID: 22243131 PMCID: PMC3273671 DOI: 10.1021/ic201580v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear resonance vibrational spectra have been obtained for six five-coordinate imidazole-ligated iron(II) porphyrinates, [Fe(Por)(L)] (Por = tetraphenylporphyrinate, octaethylporphyrinate, tetratolylporphyrinate, or protoporphyrinate IX and L = 2-methylimidazole or 1,2-dimethylimidazole). Measurements have been made on both powder and oriented crystal samples. The spectra are dominated by strong signals around 200-300 cm(-1). Although the in-plane and out-of-plane vibrations are seriously overlapped, oriented crystal spectra allow their deconvolution. Thus, oriented crystal experimental data, along with density functional theory (DFT) calculations, enable the assignment of key vibrations in the spectra. Molecular dynamics are also discussed. The nature of the Fe-N(Im) vibrations has been elaborated further than was possible from resonance Raman studies. Our study suggests that the Fe motions are coupled with the porphyrin core and peripheral groups motions. Both peripheral groups and their conformations have significant influence on the vibrational spectra (position and shape).
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Affiliation(s)
- Chuanjiang Hu
- Contribution from Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P.R. China
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Mary K. Ellison
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Marek Z. Zgierski
- Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada KIA OR6
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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10
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Dillman KL, Beck WF. Vibrational Coherence from van der Waals Modes in the Native and Molten-Globule States of Zn II-Substituted Cytochrome c. J Phys Chem B 2011; 115:8657-66. [DOI: 10.1021/jp204571m] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin L. Dillman
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Warren F. Beck
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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11
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12
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Meyer-Ilse J, Akimov D, Dietzek B. Femtosecond Coherence Spectroscopic Study of the Onset of Chemical Denaturation of Myoglobin upon Addition of Minor Amounts of Urea. Z PHYS CHEM 2011. [DOI: 10.1524/zpch.2011.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThe interaction of urea with myoglobin, as a benchmark system for heme-containing proteins, is studiedviafemtosecond coherence spectroscopy. The work focuses on the effect of urea on the appearance of low-wavenumber oscillations, which are a measure of the geometrical structure of the heme group and its interaction with the polypeptide chain. Pursuing this approach, structural alterations (i.e.changes in the vibrational dynamics of the heme group) are detected at denaturant concentrations below the full denaturation limit of 6 M urea for myoglobin. In particular, the low-wavenumber oscillation associated with the heme-doming (i.e.the out-off-plane vibration of the propyrin macrocycle) is found to appear spectrally shifted with a concentration of only 3 M urea. These results suggest that the local environment around the heme is already altered despite the fact that macroscopic unfolding as manifested in the thermodynamic properties of the polypeptide chain is not complete at these urea concentrations.
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Affiliation(s)
- Julia Meyer-Ilse
- Friedrich-Schiller-Univesrität Jena, Institute of Physical Chemistry, Jena, Deutschland
| | - Denis Akimov
- Institute of Photonic Technology Jena e.V., Jena, Deutschland
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13
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton WE, Guo Y, Cramer SP. Observation of terahertz vibrations in the nitrogenase FeMo cofactor by femtosecond pump-probe spectroscopy. Angew Chem Int Ed Engl 2010; 49:3912-5. [PMID: 20411554 PMCID: PMC3129498 DOI: 10.1002/anie.200906787] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have used Impulsive Coherent Vibrational Spectroscopy (ICVS) to study the FeMo-cofactor of nitrogenase from Azotobacter vinelandii as the extracted small molecule ‘FeMoco’. In the ICVS experiment, a 15 fs visible laser pulse pumps the sample to an excited electronic state, and a second <10 fs pulse probes the change in transmission as a function of the time delay. FeMoco was observed to relax to the ground state by a single exponential decay with a time constant of ~200 fs. Superimposed on this relaxation are oscillations caused by the coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the FeMoco vibrational frequencies that are coherently excited by the short laser pulse. The frequencies obtained by the ICVS technique were compared with values from normal mode calculations. The strongest ICVS bands are at 215 and 420 cm−1. The 420 cm−1 band is attributed to Fe-S stretching motion, whereas the 215 cm−1 band, which is the strongest feature in the spectrum, is attributed to a breathing mode of FeMoco. Over the years, nitrogenase and FeMoco have resisted characterization by resonance Raman spectroscopy. The current results demonstrate the promise of ICVS as an alternative probe of FeMoco dynamics.
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Affiliation(s)
- Ines Delfino
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Cristian Manzoni
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Dario Polli
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Christie Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Stephen P. Cramer
- Department of Applied Science, University of California, Davis, CA 95616
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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14
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton W, Guo Y, Cramer S. Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump-Probe Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Mehlenbacher RD, Lyons B, Wilson KC, Du Y, McCamant DW. Theoretical analysis of anharmonic coupling and cascading Raman signals observed with femtosecond stimulated Raman spectroscopy. J Chem Phys 2009; 131:244512. [DOI: 10.1063/1.3276684] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Zhang Y, Straub JE. Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models. J Chem Phys 2009; 130:215101. [PMID: 19508100 DOI: 10.1063/1.3147704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The time scales and pathways of vibrational energy relaxation (VER) of the nu(4) and nu(7) modes of three nickel porphyrin models, nickel porphine (NiP), nickel protoporphyrin IX (Ni-heme), and nickel octaethylporphyrin (NiOEP), were studied using a non-Markovian time-dependent perturbation theory at the B3LYP/6-31G(d) level. When NiP is calculated with D(4h) symmetry, it has the planar structure and the same VER properties as ferrous iron porphine (FeP). The porphine cores of both Ni-heme and NiOEP were distorted from a planar geometry, assuming a nonplanar structure, similar to that of the heme structure in cytochrome c. The VER time scales of Ni-heme are found to be similar to those predicted for a planar iron heme, but the derived pathways have distinctly different features. In particular, the strong coupling between the nu(7) mode and the overtone of the approximately 350 cm(-1) gamma(7) mode, observed for planar porphyrins, is absent in both nonplanar nickel porphyrins. Direct energy exchange between the nu(4) and nu(7) modes is not observed in NiOEP, but is found to play an essential role in the VER of the nu(4) mode in Ni-heme. The Ni-heme isopropionate groups are involved in the dominant VER pathways of both the nu(4) and nu(7) modes of Ni-heme. However, in contrast with VER pathways derived in planar iron heme, the isopropionate groups are not observed to play an essential role relative to other side chains in spatially directing the vibrational energy flow.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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17
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Zhang Y, Fujisaki H, Straub JE. Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model. J Chem Phys 2009; 130:025102. [DOI: 10.1063/1.3055277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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18
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Kobayashi T, Du J, Feng W, Yoshino K. Excited-state molecular vibration observed for a probe pulse preceding the pump pulse by real-time optical spectroscopy. PHYSICAL REVIEW LETTERS 2008; 101:037402. [PMID: 18764294 DOI: 10.1103/physrevlett.101.037402] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Indexed: 05/26/2023]
Abstract
It is shown experimentally that the absorbance change observed in the "negative" time range, where probe pulse precedes pump pulse in real-time vibrational spectroscopy is induced only by the excited-state wave-packet motion as theoretically expected. Coherent molecular vibration of a polymer in the excited state was observed in the real-time trace without the effect of wave-packet motion in the ground state, which usually makes it difficult to ascribe the signal either to the ground state or to the excited state.
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Affiliation(s)
- Takayoshi Kobayashi
- Department of Applied Physics and Chemistry and Institute for Laser Science, the University of Electro-communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan.
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19
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Sperling J, Nemeth A, Baum P, Šanda F, Riedle E, Kauffmann H, Mukamel S, Milota F. Exciton dynamics in a disordered conjugated polymer: Three-pulse photon-echo and transient grating experiments. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.02.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Tan ML, Bizzarri AR, Xiao Y, Cannistraro S, Ichiye T, Manzoni C, Cerullo G, Adams MWW, Jenney FE, Cramer SP. Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics. J Inorg Biochem 2007; 101:375-84. [PMID: 17204331 DOI: 10.1016/j.jinorgbio.2006.09.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 09/28/2006] [Accepted: 09/29/2006] [Indexed: 10/24/2022]
Abstract
We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.
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Affiliation(s)
- Ming-Liang Tan
- Department of Applied Science, University of California, Davis, CA 95616, USA
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Ionascu D, Gruia F, Ye X, Yu A, Rosca F, Beck C, Demidov A, Olson JS, Champion PM. Temperature-dependent studies of NO recombination to heme and heme proteins. J Am Chem Soc 2005; 127:16921-34. [PMID: 16316238 PMCID: PMC2553725 DOI: 10.1021/ja054249y] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.
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Affiliation(s)
- Dan Ionascu
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Flaviu Gruia
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Xiong Ye
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Anchi Yu
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Florin Rosca
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Chris Beck
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Andrey Demidov
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | | | - Paul M. Champion
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
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22
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Walther M, Raicu V, Ogilvie JP, Phillips R, Kluger R, Miller RJD. Determination of the Fe−CO Bond Energy in Myoglobin Using Heterodyne-Detected Transient Thermal Phase Grating Spectroscopy. J Phys Chem B 2005; 109:20605-11. [PMID: 16853667 DOI: 10.1021/jp052344n] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bond energies at active sites of proteins are intimately coupled to the structure-function relationship in biological systems. Due to the unknown nature of the protein relaxation along a reaction coordinate, it has not been possible to directly determine bond energies relevant to protein function. By embedding proteins in trehalose glasses, it is possible to freeze out protein relaxation on short time scales and determine the bond energies of photolabile ligands using photothermal spectroscopies. As a prototypical example, the photodissociation dynamics and energetics of carboxy-myoglobin (MbCO) in a trehalose glass matrix at room temperature were studied by transient absorption (or pump-probe) and transient thermal phase grating spectroscopy to determine the CO recombination dynamics and associated energetics, respectively. Both the initial energetics of the bond breaking and the energy released upon bond reformation could be used, on a time scale faster than significant protein relaxation, to determine the Fe-CO bond energy as 34 +/- 4 kcal/mol. This bond energy is significantly larger than that typically cited (25 kcal/mol) on the basis of indirect measurements but is in good agreement with recent theoretical predictions (35 kcal/mol) (Rovira, C.; Parrinello, M. Int. J. Quantum Chem. 2000, 80, 1172). This result in combination with the theoretical study suggests that protein structure plays a significant role in the bond energies at active sites which in turn provides a tuning element of the effective barrier heights independent to the transition state region.
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Affiliation(s)
- Markus Walther
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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23
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Nagy AM, Raicu V, Miller RJD. Nonlinear optical studies of heme protein dynamics: Implications for proteins as hybrid states of matter. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:148-72. [PMID: 15927874 DOI: 10.1016/j.bbapap.2005.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 02/03/2005] [Accepted: 02/15/2005] [Indexed: 10/25/2022]
Abstract
Protein structure is fundamentally related to function. However, static structures alone are insufficient to understand how a protein works. Dynamics play an equally important role. Given that proteins are highly associated aperiodic systems, it may be expected that protein dynamics would follow glass-like dynamics. However, protein functions occur on time scales orders of magnitude faster than the time scales typically associated with glassy systems. It is becoming clear that the reaction forces driving functions do not sample entirely the large number of configurations available to a protein but are highly directed along an optimized pathway. Could there be any correlation between specific topological features in protein structures and dynamics that leads to strongly correlated atomic displacements in the dynamical response to a perturbation? This review will try to provide an answer by focusing upon recent nonlinear optical studies with the aim of directly observing functionally important protein motions over the entire dynamic range of the protein response function. The specific system chosen is photoinduced dynamics of ligand dissociation at the active site in heme proteins, with myoglobin serving as the simplest model system. The energetics and nuclear motions from the very earliest events involved in bond breaking on the femtosecond time scale all the way out to ligand escape and bimolecular rebinding on the microsecond and millisecond time scale have been mapped out. The picture that is emerging is that the system consists of strongly coupled motions from the very instant the bond breaks at the active site that cascade into low frequency collective modes specific to the protein structure. It is this coupling that imparts the ability of a protein to function on time scales more commensurate with liquids while simultaneously conserving structural integrity akin to solids.
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Affiliation(s)
- A M Nagy
- Department of Chemistry, University of Toronto, Ontario, Canada
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24
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Menšı́k M, Nešpůrek S. Vibrational coherence in excited state decay: the role of the type of electron-vibrational interactions. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2004.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Leu BM, Zgierski MZ, Wyllie GRA, Scheidt WRE, Sturhahn W, Alp EE, Durbin SM, Sage JT. Quantitative vibrational dynamics of iron in nitrosyl porphyrins. J Am Chem Soc 2004; 126:4211-27. [PMID: 15053610 PMCID: PMC1570756 DOI: 10.1021/ja038526h] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.
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Affiliation(s)
- Bogdan M. Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
| | - Marek Z. Zgierski
- Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Graeme R. A. Wyllie
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - W. Rob ert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | | | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
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26
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Ye X, Demidov A, Rosca F, Wang W, Kumar A, Ionascu D, Zhu L, Barrick D, Wharton D, Champion PM. Investigations of Heme Protein Absorption Line Shapes, Vibrational Relaxation, and Resonance Raman Scattering on Ultrafast Time Scales. J Phys Chem A 2003. [DOI: 10.1021/jp0276799] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xiong Ye
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Andrey Demidov
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Florin Rosca
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Wei Wang
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Anand Kumar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Dan Ionascu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Leyun Zhu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Doug Barrick
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - David Wharton
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Paul M. Champion
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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27
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Armstrong MR, Ogilvie JP, Cowan ML, Nagy AM, Miller RJD. Observation of the cascaded atomic-to-global length scales driving protein motion. Proc Natl Acad Sci U S A 2003; 100:4990-4. [PMID: 12697894 PMCID: PMC154285 DOI: 10.1073/pnas.0936507100] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Model studies of the ligand photodissociation process of carboxymyoglobin have been conducted by using amplified few-cycle laser pulses short enough in duration (<10 fs) to capture the phase of the induced nuclear motions. The reaction-driven modes are observed directly in real time and depict the pathway by which energy liberated in the localized reaction site is efficiently channeled to functionally relevant mesoscale motions of the protein.
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Affiliation(s)
- M R Armstrong
- Department of Physics and Astronomy, University of Rochester, Bausch & Lomb Hall, Rochester, NY 14627-0171, USA
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28
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Rosca F, Kumar ATN, Ionascu D, Ye X, Demidov AA, Champion PM. Low Frequency Modes in Heme Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Rosca F, Kumar ATN, Ionascu D, Ye X, Demidov AA, Sjodin T, Wharton D, Barrick D, Sligar SG, Yonetani T, Champion PM. Investigations of Anharmonic Low-Frequency Oscillations in Heme Proteins. J Phys Chem A 2001. [DOI: 10.1021/jp0129277] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florin Rosca
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Anand T. N. Kumar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Dan Ionascu
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Xiong Ye
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Andrey A. Demidov
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Theodore Sjodin
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - David Wharton
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Douglas Barrick
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Stephen G. Sligar
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Takashi Yonetani
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Paul M. Champion
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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