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Toutounji M. Mixed Quantum-Classical Liouville Equation Treatment of Electronic Spectroscopy of Condensed Systems: Harmonic and Anharmonic Electron-Phonon Coupling. J Chem Theory Comput 2023. [PMID: 37365487 DOI: 10.1021/acs.jctc.2c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
This Review integrates the use of electronic optical response function theory and the mixed quantum-classical (MQC) Liouville equation (MQCLE), thereby leading to electronic spectroscopy in MQC media. It further sheds light on the applicability, utility, and efficiency of the mixed quantum-classical dynamics (MQCD) formalism, which starts off with the MQCLE, in probing spectroscopy and dynamics of condensed systems, whereby quantum mechanics and classical mechanics are combined systematically. The author has been exploring and implementing MQCD to investigate electron-phonon coupling effects on electronic dephasing in harmonic and anharmonic systems by calculating linear and nonlinear optical transition analytically and numerically dipole moment time correlation functions in an MQC environment, thereby presenting an in depth spectral profile analysis and their shape and symmetry. The distinctive capability of the MQC time correlation functions is that ergodicity and stationarity properties are inherently satisfied as part of the mixed quantum-classical dynamics (MQCD) framework, unlike classical correlation functions. While some research groups have applied MQCLE to calculate vibrational spectra to study hydrogen-bonded complexes in a MQC environment and other groups calculated Optical response function to probe electron transfer dynamics using the basis mapping technique, the approach, purpose, rigor, applications, and path to the end results reported herein are different. Finally, the same framework is employed to study dissipative systems in the MQC limit, whereby the zero-phonon line adopts the correct width and eliminates its asymmetry. While the full quantum mechanical model, like the multimode Brownian oscillator (MBO) model, yields the correct width and inaccurate shape in the low-temperature limit, the MQCD formalism seems to produce an accurate zero-phonon profile. Nonlinear optical signals are also reviewed in MQC media to show the applicability and utility of this approach. The vibronic optical response functions developed here will account for geometry change, frequency change, and anharmonicity upon electronic excitation to accurately probe electronic dephasing, electron-phonon coupling, shape, and symmetry of profiles and present differences and similarities to the MBO model on pure electronic dephasing. Frequency change and anharmonicity are vitally crucial for accurately assessing electron-phonon coupling upon electronic excitation. This is an additional unique result obtained by the author to further demonstrate the applicability and utility of this approach over other approximation schemes in probing electronic dephasing including that of the MBO model.
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Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, P.O. Box 15551, UAE University, Al-Ain, 33000, UAE
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2
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Lu Y, Zhong D. Nonequilibrium dynamics of photoinduced forward and backward electron transfer reactions. J Chem Phys 2020; 152:065102. [PMID: 32061242 DOI: 10.1063/1.5132814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The biological functions of photoenzymes are often triggered by photoinduced electron transfer (ET) reactions. An ultrafast backward ET (BET) reaction follows the initial photoinduced forward ET (FET), which dissipates the energy of absorbed photons and terminates the biological function in vain. Based upon our previous works, we reasoned that the dynamics of the BET is coupled with that of the FET and other local motions. In this work, the dynamics of the FET and BET is modeled as the master equation of the reduced density operator of a three-state system coupled with a classical harmonic reservoir. The coupling of the FET and BET is reflected in the time-evolution of the charge-transfer state's population, which is generated by a source, the reaction flux for the FET, and annihilated by a sink, the reaction flux for the BET. Surprisingly, numerical simulations show that when the BET is in the Marcus normal region, the BET can be accelerated by nonequilibrium local motions and becomes faster than what is predicted by the Marcus theory. The experimental confirmation of this novel dynamics would provide qualitative evidence for nonequilibrium effects on ultrafast ET dynamics. Additionally, the effects of quantum vibrational modes on the dynamics are discussed. This work can help understand the dynamical interactions between the chain of ultrafast reactions and the complex local environmental motions, revealing the physical nature underlying biological functions.
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Affiliation(s)
- Yangyi Lu
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Adhikary R, Yu W, Oda M, Walker RC, Chen T, Stanfield RL, Wilson IA, Zimmermann J, Romesberg FE. Adaptive mutations alter antibody structure and dynamics during affinity maturation. Biochemistry 2015; 54:2085-93. [PMID: 25756188 PMCID: PMC5061043 DOI: 10.1021/bi501417q] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.
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Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wayne Yu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ross C. Walker
- Department of Chemistry and Biochemistry, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Nagasawa Y, Miyasaka H. Ultrafast solvation dynamics and charge transfer reactions in room temperature ionic liquids. Phys Chem Chem Phys 2014; 16:13008-26. [DOI: 10.1039/c3cp55465a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we review the recent studies concerning the liquid structure and solvation dynamics of ionic liquids, and their influence upon electron transfer and charge transfer reactions.
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Affiliation(s)
- Yutaka Nagasawa
- Division of Frontier Materials Science
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka, Japan
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka, Japan
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5
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Adhikary R, Yu W, Oda M, Zimmermann J, Romesberg FE. Protein dynamics and the diversity of an antibody response. J Biol Chem 2012; 287:27139-47. [PMID: 22685303 PMCID: PMC3411056 DOI: 10.1074/jbc.m112.372698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/25/2012] [Indexed: 01/08/2023] Open
Abstract
The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.
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Affiliation(s)
- Ramkrishna Adhikary
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Wayne Yu
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Masayuki Oda
- the Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Jörg Zimmermann
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
| | - Floyd E. Romesberg
- From the Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 and
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6
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Colby KA, Bardeen CJ. Electronic Energy Migration in Solid versus Liquid Host Matrices for Concentrated Perylenediimide Dye Solutions. J Phys Chem A 2011; 115:7574-81. [DOI: 10.1021/jp202654v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathryn A. Colby
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Christopher J. Bardeen
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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7
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Zhu R, Lü R, Yu A. Aggregation Behaviors of Tricarbocyanine Dye in Water and in AOT Reverse Micelles. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Muramatsu M, Nagasawa Y, Miyasaka H. Ultrafast Solvation Dynamics in Room Temperature Ionic Liquids Observed by Three-Pulse Photon Echo Peak Shift Measurements. J Phys Chem A 2011; 115:3886-94. [DOI: 10.1021/jp108282v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Masayasu Muramatsu
- Division of Frontier Materials Science, Graduate School of Engineering Science, Center for Quantum Science and Technology under Extreme Conditions, Osaka University and CREST, JST, Toyonaka, Osaka 560-8531, Japan
| | - Yutaka Nagasawa
- Division of Frontier Materials Science, Graduate School of Engineering Science, Center for Quantum Science and Technology under Extreme Conditions, Osaka University and CREST, JST, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science, Graduate School of Engineering Science, Center for Quantum Science and Technology under Extreme Conditions, Osaka University and CREST, JST, Toyonaka, Osaka 560-8531, Japan
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9
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Donehue JE, Varnavski OP, Cemborski R, Iyoda M, Goodson T. Probing Coherence in Synthetic Cyclic Light-Harvesting Pigments. J Am Chem Soc 2011; 133:4819-28. [DOI: 10.1021/ja108359w] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jessica E. Donehue
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Oleg P. Varnavski
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert Cemborski
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Masahiko Iyoda
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Nagasawa Y. Ultrafast photon echo experiments in condensed phase: Detection of solvation dynamics, coherent wavepacket motions and static inhomogeneity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Zhu R, Lu R, Yu A. Photophysics and locations of IR125 and C152 in AOT reverse micelles. Phys Chem Chem Phys 2011; 13:20844-54. [DOI: 10.1039/c1cp21946d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Hildner R, Brinks D, Stefani FD, van Hulst NF. Electronic coherences and vibrational wave-packets in single molecules studied with femtosecond phase-controlled spectroscopy. Phys Chem Chem Phys 2011; 13:1888-94. [DOI: 10.1039/c0cp02231d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Nagasawa Y, Mukai R, Mori K, Muramatsu M, Miyasaka H. Effect of ultrafast electron transfer on photon echo signal: Decoherence process in electron-donating solvents. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Christensson N, Dietzek B, Yartsev A, Pullerits T. Solute specific polar solvation studied by photon echo spectroscopy. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Christensson N, Dietzek B, Yartsev A, Pullerits T. Probing the strength of the system-bath interaction by three-pulse photon echoes. J Chem Phys 2009; 130:024510. [DOI: 10.1063/1.2990652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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16
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Gibson EA, Shen Z, Jimenez R. Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding. Chem Phys Lett 2009; 473:330-335. [PMID: 21103002 PMCID: PMC2983487 DOI: 10.1016/j.cplett.2009.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.
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Affiliation(s)
- Emily A. Gibson
- Department of Physics, University of Colorado Denver, Denver, CO 80217, USA
| | - Zhaochuan Shen
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
- Department of Physics, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Ralph Jimenez
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
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17
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Thielges MC, Zimmermann J, Yu W, Oda M, Romesberg FE. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. Biochemistry 2008; 47:7237-47. [PMID: 18549243 DOI: 10.1021/bi800374q] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.
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Affiliation(s)
- Megan C Thielges
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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18
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Toutounji M. Algebraic approach to electronic spectroscopy and dynamics. J Chem Phys 2008; 128:164103. [DOI: 10.1063/1.2903748] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Ikeda-Fukazawa T, Kita D, Nagashima K. Raman spectroscopic study of CO2sorption process in poly methyl methacrylate. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/polb.21421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Theoretical Study on the Absorption Spectrum of a Chromophore in Liquid. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2008. [DOI: 10.5012/jkcs.2008.52.1.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Cheng YC, Lee H, Fleming GR. Efficient Simulation of Three-Pulse Photon-Echo Signals with Application to the Determination of Electronic Coupling in a Bacterial Photosynthetic Reaction Center. J Phys Chem A 2007; 111:9499-508. [PMID: 17696328 DOI: 10.1021/jp0735177] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A time-nonlocal quantum master equation coupled with a perturbative scheme to evaluate the third-order polarization in the phase-matching direction k(s) = -k(1) + k(2) + k(3) is used to efficiently simulate three-pulse photon-echo signals. The present method is capable of describing photon-echo peak shifts including pulse overlap and bath memory effects. In addition, the method treats the non-Markovian evolution of the density matrix and the third-order polarization in a consistent manner, thus is expected to be useful in systems with rapid and complex dynamics. We apply the theoretical method to describe one- and two-color three-pulse photon-echo peak shift experiments performed on a bacterial photosynthetic reaction center and demonstrate that, by properly incorporating the pulse overlap effects, the method can be used to describe simultaneously all peak shift experiments and determine the electronic coupling between the localized Q(y) excitations on the bacteriopheophytin (BPhy) and accessory bateriochlorophyll (BChl) in the reaction center. A value of J = 250 cm(-1) is found for the coupling between BPhy and BChl.
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Affiliation(s)
- Yuan-Chung Cheng
- Department of Chemistry and QB3 Institute, University of California Berkeley, Berkeley, California 94720, USA
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22
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Parkinson DY, Lee H, Fleming GR. Measuring Electronic Coupling in the Reaction Center of Purple Photosynthetic Bacteria by Two-Color, Three-Pulse Photon Echo Peak Shift Spectroscopy. J Phys Chem B 2007; 111:7449-56. [PMID: 17530796 DOI: 10.1021/jp070029q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One- and two-color, three-pulse photon echo peak shift spectroscopy (1C and 2C3PEPS) was used to estimate the electronic coupling between the accessory bacteriochlorophyll (B) and the bacteriopheophytin (H) in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides as approximately 170 +/- 30 cm-1. This is the first direct experimental determination of this parameter; it is within the range of values found in previously published calculations. The 1C3PEPS signal of the Qy band of the bacteriochlorophyll B shows that it is weakly coupled to nuclear motions of the bath, whereas the 1C3PEPS signal of the Qy band of the bacteriopheophytin, H, shows that it is more strongly coupled to the bath, but has minimal inhomogeneous broadening. Our simulations capture the major features of the data with the theoretical framework developed in our group to separately calculate the response functions and population dynamics.
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Affiliation(s)
- Dilworth Y Parkinson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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23
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Cho M, Fleming GR. Electron Transfer and Solvent Dynamics in Two- and Three-State Systems. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470141663.ch5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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24
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Dietzek B, Christensson N, Kjellberg P, Pascher T, Pullerits T, Yartsev A. Appearance of intramolecular high-frequency vibrations in two-dimensional, time-integrated three-pulse photon echo data. Phys Chem Chem Phys 2007; 9:701-10. [PMID: 17268681 DOI: 10.1039/b614332f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An alternative experimental outline to measure homodyne detected three-pulse photon-echo data is presented. The novel experimental approach allowing for online monitoring and correction of experimental timing and stability is discussed in detail using the paradigm system of Nile blue in alcohol solution. It is shown that excellent signal-to-noise ratios together with high reproducibility of the data can be routinely achieved. We report in detail on the appearance of high-frequency intramolecular vibrations in the two-dimensional three-pulse photon-echo data and suggest that besides the conventionally discussed three-pulse photon-echo peak-shift the width of the integrated echo signal as a function of population time contains identical and easily accessible information on high-frequency intramolecular vibrations. A comparison of experimental data with theoretical modeling is performed showing that the observed echo-width oscillations are in line with predictions of the Brownian oscillator model.
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Affiliation(s)
- Benjamin Dietzek
- Department of Chemical Physics, Lund University, SE-22100, Lund, Sweden.
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25
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Abstract
Exposure brings risk to all living organisms. Using a remarkably effective strategy, higher vertebrates mitigate risk by mounting a complex and sophisticated immune response to counter the potentially toxic invasion by a virtually limitless army of chemical and biological antagonists. Mutations are almost always deleterious, but in the case of antibody diversification there are mutations occurring at hugely elevated rates within the variable (V) and switch regions (SR) of the immunoglobulin (Ig) genes that are responsible for binding to and neutralizing foreign antigens throughout the body. These mutations are truly purposeful. This chapter is centered on activation-induced cytidine deaminase (AID). AID is required for initiating somatic hypermutation (SHM) in the V regions and class switch recombination (CSR) in the SR portions of Ig genes. By converting C --> U, while transcription takes place, AID instigates a cascade of mutational events involving error-prone DNA polymerases, base excision and mismatch repair enzymes, and recombination pathways. Together, these processes culminate in highly mutated antibody genes and the B cells expressing antibodies that have achieved optimal antigenic binding undergo positive selection in germinal centers. We will discuss the biological role of AID in this complex process, primarily in terms of its biochemical properties in relation to SHM in vivo. The chapter also discusses recent advances in experimental methods to characterize antibody dynamics as a function of SHM to help elucidate the role that the AID-induced mutations play in tailoring molecular recognition. The emerging experimental techniques help to address long-standing conundrums concerning evolution-imposed constraints on antibody structure and function.
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Affiliation(s)
- Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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Dietzek B, Kiefer W, Blumhoff J, Böttcher L, Rau S, Walther D, Uhlemann U, Schmitt M, Popp J. Ultrafast Excited-State Excitation Dynamics in a Quasi-Two-Dimensional Light-Harvesting Antenna Based on Ruthenium(II) and Palladium(II) Chromophores. Chemistry 2006; 12:5105-15. [PMID: 16628758 DOI: 10.1002/chem.200501093] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A detailed study on the excited-state-excitation migration taking place within the tetranuclear complex [{(tbbpy)(2)Ru(tmbi)}(2){Pd(allyl)}(2)](PF(6))(2) (tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine and tmbi = 5,6,5',6'-tetramethyl-2,2'-bibenzimidazolate) is presented. The charge transfer is initiated by the photoexcitation into the lowest metal-to-ligand charge-transfer (MLCT) band of one of the peripheral ruthenium(II) chromophores and terminates on the central structurally complex Pd(2) (II)(allyl)(2) subunit. Thus, the system under investigation can be thought of as a functional model for the photosynthesis reaction center in plants. The kinetic steps involved in the overall process are inferred from femtosecond time-resolved transient-grating kinetics recorded at spectral positions within the regions of ground-state bleach and transient absorption. The kinetics features a complex non-exponential time behavior and can be fitted to a bi-exponential rise (tau(1)> or =200 fs, tau(2) approximately 1.5 ps) and a mono- or bi-exponential decay, depending on the experimental situation. The data leads to the formulation of a model for the intramolecular excitation-hopping ascribing intersystem crossing and subsequent cooling as the two fastest observed processes. Following these initial steps, charge transfer from the ruthenium to the central complex Pd(2)(allyl)(2) moiety is observed with a characteristic time constant of 50 ps. A 220-ps component that is observed in the ground-state recovery only is attributed to excitation equilibration between the two identical Pd(allyl) chromophores.
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Affiliation(s)
- Benjamin Dietzek
- Institut für Physikalische Chemie, Bayerische Julius-Maximilians Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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27
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Cho BM, Carlsson CF, Jimenez R. Photon echo spectroscopy of porphyrins and heme proteins: Effects of quasidegenerate electronic structure on the peak shift decay. J Chem Phys 2006; 124:144905. [PMID: 16626243 DOI: 10.1063/1.2186318] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three pulse photon echo peak shift spectroscopy and transient grating measurements on Zn-substituted cytochrome c, Zn-tetraphenylporphyrin, and Zn-protoporphyrin IX are reported. The effects of protein conformation, axial ligation, and solvent are investigated. Numerical simulations of the peak shift and transient grating experiments are presented. The simulations employed recently derived optical response functions for square-symmetric molecules with doubly degenerate excited states. Simulations exploring the effects of excited-state energy splitting, symmetric and asymmetric fluctuations, and excited-state lifetime show that the time scales of the peak shift decay in the three-level system largely reflect the same dynamics as in the two-level system. However, the asymptotic peak shift, which is a clear indicator of inhomogeneous broadening in a two-level system, must be interpreted more carefully for three-level systems, as it is also influenced by the magnitude of the excited-state splitting. The calculated signals qualitatively reproduce the data.
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Affiliation(s)
- Byung Moon Cho
- JILA, University of Colorado and National Institute of Standards and Technology, Boulder, Colorado 80309-0440, USA
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28
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Dietzek B, Maksimenka R, Kiefer W, Hermann G, Popp J, Schmitt M. The excited-state dynamics of magnesium octaethylporphyrin studied by femtosecond time-resolved four-wave-mixing. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.08.136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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Ohta K, Tominaga K. Dynamical Interactions between Solute and Solvent Studied by Three-Pulse Photon Echo Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.1581] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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30
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Benten H, Ohkita H, Ito S, Yamamoto M, Tohda Y, Tani K. Photoinduced intramolecular charge separation in a polymer solid below the glass transition temperature. J Chem Phys 2005; 123:084901. [PMID: 16164324 DOI: 10.1063/1.2008249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photoinduced intramolecular charge separation (CS) in a polar polymer glass, cyanoethylated pullulan (CN-PUL), was studied below the glass transition temperature (Tg=395 K). A series of three carbazole (Cz: donor)-cyclohexane (S: spacer)-acceptor (A: acceptor) molecules (Cz-S-A) was used as intramolecular donor-acceptor dyads. The photoinduced CS rate was evaluated by the fluorescence decay measurement at temperatures from 100 to 400 K. The CS rate (kCS) increased above 200 K even far below Tg where micro-Brownian motions of the whole polymer chain are frozen. Below 200 K, on the other hand, kCS showed weak dependence on temperature. The temperature dependence of kCS is discussed in terms of the dielectric relaxation time of the polymer matrix. Consequently, CS below Tg was well explained by a thermally nonequilibrium electron transfer (ET) formula above 200 K and by a two-mode quantum-mechanical ET formula below 200 K. The increase in kCS above 200 K is mainly caused by a thermally activated low-frequency matrix mode originating from the side-chain relaxation of polar cyano groups. The weak temperature dependence of kCS can be explained by a nuclear-tunneling effect caused by a high-frequency matrix mode (variant Planck's over 2piomegH=250 cm-1) and an intramolecular vibrational mode (variant Planck's over 2piomegaQ=1300 cm-1). The high-frequency mode of the polymer matrix was attributed to a vibrational or librational motion of polar groups in the CN-PUL glassy solid.
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Affiliation(s)
- Hiroaki Benten
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
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31
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Nagasawa Y, Mori Y, Nakagawa Y, Miyasaka H, Okada T. Enhancement and Suppression of Vibrational Coherence in Degenerate Four-Wave-Mixing Signal Generated from Dye-Doped Polymer Films. J Phys Chem B 2005; 109:11946-52. [PMID: 16852472 DOI: 10.1021/jp051187p] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vibrational coherence in the degenerate four-wave-mixing (DFWM) signal generated from polymer films doped with a dye, oxazine 4 (Ox4), at 10 K was investigated. It was found that the amplitudes of some low-frequency oscillations (<400 cm(-1)) were enhanced when the delay between the first and second femtosecond pulses was set out of phase with the oscillation period. Frequency and reorganization energy dependence was investigated by computer simulation based on the response function formalism which considers all the possible Liouville space pathways for the DFWM signal. It was revealed that low-frequency oscillations with weak coupling to the optical transition can be enhanced in the stimulated photon echo signal compared to the transient grating signal.
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Affiliation(s)
- Yutaka Nagasawa
- Division of Frontier Materials Science, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan.
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32
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Larsen DS. Stimulated emission three-pulse photo-echo peakshift: A mixed pump–probe and photon-echo technique for studying excited-state dynamics. J Chem Phys 2004; 121:5039-42. [PMID: 15352793 DOI: 10.1063/1.1794694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A novel four-pulse photon-echo technique for exploring condensed phase dynamics at different parts of the excited-state potential energy surface is presented. In contrast to traditional three-pulse photon-echo signals, the introduction of a fourth pump pulse allows the use of photon-echo techniques to probe excited-state phenomena. Here, a "proof of principle" experiment is presented where the excited-state solvent dynamics of the coumarin 153 chromophore dissolved in methanol is explored. The fluctuations of the stimulated emission transition is probed, in contrast to the ground-state absorption transition explored in traditional echo measurements. Distinctly different excited-state dynamics, in contrast to ground-state signals, is observed and discussed.
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Affiliation(s)
- Delmar S Larsen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
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33
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Toutounji M. Optical linear response function with linear and diagonal quadratic electron-vibration coupling in mixed quantum-classical systems. J Chem Phys 2004; 121:2228-38. [PMID: 15260777 DOI: 10.1063/1.1761052] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Optical linear response function of linearly and quadratically coupled mixed quantum-classical condensed phase systems is derived. The linear response function is derived using Kapral's formalism of statistical mechanics in mixed quantum-classical systems. Our mixed quantum-classical linear dipole moment correlation function J(t) is compared with the full quantum J(t) [Y. J. Yan and S. Mukamel, J. Chem. Phys. 85, 5908 (1986)] in the high temperature limit. Model calculations and discussion of our results are presented. Various formulas of Franck-Condon factors for both linear and quadratic coupling are discussed.
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Affiliation(s)
- Mohamad Toutounji
- Department of Chemistry, College of Science, United Arab Emirates University, PO Box 17551, Al-Ain
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34
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Varnavski O, Goodson T, Sukhomlinova L, Twieg R. Ultrafast Exciton Dynamics in a Branched Molecule Investigated by Time-Resolved Fluorescence, Transient Absorption, and Three-Pulse Photon Echo Peak Shift Measurements. J Phys Chem B 2004. [DOI: 10.1021/jp0495996] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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35
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Thomson MD, Novosel M, Roskos HG, Müller T, Scheibitz M, Wagner M, Fabrizi de Biani F, Zanello P. Electronic Structure, Photophysics, and Relaxation Dynamics of Charge Transfer Excited States in Boron−Nitrogen-Bridged Ferrocene-Donor Organic-Acceptor Compounds. J Phys Chem A 2004. [DOI: 10.1021/jp037044p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Carson EA, Diffey WM, Shelly KR, Lampa-Pastirk S, Dillman KL, Schleicher JM, Beck WF. Dynamic-Absorption Spectral Contours: Vibrational Phase-Dependent Resolution of Low-Frequency Coherent Wave-Packet Motion of IR144 on the Ground-State and Excited-State π → π* Surfaces. J Phys Chem A 2004. [DOI: 10.1021/jp035176c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth A. Carson
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - William M. Diffey
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - Katherine R. Shelly
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - Sanela Lampa-Pastirk
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - Kevin L. Dillman
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - James M. Schleicher
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
| | - Warren F. Beck
- Department of Chemistry, Michigan State University, 3 Chemistry Building, East Lansing, Michigan 48824
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37
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Yang M, Damjanović A, Vaswani HM, Fleming GR. Energy transfer in photosystem I of cyanobacteria Synechococcus elongatus: model study with structure-based semi-empirical Hamiltonian and experimental spectral density. Biophys J 2003; 85:140-58. [PMID: 12829471 PMCID: PMC1303072 DOI: 10.1016/s0006-3495(03)74461-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2002] [Accepted: 03/07/2003] [Indexed: 10/21/2022] Open
Abstract
We model the energy transfer and trapping kinetics in PSI. Rather than simply applying Förster theory, we develop a new approach to self-consistently describe energy transfer in a complex with heterogeneous couplings. Experimentally determined spectral densities are employed to calculate the energy transfer rates. The absorption spectrum and fluorescence decay time components of the complex at room temperature were reasonably reproduced. The roles of the special chlorophylls (red, linker, and reaction center, respectively) molecules are discussed. A formally exact expression for the trapping time is derived in terms of the intrinsic trapping time, mean first passage time to trap, and detrapping time. The energy transfer mechanism is discussed and the slowest steps of the arrival at the primary electron donor are found to contain two dominant steps: transfer-to-reaction-center, and transfer-to-trap-from-reaction-center. The intrinsic charge transfer time is estimated to be 0.8 approximately 1.7 ps. The optimality with respect to the trapping time of the calculated transition energies and the orientation of Chls is discussed.
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Affiliation(s)
- Mino Yang
- Department of Chemistry, University of California, Berkeley, California, USA
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38
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Shirota H, Segawa H. Time-Resolved Fluorescence Study on Liquid Oligo(ethylene oxide)s: Coumarin 153 in Poly(ethylene glycol)s and Crown Ethers. J Phys Chem A 2003. [DOI: 10.1021/jp022514l] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hideaki Shirota
- Department of General Systems Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hiroshi Segawa
- Department of General Systems Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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39
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Nagasawa Y, Seike K, Muromoto T, Okada T. Two-Dimensional Analysis of Integrated Three-Pulse Photon Echo Signals of Nile Blue Doped in PMMA. J Phys Chem A 2003. [DOI: 10.1021/jp027012m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yutaka Nagasawa
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazushige Seike
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Takayuki Muromoto
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadashi Okada
- Department of Chemistry, Graduate School of Engineering Science, and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
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40
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Nagasawa Y, Watanabe A, Takikawa H, Okada T. Solute Dependence of Three Pulse Photon Echo Peak Shift Measurements in Methanol Solution. J Phys Chem A 2003. [DOI: 10.1021/jp0271559] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yutaka Nagasawa
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ayako Watanabe
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroko Takikawa
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadashi Okada
- Department of Chemistry, Graduate School of Engineering Science and Research Center for Materials Science at Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
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41
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Yu A, Tolbert CA, Farrow DA, Jonas DM. Solvatochromism and Solvation Dynamics of Structurally Related Cyanine Dyes. J Phys Chem A 2002. [DOI: 10.1021/jp0205867] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anchi Yu
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Catherine A. Tolbert
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Darcie A. Farrow
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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42
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Toutounji M. Ohmic Brownian Oscillator Approach to Hole-Burning and Photon-Echo Spectroscopies. J Phys Chem A 2002. [DOI: 10.1021/jp025686r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, United Arab Emirates University, Al-Ain, UAE
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43
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Merchant KA, Xu QH, Thompson DE, Fayer MD. Frequency Selected Ultrafast Infrared Vibrational Echo Studies of Liquids, Glasses, and Proteins. J Phys Chem A 2002. [DOI: 10.1021/jp021145q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- K. A. Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Qing-Hua Xu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - David E. Thompson
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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44
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Xu QH, Fayer MD. Temperature-dependent vibrational dephasing: Comparison of liquid and glassy solvents using frequency-selected vibrational echoes. J Chem Phys 2002. [DOI: 10.1063/1.1492280] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Jimenez R, Romesberg FE. Excited State Dynamics and Heterogeneity of Folded and Unfolded States of Cytochrome c. J Phys Chem B 2002. [DOI: 10.1021/jp0209648] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ralph Jimenez
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, Maildrop CVN22, La Jolla, California 92037
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, Maildrop CVN22, La Jolla, California 92037
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46
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Lavoine J, Boeglin A. Influence of nonadiabatic coupling on oscillatory dephasing. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00847-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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47
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Nakamura R, Yamamoto S, Nakahara J. Broad Raman scattering and luminescence in β-carotene solution. J Chem Phys 2002. [DOI: 10.1063/1.1481060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Jimenez R, Case DA, Romesberg FE. Flexibility of an Antibody Binding Site Measured with Photon Echo Spectroscopy. J Phys Chem B 2002. [DOI: 10.1021/jp013110g] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ralph Jimenez
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., Maildrop CVN22, La Jolla, California 92037
| | - David A. Case
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., Maildrop CVN22, La Jolla, California 92037
| | - Floyd E. Romesberg
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., Maildrop CVN22, La Jolla, California 92037
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49
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Ohta K, Yang M, Fleming GR. Ultrafast exciton dynamics of J-aggregates in room temperature solution studied by third-order nonlinear optical spectroscopy and numerical simulation based on exciton theory. J Chem Phys 2001. [DOI: 10.1063/1.1403693] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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The mechanism of energy transfer in the antenna of photosynthetic purple bacteria. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00504-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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