151
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Iyama T, Kawabata H, Tachikawa H. Effects of Point Charges on the Excitation Energies of Protonated Schiff Base of Retinal. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/15533174.2010.486814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Tetsuji Iyama
- a Division of Materials Chemistry, Graduate School of Engineering , Hokkaido University , Sapporo, Japan
| | - Hiroshi Kawabata
- a Division of Materials Chemistry, Graduate School of Engineering , Hokkaido University , Sapporo, Japan
| | - Hiroto Tachikawa
- a Division of Materials Chemistry, Graduate School of Engineering , Hokkaido University , Sapporo, Japan
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152
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McClure BA, Abrams ER, Rack JJ. Excited State Distortion in Photochromic Ruthenium Sulfoxide Complexes. J Am Chem Soc 2010; 132:5428-36. [DOI: 10.1021/ja9099399] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Beth Anne McClure
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701
| | - Eric R. Abrams
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701
| | - Jeffrey J. Rack
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701
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153
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Niu K, Zhao B, Sun Z, Lee SY. Analysis of femtosecond stimulated Raman spectroscopy of excited-state evolution in bacteriorhodopsin. J Chem Phys 2010; 132:084510. [DOI: 10.1063/1.3330818] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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154
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Briand J, Bräm O, Réhault J, Léonard J, Cannizzo A, Chergui M, Zanirato V, Olivucci M, Helbing J, Haacke S. Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch. Phys Chem Chem Phys 2010; 12:3178-87. [PMID: 20237707 DOI: 10.1039/b918603d] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Femtosecond fluorescence up-conversion, UV-Vis and IR transient absorption spectroscopy are used to study the photo-isomerization dynamics of a new type of zwitterionic photoswitch based on a N-alkylated indanylidene pyrroline Schiff base framework (ZW-NAIP). The system is biomimetic, as it mimics the photophysics of retinal, in coupling excited state charge translocation and isomerization. While the fluorescence lifetime is 140 fs, excited state absorption persists over 230 fs in the form of a vibrational wavepacket according to twisting of the isomerizing double bond. After a short "dark" time window in the UV-visible spectra, which we associate with the passage through a conical intersection (CI), the wavepacket appears on the ground state potential energy surface, as evidenced by the transient mid-IR data. This allows for a precise timing of the photoreaction all the way from the initial Franck-Condon region, through the CI and into both ground state isomers, until incoherent vibrational relaxation dominates the dynamics. The photo-reaction dynamics remarkably follow those observed for retinal in rhodopsin, with the additional benefit that in ZW-NAIP the conformational change reverses the zwitterion dipole moment direction. Last, the pronounced low-frequency coherences make these molecules ideal systems for investigating wavepacket dynamics in the vicinity of a CI and for coherent control experiments.
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Affiliation(s)
- Julien Briand
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg University, CNRS, IPCMS-DON, 23, rue du Loess, 67034 Strasbourg, France
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155
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Zgrablić G, Ricci M, Novello AM, Parmigiani F. Dependence of Photochemical Reactivity of the All-trans Retinal Protonated Schiff Base on the Solvent and the Excitation Wavelength. Photochem Photobiol 2010; 86:507-12. [DOI: 10.1111/j.1751-1097.2009.00697.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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156
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Gross R, Wolf MMN, Schumann C, Friedman N, Sheves M, Li L, Engelhard M, Trentmann O, Neuhaus HE, Diller R. Primary photoinduced protein response in bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 2010; 131:14868-78. [PMID: 19778046 DOI: 10.1021/ja904218n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential for the biological function of the light-driven proton pump, bacteriorhodopsin (BR), and the light sensor, sensory rhodopsin II (SRII), is the coupling of the activated retinal chromophore to the hosting protein moiety. In order to explore the dynamics of this process we have performed ultrafast transient mid-infrared spectroscopy on isotopically labeled BR and SRII samples. These include SRII in D(2)O buffer, BR in H(2)(18)O medium, SRII with (15)N-labeled protein, and BR with (13)C(14)(13)C(15)-labeled retinal chromophore. Via observed shifts of infrared difference bands after photoexcitation and their kinetics we provide evidence for nonchromophore bands in the amide I and the amide II region of BR and SRII. A band around 1550 cm(-1) is very likely due to an amide II vibration. In the amide I region, contributions of modes involving exchangeable protons and modes not involving exchangeable protons can be discerned. Observed bands in the amide I region of BR are not due to bending vibrations of protein-bound water molecules. The observed protein bands appear in the amide I region within the system response of ca. 0.3 ps and in the amide II region within 3 ps, and decay partially in both regions on a slower time scale of 9-18 ps. Similar observations have been presented earlier for BR5.12, containing a nonisomerizable chromophore (R. Gross et al. J. Phys. Chem. B 2009, 113, 7851-7860). Thus, the results suggest a common mechanism for ultrafast protein response in the artificial and the native system besides isomerization, which could be induced by initial chromophore polarization.
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Affiliation(s)
- Ruth Gross
- University of Kaiserslautern, Department of Physics, Erwin-Schrodinger-Strasse, 67663 Kaiserslautern, Germany
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157
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Verhoefen MK, Lenz MO, Amarie S, Klare JP, Tittor J, Oesterhelt D, Engelhard M, Wachtveitl J. Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide. Biochemistry 2009; 48:9677-83. [DOI: 10.1021/bi901197c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin O. Lenz
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sergiu Amarie
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johann P. Klare
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Jörg Tittor
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Dieter Oesterhelt
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Engelhard
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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158
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Schade M, Moretto A, Crisma M, Toniolo C, Hamm P. Vibrational Energy Transport in Peptide Helices after Excitation of C−D Modes in Leu-d10. J Phys Chem B 2009; 113:13393-7. [DOI: 10.1021/jp906363a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Schade
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Alessandro Moretto
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Marco Crisma
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Claudio Toniolo
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
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159
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Comparing photochemistry of n- and tert-butylamine all-trans retinal protonated Schiff-base: Effects of C N configurational inhomogeneity. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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160
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Mizuno M, Shibata M, Yamada J, Kandori H, Mizutani Y. Picosecond Time-Resolved Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin: Primary Protein Response to the Photoisomerization of Retinal. J Phys Chem B 2009; 113:12121-8. [DOI: 10.1021/jp904388w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Mikihiro Shibata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Junya Yamada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Hideki Kandori
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
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161
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Szymczak JJ, Barbatti M, Lischka H. Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process? J Phys Chem A 2009; 113:11907-18. [DOI: 10.1021/jp903329j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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162
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Sobotta C, Braun M, Tittor J, Oesterhelt D, Zinth W. Influence of the charge at D85 on the initial steps in the photocycle of bacteriorhodopsin. Biophys J 2009; 97:267-76. [PMID: 19580764 DOI: 10.1016/j.bpj.2009.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 03/25/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022] Open
Abstract
Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.
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Affiliation(s)
- Constanze Sobotta
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
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163
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Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime. Proc Natl Acad Sci U S A 2009; 106:10896-900. [PMID: 19564608 DOI: 10.1073/pnas.0904589106] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 x 10(16) photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration.
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164
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Andresen ER, Hamm P. Site-specific difference 2D-IR spectroscopy of bacteriorhodopsin. J Phys Chem B 2009; 113:6520-7. [PMID: 19358550 DOI: 10.1021/jp810397u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.
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Affiliation(s)
- Esben Ravn Andresen
- Physikalisch-Chemisches Institut, Universitat Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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165
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Becker HC, Kilså K. Size- and solvent-dependent kinetics for cis-trans isomerization in donor-acceptor systems. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 72:1014-1019. [PMID: 19196546 DOI: 10.1016/j.saa.2008.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 12/18/2008] [Indexed: 05/27/2023]
Abstract
We have investigated, using time-resolved and steady-state optical spectroscopy, the cis-trans isomerization dynamics in a series of charge transfer, donor-acceptor compounds. The number of donor (dithiafulvene) and acceptor (p-nitrophenyl) moieties as well as their spatial arrangement around a central ethynylethene core has been varied in a systematic way. All compounds in the series are weakly fluorescent. We show that the fluorescence spectrum red-shifts within a few picoseconds, a shift which occurs concurrently with a blue-shift of the transient absorption spectrum. The kinetics following the initial relaxation are in all cases multi-exponential, and the time constants correlate with molecular size and solvent viscosity. We interpret the data as a result of conformational change where the conjugation through the central double bond is broken upon excitation into the charge-transfer transition, and the time for rotation around this bond is dependent on the molecular interactions between solute and solvent.
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Affiliation(s)
- Hans-Christian Becker
- Department of Photochemistry and Molecular Sciences, Box 523, Uppsala University, SE-751 20 Uppsala, Sweden
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166
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Shim S, Dasgupta J, Mathies RA. Femtosecond Time-Resolved Stimulated Raman Reveals the Birth of Bacteriorhodopsin’s J and K Intermediates. J Am Chem Soc 2009; 131:7592-7. [DOI: 10.1021/ja809137x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sangdeok Shim
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Jyotishman Dasgupta
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Richard A. Mathies
- Department of Chemistry, University of California, Berkeley, California 94720
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167
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Gross R, Schumann C, Wolf MMN, Herbst J, Diller R, Friedman N, Sheves M. Ultrafast Protein Conformational Alterations in Bacteriorhodopsin and Its Locked Analogue BR5.12. J Phys Chem B 2009; 113:7851-60. [PMID: 19422251 DOI: 10.1021/jp810042f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruth Gross
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Schumann
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias M. N. Wolf
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Herbst
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rolf Diller
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Noga Friedman
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
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168
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Wang J, El-Sayed MA. Rapid Thermal Tuning of Chromophore Structure in Membrane Protein. J Phys Chem B 2009; 113:4184-6. [DOI: 10.1021/jp901560m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences and State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China, and Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Mostafa A. El-Sayed
- Beijing National Laboratory for Molecular Sciences and State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China, and Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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169
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Keal TW, Wanko M, Thiel W. Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0546-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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170
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Zgrablić G, Haacke S, Chergui M. Heterogeneity and Relaxation Dynamics of the Photoexcited Retinal Schiff Base Cation in Solution. J Phys Chem B 2009; 113:4384-93. [DOI: 10.1021/jp8077216] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goran Zgrablić
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Stefan Haacke
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
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171
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Dobryakov AL, Ernsting NP. Lineshapes for resonant impulsive stimulated Raman scattering with chirped pump and supercontinuum probe pulses. J Chem Phys 2009; 129:184504. [PMID: 19045411 DOI: 10.1063/1.3009221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular vibrational coherence from impulsive stimulated Raman (SR) scattering, as observed by broadband transient absorption spectroscopy, is treated within the well-known third-order perturbation formalism. Shaped femtosecond optical pulses are used for the pump and supercontinuum probe fields. Dephasing is assumed to be homogeneous in the Bloch approximation. A key step requires threefold time integration over response functions and electric fields. For well-separated pulses the triple integral can be solved analytically, resulting in lineshape functions. These allow to describe the SR signal through absorption/emission/dispersion profiles which are associated with the inherent contributions. A clear physical interpretation of the amplitude and phase of the oscillatory signal is thereby obtained, and a direct connection with the vibronic structure of the molecular system is provided. Calculations for model molecular systems illustrate the spectral dependence of the vibrational coherence seen, for example, with perylene in cyclohexane. The nonoscillatory and oscillatory parts of the transient absorption spectra are compared to each other. Observed mode beatings are explained.
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Affiliation(s)
- A L Dobryakov
- Department of Chemistry, Humboldt University, D-12489 Berlin, Germany.
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172
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Carroll EC, Hill MP, Madsen D, Malley KR, Larsen DS. A single source femtosecond-millisecond broadband spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:026102. [PMID: 19256678 DOI: 10.1063/1.3070516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Time-resolved measurement of population dynamics extending over femtosecond to millisecond time scales typically requires a combination of transient absorption techniques involving different laser systems and detection schemes. The spectrometer design presented here facilitates transient absorption measurements over 12 decades with a single ultrafast laser system by picking pump and probe pulses independently from the laser oscillator pulse train. Unamplified pulses seed a photonic crystal fiber to a supercontinuum probe source for spectrally resolved measurements. The utility of the system is demonstrated by measuring triplet state dynamics following photoexcitation of vitamin B(6) in aqueous solution.
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Affiliation(s)
- E C Carroll
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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173
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Dietzek B, Tarnovsky AN, Yartsev A. Visualizing overdamped wavepacket motion: Excited-state isomerization of pseudocyanine in viscous solvents. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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174
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Sun Z, Fu B, Zhang DH, Lee SY. Theoretical investigation of the direct observation of anharmonic coupling in CDCl3 in the time domain with femtosecond stimulated Raman scattering. J Chem Phys 2009; 130:044312. [DOI: 10.1063/1.3068709] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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175
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Siewertsen R, Renth F, Temps F, Sönnichsen F. Parallel ultrafast E–C ring closure and E–Z isomerisation in a photochromic furylfulgide studied by femtosecond time-resolved spectroscopy. Phys Chem Chem Phys 2009; 11:5952-61. [DOI: 10.1039/b821344e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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176
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Nakamura T, Takeuchi S, Shibata M, Demura M, Kandori H, Tahara T. Ultrafast Pump−Probe Study of the Primary Photoreaction Process in pharaonis Halorhodopsin: Halide Ion Dependence and Isomerization Dynamics. J Phys Chem B 2008; 112:12795-800. [DOI: 10.1021/jp803282s] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Takumi Nakamura
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Mikihiro Shibata
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Makoto Demura
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideki Kandori
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
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177
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Marquetand P, Nuernberger P, Brixner T, Engel V. Molecular dump processes induced by chirped laser pulses. J Chem Phys 2008; 129:074303. [DOI: 10.1063/1.2960581] [Citation(s) in RCA: 9] [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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178
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Szymczak JJ, Barbatti M, Lischka H. Mechanism of Ultrafast Photodecay in Restricted Motions in Protonated Schiff Bases: The Pentadieniminium Cation. J Chem Theory Comput 2008; 4:1189-99. [DOI: 10.1021/ct800148n] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
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Abstract
Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.
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Affiliation(s)
- Villy Sundström
- Department of Chemical Physics, Lund University, S-221 00 Lund, Sweden.
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180
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Backus EHG, Nguyen PH, Botan V, Pfister R, Moretto A, Crisma M, Toniolo C, Stock G, Hamm P. Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations. J Phys Chem B 2008; 112:9091-9. [DOI: 10.1021/jp711046e] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ellen H. G. Backus
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Phuong H. Nguyen
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Virgiliu Botan
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Rolf Pfister
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Alessandro Moretto
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Marco Crisma
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Claudio Toniolo
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Gerhard Stock
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
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181
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Wu Y, Zhong S, Ai X, Hu K, Zhang J. Ultrafast isomerization dynamics of retinal in bacteriorhodopsin as revealed by femtosecond absorption spectroscopy. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0283-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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182
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Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin. Biophys J 2008; 95:2402-14. [PMID: 18515390 DOI: 10.1529/biophysj.108.132175] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cell membrane of Salinibacter ruber contains xanthorhodopsin, a light-driven transmembrane proton pump with two chromophores: a retinal and the carotenoid, salinixanthin. Action spectra for transport had indicated that light absorbed by either is utilized for function. If the carotenoid is an antenna in this protein, its excited state energy has to be transferred to the retinal and should be detected in the retinal fluorescence. From fluorescence studies, we show that energy transfer occurs from the excited singlet S(2) state of salinixanthin to the S(1) state of the retinal. Comparison of the absorption spectrum with the excitation spectrum for retinal emission yields 45 +/- 5% efficiency for the energy transfer. Such high efficiency would require close proximity and favorable geometry for the two polyene chains, but from the heptahelical crystallographic structure of the homologous retinal protein, bacteriorhodopsin, it is not clear where the carotenoid can be located near the retinal. The fluorescence excitation anisotropy spectrum reveals that the angle between their transition dipole moments is 56 +/- 3 degrees . The protein accommodates the carotenoid as a second chromophore in a distinct binding site to harvest light with both extended wavelength and polarization ranges. The results establish xanthorhodopsin as the simplest biological excited-state donor-acceptor system for collecting light.
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183
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Terahertz radiation from bacteriorhodopsin reveals correlated primary electron and proton transfer processes. Proc Natl Acad Sci U S A 2008; 105:6888-93. [PMID: 18456840 DOI: 10.1073/pnas.0706336105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The kinetics of electrogenic events associated with the different steps of the light-induced proton pump of bacteriorhodopsin is well studied in a wide range of time scales by direct electric methods. However, the investigation of the fundamental primary charge translocation phenomena taking place in the functional energy conversion process of this protein, and in other biomolecular assemblies using light energy, has remained experimentally unfeasible because of the lack of proper detection technique operating in the 0.1- to 20-THz region. Here, we show that extending the concept of the familiar Hertzian dipole emission into the extreme spatial and temporal range of intramolecular polarization processes provides an alternative way to study ultrafast electrogenic events on naturally ordered biological systems. Applying a relatively simple experimental arrangement based on this idea, we were able to observe light-induced coherent terahertz radiation from bacteriorhodopsin with femtosecond time resolution. The detected terahertz signal was analyzed by numerical simulation in the framework of different models for the elementary polarization processes. It was found that the principal component of the terahertz emission can be well described by excited-state intramolecular electron transfer within the retinal chromophore. An additional slower process is attributed to the earliest phase of the proton pump, probably occurring by the redistribution of a H bond near the retinal. The correlated electron and proton translocation supports the concept, assigning a functional role to the light-induced sudden polarization in retinal proteins.
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184
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Initial reaction dynamics of proteorhodopsin observed by femtosecond infrared and visible spectroscopy. Biophys J 2008; 94:4796-807. [PMID: 18326639 DOI: 10.1529/biophysj.107.125484] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a comparative study using femtosecond pump/probe spectroscopy in the visible and infrared of the early photodynamics of solubilized proteorhodopsin (green absorbing variant) in D(2)O with deprotonated (pD 9.2) and protonated (pD 6.4) primary proton acceptor Asp-97. The vis-pump/vis-probe experiments show a kinetic isotope effect that is more pronounced for alkaline conditions, thus decreasing the previously reported pH-dependence of the primary reaction of proteorhodopsin in H(2)O. This points to a pH dependent H-bonding network in the binding pocket of proteorhodopsin, that directly influences the primary photo-induced dynamics. The vis-pump/IR-probe experiments were carried out in two different spectral regions and allowed to monitor the retinal C=C (1500 cm(-1)-1580 cm(-1)) and C=N stretching vibration as well as the amide I mode of the protein (1590 cm(-1)-1680 cm(-1)). Like the FTIR spectra of the K intermediate (PR(K)-PR difference spectra) in this spectral range, the kinetic parameters and also the quantum efficiency of photo-intermediate formation are found to be virtually independent of the pD value.
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185
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Biesso A, Qian W, El-Sayed MA. Gold nanoparticle plasmonic field effect on the primary step of the other photosynthetic system in nature, bacteriorhodopsin. J Am Chem Soc 2008; 130:3258-9. [PMID: 18290646 DOI: 10.1021/ja7099858] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arianna Biesso
- Georgia Institute of Technology, Department of Chemistry and Biochemistry 770 State Street, Atlanta, Georgia 30332, USA
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186
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Mockus N, Rabinovich D, Petersen J, Rack J. Femtosecond Isomerization in a Photochromic Molecular Switch. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200703677] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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187
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Mockus N, Rabinovich D, Petersen J, Rack J. Femtosecond Isomerization in a Photochromic Molecular Switch. Angew Chem Int Ed Engl 2008; 47:1458-61. [DOI: 10.1002/anie.200703677] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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188
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Mutagenic Analysis of Membrane Protein Functional Mechanisms: Bacteriorhodopsin as a Model Example. Methods Cell Biol 2008. [DOI: 10.1016/s0091-679x(07)84016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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189
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Koike K, Kawaguchi K, Yamato T. Stress tensor analysis of the protein quake of photoactive yellow protein. Phys Chem Chem Phys 2007; 10:1400-5. [PMID: 18309395 DOI: 10.1039/b714618c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important, as is the atomic description of the series of conformational changes associated with the photocycle. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42, suggesting that this atom is the focus of the protein quake of PYP. This is consistent with previous experimental observations.
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Affiliation(s)
- Kana Koike
- Graduate School of Science, Nagoya University, Furo-chos, Chikusa-ku, Nagoya, Japan
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190
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Akemann W, Laage D, Plaza P, Martin MM, Blanchard-Desce M. Photoinduced intramolecular charge transfer in push-pull polyenes: effects of solvation, electron-donor group, and polyenic chain length. J Phys Chem B 2007; 112:358-68. [PMID: 17997542 DOI: 10.1021/jp075418z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subpicosecond absorption spectroscopy is used to characterize the primary photoinduced processes in a class of push-pull polyenes bearing a julolidine end group as the electron donor and a diethylthiobarbituric acid end group as the electron acceptor. The excited-state decay time and relaxation pathway have been studied for four polyenes of increasing chain length (n = 2-5 double bonds) in aprotic solvents of different solvation time, polarity, and viscosity. Intramolecular charge transfer (ICT) leading to a transient state of cyanine-like structure (fully conjugated with no bond length alternation) is observed in all polar solvents at a solvent dependent rate, but the reaction is not observed in cyclohexane, a nonpolar solvent. In polar solvents, the reaction time increases with the average solvation time but remains slightly larger, except in the viscous solvent triacetin. These facts are interpreted as an indication that both solvent reorganization and internal restructuring are involved in the ICT-state formation. The observed photodynamics resemble those we previously found for another class of polyenes bearing a dibutylaniline group as the donor, including a similar charge-transfer rate in spite of the larger electron donor character of the julolidine group. This observation brings further support to the proposal that an intramolecular coordinate is involved in the charge-transfer reaction, possibly a torsional motion of the donor end group. On the other hand, relaxation of the ICT state leads to cis-trans isomerization or crossing to the triplet state, depending on the length of the polyenic chain. In dioxane, tetrahydrofuran, and triacetin, the ICT state of the shorter chains (n = 2, 3) relaxes to the isomer with a viscosity-dependent rate, while that of the longer ones (n = 4, 5) leads to the triplet state with a viscosity-independent rate, as expected. In acetonitrile, the ICT-state lifetime is generally much shorter. A change from photoisomerization to intersystem crossing at n = 4 is also proposed in this solvent, but the formation of a photoproduct at n = 2 is not clear. In cyclohexane, where the ICT state is not formed, the relaxation pathway of the initially excited state is found to lead to an isomer for n = 2. As in polar solvents, a change to intersystem crossing at n = 4 is proposed. The direct relaxation to the ground state found at n = 3 for the series bearing a dibutylaniline group is not observed with the julolidine group. The results clearly illustrate that photoinduced reaction trajectories in push-pull polyenes are controlled by the static and dynamic properties of the solvent, the chemical nature and size of the end groups, and the conjugated-chain length and flexibility.
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Affiliation(s)
- Walther Akemann
- UMR CNRS 8640, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
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191
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Bismuth O, Friedman N, Sheves M, Ruhman S. Photochemical dynamics of all-trans retinal protonated Schiff-base in solution: Excitation wavelength dependence. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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192
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Kobayashi T, Yabushita A, Saito T, Ohtani H, Tsuda M. Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization. Photochem Photobiol 2007; 83:363-8. [PMID: 17132067 DOI: 10.1562/2006-08-19-ir-1006] [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: 11/19/2022]
Abstract
By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.
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Affiliation(s)
- Takayoshi Kobayashi
- Department of Physics, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo, Japan.
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193
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Amsden JJ, Kralj JM, Chieffo LR, Wang X, Erramilli S, Spudich EN, Spudich JL, Ziegler LD, Rothschild KJ. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction. J Phys Chem B 2007; 111:11824-31. [PMID: 17880126 DOI: 10.1021/jp073490r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.
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Affiliation(s)
- Jason J Amsden
- Department of Physics, Boston University, Boston, MA 02215, USA
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194
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195
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Substituent-controlled photoisomerization in retinal chromophore models: Fluorinated and methoxy-substituted protonated Schiff bases. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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196
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McCamant DW, Kukura P, Mathies RA. Femtosecond stimulated Raman study of excited-state evolution in bacteriorhodopsin. J Phys Chem B 2007; 109:10449-57. [PMID: 16852266 PMCID: PMC1544036 DOI: 10.1021/jp050095x] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to examine the photoisomerization dynamics in the excited state of bacteriorhodopsin. Near-IR stimulated emission is observed in the FSRS probe window that decays with a 400-600-fs time constant. Additionally, dispersive vibrational lines appear at the locations of the ground-state vibrational frequencies and decay with a 260-fs time constant. The dispersive line shapes are caused by a nonlinear effect we term Raman initiated by nonlinear emission (RINE) that generates vibrational coherence on the ground-state surface. Theoretical expressions for the RINE line shapes are developed and used to fit the spectral and temporal evolution of the spectra. The rapid 260-fs decay of the RINE peak intensity, compared to the slower evolution of the stimulated emission, indicates that the excited-state population moves in approximately 260 fs to a region on the potential energy surface where the RINE signal is attenuated. This loss of RINE signal is best explained by structural evolution of the excited-state population along multiple low-frequency modes that carry the molecule out of the harmonic photochemically inactive Franck-Condon region and into the photochemically active geometry.
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Affiliation(s)
- David W McCamant
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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197
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Sun Z, Jin Z, Lu J, Zhang DH, Lee SY. Wave packet theory of dynamic stimulated Raman spectra in femtosecond pump-probe spectroscopy. J Chem Phys 2007; 126:174104. [PMID: 17492854 DOI: 10.1063/1.2715593] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The quantum theory for stimulated Raman spectroscopy from a moving wave packet using the third-order density matrix and polarization is derived. The theory applies, in particular, to the new technique of femtosecond broadband stimulated Raman spectroscopy (FSRS). In the general case, a femtosecond actinic pump pulse first prepares a moving wave packet on an excited state surface which is then interrogated with a coupled pair of picosecond Raman pump pulse and a femtosecond Raman probe pulse and the Raman gain in the direction of the probe pulse is measured. It is shown that the third-order polarization in the time domain, whose Fourier transform governs the Raman gain, is given simply by the overlap of a first-order wave packet created by the Raman pump on the upper electronic state with a second-order wave packet on the initial electronic state that is created by the coupling of the Raman pump and probe fields acting on the molecule. Calculations are performed on model potentials to illustrate and interpret the FSRS spectra.
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Affiliation(s)
- Zhigang Sun
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637616, Singapore
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198
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Abstract
The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.
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Affiliation(s)
- Benjamin G Levine
- Department of Chemistry, Beckman Institute, Center for Biophysics and Computational Biology, and Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801, USA.
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199
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Masciangioli T, Devanathan S, Cusanovich MA, Tollin G, El-Sayed MA. Probing the Primary Event in the Photocycle of Photoactive Yellow Protein Using Photochemical Hole-burning Technique¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720639ptpeit2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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200
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Sun M, Ding Y, Cui G, Liu Y. S1 and S2 Excited States of Gas-Phase Schiff-Base Retinal Chromophores: A Time-Dependent Density Functional Theoretical Investigation. J Phys Chem A 2007; 111:2946-50. [PMID: 17388381 DOI: 10.1021/jp0709757] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In concert with the recent photoabsorption experiments of gas-phase Schiff-base retinal chromophores (Nielsen et al. Phys. Rev. Lett. 2006, 96, 018304), quantum chemical calculations using time-dependent density functional theory coupled with different functionals and under the Tamm-Dancoff approximation were made on the first two excited states (S1 and S2) of two retinal chromophores: 11-cis and all-trans protonated Schiff bases. The calculated vertical excitation energies (Tv) and oscillator strengths (f) are consistent with the experimental absorption bands. The experimentally observed phenomenon that the transition dipole moment (mu) of S2 is much smaller that of S1 was interpreted by 3D representation of transition densities. The different optical behaviors (linear and nonlinear optical responds) of the excited states were investigated by considering different strengths of external electric fields.
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Affiliation(s)
- Mengtao Sun
- National Laboratory for Condensed State Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603-146, Beijing 100080, China.
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