1
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Guo Y, Feng M, Kuang Z, Abeywickrama CS, Pang Y, Xia A. Unveiling Solvation Dynamics of Excited and Ground States via Ultrafast Pump-Dump-Probe Spectroscopy. J Phys Chem B 2023; 127:7764-7771. [PMID: 37656037 DOI: 10.1021/acs.jpcb.3c05450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The conventional ultrafast pump-probe spectroscopy has primarily focused on examining the formation and decay of the excited state intermediates, but it is very difficult to detect those intermediates while the formation is slow and dissipation is much fast because of the limited concentration during the intrinsic photocycle. To address this issue, a multipulse ultrafast pump-dump-probe spectroscopy was employed to generate and probe the short-lived ground state intermediates (GSIs) in an electronic push-pull pyrene derivative (EPP). This particular derivative undergoes planarized intramolecular charge transfer (PICT) in the excited state upon initial femtosecond pulse excitation. After applying the dump pulse once the PICT was formed, the blue-shifted transient absorption GSIs with the ground state dynamics of the structure recovery was directly observed. It is found that GSIs undergo slower reorganization than the PICT formation in the excited state of EPP due to the solvation effect with different dipole moments of ground states and excited states. These findings provide a comprehensive understanding of the full photocycle dynamics of both the ground and excited states, shedding light on the presence of hidden ground state behaviors.
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Affiliation(s)
- Yuanyuan Guo
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Minjun Feng
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Zhuoran Kuang
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
| | | | - Yi Pang
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Andong Xia
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
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2
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Boichenko AN, Bochenkova AV. Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution. J Chem Theory Comput 2023. [PMID: 37146177 DOI: 10.1021/acs.jctc.2c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We introduce a new methodology for calculating vertical electron detachment energies (VDEs) of biologically relevant chromophores in their deprotonated anionic forms in aqueous solution. It combines a large-scale mixed DFT/EFP/MD approach with the high-level multireference perturbation theory XMCQDPT2 and the Effective Fragment Potential (EFP) method. The methodology includes a multiscale flexible treatment of inner (∼1000 water molecules) and outer (∼18000 water molecules) water shells around a charged solute, capturing both the effects of specific solvation and the properties of bulk water. VDEs are calculated as a function of system size for getting a converged value at the DFT/EFP level of theory. The XMCQDPT2/EFP approach, adapted for calculating VDEs, supports the DFT/EFP results. When corrected for a solvent polarization contribution, the XMCQDPT2/EFP method yields the most accurate estimate to date of the first VDE for aqueous phenolate (7.3 ± 0.1 eV), which agrees well with liquid-jet X-ray photoelectron spectroscopy data (7.1 ± 0.1 eV). We show that the geometry of the water shell and its size are essential for accurate VDE calculations of aqueous phenolate and its biologically relevant derivatives. By simulating photoelectron spectra of aqueous phenolate upon two-photon excitation at wavelengths resonant with the S0 → S1 transition, we also provide interpretation of recent multiphoton UV liquid-microjet photoelectron spectroscopy experiments. We show that its first VDE is consistent with our estimate of 7.3 eV, when experimental two-photon binding energies are corrected for the resonant contribution.
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Affiliation(s)
- Anton N Boichenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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3
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Mix LT, Hara M, Fuzell J, Kumauchi M, Kaledhonkar S, Xie A, Hoff WD, Larsen DS. Not All Photoactive Yellow Proteins Are Built Alike: Surprises and Insights into Chromophore Photoisomerization, Protonation, and Thermal Reisomerization of the Photoactive Yellow Protein Isolated from Salinibacter ruber. J Am Chem Soc 2021; 143:19614-19628. [PMID: 34780163 DOI: 10.1021/jacs.1c08910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We demonstrate that the Halorhodospira halophila (Hhal) photoactive yellow protein (PYP) is not representative of the greater PYP family. The photodynamics of the PYP isolated from Salinibacter ruber (Srub) is characterized with a comprehensive range of spectroscopic techniques including ultrafast transient absorption, photostationary light titrations, Fourier transform infrared, and cryokinetics spectroscopies. We demonstrate that the dark-adapted pG state consists of two subpopulations differing in the protonation state of the chromophore and that both are photoactive, with the protonated species undergoing excited-state proton transfer. However, the primary I0 photoproduct observed in the Hhal PYP photocycle is absent in the Srub PYP photodynamics, which indicates that this intermediate, while important in Hhal photodynamics, is not a critical intermediate in initiating all PYP photocycles. The excited-state lifetime of Srub PYP is the longest of any PYP resolved to date (∼30 ps), which we ascribe to the more constrained chromophore binding pocket of Srub PYP and the absence of the critical Arg52 residue found in Hhal PYP. The final stage of the Srub PYP photocycle involves the slowest known thermal dark reversion of a PYP (∼40 min vs 350 ms in Hhal PYP). This property allowed the characterization of a pH-dependent equilibrium between the light-adapted pB state with a protonated cis chromophore and a newly resolved pG' intermediate with a deprotonated cis chromophore and pG-like protein conformation. This result demonstates that protein conformational changes and chromophore deprotonation precede chromophore reisomerization during the thermal recovery of the PYP photocycle.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jack Fuzell
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Sandip Kaledhonkar
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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4
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
- Correspondence:
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5
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Mustalahti S, Morozov D, Luk HL, Pallerla RR, Myllyperkiö P, Pettersson M, Pihko PM, Groenhof G. Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked. J Phys Chem Lett 2020; 11:2177-2181. [PMID: 32109070 PMCID: PMC7145348 DOI: 10.1021/acs.jpclett.0c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Photoactivation in the Photoactive Yellow Protein, a bacterial blue-light photoreceptor, proceeds via photoisomerization of the double C═C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double-bond photoisomerization, the isolated chromophore and many of its analogues can isomerize around a single C-C bond as well. Whereas double-bond photoisomerization has been observed with X-ray crystallography, experimental evidence of single-bond photoisomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring, and carried out transient absorption spectroscopy experiments in combination with nonadiabatic molecular dynamics simulations to reveal that the locked chromophore isomerizes around the single bond upon photoactivation. Our work thus provides experimental evidence of single-bond photoisomerization in a photoactive yellow protein chromophore analogue and suggests that photoisomerization is not restricted to the double bonds in conjugated systems. This insight may be useful for designing light-driven molecular switches or motors.
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6
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Maiuri M, Garavelli M, Cerullo G. Ultrafast Spectroscopy: State of the Art and Open Challenges. J Am Chem Soc 2019; 142:3-15. [DOI: 10.1021/jacs.9b10533] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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7
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van Thor JJ. Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:050901. [PMID: 31559317 PMCID: PMC6759419 DOI: 10.1063/1.5110685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/29/2019] [Indexed: 05/02/2023]
Abstract
Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.
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Affiliation(s)
- Jasper J. van Thor
- Molecular Biophysics, Imperial College London, London SW7 2AZ, United Kingdom
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8
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Zhao L, Liu J, Zhou P. Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:203-211. [PMID: 30544011 DOI: 10.1016/j.saa.2018.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S2 state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S1 state decay process. In contrast, for the decay process of the S2 state, an ultrafast transition from the S2 to the S1 state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S2 to S0 is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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9
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Tyson AL, Verlet JRR. On the Mechanism of Phenolate Photo-Oxidation in Aqueous Solution. J Phys Chem B 2019; 123:2373-2379. [PMID: 30768899 DOI: 10.1021/acs.jpcb.8b11766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photo-oxidation dynamics following ultraviolet (257 nm) excitation of the phenolate anion in aqueous solution is studied using broadband (550-950 nm) transient absorption spectroscopy. A clear signature from electron ejection is observed on a sub-picosecond timescale, followed by cooling dynamics and the decay of the signal to a constant offset that is assigned to the hydrated electron. The dynamics are compared to the charge-transfer-to-solvent dynamics from iodide at the same excitation wavelength and are shown to be very similar to these. This is in stark contrast to a previous study on the phenolate anion excited at 266 nm, in which electron emission was observed over longer timescales. We account for the differences using a simple Marcus picture for electron emission in which the electron tunneling rate depends sensitively on the initial excitation energy. After electron emission, a contact pair is formed which undergoes geminate recombination and dissociation to form the free hydrated electron at rates that are slightly faster than those for the iodide system. Our results show that, although the underlying chemical physics of electron emission differs between iodide and phenolate, the observed dynamics can appear very similar.
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Affiliation(s)
| | - Jan R R Verlet
- Department of Chemistry , Durham University , Durham DH1 3LE , U.K
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10
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Koga M, Yoneda Y, Sotome H, Miyasaka H. Ionization dynamics of a phenylenediamine derivative in solutions as revealed by femtosecond simultaneous and stepwise two-photon excitation. Phys Chem Chem Phys 2019; 21:2889-2898. [PMID: 30451254 DOI: 10.1039/c8cp06530f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Femtosecond transient absorption spectroscopy with off-resonant simultaneous and resonant stepwise two-photon excitation methods were applied to the direct observation of photoionization dynamics of a phenylenediamine derivative in n-hexane, ethanol and acetonitrile solutions. Upon the selective excitation of the solute via the off-resonant two-photon excitation to the energy level almost equivalent with the ionization potential in the gas phase, rapid appearance of the radical cation (within ca. 100-200 fs) was observed in polar and nonpolar solutions. On the other hand, in the case where the excited energy level from the ground state is 0.8 eV lower than the ionization potential in the gas phase, the radical cation appears only in polar solutions in sub-ps to ps time scales, indicating that the photoionization does not occur directly from the highly electronically excited state even in the polar solution. Comparison of the dynamics between ethanol and acetonitrile solutions strongly suggested that the solvation process of the precursor species leading to the ionization took a crucial role in the electron ejection process with lower energy in polar solutions.
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Affiliation(s)
- Masafumi Koga
- Division of Frontier Materials Science and Center for Advanced Interdisciplinary Research, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
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11
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
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12
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Henley A, Patel AM, Parkes MA, Anderson JC, Fielding HH. Role of Photoisomerization on the Photodetachment of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2018; 122:8222-8228. [PMID: 30234981 DOI: 10.1021/acs.jpca.8b07770] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photocycle of photoactive yellow protein (PYP) is initiated by a photoinduced trans-cis isomerization around a C═C bond in the chromophore that lies at the heart of the protein; however, in addition to the desired photochemical pathway, the chromophore can undergo competing electronic relaxation processes. Here we combine gas-phase anion photoelectron spectroscopy and quantum chemistry calculations to investigate how locking the C═C bond in the chromophore controls the competition between these electronic relaxation processes following photoexcitation in the range 400-310 nm. We find evidence to suggest that preventing trans-cis isomerization effectively turns off internal conversion to the ground electronic state and enhances electron emission from the first electronically excited state.
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Affiliation(s)
- Alice Henley
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Anand M Patel
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Michael A Parkes
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - James C Anderson
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Helen H Fielding
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
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13
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Kuang Z, Guo Q, Wang X, Song H, Maroncelli M, Xia A. Ultrafast Ground-State Intramolecular Proton Transfer in Diethylaminohydroxyflavone Resolved with Pump-Dump-Probe Spectroscopy. J Phys Chem Lett 2018; 9:4174-4181. [PMID: 29991264 DOI: 10.1021/acs.jpclett.8b01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
4'- N, N-Diethylamino-3-hydroxyflavone (DEAHF), due to excited-state intramolecular proton transfer (ESIPT) reaction, exhibits two solvent-dependent emission bands. Because of the slow formation and fast decay of the ground-state tautomer, its population does not accumulate enough for its detection during the normal photocycle. As a result, the details of the ground-state intramolecular proton-transfer (GSIPT) reaction have remained unknown. The present work uses femtosecond pump-dump-probe spectroscopy to prepare the short-lived ground-state tautomer and track this GSIPT process in solution. By simultaneously measuring femtosecond pump-probe and pump-dump-probe spectra, ultrafast kinetics of the ESIPT and GSIPT reactions are obtained. The GSIPT reaction is shown to be a solvent-dependent irreversible two-state process in two solvents, with estimated time constants of 1.7 ps in toluene and 10 ps in the more polar tetrahydrofuran. These results are of great value in both fully describing the photocycle of this four-level proton transfer molecule and for providing a deeper understanding of dynamical solvent effects on tautomerization.
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Affiliation(s)
- Zhuoran Kuang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Qianjin Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
| | - Xian Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Hongwei Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Mark Maroncelli
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Andong Xia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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14
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Henley A, Diveky ME, Patel AM, Parkes MA, Anderson JC, Fielding HH. Electronic structure and dynamics of torsion-locked photoactive yellow protein chromophores. Phys Chem Chem Phys 2017; 19:31572-31580. [PMID: 29165495 DOI: 10.1039/c7cp06950b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photocycle of photoactive yellow protein (PYP) begins with small-scale torsional motions of the chromophore leading to large-scale movements of the protein scaffold triggering a biological response. The role of single-bond torsional molecular motions of the chromophore in the initial steps of the PYP photocycle are not fully understood. Here, we employ anion photoelectron spectroscopy measurements and quantum chemistry calculations to investigate the electronic relaxation dynamics following photoexcitation of four model chromophores, para-coumaric acid, its methyl ester, and two analogues with aliphatic bridges hindering torsional motions around the single bonds adjacent to the alkene group. Following direct photoexcitation of S1 at 400 nm, we find that both single bond rotations play a role in steering the PYP chromophore through the S1/S0 conical intersection but that rotation around the single bond between the alkene moiety and the phenoxide group is particularly important. Following photoexcitation of higher lying electronic states in the range 346-310 nm, we find that rotation around the single bond between the alkene and phenoxide groups also plays a key role in the electronic relaxation from higher lying states to the S1 state. These results have potential applications in tuning the photoresponse of photoactive proteins and materials with chromophores based on PYP.
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Matus E Diveky
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Anand M Patel
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - James C Anderson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Helen H Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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15
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Milanese JM, Provorse MR, Alameda E, Isborn CM. Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. J Chem Theory Comput 2017; 13:2159-2171. [DOI: 10.1021/acs.jctc.7b00159] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel M. Milanese
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Enrique Alameda
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
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16
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Horbury MD, Baker LA, Rodrigues ND, Quan WD, Stavros VG. Photoisomerization of ethyl ferulate: A solution phase transient absorption study. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Redeckas K, Voiciuk V, Zigmantas D, Hiller RG, Vengris M. Unveiling the excited state energy transfer pathways in peridinin-chlorophyll a- protein by ultrafast multi-pulse transient absorption spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:297-307. [DOI: 10.1016/j.bbabio.2017.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/15/2017] [Accepted: 01/31/2017] [Indexed: 11/27/2022]
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18
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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19
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Ahamed G, Batuta S, Ghosh D, Begum NA, Mandal D. Photophysical studies on a photoactive yellow protein fluorophore analog with the 4-Hydroxy group replaced by 4-Dimethylamino group. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.11.017] [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]
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20
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Mix LT, Hara M, Rathod R, Kumauchi M, Hoff WD, Larsen DS. Noncanonical Photocycle Initiation Dynamics of the Photoactive Yellow Protein (PYP) Domain of the PYP-Phytochrome-Related (Ppr) Photoreceptor. J Phys Chem Lett 2016; 7:5212-5218. [PMID: 27973895 DOI: 10.1021/acs.jpclett.6b02253] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The photoactive yellow protein (PYP) from Halorhodospira halophila (Hhal) is a bacterial photoreceptor and model system for exploring functional protein dynamics. We report ultrafast spectroscopy experiments that probe photocycle initiation dynamics in the PYP domain from the multidomain PYP-phytochrome-related photoreceptor from Rhodospirillum centenum (Rcen). As with Hhal PYP, Rcen PYP exhibits similar excited-state dynamics; in contrast, Rcen PYP exhibits altered photoproduct ground-state dynamics in which the primary I0 intermediate as observed in Hhal PYP is absent. This property is attributed to a tighter, more sterically constrained binding pocket around the p-coumaric acid chromophore due to a change in the Rcen PYP protein structure that places Phe98 instead of Met100 in contact with the chromophore. Hence, the I0 state is not a necessary step for the initiation of productive PYP photocycles and the ubiquitously studied Hhal PYP may not be representative of the broader PYP family of photodynamics.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Rachana Rathod
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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21
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Mix LT, Kirpich J, Kumauchi M, Ren J, Vengris M, Hoff WD, Larsen DS. Bifurcation in the Ultrafast Dynamics of the Photoactive Yellow Proteins from Leptospira biflexa and Halorhodospira halophila. Biochemistry 2016; 55:6138-6149. [DOI: 10.1021/acs.biochem.6b00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- L. Tyler Mix
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Julia Kirpich
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jie Ren
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Mikas Vengris
- Faculty
of Physics, Laser Research Centre, Vilnius University, Sauletekio
10, LT-10233 Vilnius, Lithuania
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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22
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Hutchison CD, Kaucikas M, Tenboer J, Kupitz C, Moffat K, Schmidt M, van Thor JJ. Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Pande K, Hutchison CDM, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Šrajer V, Henning R, Spence JCH, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt M. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 2016; 352:725-9. [PMID: 27151871 DOI: 10.1126/science.aad5081] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 04/05/2016] [Indexed: 11/02/2022]
Abstract
A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
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Affiliation(s)
- Kanupriya Pande
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Andy Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Josef S Robinson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason Tenboer
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Shibom Basu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jennifer Brayshaw
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Chelsie Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse D Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Markus Metz
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas D Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gihan Ketawala
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J van Thor
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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24
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Parkes MA, Phillips C, Porter MJ, Fielding HH. Controlling electron emission from the photoactive yellow protein chromophore by substitution at the coumaric acid group. Phys Chem Chem Phys 2016; 18:10329-36. [PMID: 27025529 DOI: 10.1039/c6cp00565a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding how the interactions between a chromophore and its surrounding protein control the function of a photoactive protein remains a challenge. Here, we present the results of photoelectron spectroscopy measurements and quantum chemistry calculations aimed at investigating how substitution at the coumaryl tail of the photoactive yellow protein chromophore controls competing relaxation pathways following photoexcitation of isolated chromophores in the gas phase with ultraviolet light in the range 350-315 nm. The photoelectron spectra are dominated by electrons resulting from direct detachment and fast detachment from the 2(1)ππ* state but also have a low electron kinetic energy component arising from autodetachment from lower lying electronically excited states or thermionic emission from the electronic ground state. We find that substituting the hydrogen atom of the carboxylic acid group with a methyl group lowers the threshold for electron detachment but has very little effect on the competition between the different relaxation pathways, whereas substituting with a thioester group raises the threshold for electron detachment and appears to 'turn off' the competing electron emission processes from lower lying electronically excited states. This has potential implications in terms of tuning the light-induced electron donor properties of photoactive yellow protein.
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Affiliation(s)
- Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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25
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García-Prieto FF, Muñoz-Losa A, Luz Sánchez M, Elena Martín M, Aguilar MA. Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore. Phys Chem Chem Phys 2016; 18:27476-27485. [DOI: 10.1039/c6cp03541h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.
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Affiliation(s)
| | - Aurora Muñoz-Losa
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - M. Luz Sánchez
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
| | - M. Elena Martín
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
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26
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Fudim R, Mehlhorn J, Berthold T, Weber S, Schleicher E, Kennis JTM, Mathes T. Photoinduced formation of flavin radicals in BLUF domains lacking the central glutamine. FEBS J 2015; 282:3161-74. [DOI: 10.1111/febs.13297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Roman Fudim
- Institut für Biologie/Experimentelle Biophysik; Humboldt Universität zu Berlin; Berlin Germany
| | - Jennifer Mehlhorn
- Institut für Biologie/Experimentelle Biophysik; Humboldt Universität zu Berlin; Berlin Germany
| | - Thomas Berthold
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Freiburg Germany
| | - Stefan Weber
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS); Albert-Ludwigs-Universität Freiburg; Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Freiburg Germany
- Inorganic Chemistry Laboratory; University of Oxford; UK
| | - John T. M. Kennis
- Biophysics Section; Department of Physics and Astronomy; Faculty of Sciences; VU University; Amsterdam The Netherlands
| | - Tilo Mathes
- Institut für Biologie/Experimentelle Biophysik; Humboldt Universität zu Berlin; Berlin Germany
- Biophysics Section; Department of Physics and Astronomy; Faculty of Sciences; VU University; Amsterdam The Netherlands
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27
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Mooney CRS, Parkes MA, Iskra A, Fielding HH. Controlling Radical Formation in the Photoactive Yellow Protein Chromophore. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Mooney CRS, Parkes MA, Iskra A, Fielding HH. Controlling Radical Formation in the Photoactive Yellow Protein Chromophore. Angew Chem Int Ed Engl 2015; 54:5646-9. [DOI: 10.1002/anie.201500549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 11/05/2022]
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29
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Zhang Y, Dood J, Beckstead AA, Li XB, Nguyen KV, Burrows CJ, Improta R, Kohler B. Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine. J Phys Chem B 2015; 119:7491-502. [PMID: 25660103 DOI: 10.1021/jp511220x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Femtosecond time-resolved IR spectroscopy is used to investigate the excited-state dynamics of a dinucleotide containing an 8-oxoguanine anion at the 5'-end and neutral adenine at the 3'-end. UV excitation of the dinucleotide transfers an electron from deprotonated 8-oxoguanine to its π-stacked neighbor adenine in less than 1 ps, generating a neutral 8-oxoguanine radical and an adenine radical anion. These species are identified by the excellent agreement between the experimental and calculated IR difference spectra. The quantum efficiency of this ultrafast charge shift reaction approaches unity. Back electron transfer from the adenine radical anion to the 8-oxguanine neutral radical occurs in 9 ps, or approximately 6 times faster than between the adenine radical anion and the 8-oxoguanine radical cation (Zhang, Y. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 11612-11617). The large asymmetry in forward and back electron transfer rates is fully rationalized by semiclassical nonadiabatic electron transfer theory. Forward electron transfer is ultrafast because the driving force is nearly equal to the reorganization energy, which is estimated to lie between 1 and 2 eV. Back electron transfer is highly exergonic and takes place much more slowly in the Marcus inverted region.
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Affiliation(s)
- Yuyuan Zhang
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Jordan Dood
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ashley A Beckstead
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Xi-Bo Li
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Khiem V Nguyen
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Cynthia J Burrows
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Roberto Improta
- §CNR-Consiglio Nazionale delle Ricerche Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, 80136 Napoli, Italy
| | - Bern Kohler
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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30
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Vegh RB, Bloch DA, Bommarius AS, Verkhovsky M, Pletnev S, Iwaï H, Bochenkova AV, Solntsev KM. Hidden photoinduced reactivity of the blue fluorescent protein mKalama1. Phys Chem Chem Phys 2015; 17:12472-85. [DOI: 10.1039/c5cp00887e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report a complete photocycle of the blue fluorescent protein exhibiting two delayed branches coupled to hidden proton transfer events.
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Affiliation(s)
- Russell B. Vegh
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Dmitry A. Bloch
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Andreas S. Bommarius
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Michael Verkhovsky
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Sergei Pletnev
- Synchrotron Radiation Research Section
- Macromolecular Crystallography Laboratory
- National Cancer Institute
- Argonne
- USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | | | - Kyril M. Solntsev
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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31
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Pepino AJ, Burgos Paci MA, Peláez WJ, Argüello GA. An experimental and theoretical study of the photoisomerization and thermal reversion on 5-arylmethylene-2-thioxoimidazolidin-4-one. Phys Chem Chem Phys 2015; 17:12927-34. [DOI: 10.1039/c4cp04748f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unraveling the photochemical behaviour of the GFP chromophore has attracted widespread attention among scientists. Results for a new chromophore analog are presented.
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Affiliation(s)
- A. J. Pepino
- INFIQC-Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- UNC
- Córdoba
- Argentina
| | - M. A. Burgos Paci
- INFIQC-Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- UNC
- Córdoba
- Argentina
| | - W. J. Peláez
- INFIQC-Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- UNC
- Córdoba
- Argentina
| | - G. A. Argüello
- INFIQC-Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- UNC
- Córdoba
- Argentina
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32
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Kee TW. Femtosecond Pump-Push-Probe and Pump-Dump-Probe Spectroscopy of Conjugated Polymers: New Insight and Opportunities. J Phys Chem Lett 2014; 5:3231-40. [PMID: 26276338 DOI: 10.1021/jz501549h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Conjugated polymers are an important class of soft materials that exhibit a wide range of applications. The excited states of conjugated polymers, often referred to as excitons, can either deactivate to yield the ground state or dissociate in the presence of an electron acceptor to form charge carriers. These interesting properties give rise to their luminescence and the photovoltaic effect. Femtosecond spectroscopy is a crucial tool for studying conjugated polymers. Recently, more elaborate experimental configurations utilizing three optical pulses, namely, pump-push-probe and pump-dump-probe, have been employed to investigate the properties of excitons and charge-transfer states of conjugated polymers. These studies have revealed new insight into femtosecond torsional relaxation and detrapping of bound charge pairs of conjugated polymers. This Perspective highlights (1) the recent achievements by several research groups in using pump-push-probe and pump-dump-probe spectroscopy to study conjugated polymers and (2) future opportunities and potential challenges of these techniques.
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Affiliation(s)
- Tak W Kee
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
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33
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Zhu J, Vreede J, Hospes M, Arents J, Kennis JTM, van Stokkum IHM, Hellingwerf KJ, Groot ML. Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield. J Phys Chem B 2014; 119:2372-83. [DOI: 10.1021/jp506785q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingyi Zhu
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | | | | | - John T. M. Kennis
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | - Marie Louise Groot
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. Faraday Discuss 2014; 171:439-55. [PMID: 25415305 DOI: 10.1039/c4fd00011k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Femtosecond time resolved pump-probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63 crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a 'quasi-cw' approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the 'quasi-cw' rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.
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Affiliation(s)
- Jasper J van Thor
- Imperial College London, Division of Molecular Biosciences, South Kensington Campus, London SW7 2AZ, UK.
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Redeckas K, Voiciuk V, Steponavičiu̅tė R, Martynaitis V, Šačkus A, Vengris M. Optically Controlled Molecular Switching of an Indolobenzoxazine-Type Photochromic Compound. J Phys Chem A 2014; 118:5642-51. [DOI: 10.1021/jp505723q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kipras Redeckas
- Quantum
Electronics Department, Vilnius University, Saulėtekio 10, LT-10223 Vilnius, Lithuania
| | - Vladislava Voiciuk
- Quantum
Electronics Department, Vilnius University, Saulėtekio 10, LT-10223 Vilnius, Lithuania
| | - Rasa Steponavičiu̅tė
- Department
of Organic Chemistry, Kaunas University of Technology, Radvilėnų
19, LT-50254 Kaunas, Lithuania
| | - Vytas Martynaitis
- Department
of Organic Chemistry, Kaunas University of Technology, Radvilėnų
19, LT-50254 Kaunas, Lithuania
| | - Algirdas Šačkus
- Department
of Organic Chemistry, Kaunas University of Technology, Radvilėnų
19, LT-50254 Kaunas, Lithuania
| | - Mikas Vengris
- Quantum
Electronics Department, Vilnius University, Saulėtekio 10, LT-10223 Vilnius, Lithuania
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36
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Gottlieb SM, Kim PW, Rockwell NC, Hirose Y, Ikeuchi M, Lagarias JC, Larsen DS. Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon. Biochemistry 2013; 52:8198-208. [DOI: 10.1021/bi400946q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean M. Gottlieb
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Nathan C. Rockwell
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Yuu Hirose
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Masahiko Ikeuchi
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
- Department
of Life Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - J. Clark Lagarias
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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37
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Song SH, Madsen D, van der Steen JB, Pullman R, Freer LH, Hellingwerf KJ, Larsen DS. Primary Photochemistry of the Dark- and Light-Adapted States of the YtvA Protein from Bacillus subtilis. Biochemistry 2013; 52:7951-63. [DOI: 10.1021/bi4012258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sang-Hun Song
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dorte Madsen
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jeroen B. van der Steen
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences
(SILS), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Robert Pullman
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Lucy H. Freer
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Klaas J. Hellingwerf
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences
(SILS), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Delmar S. Larsen
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
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38
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Naseem S, Laurent AD, Carroll EC, Vengris M, Kumauchi M, Hoff WD, Krylov AI, Larsen DS. Photo-isomerization upshifts the pKa of the Photoactive Yellow Protein chromophore to contribute to photocycle propagation. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Mendonça L, Hache F, Changenet-Barret P, Plaza P, Chosrowjan H, Taniguchi S, Imamoto Y. Ultrafast Carbonyl Motion of the Photoactive Yellow Protein Chromophore Probed by Femtosecond Circular Dichroism. J Am Chem Soc 2013; 135:14637-43. [DOI: 10.1021/ja404503q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lucille Mendonça
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | - François Hache
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | | | - Pascal Plaza
- Ecole Normale Supérieure,
Département de Chimie, UMR 8640 CNRS-ENS-UPMC, 24 rue Lhomond,
75005 Paris, France
| | - Haik Chosrowjan
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seiji Taniguchi
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasushi Imamoto
- Department
of Biophysics, Graduate School of Sciences, Kyoto University, Kyoto 6068502, Japan
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40
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Kim PW, Rockwell NC, Freer LH, Chang CW, Martin SS, Lagarias JC, Larsen DS. Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations. J Phys Chem Lett 2013; 4:2605-2609. [PMID: 24143267 PMCID: PMC3798021 DOI: 10.1021/jz401443q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ultrafast mechanisms underlying the initial photoisomerization (Pr → Lumi-R) in the forward reaction of the cyanobacterial photoreceptor Cph1 were explored with multipulse pump-dump-probe transient spectroscopy. A recently postulated multi-population model was used to fit the transient pump-dump-probe and dump-induced depletion signals. We observed dump-induced depletion of the Lumi-R photoproduct, demonstrating that photoisomerization occurs via evolution on both the excited- and ground-state electronic surfaces. Excited-state equilibrium was not observed, as shown via the absence of a dump-induced excited-state "Le Châtelier redistribution" of excited-state populations. The importance of incorporating the inhomogeneous dynamics of Cph1 in interpreting measured transient data is discussed.
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Affiliation(s)
- Peter W. Kim
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Lucy H. Freer
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Che-Wei Chang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
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41
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Chang CW, Gottlieb SM, Kim PW, Rockwell NC, Lagarias JC, Larsen DS. Reactive Ground-State Pathways Are Not Ubiquitous in Red/Green Cyanobacteriochromes. J Phys Chem B 2013; 117:11229-38. [DOI: 10.1021/jp402112u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Che-Wei Chang
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
| | - Sean M. Gottlieb
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
| | - Peter W. Kim
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
| | - Nathan C. Rockwell
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
| | - J. Clark Lagarias
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
| | - Delmar S. Larsen
- Department of Chemistry and ‡Department of
Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California
95616
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42
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Vengris M, Larsen DS, Valkunas L, Kodis G, Herrero C, Gust D, Moore T, Moore A, van Grondelle R. Separating annihilation and excitation energy transfer dynamics in light harvesting systems. J Phys Chem B 2013; 117:11372-82. [PMID: 23662680 DOI: 10.1021/jp403301c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The dependence of excitation energy transfer kinetics on the electronic state of the acceptor (ground vs excited) has been resolved with a novel multipulse prePump-Pump-Probe spectroscopy. The primary energy transfer and annihilation dynamics in two model light-harvesting systems were explored: an artificially synthesized carotenoid-zinc-phthalocyanine dyad and a naturally occurring light-harvesting peridinin-chlorophyll protein complex from Amphidinium carterae. Both systems use carotenoid as the primary excitation energy donor with porphyrin chromophores as the acceptor molecules. The prePump-Pump-Probe transient signals were analyzed with Monte Carlo modeling to explicitly address the underlying step-by-step kinetics involved in both excitation migration and annihilation processes. Both energy transfer and annihilation dynamics were demonstrated to occur with approximately the same rate in both systems, regardless of the excitation status of the acceptor pigments. The possible reasons for these observations are discussed in the framework of the Förster energy transfer model.
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Affiliation(s)
- Mikas Vengris
- Quantum Electronics Department, Faculty of Physics, Vilnius University , Saulėtekio 9-III, 10222 Vilnius, Lithuania
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43
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Zhu J, Paparelli L, Hospes M, Arents J, Kennis JTM, van Stokkum IHM, Hellingwerf KJ, Groot ML. Photoionization and Electron Radical Recombination Dynamics in Photoactive Yellow Protein Investigated by Ultrafast Spectroscopy in the Visible and Near-Infrared Spectral Region. J Phys Chem B 2013; 117:11042-8. [DOI: 10.1021/jp311906f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingyi Zhu
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Laura Paparelli
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Marijke Hospes
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - Jos Arents
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - John T. M. Kennis
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - Marie Louise Groot
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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44
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Lincoln CN, Fitzpatrick AE, van Thor JJ. Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein. Phys Chem Chem Phys 2012; 14:15752-64. [PMID: 23090503 DOI: 10.1039/c2cp41718a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quantum yield of photoisomerisation of the photoactive yellow protein (PYP) strongly depends on peak power and wavelength with femtosecond optical excitation. Using systematic power titrations and addition of second order dispersion resulting in 140, 300 and 600 fs pulse durations, the one and multi-photon cross-sections at 400, 450 and 490 nm have been assessed from transient absorption spectroscopy and additionally the Z-scan technique. Applying a target model that incorporates photoselection theory, estimates for the cross-sections for stimulated emission and absorption of the first excited state, the amount of ultrafast internal conversion and the underlying species associated dynamics have been determined. The final quantum yields for photoisomerisation were found to be 0.06, 0.14-0.19 and 0.02 for excitation wavelengths 400, 450 and 490 nm and found to increase with increasing pulse durations. Transient absorption measurements and Z-scan measurements at 450 nm, coinciding with the maximum wavelength of the ground state absorption, indicate that the photochemical quantum yield is intrinsically limited by an ultrafast internal conversion reaction as well as by stimulated emission cross-section. With excitation at 400 nm photoisomerisation quantum yield is further significantly limited by competing multi-photon excitation into excited state absorption at 385 nm previously proposed to result in photoionisation. With excitation at 490 nm the photoisomerisation quantum yield is predominantly limited further by the significantly higher stimulated emission cross-section compared to ground state cross-section as well as multi-photon processes. In addition to photoionisation, a second product of multi-photon excitation is identified and characterised by an induced absorption at 500 nm and a time constant of 2 ps for relaxation. With power densities up to 138 GW cm(-2) the measurements have not provided indication for coherent multi-photon absorption of PYP. In the saturation regime with 450 nm excitation, the limit for the photoisomerisation quantum yield was found to be 0.14-0.19 and the excited state absorption cross-section 6.1 × 10(-17) cm(2) or 0.36 times the ground state cross-section of 1.68 × 10(-16) cm(2) per molecule. This places a fundamental restriction on the maximum populations and sample penetration that may be achieved for instance in femtosecond pump-probe experiments with molecular crystals of PYP.
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Affiliation(s)
- Craig N Lincoln
- Imperial College London, Division of Molecular Biosciences, South Kensington campus, SW7 2AZ, London, UK
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45
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Changenet-Barret P, Lacombat F, Plaza P. Reaction-coordinate tracking in the excited-state deactivation of the photoactive yellow protein chromophore in solution. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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46
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Fitzpatrick AE, Lincoln CN, van Wilderen LJGW, van Thor JJ. Pump–Dump–Probe and Pump–Repump–Probe Ultrafast Spectroscopy Resolves Cross Section of an Early Ground State Intermediate and Stimulated Emission in the Photoreactions of the Pr Ground State of the Cyanobacterial Phytochrome Cph1. J Phys Chem B 2012; 116:1077-88. [DOI: 10.1021/jp206298n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ann E. Fitzpatrick
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | - Craig N. Lincoln
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | | | - Jasper J. van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
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47
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Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Second-chance forward isomerization dynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. J Am Chem Soc 2012; 134:130-3. [PMID: 22107125 PMCID: PMC3261522 DOI: 10.1021/ja209533x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump-dump-probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the forward reaction of NpR6012g4.
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Affiliation(s)
- Peter W. Kim
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Lucy H. Freer
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
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48
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Boggio-Pasqua M, Burmeister CF, Robb MA, Groenhof G. Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations. Phys Chem Chem Phys 2012; 14:7912-28. [DOI: 10.1039/c2cp23628a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Zuev D, Bravaya KB, Makarova MV, Krylov AI. Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins. J Chem Phys 2011; 135:194304. [DOI: 10.1063/1.3660350] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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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Wei Z, Nakamura T, Takeuchi S, Tahara T. Tracking of the Nuclear Wavepacket Motion in Cyanine Photoisomerization by Ultrafast Pump–Dump–Probe Spectroscopy. J Am Chem Soc 2011; 133:8205-10. [DOI: 10.1021/ja110716b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zhengrong Wei
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Takumi Nakamura
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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