1
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Salvadori G, Mennucci B. Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling. J Phys Chem Lett 2024:8078-8084. [PMID: 39087732 DOI: 10.1021/acs.jpclett.4c01823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Bacteriophytochromes are light-sensing biological machines that switch between two photoreversible states, Pr and Pfr. Their relative stability is opposite in canonical and bathy bacteriophytochromes, but in both cases the switch between them is triggered by the photoisomerization of an embedded bilin chromophore. We applied an integrated multiscale strategy of excited-state QM/MM nonadiabatic dynamics and (QM/)MM molecular dynamics simulations with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that photoactivation in both phytochromes is triggered by the same hula-twist motion of the bilin chromophore. However, only in the bathy phytochrome, the bilin reaches the final rotated structure already in the first intermediate. This allows a reorientation of the binding pocket in a microsecond time scale, which can propagate through the entire protein causing the spine to tilt.
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Affiliation(s)
- Giacomo Salvadori
- Institute for Computational Biomedicine (INM-9/IAS-5), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, 56124 Pisa, Italy
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2
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Pieri E, Walker AR, Zhu M, Martínez TJ. Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. J Am Chem Soc 2024; 146:17646-17658. [PMID: 38885641 DOI: 10.1021/jacs.4c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).
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Affiliation(s)
- Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alice R Walker
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Mingning Zhu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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3
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Nagae T, Fujita Y, Tsuchida T, Kamo T, Seto R, Hamada M, Aoyama H, Sato-Tomita A, Fujisawa T, Eki T, Miyanoiri Y, Ito Y, Soeta T, Ukaji Y, Unno M, Mishima M, Hirose Y. Green/red light-sensing mechanism in the chromatic acclimation photosensor. SCIENCE ADVANCES 2024; 10:eadn8386. [PMID: 38865454 PMCID: PMC11168458 DOI: 10.1126/sciadv.adn8386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/26/2024] [Indexed: 06/14/2024]
Abstract
Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.
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Affiliation(s)
- Takayuki Nagae
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yuya Fujita
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tatsuya Tsuchida
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Ryoka Seto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Masako Hamada
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Hiroshi Aoyama
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ayana Sato-Tomita
- Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Takahiro Soeta
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yutaka Ukaji
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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4
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Nagami S, Kaguchi R, Akahane T, Harabuchi Y, Taniguchi T, Monde K, Maeda S, Ichikawa S, Katsuyama A. Photoinduced dual bond rotation of a nitrogen-containing system realized by chalcogen substitution. Nat Chem 2024; 16:959-969. [PMID: 38418536 DOI: 10.1038/s41557-024-01461-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Photoinduced concerted multiple-bond rotation has been proposed in some biological systems. However, the observation of such phenomena in synthetic systems, in other words, the synthesis of molecules that undergo photoinduced multiple-bond rotation upon photoirradiation, has been a challenge in the photochemistry field. Here we describe a chalcogen-substituted benzamide system that exhibits photoinduced dual bond rotation in heteroatom-containing bonds. Introduction of the chalcogen substituent into a sterically hindered benzamide system provides sufficient kinetic stability and photosensitivity to enable the photoinduced concerted rotation. The presence of two different substituents on the phenyl ring in the thioamide derivative enables the generation of a pair of enantiomers and E/Z isomers. Using these four stereoisomers as indicators of which bonds are rotated, we monitor the photoinduced C-N/C-C concerted bond rotation in the thioamide derivative depending on external stimuli such as temperature and photoirradiation. Theoretical calculations provide insight on the mechanism of this selective photoinduced C-N/C-C concerted rotation.
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Affiliation(s)
- Shotaro Nagami
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Rintaro Kaguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Taichi Akahane
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- JST, ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Sapporo, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Tohru Taniguchi
- Frontier Research Center of Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kenji Monde
- Frontier Research Center of Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- JST, ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Sapporo, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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5
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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6
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Ikejiri M, Yoshimizu A, Shiota F, Nagayama A, Fujisaka A, Kuboki Y, Miyashita K. Viscosity-Induced Emission of 5-(Diarylmethylene)imidazolone with Extended Conjugation via Attachment of N-Methylpyrrole at the 2-Position. Chem Pharm Bull (Tokyo) 2024; 72:518-523. [PMID: 38825446 DOI: 10.1248/cpb.c24-00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
We have developed a series of 2-monoaryl-5-diarylmethylene analogs of the green fluorescent protein chromophore to study their viscosity-induced emission (VIE) properties. The analogs were synthesized by a condensation with methyl imidate and N-(diarylmethylene)glycinate. Among the analogs, the N-methylpyrrol-2-yl-substituted analog 1h induced the most remarkable VIE behavior in triglyceride and lipid bilayers probably due to the high π-electron-rich property of the pyrrole ring. The pyrrole substituent in imidazolone analogs can be expected to become a common template for introducing VIE behavior.
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Affiliation(s)
| | | | | | - Ai Nagayama
- Faculty of Pharmacy, Osaka Ohtani University
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7
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Arcidiacono A, Accomasso D, Cupellini L, Mennucci B. How orange carotenoid protein controls the excited state dynamics of canthaxanthin. Chem Sci 2023; 14:11158-11169. [PMID: 37860660 PMCID: PMC10583711 DOI: 10.1039/d3sc02662k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Orange Carotenoid Protein (OCP) is a ketocarotenoid-binding protein essential for photoprotection in cyanobacteria. The main steps of the photoactivated conversion which converts OCP from its resting state to the active one have been extensively investigated. However, the initial photochemical event in the ketocarotenoid which triggers the large structural changes finally leading to the active state is still not understood. Here we employ QM/MM surface hopping nonadiabatic dynamics to investigate the excited-state decay of canthaxanthin in OCP, both in the ultrafast S2 to S1 internal conversion and the slower decay leading back to the ground state. For the former step we show the involvement of an additional excited state, which in the literature has been often named the SX state, and we characterize its nature. For the latter step, we reveal an excited state decay characterized by multiple timescales, which are related to the ground-state conformational heterogeneity of the ketocarotenoid. We assigned the slowly decaying population to the so-called S* state. Finally, we identify a minor decay pathway involving double-bond photoisomerization, which could be the initial trigger to photoactivation of OCP.
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Affiliation(s)
- Amanda Arcidiacono
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Davide Accomasso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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8
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Kanagaraj K, Rebek J, Yu Y. Control of reactivity and selectivity in isomerization and rearrangement reactions inside confined spaces. Chem Commun (Camb) 2023. [PMID: 37377149 DOI: 10.1039/d3cc01198d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In the confined space of supramolecular systems, the substrate can be forced into a reactive conformation and labile intermediates may be stabilized while isolated from the bulk solution. In this highlight, unusual processes mediated by supramolecular hosts are described. These include unfavourable conformational equilibria, unusual product selectivities in bond and ring-chain isomerizations, accelerated rearrangement reactions through labile intermediates, and encapsulated oxidations. In the host, controlled or altered isomerization of the guests can occur via hydrophobic, photochemical and thermal interventions. The inner spaces of the hosts resemble enzyme cavities that stabilize labile intermediates not accessible in the bulk solvent. The effects of confinement and the binding forces involved are discussed and further applications are suggested.
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Affiliation(s)
- Kuppusamy Kanagaraj
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| | - Julius Rebek
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
- Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
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9
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Corra S, Curcio M, Credi A. Photoactivated Artificial Molecular Motors. JACS AU 2023; 3:1301-1313. [PMID: 37234111 PMCID: PMC10207102 DOI: 10.1021/jacsau.3c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Accurate control of long-range motion at the molecular scale holds great potential for the development of ground-breaking applications in energy storage and bionanotechnology. The past decade has seen tremendous development in this area, with a focus on the directional operation away from thermal equilibrium, giving rise to tailored man-made molecular motors. As light is a highly tunable, controllable, clean, and renewable source of energy, photochemical processes are appealing to activate molecular motors. Nonetheless, the successful operation of molecular motors fueled by light is a highly challenging task, which requires a judicious coupling of thermal and photoinduced reactions. In this paper, we focus on the key aspects of light-driven artificial molecular motors with the aid of recent examples. A critical assessment of the criteria for the design, operation, and technological potential of such systems is provided, along with a perspective view on future advances in this exciting research area.
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Affiliation(s)
- Stefano Corra
- CLAN-Center
for Light Activated Nanostructures, Istituto
per la Sintesi Organica e Fotoreattività, CNR area della ricerca
Bologna, via Gobetti,
101, 40129 Bologna, Italy
- Dipartimento
di Chimica Industriale “Toso-Montanari”, Alma Mater Studiorum - Università di Bologna, viale del Risorgimento, 8, 40136 Bologna, Italy
| | - Massimiliano Curcio
- CLAN-Center
for Light Activated Nanostructures, Istituto
per la Sintesi Organica e Fotoreattività, CNR area della ricerca
Bologna, via Gobetti,
101, 40129 Bologna, Italy
- Dipartimento
di Chimica Industriale “Toso-Montanari”, Alma Mater Studiorum - Università di Bologna, viale del Risorgimento, 8, 40136 Bologna, Italy
| | - Alberto Credi
- CLAN-Center
for Light Activated Nanostructures, Istituto
per la Sintesi Organica e Fotoreattività, CNR area della ricerca
Bologna, via Gobetti,
101, 40129 Bologna, Italy
- Dipartimento
di Chimica Industriale “Toso-Montanari”, Alma Mater Studiorum - Università di Bologna, viale del Risorgimento, 8, 40136 Bologna, Italy
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10
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Liu L, Fang WH, Martinez TJ. A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors. J Am Chem Soc 2023; 145:6888-6898. [PMID: 36920260 DOI: 10.1021/jacs.3c00275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.
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Affiliation(s)
- Lihong Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.,Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Todd J Martinez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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11
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Krishnan SB, Clark RJ, Lin X, Dmitrenko O, Hilinski EF, Kuhn LR, Alabugin IV, Saltiel J. α-Methylstilbene Isomers: Relationship of Structure to Photophysics and Photochemistry. J Phys Chem A 2022; 126:8976-8987. [PMID: 36414392 DOI: 10.1021/acs.jpca.2c06319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Significant differences in the photochemical and photophysical behavior of trans-α-methylstilbene and trans-stilbene have been attributed to structural changes caused by the steric requirements of the methyl group. We present here the X-ray structures of cis- and trans-α-methylstilbene (c- and t-MeSt). This is the first X-ray structure of a cis-stilbene. Despite the pronounced departure from phenyl group coplanarity, the solid-state packing of t-MeSt resembles that of trans-stilbene in that both exhibit disorder with a bicycle pedal structural relationship, dynamic in t-St but static in t-MeSt. We compare the X-ray structures with calculated structures. We also compare our steady state and transient photochemical and spectroscopic results with predictions in a recent theoretical paper that anticipated some of our experiments. Deviations from planarity imposed by the methyl substitution account for the shorter lifetimes of the trans excited states. The rapid torsional relaxation of 1t-MeSt* to the twisted intermediate 1p*, ktp = 2.9 × 1012 s-1, observed using fs transient absorption spectroscopy, explains the sharp decrease in the fluorescence quantum yield of t-MeSt. We correct misconceptions that have appeared in the literature concerning the shape of the stilbene potential energy surface in S1. The nonplanarity due to methyl substitution leads to chirality issues that are relevant in biological molecules such as the protonated Schiff bases of retinal in the opsins.
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Affiliation(s)
- Sumesh B Krishnan
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Ronald J Clark
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Xinsong Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Edwin F Hilinski
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Leah R Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Jack Saltiel
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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12
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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13
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Rajbongshi BK, Rafiq S, Bhowmik S, Sen P. Ultrafast Excited State Relaxation of a Model Green Fluorescent Protein Chromophore: Femtosecond Fluorescence and Transient Absorption Study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Jones CM, List NH, Martínez TJ. Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins. J Am Chem Soc 2022; 144:12732-12746. [PMID: 35786916 DOI: 10.1021/jacs.2c02946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent proteins have become routine tools for biological imaging. However, their nanosecond lifetimes on the excited state present computational hurdles to a full understanding of these photoactive proteins. In this work, we simulate approximately 0.5 nanoseconds of ab initio molecular dynamics to elucidate steric and electronic features responsible for fluorescent protein behavior. Using green fluorescent protein (GFP) and Dronpa2─widely used fluorescent proteins with contrasting functionality─as case studies, we leverage previous findings in the gas phase and solution to explore the deactivation mechanisms available to these proteins. Starting with ground-state analyses, we identify steric (the distribution of empty pockets near the chromophore) and electronic (electric fields exerted on chromophore moieties) factors that offer potential avenues for rational design. Picosecond timescale simulations on the excited state reveal that the chromophore can access twisted structures in Dronpa2, while the chromophore is largely confined to planarity in GFP. We couple ab initio multiple spawning (AIMS) and enhanced sampling simulations to discover and characterize conical intersection seams that facilitate internal conversion, which is a rare event in both systems. Our AIMS simulations correctly capture the relative fluorescence profiles of GFP and Dronpa2 within the first few picoseconds, and we attribute the diminished fluorescence intensity of Dronpa2, relative to GFP, to flexible chromophore intermediates on the excited state. Furthermore, we predict that twisted chromophore intermediates produce red-shifted intensities in the Dronpa2 fluorescence spectrum. If confirmed experimentally, this spectroscopic signature would provide valuable insights when screening and developing novel fluorescent proteins.
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Affiliation(s)
- Chey M Jones
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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15
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Lea MR, Stavros VG, Maurer RJ. Effect of electron donating/withdrawing groups on molecular photoswitching of functionalized hemithioindigo derivatives: a computational multireference study. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202100290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin R. Lea
- University of Warwick Department of Chemistry Gibbet Hill Road CV4 7AL Coventry UNITED KINGDOM
| | - Vasilios G. Stavros
- University of Warwick Department of Chemistry Gibbet Hill Road CV4 7AL Coventry UNITED KINGDOM
| | - Reinhard J Maurer
- University of Warwick Department of Chemistry Department of Chemistry Gibbet Hill Road CV4 7AL Coventry UNITED KINGDOM
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16
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Gordeev EG, Erokhin KS, Kobelev AD, Burykina JV, Novikov PV, Ananikov VP. Exploring metallic and plastic 3D printed photochemical reactors for customizing chemical synthesis. Sci Rep 2022; 12:3780. [PMID: 35260601 PMCID: PMC8904794 DOI: 10.1038/s41598-022-07583-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Visible light photocatalysis is a rapidly developing branch of chemical synthesis with outstanding sustainable potential and improved reaction design. However, the challenge is that many particular chemical reactions may require dedicated tuned photoreactors to achieve maximal efficiency. This is a critical stumbling block unless the possibility for reactor design becomes available directly in the laboratories. In this work, customized laboratory photoreactors were developed with temperature stabilization and the ability to adapt different LED light sources of various wavelengths. We explore two important concepts for the design of photoreactors: reactors for performing multiple parallel experiments and reactors suitable for scale-up synthesis, allowing a rapid increase in the product amount. Reactors of the first type were efficiently made of metal using metal laser sintering, and reactors of the second type were successfully manufactured from plastic using fused filament fabrication. Practical evaluation has shown good accuracy of the temperature stabilization in the range typically required for organic synthesis for both types of reactors. Synthetic application of 3D printed reactors has shown good utility in test reactions-furan C-H arylation and thiol-yne coupling. The critical effect of temperature stabilization was established for the furan arylation reaction: heating of the reaction mixture may lead to the total vanishing of photochemical effect.
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Affiliation(s)
- Evgeniy G Gordeev
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991
| | - Kirill S Erokhin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991
| | - Andrey D Kobelev
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991
- Lomonosov Moscow State University, Leninskie Gory GSP-1, 1-3, Moscow, Russia, 119991
| | - Julia V Burykina
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991
| | - Pavel V Novikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, Russia, 119991.
- Lomonosov Moscow State University, Leninskie Gory GSP-1, 1-3, Moscow, Russia, 119991.
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17
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Gerwien A, Jehle B, Irmler M, Mayer P, Dube H. An Eight-State Molecular Sequential Switch Featuring a Dual Single-Bond Rotation Photoreaction. J Am Chem Soc 2022; 144:3029-3038. [PMID: 35157802 PMCID: PMC8874910 DOI: 10.1021/jacs.1c11183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Typical photoswitches
interconvert between two different states
by simple isomerization reactions, which represents a fundamental
limit for applications. To expand the switching capacity usually different
photoswitches have to be linked together leading to strong increase
in molecular weight, diminished switching function, and less precision
and selectivity of switching events. Herein we present an approach
for solving this essential problem with a different photoswitching
concept. A basic molecular switch architecture provides precision
photoswitching between eight different states via controlled rotations
around three adjacent covalent bonds. All eight states can be populated
one after another in an eight-step cycle by alternating between photochemical
Hula-Twist isomerizations and thermal single-bond rotations. By simply
changing solvent and temperature the same switch can also undergo
a different cycle instead interconverting just five isomers in a selective
sequence. This behavior is enabled through the discovery of an unprecedented
photoreaction, a one-photon dual single-bond rotation.
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Affiliation(s)
- Aaron Gerwien
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Benjamin Jehle
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Marvin Irmler
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Peter Mayer
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Henry Dube
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Strasse 10, 91058 Erlangen, Germany
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18
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Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging. Nat Biotechnol 2022; 40:598-605. [PMID: 34845372 PMCID: PMC9005348 DOI: 10.1038/s41587-021-01100-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/17/2021] [Indexed: 02/07/2023]
Abstract
Reversibly photo-switchable proteins are essential for many super-resolution fluorescence microscopic and optoacoustic imaging methods. However, they have yet to be used as sensors that measure the distribution of specific analytes at the nanoscale or in the tissues of live animals. Here we constructed the prototype of a photo-switchable Ca2+ sensor based on GCaMP5G that can be switched with 405/488-nm light and describe its molecular mechanisms at the structural level, including the importance of the interaction of the core barrel structure of the fluorescent protein with the Ca2+ receptor moiety. We demonstrate super-resolution imaging of Ca2+ concentration in cultured cells and optoacoustic Ca2+ imaging in implanted tumor cells in mice under controlled Ca2+ conditions. Finally, we show the generalizability of the concept by constructing examples of photo-switching maltose and dopamine sensors based on periplasmatic binding protein and G-protein-coupled receptor-based sensors.
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19
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Sussardi A, Marshall RJ, Moggach SA, Jones AC, Forgan RS. Photophysics of Azobenzene Constrained in a UiO Metal-Organic Framework: Effects of Pressure, Solvation and Dynamic Disorder. Chemistry 2021; 27:14871-14875. [PMID: 34468054 PMCID: PMC8596631 DOI: 10.1002/chem.202101879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/04/2022]
Abstract
Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter‐chromophore interactions. Furthermore, high‐pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans‐azobenzene chromophore, constrained in the form of the 4,4’‐azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure‐induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans‐azobenzene remains non‐fluorescent (with a quantum yield less than 10−4) despite the prevention of trans‐cis isomerization by the constraining MOF structure. We propose that efficient non‐radiative decay is mediated by the local, pedal‐like twisting of the azo group that is evident as dynamic disorder in the crystal structure.
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Affiliation(s)
- Alif Sussardi
- EaStCHEM, School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Ross J Marshall
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Stephen A Moggach
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, Western Australia, 6009, Australia
| | - Anita C Jones
- EaStCHEM, School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Ross S Forgan
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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20
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Heisler IA, Meech SR. Altered relaxation dynamics of excited state reactions by confinement in reverse micelles probed by ultrafast fluorescence up-conversion. Chem Soc Rev 2021; 50:11486-11502. [PMID: 34661209 DOI: 10.1039/d1cs00516b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chemical reactions in confined environments are important in areas as diverse as heterogenous catalysis, environmental chemistry and biochemistry, yet they are much less well understood than the equivalent reactions in either the gas phase or in free solution. The understanding of chemical reactions in solution was greatly enhanced by real time studies of model reactions, through ultrafast spectroscopy (especially when supported by molecular dynamics simulation). Here we review some of the efforts that have been made to adapt this approach to the investigation of reactions in confined media. Specifically, we review the application of ultrafast fluorescence spectroscopy to measure reaction dynamics in the nanoconfined water phase of reverse micelles, as a function of the droplet radius and the charge on the interface. Methods of measurement and modelling of the reactions are outlined. In all of the cases studied (which are focused on ultrafast intramolecular reactions) the effect of confinement was to suppress the reaction. Even in the largest micelles the result in the bulk aqueous phase was not usually recovered, suggesting an important role for specific interactions between reactant and environment, for example at the interface. There was no simple one-to-one correspondence with direct measures of the dynamics of the confined phase. Thus, understanding the effect of confinement on reaction rate appears to require not only knowledge of the dynamics of the reaction in solutions and the effect of confinement on the medium, but also of the interaction between reactant and confining medium.
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Affiliation(s)
- Ismael A Heisler
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
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21
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Kochman MA, Palczewski K, Kubas A. Theoretical Study of the Photoisomerization Mechanism of All- Trans-Retinyl Acetate. J Phys Chem A 2021; 125:8358-8372. [PMID: 34546761 PMCID: PMC8488936 DOI: 10.1021/acs.jpca.1c05533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor
to 9-cis-retinal,
which has potential application in the treatment of some hereditary
diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the
readily available all-trans-RAc. In the present study,
we examine the mechanism of the photoisomerization reaction with the
use of state-of-the-art electronic structure calculations for two
polyenic model compounds: tEtEt-octatetraene and tEtEtEc-2,6-dimethyl-1,3,5,7,9-decapentaene. The occurrence
of photoisomerization is attributed to a chain-kinking mechanism,
whereby a series of S1/S0 conical intersections
associated with kinking deformations at different positions along
the polyenic chain mediate internal conversion to the S0 state, and subsequent isomerization around one of the double bonds.
Two other possible photoisomerization mechanisms are taken into account,
but they are rejected as incompatible with simulation results and/or
the available spectroscopic data.
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Affiliation(s)
- Michał Andrzej Kochman
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States.,Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
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22
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Jones CM, List NH, Martínez TJ. Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water. Chem Sci 2021; 12:11347-11363. [PMID: 34667545 PMCID: PMC8447926 DOI: 10.1039/d1sc02508b] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022] Open
Abstract
The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.
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Affiliation(s)
- Chey M Jones
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
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23
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Bandara S, Rockwell NC, Zeng X, Ren Z, Wang C, Shin H, Martin SS, Moreno MV, Lagarias JC, Yang X. Crystal structure of a far-red-sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism. Proc Natl Acad Sci U S A 2021; 118:e2025094118. [PMID: 33727422 PMCID: PMC8000052 DOI: 10.1073/pnas.2025094118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cyanobacteriochromes (CBCRs) are small, linear tetrapyrrole (bilin)-binding photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. More spectrally diverse than canonical red/far-red-sensing phytochromes, CBCRs were thought to be restricted to sensing visible and near UV light until recently when several subfamilies with far-red-sensing representatives (frCBCRs) were discovered. Two of these frCBCRs subfamilies have been shown to incorporate bilin precursors with larger pi-conjugated chromophores, while the third frCBCR subfamily uses the same phycocyanobilin precursor found in the bulk of the known CBCRs. To elucidate the molecular basis of far-red light perception by this third frCBCR subfamily, we determined the crystal structure of the far-red-absorbing dark state of one such frCBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 which exhibits a reversible far-red/orange photocycle. Determined by room temperature serial crystallography and cryocrystallography, the refined 2.7-Å structure reveals an unusual all-Z,syn configuration of the phycocyanobilin (PCB) chromophore that is considerably less extended than those of previously characterized red-light sensors in the phytochrome superfamily. Based on structural and spectroscopic comparisons with other bilin-binding proteins together with site-directed mutagenesis data, our studies reveal protein-chromophore interactions that are critical for the atypical bathochromic shift. Based on these analyses, we propose that far-red absorption in Anacy_2551g3 is the result of the additive effect of two distinct red-shift mechanisms involving cationic bilin lactim tautomers stabilized by a constrained all-Z,syn conformation and specific interactions with a highly conserved anionic residue.
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Affiliation(s)
- Sepalika Bandara
- Department of Chemistry, University of Illinois, Chicago, IL 60607
| | - Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Xiaoli Zeng
- Department of Chemistry, University of Illinois, Chicago, IL 60607
| | - Zhong Ren
- Department of Chemistry, University of Illinois, Chicago, IL 60607
| | - Cong Wang
- Department of Chemistry, University of Illinois, Chicago, IL 60607
| | - Heewhan Shin
- Department of Chemistry, University of Illinois, Chicago, IL 60607
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616;
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois, Chicago, IL 60607;
- Department of Ophthalmology and Vision Sciences, University of Illinois, Chicago, IL 60607
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24
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Fluorescent Orthopalladated Complexes of 4-Aryliden-5(4 H)-oxazolones from the Kaede Protein: Synthesis and Characterization. Molecules 2021; 26:molecules26051238. [PMID: 33669118 PMCID: PMC7956804 DOI: 10.3390/molecules26051238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 11/18/2022] Open
Abstract
The goal of the work reported here was to amplify the fluorescent properties of 4-aryliden-5(4H)-oxazolones by suppression of the hula-twist non-radiative deactivation pathway. This aim was achieved by simultaneous bonding of a Pd center to the N atom of the heterocycle and the ortho carbon of the arylidene ring. Two different 4-((Z)-arylidene)-2-((E)-styryl)-5(4H)-oxazolones, the structures of which are closely related to the chromophore of the Kaede protein and substituted at the 2- and 4-positions of the arylidene ring (1a OMe; 1b F), were used as starting materials. Oxazolones 1a and 1b were reacted with Pd(OAc)2 to give the corresponding dinuclear orthometalated palladium derivates 2a and 2b by regioselective C–H activation of the ortho-position of the arylidene ring. Reaction of 2a (2b) with LiCl promoted the metathesis of the bridging carboxylate by chloride ligands to afford dinuclear 3a (3b). Mononuclear complexes containing the orthopalladated oxazolone and a variety of ancillary ligands (acetylacetonate (4a, 4b), hydroxyquinolinate (5a), aminoquinoline (6a), bipyridine (7a), phenanthroline (8a)) were prepared from 3a or 3b through metathesis of anionic ligands or substitution of neutral weakly bonded ligands. All species were fully characterized and the X-ray determination of the molecular structure of 7a was carried out. This structure has strongly distorted ligands due to intramolecular interactions. Fluorescence measurements showed an increase in the quantum yield (QY) by up to one order of magnitude on comparing the free oxazolone (QY < 1%) with the palladated oxazolone (QY = 12% for 6a). This fact shows that the coordination of the oxazolone to the palladium efficiently suppresses the hula-twist deactivation pathway.
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25
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Gurchiek JK, Rose JB, Guberman-Pfeffer MJ, Tilluck RW, Ghosh S, Gascón JA, Beck WF. Fluorescence Anisotropy Detection of Barrier Crossing and Ultrafast Conformational Dynamics in the S 2 State of β-Carotene. J Phys Chem B 2020; 124:9029-9046. [PMID: 32955881 DOI: 10.1021/acs.jpcb.0c06961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carotenoids are usually only weakly fluorescent despite being very strong absorbers in the mid-visible region because their first two excited singlet states, S1 and S2, have very short lifetimes. To probe the structural mechanisms that promote the nonradiative decay of the S2 state to the S1 state, we have carried out a series of fluorescence lineshape and anisotropy measurements with a prototype carotenoid, β-carotene, in four aprotic solvents. The anisotropy values observed in the fluorescence emission bands originating from the S2 and S1 states reveal that the large internal rotations of the emission transition dipole moment, as much as 50° relative to that of the absorption transition dipole moment, are initiated during ultrafast evolution on the S2 state potential energy surface and persist upon nonradiative decay to the S1 state. Electronic structure calculations of the orientation of the transition dipole moment account for the anisotropy results in terms of torsional and pyramidal distortions near the center of the isoprenoid backbone. The excitation wavelength dependence of the fluorescence anisotropy indicates that these out-of-plane conformational motions are initiated by passage over a low-activation energy barrier from the Franck-Condon S2 structure. This conclusion is consistent with detection over the 80-200 K range of a broad, red-shifted fluorescence band from a dynamic intermediate evolving on a steep gradient of the S2 state potential energy surface after crossing the activation barrier. The temperature dependence of the oscillator strength and anisotropy indicate that nonadiabatic passage from S2 through a conical intersection seam to S1 is promoted by the out-of-plane motions of the isoprenoid backbone with strong hindrance by solvent friction.
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Affiliation(s)
- J K Gurchiek
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Justin B Rose
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Matthew J Guberman-Pfeffer
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06268-1712, United States
| | - Ryan W Tilluck
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Soumen Ghosh
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milan, Lombardy 20133, Italy
| | - José A Gascón
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06268-1712, United States
| | - Warren F Beck
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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26
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Marefat Khah A, Reinholdt P, Nuernberger P, Kongsted J, Hättig C. Relaxation Dynamics of the Triazene Compound Berenil in DNA-Minor-Groove Confinement after Photoexcitation. J Chem Theory Comput 2020; 16:5203-5211. [DOI: 10.1021/acs.jctc.0c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Christof Hättig
- Quantum Chemistry Group, Ruhr University of Bochum, D-44780 Bochum, Germany
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27
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Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA, Lakhno VD. Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Weir H, Williams M, Parrish RM, Hohenstein EG, Martínez TJ. Nonadiabatic Dynamics of Photoexcited cis-Stilbene Using Ab Initio Multiple Spawning. J Phys Chem B 2020; 124:5476-5487. [DOI: 10.1021/acs.jpcb.0c03344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hayley Weir
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Monika Williams
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Robert M. Parrish
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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29
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Zimányi L, Krishnan SB, Williford E, Gupta S, Sepulveda J, Schwartz H, Mallory FB, Mallory CW, Dmitrenko O, Saltiel J. Translational Diffusion and Unstable Conformer Trapping in Glassy Isopentane at 77 K. J Phys Chem A 2019; 123:9102-9112. [PMID: 31557030 DOI: 10.1021/acs.jpca.9b07964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diffusional quenching in isopentane (IP) glass at 77 K is demonstrated by the reduction of triphenylene phosphorescence lifetimes in the presence of 1,3-pentadiene and/or molecular oxygen. Fluorescence spectra and lifetimes of cis- and trans-1,2-di(1-methyl-2-naphthyl)ethene in IP glass at 77 K reveal that the cis → trans photoisomerization leads to the trapping of unstable conformers of the trans isomer. The claim that IP at 77 K is not sufficiently viscous to trap unstable photoproduct conformers is invalidated.
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Affiliation(s)
- László Zimányi
- Institute of Biophysics , Biological Research Centre, Hungarian Academy of Sciences , P.O. Box 521, Szeged , Hungary , H-6701
| | - Sumesh B Krishnan
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
| | - Emily Williford
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
| | - Shipra Gupta
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
| | - Jonathan Sepulveda
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
| | - Hadleigh Schwartz
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
| | - Frank B Mallory
- Department of Chemistry , Bryn Mawr College , Bryn Mawr , Pennsylvania 19010 , United States
| | - Clelia W Mallory
- Department of Chemistry , Bryn Mawr College , Bryn Mawr , Pennsylvania 19010 , United States.,Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jack Saltiel
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306-4390 , United States
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30
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Chang J, Romei MG, Boxer SG. Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins. J Am Chem Soc 2019; 141:15504-15508. [PMID: 31533429 PMCID: PMC7036281 DOI: 10.1021/jacs.9b08356] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of cis and trans rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the trans state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas, in a tighter packing (7% smaller unit cell size), the hula-twist occurs.
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Affiliation(s)
- Jeffrey Chang
- Department of Physics, Stanford University, Stanford, California 94305, United States
| | - Matthew G. Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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31
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Abstract
Directed motion at the nanoscale is a central attribute of life, and chemically driven motor proteins are nature's choice to accomplish it. Motivated and inspired by such bionanodevices, in the past few decades chemists have developed artificial prototypes of molecular motors, namely, multicomponent synthetic species that exhibit directionally controlled, stimuli-induced movements of their parts. In this context, photonic and redox stimuli represent highly appealing modes of activation, particularly from a technological viewpoint. Here we describe the evolution of the field of photo- and redox-driven artificial molecular motors, and we provide a comprehensive review of the work published in the past 5 years. After an analysis of the general principles that govern controlled and directed movement at the molecular scale, we describe the fundamental photochemical and redox processes that can enable its realization. The main classes of light- and redox-driven molecular motors are illustrated, with a particular focus on recent designs, and a thorough description of the functions performed by these kinds of devices according to literature reports is presented. Limitations, challenges, and future perspectives of the field are critically discussed.
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Affiliation(s)
- Massimo Baroncini
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Scienze e Tecnologie Agro-alimentari , Università di Bologna , viale Fanin 44 , 40127 Bologna , Italy
| | - Serena Silvi
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Chimica "G. Ciamician" , Università di Bologna , via Selmi 2 , 40126 Bologna , Italy
| | - Alberto Credi
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Scienze e Tecnologie Agro-alimentari , Università di Bologna , viale Fanin 44 , 40127 Bologna , Italy
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32
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Zhao X, Luo J, Yang S, Han K. New Insight into the Photoprotection Mechanism of Plant Sunscreens: Adiabatic Relaxation Competing with Nonadiabatic Relaxation in the cis → trans Photoisomerization of Methyl Sinapate. J Phys Chem Lett 2019; 10:4197-4202. [PMID: 31287701 DOI: 10.1021/acs.jpclett.9b01651] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A great deal of thermally instable cis form photoisomerization products will be formed from the thermally stable trans form of the plant sunscreens sinapate esters upon ultraviolet radiation. To reveal the photoisomerization mechanism of the cis-isomer, we explore the photodynamics of a model plant sunscreen methyl sinapate (MS) in the cis form in organic solution. The high photoisomerization quantum yield of the cis-isomer results in the relatively higher photostability of trans-MS. By utilizing femtosecond transient absorption spectroscopy and quantum chemical calculation, we propose that an adiabatic relaxation competes with nonadiabatic relaxation for the excited-state cis form of methyl sinapate. These results suggest that the photoprotection mechanism of the cis form of sinapate esters is significantly different from that of the trans form of sinapate esters and plays an important role in the overall photoprotection effect.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics (DICP) , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian , Liaoning 116023 , China
- University of Chinese Academy of Sciences , Beijing 10049 , China
| | - Jian Luo
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics (DICP) , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian , Liaoning 116023 , China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics (DICP) , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian , Liaoning 116023 , China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics (DICP) , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian , Liaoning 116023 , China
- Institute of Molecular Sciences and Engineering , Shandong University , Qingdao 266237 , P.R. China
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33
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Raj AM, Sharma G, Prabhakar R, Ramamurthy V. Space Constrained Stereoselective Geometric Isomerization of 1,2-Diphenylcyclopropane and Stilbenes in an Aqueous Medium. Org Lett 2019; 21:5243-5247. [PMID: 31247756 DOI: 10.1021/acs.orglett.9b01176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Confinement provided by the reaction space alters the photostationary state isomer distribution during the geometric isomerization of excited 1,2-diphenylcyclopropane and stilbenes. The selectivity in 1,2-diphenylcyclopropane is suggested to result from the supramolecular steric hindrance exerted by the medium for the rotational motion. The alteration in the selectivity between a dimethyl and n-propyl substituted stilbenes is attributed to the medium influence on the location of the transition state on the ground state surface.
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Affiliation(s)
- A Mohan Raj
- Department of Chemistry , University of Miami , Coral Cables , Florida 33124 , United States
| | - Gaurav Sharma
- Department of Chemistry , University of Miami , Coral Cables , Florida 33124 , United States
| | - Rajeev Prabhakar
- Department of Chemistry , University of Miami , Coral Cables , Florida 33124 , United States
| | - V Ramamurthy
- Department of Chemistry , University of Miami , Coral Cables , Florida 33124 , United States
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34
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MacDonell RJ, Schuurman MS. Site-Selective Isomerization of Cyano-Substituted Butadienes: Chemical Control of Nonadiabatic Dynamics. J Phys Chem A 2019; 123:4693-4701. [DOI: 10.1021/acs.jpca.9b02446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ryan J. MacDonell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, D’Iorio Hall, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S. Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, D’Iorio Hall, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
- National Research of Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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35
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Fuß W. Previtamin D: Z-E photoisomerization via a Hula-twist conical intersection. Phys Chem Chem Phys 2019; 21:6776-6789. [PMID: 30887977 DOI: 10.1039/c9cp00500e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On photoisomerization of previtamin D - a steroid Z-triene - produced in situ by ring opening of 7-dehydrocholesterol in a cold matrix, it was found in A. M. Müller et al. [Angew. Chem., Int. Ed., 1998, 37, 505-507] that the product (tachysterol) had rotated not only its central double bond but also an adjacent single bond. This is called a Hula twist (HT) due to the alternative description, in which it is just one central CH group that rotates. It was pointed out that the results directly support the calculated molecular structure at a conical intersection, which mediates the Z-E isomerization of polyenes. With a more sophisticated technique, Saltiel et al. (J. Phys. Chem. Lett., 2013, 4, 716-721) confirmed this tachysterol rotamer as the main product but found two additional conformers. They believed to have seen also three previtamin D conformers, suggested to be a result of hot-ground-state reactions from the primary rotamer, and interpreted all tachysterol products to be a result of a double-bond twist (DBT), not a HT. On the basis of published circular dichroism data and consideration of other reactions, it is here shown that under these conditions hot-ground-state reactions are unimportant or even negligible and that there is practically only a single conformer of previtamin D after ring opening. All products can be easily understood on the basis of an HT-type conical intersection, which is thus further supported. Invoking a published pretwist model even rationalizes product ratios. The two twists in HT are concerted. Furthermore HT is fully consistent with the NEER principle (nonequilibration of excited rotamers) and even offers additional possibilities for conformer control.
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36
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Zhang JQ, Zhang DS, Chen QJ, Xu HB, Kurmoo M, Zeng MH. Thermally Induced trans-to-cis Isomerization and Its Photoinduced Reversal Monitored using Absorption and Luminescence: Cooperative Effect of Metal Coordination and Steric Substituent. Chemistry 2019; 25:5177-5185. [PMID: 30740800 DOI: 10.1002/chem.201900204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 11/07/2022]
Abstract
For ethene derivatives with large groups the cis-isomer is often quite unstable and unavailable. Herein, we report an exception of two stable coordination complexes, (cis-L)ZnCl2 , starting from trans-1,2-bis(1-R-benzo[d]imidazol-2-yl)ethene (R=H, L1; R=CH3 , L2) ligands under solvothermal condition (T ≥140 °C). Using the intensity of the absorption and luminescence spectra as probes we proposed its progressive cis-to-trans reversal upon irradiation with UV light, which was confirmed by powder X-ray diffraction (PXRD). Similar results observed in the series of (cis-L2)MII Cl2 [M=Fe (4), Co (5), Ni (6)] demonstrate the universal strategy. The results of PXRD, NMR spectroscopy, ESI-MS and DFT calculations support the above conclusion. NMR spectroscopy indicates that irradiation of 1 converts an optimized 71 % of the cis-isomer to trans, whereas the free trans-L1 ligand transforms to only 15 % cis-isomer under similar conditions.
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Affiliation(s)
- Jun-Quan Zhang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, P. R. China
| | - De-Shan Zhang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, P. R. China
| | - Qiu-Jie Chen
- Key Laboratory for the Synthesis and Application of, Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, P. R. China
| | - Hai-Bing Xu
- Key Laboratory for the Synthesis and Application of, Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, P. R. China
| | - Mohamedally Kurmoo
- Université de Strasbourg, Institut de Chimie de Strasbourg, CNRS-UMR7177, 4 rue Blaise Pascal, Strasbourg Cedex, 67070, France
| | - Ming-Hua Zeng
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, P. R. China.,Key Laboratory for the Synthesis and Application of, Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, P. R. China
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37
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Ghanbarpour A, Nairat M, Nosrati M, Santos EM, Vasileiou C, Dantus M, Borhan B, Geiger JH. Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. J Am Chem Soc 2019; 141:1735-1741. [PMID: 30580520 DOI: 10.1021/jacs.8b12493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteriorhodopsin represents the simplest, and possibly most abundant, phototropic system requiring only a retinal-bound transmembrane protein to convert photons of light to an energy-generating proton gradient. The creation and interrogation of a microbial rhodopsin mimic, based on an orthogonal protein system, would illuminate the design elements required to generate new photoactive proteins with novel function. We describe a microbial rhodopsin mimic, created using a small soluble protein as a template, that specifically photoisomerizes all- trans to 13- cis retinal followed by thermal relaxation to the all- trans isomer, mimicking the bacteriorhodopsin photocycle, in a single crystal. The key element for selective isomerization is a tuned steric interaction between the chromophore and protein, similar to that seen in the microbial rhodopsins. It is further demonstrated that a single mutation converts the system to a protein photoswitch without chromophore photoisomerization or conformational change.
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Affiliation(s)
- Alireza Ghanbarpour
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Muath Nairat
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Meisam Nosrati
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Elizabeth M Santos
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Chrysoula Vasileiou
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Marcos Dantus
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Babak Borhan
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - James H Geiger
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
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38
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Dokukina I, Nenov A, Garavelli M, Marian CM, Weingart O. QM/MM Photodynamics of Retinal in the Channelrhodopsin Chimera C1C2 with OM3/MRCI. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Irina Dokukina
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Christel M. Marian
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
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39
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Kraack JP, Motzkus M, Buckup T. Excited State Vibrational Spectra of All- trans Retinal Derivatives in Solution Revealed By Pump-DFWM Experiments. J Phys Chem B 2018; 122:12271-12281. [PMID: 30507189 DOI: 10.1021/acs.jpcb.8b08495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The ultrafast structural changes during the photoinduced isomerization of the retinal-protonated Schiff base (RPSB) is still a poorly understood aspect in the retinal's photochemistry. In this work, we apply pump-degenerate four-wave mixing (pump-DFWM) to all- trans retinal (ATR) and retinal Schiff bases (RSB) to resolve coherent high- and low-frequency vibrational signatures from excited electronic states. We show that the vibrational spectra of excited singlet states in these samples exhibit pronounced differences compared to the relaxed ground state. Pump-DFWM results indicate three major features for ATR and RSB. (i) Excited state vibrational spectra of ATR and RSB consist predominately of low-frequency modes in the energetic range 100-500 cm-1. (ii) Excited state vibrational spectra show distinct differences for excitation in specific regions of electronic transitions of excited state absorption and emission. (iii) Low-frequency modes in ATR and RSB are inducible during the entire lifetime of the excited electronic states. This latter effect points to a transient molecular structure that, following initial relaxation between different excited electronic states, does not change anymore over the lifetime of the finally populated excited electronic state.
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Affiliation(s)
- Jan Philip Kraack
- Physikalisch-Chemisches Institut , Ruprecht-Karls Universität Heidelberg , D-69210 Heidelberg , Germany
| | - Marcus Motzkus
- Physikalisch-Chemisches Institut , Ruprecht-Karls Universität Heidelberg , D-69210 Heidelberg , Germany
| | - Tiago Buckup
- Physikalisch-Chemisches Institut , Ruprecht-Karls Universität Heidelberg , D-69210 Heidelberg , Germany
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40
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Aldaz C, Kammeraad JA, Zimmerman PM. Discovery of conical intersection mediated photochemistry with growing string methods. Phys Chem Chem Phys 2018; 20:27394-27405. [PMID: 30357173 PMCID: PMC6532651 DOI: 10.1039/c8cp04703k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Conical intersections (CIs) are important features of photochemistry that determine yields and selectivity. Traditional CI optimizers require significant human effort and chemical intuition, which typically restricts searching to only a small region of the CI space. Herein, a systematic approach utilizing the growing string method is introduced to locate multiple CIs. Unintuitive MECI are found using driving coordinates that can be generated using a combinatorial search, and subsequent optimization allows reaction pathways, transition states, products, and seam-space pathways to be located. These capabilities are demonstrated by application to two prototypical photoisomerization reactions and the dimerization of butadiene. In total, many reaction pathways were uncovered, including the elusive stilbene hula-twist mechanism, and a previously unidentified product in butadiene dimerization. Overall, these results suggest that growing string methods provide a predictive strategy for exploring photochemistry.
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Affiliation(s)
- Cody Aldaz
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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41
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Glover WJ, Mori T, Schuurman MS, Boguslavskiy AE, Schalk O, Stolow A, Martínez TJ. Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations. J Chem Phys 2018; 148:164303. [DOI: 10.1063/1.5018130] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- William J. Glover
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Toshifumi Mori
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Institute for Molecular Science, Myodaji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Michael S. Schuurman
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1A 0R6, Canada
| | - Andrey E. Boguslavskiy
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1A 0R6, Canada
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Oliver Schalk
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Albert Stolow
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1A 0R6, Canada
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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42
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Domratcheva T, Schlichting I. Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins. Faraday Discuss 2018; 207:9-26. [PMID: 29583144 DOI: 10.1039/c8fd00058a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light is an important environmental variable and most organisms have evolved means to sense, exploit or avoid it and to repair detrimental effects on their genome. In general, light absorption is the task of specific chromophores, however other biomolecules such as oligonucleotides also do so which can result in undesired outcomes such as mutations and cancer. Given the biological importance of light-induced processes and applications for imaging, optogenetics, photodynamic therapy or photovoltaics, there is a great interest in understanding the detailed molecular mechanisms of photoinduced processes in proteins and nucleic acids. The processes are typically characterized by time-resolved spectroscopic approaches or computation, inferring structural information on transient species from stable ground state structures. Recently, however, structure determination of excited states or other short-lived species has become possible with the advent of X-ray free-electron lasers. This review gives an overview of the impact of structure on the understanding of photoinduced processes in macromolecules, focusing on systems presented at this Faraday Discussion meeting.
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Affiliation(s)
- Tatiana Domratcheva
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
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43
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Sonoda Y, Goto M, Ichimura K. Solid-state one-way photoisomerisation of Z,E,Z-1,6-(4,4'-diphenyl)hexa-1,3,5-triene dicarboxylate examined using higher-order derivative spectra and powder XRD patterns. Photochem Photobiol Sci 2018; 17:271-280. [PMID: 29364307 DOI: 10.1039/c7pp00247e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Higher order derivative spectra were applied at first to one-way ZEZ-to-EEE photoisomerisation of dimethyl ester (ZEZ-DPH1) of the titled compound in a methylcyclohexane solution. Many common crossing points emerged in UV-induced derivative-spectral changes to reveal the direct ZEZ-to-EEE photoisomerisation without the transient formation of an intermediate to suggest the bicycle-pedal mechanism. The solid-state photoisomerisation was subsequently monitored by tracing changes in the fourth-order derivatives of absorption spectra of a thin crystalline layer of ZEZ-DPH1 prepared by the drop-casting method, because the distortion of absorption spectra due to light scattering is cancelled. It was suggested that the solid-state photochemical event consists of three steps: fast ZEZ-to-EEE photoisomerisation, a subsequent slow ZEZ-to-EEE photoisomerisation and very slow disappearance of the EEE-isomer. Studies on powder XRD were also carried out for a drop-cast solid layer of ZEZ-DPH1 to disclose the coexistence of a crystal form other than the original one, and the former exhibited faster ZEZ-to-EEE photoisomerisation when compared with the original crystal form. The results revealed by XRD analysis are in line with those obtained by higher-order derivative spectra, confirming the solid-state one-way photoisomerisation to take place through the bicycle-pedal process.
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Affiliation(s)
- Yoriko Sonoda
- Electronics and Photonics Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki 305-8565, Japan
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44
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Amirjalayer S, Martinez‐Cuezva A, Berna J, Woutersen S, Buma WJ. Photoinduced Pedalo-Type Motion in an Azodicarboxamide-Based Molecular Switch. Angew Chem Int Ed Engl 2018; 57:1792-1796. [PMID: 29139183 PMCID: PMC5814897 DOI: 10.1002/anie.201709666] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/23/2017] [Indexed: 01/05/2023]
Abstract
Well-defined structural changes of molecular units that can be triggered by light are crucial for the development of photoactive functional materials. Herein, we report on a novel switch that has azodicarboxamide as its photo-triggerable element. Time-resolved UV-pump/IR probe spectroscopy in combination with quantum-chemical calculations shows that the azodicarboxamide functionality, in contrast to other azo-based chromophores, does not undergo trans-cis photoisomerization. Instead, a photoinduced pedalo-type motion occurs, which because of its volume-conserving properties enables the design of functional molecular systems with controllable motion in a confined space.
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Affiliation(s)
- Saeed Amirjalayer
- Physikalisches Institut and Center for Multiscale Theory and ComputationWestfälische Wilhelms-Universität MünsterWillhelm-Klemm-Strasse 1048149MünsterGermany
- Center for Nanotechnology (CeNTech)Heisenbergstrasse 1148149MünsterGermany
| | | | - Jose Berna
- Departamento de Química OrgánicaFacultad de QuímicaUniversidad de Murcia30100MurciaSpain
| | - Sander Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
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45
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Guo Y, Wolff FE, Schapiro I, Elstner M, Marazzi M. Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2. Phys Chem Chem Phys 2018; 20:27501-27509. [DOI: 10.1039/c8cp05210g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Franziska E. Wolff
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research
- Institute of Chemistry
- Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Marcus Elstner
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
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46
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Amirjalayer S, Martinez-Cuezva A, Berna J, Woutersen S, Buma WJ. Photoinduced Pedalo-Type Motion in an Azodicarboxamide-Based Molecular Switch. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Saeed Amirjalayer
- Physikalisches Institut and Center for Multiscale Theory and Computation; Westfälische Wilhelms-Universität Münster; Willhelm-Klemm-Strasse 10 48149 Münster Germany
- Center for Nanotechnology (CeNTech); Heisenbergstrasse 11 48149 Münster Germany
| | - Alberto Martinez-Cuezva
- Departamento de Química Orgánica; Facultad de Química; Universidad de Murcia; 30100 Murcia Spain
| | - Jose Berna
- Departamento de Química Orgánica; Facultad de Química; Universidad de Murcia; 30100 Murcia Spain
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
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47
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Di Donato M, Lerch MM, Lapini A, Laurent AD, Iagatti A, Bussotti L, Ihrig SP, Medved’ M, Jacquemin D, Szymański W, Buma WJ, Foggi P, Feringa BL. Shedding Light on the Photoisomerization Pathway of Donor-Acceptor Stenhouse Adducts. J Am Chem Soc 2017; 139:15596-15599. [PMID: 29039920 PMCID: PMC5680540 DOI: 10.1021/jacs.7b09081] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 12/20/2022]
Abstract
Donor-acceptor Stenhouse adducts (DASAs) are negative photochromes that hold great promise for a variety of applications. Key to optimizing their switching properties is a detailed understanding of the photoswitching mechanism, which, as yet, is absent. Here we characterize the actinic step of DASA-photoswitching and its key intermediate, which was studied using a combination of ultrafast visible and IR pump-probe spectroscopies and TD-DFT calculations. Comparison of the time-resolved IR spectra with DFT computations allowed to unambiguously identify the structure of the intermediate, confirming that light absorption induces a sequential reaction path in which a Z-E photoisomerization of C2-C3 is followed by a rotation around C3-C4 and a subsequent thermal cyclization step. First and second-generation DASAs share a common photoisomerization mechanism in chlorinated solvents with notable differences in kinetics and lifetimes of the excited states. The photogenerated intermediate of the second-generation DASA was photo-accumulated at low temperature and probed with time-resolved spectroscopy, demonstrating the photoreversibility of the isomerization process. Taken together, these results provide a detailed picture of the DASA isomerization pathway on a molecular level.
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Affiliation(s)
- Mariangela Di Donato
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, via della
Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Michael M. Lerch
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Andrea Lapini
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, via della
Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Adèle D. Laurent
- CEISAM, UMR CNRS 6230,
BP 92208, 2 Rue de
la Houssinière, 44322 Nantes Cedex 3, France
| | - Alessandro Iagatti
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
| | - Laura Bussotti
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Svante P. Ihrig
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Miroslav Medved’
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University in Olomouc, 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovak Republic
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230,
BP 92208, 2 Rue de
la Houssinière, 44322 Nantes Cedex 3, France
- Institut Universitaire de France, 103 bd St Michael, 75005 Paris Cedex 5, France
| | - Wiktor Szymański
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
- Department
of Radiology, University of Groningen, University
Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Wybren Jan Buma
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
| | - Paolo Foggi
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
- Dipartimento
di Chimica, Università di Perugia, via Elce di Sotto 8, 06100 Perugia, Italy
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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48
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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49
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Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nat Chem 2017; 10:31-37. [PMID: 29256511 DOI: 10.1038/nchem.2853] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/27/2017] [Indexed: 12/23/2022]
Abstract
Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.
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50
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Grimmelsmann L, Marefat Khah A, Spies C, Hättig C, Nuernberger P. Ultrafast Dynamics of a Triazene: Excited-State Pathways and the Impact of Binding to the Minor Groove of DNA and Further Biomolecular Systems. J Phys Chem Lett 2017; 8:1986-1992. [PMID: 28426228 DOI: 10.1021/acs.jpclett.7b00472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many synthetic DNA minor groove binders exhibit a strong increase in fluorescence when bound to DNA. The pharmaceutical-relevant berenil (diminazene aceturate) is an exception with an extremely low fluorescence quantum yield (on the order of 10-4). We investigate the ultrafast excited-state dynamics of this triazene by femtosecond time-resolved fluorescence experiments in water, ethylene glycol, and buffer and bound to the enzyme β-trypsin, the minor groove of AT-rich DNA, and G-quadruplex DNA. Ab initio calculations provide additional mechanistic insight. The complementing studies unveil that the excited-state motion initiated by ππ* excitation occurs in two phases: a subpicosecond phase associated with the lengthening of the central N═N double bond, followed by a bicycle-pedal-type motion of the triazene bridge, which is almost volume-conserving and can proceed efficiently within only a few picoseconds even under spatially confined conditions. Our results elucidate the excited-state relaxation mechanism of aromatic triazenes and explain the modest sensitivity of the fluorescence quantum yield of berenil even when it is bound to various biomolecules.
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Affiliation(s)
- Lena Grimmelsmann
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Alireza Marefat Khah
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christian Spies
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christof Hättig
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Patrick Nuernberger
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
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