1
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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2
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, Mancuso A. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:141-162. [PMID: 38507205 DOI: 10.1007/978-3-031-52193-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.
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Affiliation(s)
| | | | | | | | | | - Chan Kim
- European XFEL, Schenefeld, Germany
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3
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Lee Y, Ki H, Im D, Eom S, Gu J, Lee S, Kim J, Cha Y, Lee KW, Zerdane S, Levantino M, Ihee H. Cerium Photocatalyst in Action: Structural Dynamics in the Presence of Substrate Visualized via Time-Resolved X-ray Liquidography. J Am Chem Soc 2023; 145:23715-23726. [PMID: 37856865 PMCID: PMC10623567 DOI: 10.1021/jacs.3c08166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Indexed: 10/21/2023]
Abstract
[Ce(III)Cl6]3-, with its earth-abundant metal element, is a promising photocatalyst facilitating carbon-halogen bond activation. Still, the structure of the reaction intermediate has yet to be explored. Here, we applied time-resolved X-ray liquidography (TRXL), which allows for direct observation of the structural details of reaction intermediates, to investigate the photocatalytic reaction of [Ce(III)Cl6]3-. Structural analysis of the TRXL data revealed that the excited state of [Ce(III)Cl6]3- has Ce-Cl bonds that are shorter than those of the ground state and that the Ce-Cl bond further contracts upon oxidation. In addition, this study represents the first application of TRXL to both photocatalyst-only and photocatalyst-and-substrate samples, providing insights into the substrate's influence on the photocatalyst's reaction dynamics. This study demonstrates the capability of TRXL in elucidating the reaction dynamics of photocatalysts under various conditions and highlights the importance of experimental determination of the structures of reaction intermediates to advance our understanding of photocatalytic mechanisms.
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Affiliation(s)
- Yunbeom Lee
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hosung Ki
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Donghwan Im
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seunghwan Eom
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jain Gu
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seonggon Lee
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jungmin Kim
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yongjun Cha
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Kyung Won Lee
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Serhane Zerdane
- European
Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matteo Levantino
- European
Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Hyotcherl Ihee
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon, 34141, Republic
of Korea
- Department
of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
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4
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [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] [Received: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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5
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Pounot K, Schirò G, Levantino M. Tracking the structural dynamics of proteins with time-resolved X-ray solution scattering. Curr Opin Struct Biol 2023; 82:102661. [PMID: 37536065 DOI: 10.1016/j.sbi.2023.102661] [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] [Received: 02/23/2023] [Revised: 05/03/2023] [Accepted: 06/29/2023] [Indexed: 08/05/2023]
Abstract
Relevant events during protein function such as ligand binding/release and interaction with substrates or with light are often accompanied by out-of-equilibrium structural dynamics. Time-resolved experimental techniques have been developed to follow protein structural changes as they happen in real time after a given reaction-triggering event. Time-resolved X-ray solution scattering is a promising approach that bears structural sensitivity with temporal resolution in the femto-to-millisecond time range, depending on the X-ray source characteristics and the triggering method. Here we present the basic principles of the technique together with a description of the most relevant results recently published and a discussion on the computational methods currently developed to achieve a structural interpretation of the time-resolved X-ray solution scattering experimental data.
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Affiliation(s)
- Kevin Pounot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.
| | - Matteo Levantino
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France.
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6
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Ki H, Gu J, Cha Y, Lee KW, Ihee H. Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:034103. [PMID: 37388296 PMCID: PMC10306411 DOI: 10.1063/4.0000189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles. Proper data analysis is key to extracting the information of the kinetics and structural dynamics of the studied system encrypted in the TRXL data. In typical TRXL data, the signals from solute scattering, solvent scattering, and solute-solvent cross scattering are mixed in the q-space, and the solute kinetics and solvent hydrodynamics are mixed in the time domain, thus complicating the data analysis. Various methods developed so far generally require prior knowledge of the molecular structures of candidate species involved in the reaction. Because such information is often unavailable, a typical data analysis often involves tedious trial and error. To remedy this situation, we have developed a method named projection to extract the perpendicular component (PEPC), capable of removing the contribution of solvent kinetics from TRXL data. The resulting data then contain only the solute kinetics, and, thus, the solute kinetics can be easily determined. Once the solute kinetics is determined, the subsequent data analysis to extract the structural information can be performed with drastically improved convenience. The application of the PEPC method is demonstrated with TRXL data from the photochemistry of two molecular systems: [Au(CN)2-]3 in water and CHI3 in cyclohexane.
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Affiliation(s)
| | | | | | | | - H. Ihee
- Author to whom correspondence should be addressed:
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7
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Nam Y, Song H, Freixas VM, Keefer D, Fernandez-Alberti S, Lee JY, Garavelli M, Tretiak S, Mukamel S. Monitoring vibronic coherences and molecular aromaticity in photoexcited cyclooctatetraene with an X-ray probe: a simulation study. Chem Sci 2023; 14:2971-2982. [PMID: 36937575 PMCID: PMC10016608 DOI: 10.1039/d2sc04335a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding conical intersection (CI) dynamics and subsequent conformational changes is key for exploring and controlling photo-reactions in aromatic molecules. Monitoring of their time-resolved dynamics remains a formidable experimental challenge. In this study, we simulate the photoinduced S3 to S1 non-adiabatic dynamics of cyclooctatetraene (COT), involving multiple CIs with relaxation times in good agreement with experiment. We further investigate the possibility to directly probe the CI passages in COT by off-resonant X-ray Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). We find that these signals sensitively monitor key chemical features during the ultrafast dynamics. First, we distinguish two CIs by using TRUECARS signals with their appearances at different Raman shifts. Second, we demonstrate that TRXD, where X-ray photons scatter off electron densities, can resolve ultrafast changes in the aromaticity of COT. It can further distinguish between planar and non-planar geometries explored during the dynamics, as e.g. two different tetraradical-type CIs. The knowledge gained from these measurements can give unique insight into fundamental chemical properties that dynamically change during non-adiabatic passages.
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Affiliation(s)
- Yeonsig Nam
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory Los Alamos New Mexico 87545 USA
| | - Victor M Freixas
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET B1876BXD Bernal Argentina
| | - Daniel Keefer
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | | | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University Suwon 16419 Korea
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari,", Universita' degli Studi di Bologna I-40136 Bologna Italy
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory Los Alamos New Mexico 87545 USA
| | - Shaul Mukamel
- Department of Chemistry, University of California Irvine California 92697-2025 USA
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8
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Katayama T, Choi TK, Khakhulin D, Dohn AO, Milne CJ, Vankó G, Németh Z, Lima FA, Szlachetko J, Sato T, Nozawa S, Adachi SI, Yabashi M, Penfold TJ, Gawelda W, Levi G. Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer. Chem Sci 2023; 14:2572-2584. [PMID: 36908966 PMCID: PMC9993854 DOI: 10.1039/d2sc06600a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Photochemical reactions in solution are governed by a complex interplay between transient intramolecular electronic and nuclear structural changes and accompanying solvent rearrangements. State-of-the-art time-resolved X-ray solution scattering has emerged in the last decade as a powerful technique to observe solute and solvent motions in real time. However, disentangling solute and solvent dynamics and how they mutually influence each other remains challenging. Here, we simultaneously measure femtosecond X-ray emission and scattering to track both the intramolecular and solvation structural dynamics following photoexcitation of a solvated copper photosensitizer. Quantitative analysis assisted by molecular dynamics simulations reveals a two-step ligand flattening strongly coupled to the solvent reorganization, which conventional optical methods could not discern. First, a ballistic flattening triggers coherent motions of surrounding acetonitrile molecules. In turn, the approach of acetonitrile molecules to the copper atom mediates the decay of intramolecular coherent vibrations and induces a further ligand flattening. These direct structural insights reveal that photoinduced solute and solvent motions can be intimately intertwined, explaining how the key initial steps of light harvesting are affected by the solvent on the atomic time and length scale. Ultimately, this work takes a step forward in understanding the microscopic mechanisms of the bidirectional influence between transient solvent reorganization and photoinduced solute structural dynamics.
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Affiliation(s)
- Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute Kouto 1-1-1, Sayo Hyogo 679-5198 Japan.,RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Tae-Kyu Choi
- XFEL Division, Pohang Accelerator Laboratory Jigok-ro 127-80 Pohang 37673 Republic of Korea
| | | | - Asmus O Dohn
- Science Institute, University of Iceland 107 Reykjavík Iceland .,DTU Physics, Technical University of Denmark Kongens Lyngby Denmark
| | | | - György Vankó
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | - Zoltán Németh
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | | | - Jakub Szlachetko
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University PL-30392 Kraków Poland
| | - Tokushi Sato
- European XFEL Holzkoppel 4, Schenefeld 22869 Germany
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Thomas J Penfold
- Chemistry-School of Natural and Environmental Sciences, Newcastle University Newcastle Upon-Tyne NE1 7RU UK
| | - Wojciech Gawelda
- Departamento de Química, Universidad Autónoma de Madrid, Campus Cantoblanco 28047 Madrid Spain.,IMDEA-Nanociencia, Campus Cantoblanco C/Faraday 9 28049 Madrid Spain.,Faculty of Physics, Adam Mickiewicz University 61-614 Poznań Poland
| | - Gianluca Levi
- Science Institute, University of Iceland 107 Reykjavík Iceland
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9
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Kosheleva I, Henning R, Kim I, Kim SO, Kusel M, Srajer V. Sample-minimizing co-flow cell for time-resolved pump-probe X-ray solution scattering. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:490-499. [PMID: 36891863 PMCID: PMC10000795 DOI: 10.1107/s1600577522012127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 06/10/2023]
Abstract
A fundamental problem in biological sciences is understanding how macromolecular machines work and how the structural changes of a molecule are connected to its function. Time-resolved techniques are vital in this regard and essential for understanding the structural dynamics of biomolecules. Time-resolved small- and wide-angle X-ray solution scattering has the capability to provide a multitude of information about the kinetics and global structural changes of molecules under their physiological conditions. However, standard protocols for such time-resolved measurements often require significant amounts of sample, which frequently render time-resolved measurements impossible. A cytometry-type sheath co-flow cell, developed at the BioCARS 14-ID beamline at the Advanced Photon Source, USA, allows time-resolved pump-probe X-ray solution scattering measurements to be conducted with sample consumption reduced by more than ten times compared with standard sample cells and protocols. The comparative capabilities of the standard and co-flow experimental setups were demonstrated by studying time-resolved signals in photoactive yellow protein.
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Affiliation(s)
- Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Robert Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Insik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, E6-6 #513, 291 Daehak-ro, Daejeon, Yuseong-gu 34141, Republic of Korea
| | - Michael Kusel
- Kusel Design, 12 Coghlan Street, Niddrie, Wurundjeri Country 3042, Australia
| | - Vukica Srajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
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10
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Du DX, Simjanoska M, Fitzpatrick AWP. Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. J Struct Biol 2023; 215:107941. [PMID: 36773734 DOI: 10.1016/j.jsb.2023.107941] [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] [Received: 10/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
As structural determination of protein complexes approaches atomic resolution, there is an increasing focus on conformational dynamics. Here we conceptualize the combination of two techniques which have become established in recent years: microcrystal electron diffraction and ultrafast electron microscopy. We show that the extremely low dose of pulsed photoemission still enables microED due to the strength of the electron bunching from diffraction of the protein crystals. Indeed, ultrafast electron diffraction experiments on protein crystals have already been demonstrated to be effective in measuring intermolecular forces in protein microcrystals. We discuss difficulties that may arise in the acquisition and processing of data and the overall feasibility of the experiment, paying specific attention to dose and signal-to-noise ratio. In doing so, we outline a detailed workflow that may be effective in minimizing the dose on the specimen. A series of model systems that would be good candidates for initial experiments is provided.
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Affiliation(s)
- Daniel X Du
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Marija Simjanoska
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Anthony W P Fitzpatrick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
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11
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Lu Y, Yang GZ, Yang D. Effects of ligand binding on dynamics of fatty acid binding protein and interactions with membranes. Biophys J 2022; 121:4024-4032. [PMID: 36196055 PMCID: PMC9675020 DOI: 10.1016/j.bpj.2022.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Intracellular transport of fatty acids involves binding of ligands to their carrier fatty acid binding proteins (FABPs) and interactions of ligand-free and -bound FABPs with membranes. Previous studies focused on ligand-free FABPs. Here, our amide hydrogen exchange data showed that oleic acid binding to human intestinal FABP (hIFABP) stabilizes the protein, most likely through enhancing the hydrogen-bonding network, and induces rearrangement of sidechains even far away from the ligand binding site. Using NMR relaxation techniques, we found that the ligand binding affects not only conformational exchanges between major and minor states but also the affinity of hIFABP to nanodiscs. Analyses of the relaxation and amide exchange data suggested that two minor native-like states existing in both ligand-free and -bound hIFABPs originate from global "breathing" motions, while one minor native-like state comes from local motions. The amide hydrogen exchange data also indicated that helix αII undergoes local unfolding through which ligands can exit from the binding cavity.
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Affiliation(s)
- Yimei Lu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Gabriel Zhang Yang
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore.
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12
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Ki H, Kim TW, Moon J, Kim J, Lee Y, Heo J, Kim KH, Kong Q, Khakhulin D, Newby G, Kim J, Kim J, Wulff M, Ihee H. Photoactivation of triosmium dodecacarbonyl at 400 nm probed with time-resolved X-ray liquidography. Chem Commun (Camb) 2022; 58:7380-7383. [PMID: 35695475 DOI: 10.1039/d2cc02438a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoactivation mechanism of Os3(CO)12 at 400 nm is examined with time-resolved X-ray liquidography. The data reveal two pathways: the vibrational relaxation following an internal conversion to the electronic ground state and the ligand dissociation to form Os3(CO)11 with a ligand vacancy at the axial position.
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Affiliation(s)
- Hosung Ki
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea. .,Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Mokpo National University, Muan-gun, Jeollanam-do 58554, Republic of Korea
| | - Jiwon Moon
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Jungmin Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea. .,Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yunbeom Lee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea. .,Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jun Heo
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea. .,Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyung Hwan Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Qingyu Kong
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
| | | | - Gemma Newby
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 22212, Republic of Korea
| | - Michael Wulff
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - Hyotcherl Ihee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea. .,Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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13
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Lee SJ, Kim TW, Kim JG, Yang C, Yun SR, Kim C, Ren Z, Kumarapperuma I, Kuk J, Moffat K, Yang X, Ihee H. Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering. SCIENCE ADVANCES 2022; 8:eabm6278. [PMID: 35622911 PMCID: PMC9140987 DOI: 10.1126/sciadv.abm6278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/13/2022] [Indexed: 05/25/2023]
Abstract
Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Mokpo National University, Muan-gun, Jeollanam-do, 58554, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Changin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jane Kuk
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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14
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Heo J, Kim JG, Choi EH, Ki H, Ahn DS, Kim J, Lee S, Ihee H. Determining the charge distribution and the direction of bond cleavage with femtosecond anisotropic x-ray liquidography. Nat Commun 2022; 13:522. [PMID: 35082327 PMCID: PMC8792042 DOI: 10.1038/s41467-022-28168-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Energy, structure, and charge are fundamental quantities characterizing a molecule. Whereas the energy flow and structure change in chemical reactions are experimentally characterized, determining the atomic charges of a molecule in solution has been elusive, even for a triatomic molecule such as triiodide ion, I3-. Moreover, it remains to be answered how the charge distribution is coupled to the molecular geometry; which I-I bond, if two I-I bonds are unequal, dissociates depending on the electronic state. Here, femtosecond anisotropic x-ray solution scattering allows us to provide the following answers in addition to the overall rich structural dynamics. The analysis unravels that the negative charge of I3- is highly localized on the terminal iodine atom forming the longer bond with the central iodine atom, and the shorter I-I bond dissociates in the excited state, whereas the longer one in the ground state. We anticipate that this work may open a new avenue for studying the atomic charge distribution of molecules in solution and taking advantage of orientational information in anisotropic scattering data for solution-phase structural dynamics.
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Affiliation(s)
- Jun Heo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Doo-Sik Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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15
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Jeong H, Ki H, Kim JG, Kim J, Lee Y, Ihee H. Sensitivity of
time‐resolved
diffraction data to changes in internuclear distances and atomic positions. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Haeyun Jeong
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
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16
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Heyne K. Impact of Ultrafast Electric Field Changes on Photoreceptor Protein Dynamics. J Phys Chem B 2022; 126:581-587. [PMID: 35026113 DOI: 10.1021/acs.jpcb.1c08131] [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
Studies on photoreceptors provide a wealth of information on cofactor and protein dynamics on the microsecond to seconds time-scale. Up to now, ultrafast dynamics addresses mainly the cofactor or chromophore, but ultrafast protein dynamics are poorly understood. Increasing evidence show that protein responses can occur even faster than the cofactor dynamics. The causal reason for the ultrafast protein response cannot be explained by the localized cofactor excitation or its excited-state decay, alone. We propose a Coulomb interaction mechanism started by a shock wave and stabilized by a dipole moment change at least partially responsible for coherent oscillations in proteins, protonation changes, water dislocations, and protein changes prior to and beyond chromophore's excited-state decay. Photoexcitation changes the electron density distribution of the chromophore within a few femtoseconds: The Coulomb shock wave affects polar groups, hydrogen bonds, and protein bound water molecules. The process occurs on a time-scale even faster than excited-state decay of the chromophore. We discuss studies on selected photoreceptors in light of this mechanism and its impact on a detailed understanding of protein dynamics.
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Affiliation(s)
- Karsten Heyne
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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17
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Choi EH, Lee Y, Heo J, Ihee H. Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers. Chem Sci 2022; 13:8457-8490. [PMID: 35974755 PMCID: PMC9337737 DOI: 10.1039/d2sc00502f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet. Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.![]()
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Affiliation(s)
- Eun Hyuk Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jun Heo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
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18
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Kim Y, Ma R, Lee J, Harich J, Nam D, Kim S, Kim M, Ochmann M, Eom I, Huse N, Lee JH, Kim TK. Ligand-Field Effects in a Ruthenium(II) Polypyridyl Complex Probed by Femtosecond X-ray Absorption Spectroscopy. J Phys Chem Lett 2021; 12:12165-12172. [PMID: 34914396 DOI: 10.1021/acs.jpclett.1c02400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We employ femtosecond X-ray absorption spectroscopy of [Ru(m-bpy)3]2+ (m-bpy = 6-methyl-2,2'-bipyridine) to elucidate the time evolution of the spin and charge density upon metal-to-ligand charge-transfer (MLCT) excitation. The core-level transitions at the Ru L3-edge reveal a very short MLCT lifetime of 0.9 ps and relaxation to the lowest triplet metal-centered state (3MC) which exhibits a lifetime of about 300 ps. Time-dependent density functional theory relates ligand methylation to a lower ligand field strength that stabilizes the 3MC state. A quarter of the 3MLCT population appears to be trapped which may be attributed to intramolecular vibrational relaxation or further electron transfer to the solvent. Our results demonstrate that small changes in the ligand field allow control of the photophysical properties. Moreover, this study underscores the high information content of femtosecond L-edge spectroscopy as a probe of valence charge density and spin-state in 4d transition metals.
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Affiliation(s)
- Yujin Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | | | - Junho Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Jessica Harich
- Department of Physics, University of Hamburg and Center for Free-Electron Laser Science, 22761 Hamburg, Germany
| | | | | | | | - Miguel Ochmann
- Department of Physics, University of Hamburg and Center for Free-Electron Laser Science, 22761 Hamburg, Germany
| | | | - Nils Huse
- Department of Physics, University of Hamburg and Center for Free-Electron Laser Science, 22761 Hamburg, Germany
| | | | - Tae Kyu Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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19
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Orädd F, Ravishankar H, Goodman J, Rogne P, Backman L, Duelli A, Nors Pedersen M, Levantino M, Wulff M, Wolf-Watz M, Andersson M. Tracking the ATP-binding response in adenylate kinase in real time. SCIENCE ADVANCES 2021; 7:eabi5514. [PMID: 34788091 PMCID: PMC8597995 DOI: 10.1126/sciadv.abi5514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
Abstract
The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a “cracking mechanism” proposed to underlie global structural transformation, such as allostery, in proteins.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Harsha Ravishankar
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Jack Goodman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Martin Nors Pedersen
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Matteo Levantino
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Michael Wulff
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
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20
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Gu J, Lee S, Eom S, Ki H, Choi EH, Lee Y, Nozawa S, Adachi SI, Kim J, Ihee H. Structural Dynamics of C 2F 4I 2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography. Int J Mol Sci 2021; 22:9793. [PMID: 34575954 PMCID: PMC8469616 DOI: 10.3390/ijms22189793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/28/2022] Open
Abstract
The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute-solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase.
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Affiliation(s)
- Jain Gu
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Seunghwan Eom
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Eun Hyuk Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Ibaraki, Japan; (S.N.); (S.-i.A.)
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba 305-0801, Ibaraki, Japan
| | - Shin-ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Ibaraki, Japan; (S.N.); (S.-i.A.)
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba 305-0801, Ibaraki, Japan
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Korea;
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (J.G.); (S.L.); (S.E.); (H.K.); (E.H.C.); (Y.L.)
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Korea
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21
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
- Correspondence:
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22
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Filming ultrafast roaming-mediated isomerization of bismuth triiodide in solution. Nat Commun 2021; 12:4732. [PMID: 34354075 PMCID: PMC8342516 DOI: 10.1038/s41467-021-25070-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/20/2021] [Indexed: 12/19/2022] Open
Abstract
Roaming reaction, defined as a reaction yielding products via reorientational motion in the long-range region (3 - 8 Å) of the potential, is a relatively recently proposed reaction pathway and is now regarded as a universal mechanism that can explain the unimolecular dissociation and isomerization of various molecules. The structural movements of the partially dissociated fragments originating from the frustrated bond fission at the onset of roaming, however, have been explored mostly via theoretical simulations and rarely observed experimentally. Here, we report an investigation of the structural dynamics during a roaming-mediated isomerization reaction of bismuth triiodide (BiI3) in acetonitrile solution using femtosecond time-resolved x-ray liquidography. Structural analysis of the data visualizes the atomic movements during the roaming-mediated isomerization process including the opening of the Bi-Ib-Ic angle and the closing of Ia-Bi-Ib-Ic dihedral angle, each by ~40°, as well as the shortening of the Ib···Ic distance, following the frustrated bond fission.
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