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De Angelis D, Longetti L, Bonano G, Pelli Cresi JS, Foglia L, Pancaldi M, Capotondi F, Pedersoli E, Bencivenga F, Krstulovic M, Menk RH, D'Addato S, Orlando S, de Simone M, Ingle RA, Bleiner D, Coreno M, Principi E, Chergui M, Masciovecchio C, Mincigrucci R. A sub-100 nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:605-612. [PMID: 38592969 DOI: 10.1107/s1600577524001875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Experimental characterization of the structural, electronic and dynamic properties of dilute systems in aqueous solvents, such as nanoparticles, molecules and proteins, are nowadays an open challenge. X-ray absorption spectroscopy (XAS) is probably one of the most established approaches to this aim as it is element-specific. However, typical dilute systems of interest are often composed of light elements that require extreme-ultraviolet to soft X-ray photons. In this spectral regime, water and other solvents are rather opaque, thus demanding radical reduction of the solvent volume and removal of the liquid to minimize background absorption. Here, we present an experimental endstation designed to operate a liquid flat jet of sub-micrometre thickness in a vacuum environment compatible with extreme ultraviolet/soft XAS measurements in transmission geometry. The apparatus developed can be easily connected to synchrotron and free-electron-laser user-facility beamlines dedicated to XAS experiments. The conditions for stable generation and control of the liquid flat jet are analyzed and discussed. Preliminary soft XAS measurements on some test solutions are shown.
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Affiliation(s)
- Dario De Angelis
- CNR - Istituto Officina dei Materiali (IOM), Basovizza, Area Science Park, 34149 Trieste, Italy
| | - Luca Longetti
- Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Gabriele Bonano
- Dipartimento FIM, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/a, 41125 Modena, Italy
| | | | - Laura Foglia
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Matteo Pancaldi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Flavio Capotondi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Emanuele Pedersoli
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Filippo Bencivenga
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Marija Krstulovic
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Ralf Hendrik Menk
- Sezione di Trieste, Istituto Nazionale di Fisica Nucleare, Via Valerio 2, 34127 Trieste, Italy
| | - Sergio D'Addato
- Dipartimento FIM, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/a, 41125 Modena, Italy
| | - Stefano Orlando
- ISM-CNR, Trieste Branch, in Basovizza Area Science Park, 34149 Trieste, Italy
| | - Monica de Simone
- CNR - Istituto Officina dei Materiali (IOM), Basovizza, Area Science Park, 34149 Trieste, Italy
| | - Rebecca A Ingle
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Davide Bleiner
- Laboratory for Advanced Analytical Technologies, EMPA, Uberlandstrasse 129, CH-8600 Dübendorf, Switzerland
| | - Marcello Coreno
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Emiliano Principi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Majed Chergui
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Riccardo Mincigrucci
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
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2
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Guo M, Braun A, Sokaras D, Kroll T. Iron Kβ X-ray Emission Spectroscopy: The Origin of Spectral Features from Atomic to Molecular Systems Using Multi-configurational Calculations. J Phys Chem A 2024; 128:1260-1273. [PMID: 38329897 DOI: 10.1021/acs.jpca.3c07949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Kβ X-ray emission spectroscopy (XES) is widely used to fingerprint the local spin of transition-metal ions, including in pump-probe experiments, to identify excited states or in chemical and biological reactions to characterize short-lived intermediates. In this study, the spectra of ferrous and ferric complexes for various spin states were measured experimentally and described theoretically through restricted active space (RAS) calculations including dynamic correlations. Through the RAS calculations from simple atomic models to complex molecular systems, spectral effects such as the exchange interactions, crystal-field strength, and covalent orbital mixing were evaluated and discussed. The calculations find that only the spectral features of low-spin cases show a dependence on the crystal-field strength, particularly for ferrous low spin. The effect of the covalent orbital mixing strength on the first moment of the Kβ1,3 main line and the Kβ1,3-Kβ' energy splitting is quantitatively described. Clear relationships are found within a given nominal spin but less between different spin states, which calls for careful selection of reference spectra in future experiments. This study further advances our understanding of the correlation between changes in experimental spectral features and their corresponding electronic structure information.
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Affiliation(s)
- Meiyuan Guo
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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3
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Lima FA, Otte F, Vakili M, Ardana-Lamas F, Biednov M, Dall’Antonia F, Frankenberger P, Gawelda W, Gelisio L, Han H, Huang X, Jiang Y, Kloos M, Kluyver T, Knoll M, Kubicek K, Bermudez Macias IJ, Schulz J, Turkot O, Uemura Y, Valerio J, Wang H, Yousef H, Zalden P, Khakhulin D, Bressler C, Milne C. Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:1168-1182. [PMID: 37860937 PMCID: PMC10624029 DOI: 10.1107/s1600577523008159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.
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Affiliation(s)
- F. A. Lima
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - F. Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Fakultät für Physik, Technical University Dortmund, Dortmund, Germany
| | - M. Vakili
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - M. Biednov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - W. Gawelda
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - L. Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - X. Huang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T. Kluyver
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Knoll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - K. Kubicek
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | | | - J. Schulz
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - O. Turkot
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Wang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. Zalden
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D. Khakhulin
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Bressler
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | - C. Milne
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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4
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Kurta RP, van Driel TB, Dohn AO, Berberich TB, Nelson S, Zaluzhnyy IA, Mukharamova N, Lapkin D, Zederkof DB, Seaberg M, Pedersen KS, Kjær KS, Rippy GI, Biasin E, Møller KB, Gelisio L, Haldrup K, Vartanyants IA, Nielsen MM. Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser. Phys Chem Chem Phys 2023; 25:23417-23434. [PMID: 37486006 DOI: 10.1039/d3cp01257c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
We apply ultrashort X-ray laser pulses to track optically excited structural dynamics of [Ir2(dimen)4]2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered X-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir2(dimen)4]2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir2(dimen)4]2+ with a larger Ir-Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. The proposed X-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.
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Affiliation(s)
- Ruslan P Kurta
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
| | - Tim B van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Asmus O Dohn
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Lyngby, Denmark.
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Iceland
| | | | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A Zaluzhnyy
- Department of Physics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | | | - Dmitry Lapkin
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Diana B Zederkof
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Lyngby, Denmark.
| | - Matthew Seaberg
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kasper S Pedersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Lyngby, Denmark
| | - Kasper S Kjær
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Geoffery Ian Rippy
- Department of Materials Science and Engineering, University of California Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Lyngby, Denmark
| | - Luca Gelisio
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Lyngby, Denmark.
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Martin M Nielsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Lyngby, Denmark.
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5
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Zhang J, Liu L, Zheng C, Li W, Wang C, Wang T. Embedded nano spin sensor for in situ probing of gas adsorption inside porous organic frameworks. Nat Commun 2023; 14:4922. [PMID: 37582960 PMCID: PMC10427628 DOI: 10.1038/s41467-023-40683-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023] Open
Abstract
Spin-based sensors have attracted considerable attention owing to their high sensitivities. Herein, we developed a metallofullerene-based nano spin sensor to probe gas adsorption within porous organic frameworks. For this, spin-active metallofullerene, Sc3C2@C80, was selected and embedded into a nanopore of a pyrene-based covalent organic framework (Py-COF). Electron paramagnetic resonance (EPR) spectroscopy recorded the EPR signals of Sc3C2@C80 within Py-COF after adsorbing N2, CO, CH4, CO2, C3H6, and C3H8. Results indicated that the regularly changing EPR signals of embedded Sc3C2@C80 were associated with the gas adsorption performance of Py-COF. In contrast to traditional adsorption isotherm measurements, this implantable nano spin sensor could probe gas adsorption and desorption with in situ, real-time monitoring. The proposed nano spin sensor was also employed to probe the gas adsorption performance of a metal-organic framework (MOF-177), demonstrating its versatility. The nano spin sensor is thus applicable for quantum sensing and precision measurements.
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Affiliation(s)
- Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linshan Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
| | - Chaofeng Zheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wang Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
| | - Chunru Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
| | - Taishan Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China.
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6
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Sension RJ, McClain TP, Lamb RM, Alonso-Mori R, Lima FA, Ardana-Lamas F, Biednov M, Chollet M, Chung T, Deb A, Dewan PA, Gee LB, Huang Ze En J, Jiang Y, Khakhulin D, Li J, Michocki LB, Miller NA, Otte F, Uemura Y, van Driel TB, Penner-Hahn JE. Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J Am Chem Soc 2023. [PMID: 37327324 DOI: 10.1021/jacs.3c04099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Femtosecond time-resolved X-ray absorption (XANES) at the Co K-edge, X-ray emission (XES) in the Co Kβ and valence-to-core regions, and broadband UV-vis transient absorption are combined to probe the femtosecond to picosecond sequential atomic and electronic dynamics following photoexcitation of two vitamin B12 compounds, hydroxocobalamin and aquocobalamin. Polarized XANES difference spectra allow identification of sequential structural evolution involving first the equatorial and then the axial ligands, with the latter showing rapid coherent bond elongation to the outer turning point of the excited state potential followed by recoil to a relaxed excited state structure. Time-resolved XES, especially in the valence-to-core region, along with polarized optical transient absorption suggests that the recoil results in the formation of a metal-centered excited state with a lifetime of 2-5 ps. This combination of methods provides a uniquely powerful tool to probe the electronic and structural dynamics of photoactive transition-metal complexes and will be applicable to a wide variety of systems.
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Affiliation(s)
- Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Taylor P McClain
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Ryan M Lamb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Frederico Alves Lima
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fernando Ardana-Lamas
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mykola Biednov
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Taewon Chung
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Paul A Dewan
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Joel Huang Ze En
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Yifeng Jiang
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Dmitry Khakhulin
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Jianhao Li
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Lindsay B Michocki
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Florian Otte
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tim B van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
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7
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Zhao Y, Adiyeri Saseendran DP, Huang C, Triana CA, Marks WR, Chen H, Zhao H, Patzke GR. Oxygen Evolution/Reduction Reaction Catalysts: From In Situ Monitoring and Reaction Mechanisms to Rational Design. Chem Rev 2023; 123:6257-6358. [PMID: 36944098 DOI: 10.1021/acs.chemrev.2c00515] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) are core steps of various energy conversion and storage systems. However, their sluggish reaction kinetics, i.e., the demanding multielectron transfer processes, still render OER/ORR catalysts less efficient for practical applications. Moreover, the complexity of the catalyst-electrolyte interface makes a comprehensive understanding of the intrinsic OER/ORR mechanisms challenging. Fortunately, recent advances of in situ/operando characterization techniques have facilitated the kinetic monitoring of catalysts under reaction conditions. Here we provide selected highlights of recent in situ/operando mechanistic studies of OER/ORR catalysts with the main emphasis placed on heterogeneous systems (primarily discussing first-row transition metals which operate under basic conditions), followed by a brief outlook on molecular catalysts. Key sections in this review are focused on determination of the true active species, identification of the active sites, and monitoring of the reactive intermediates. For in-depth insights into the above factors, a short overview of the metrics for accurate characterizations of OER/ORR catalysts is provided. A combination of the obtained time-resolved reaction information and reliable activity data will then guide the rational design of new catalysts. Strategies such as optimizing the restructuring process as well as overcoming the adsorption-energy scaling relations will be discussed. Finally, pending current challenges and prospects toward the understanding and development of efficient heterogeneous catalysts and selected homogeneous catalysts are presented.
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Affiliation(s)
- Yonggui Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | | - Chong Huang
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Carlos A Triana
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Walker R Marks
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hang Chen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Han Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Greta R Patzke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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8
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Bacellar C, Rouxel JR, Ingle RA, Mancini GF, Kinschel D, Cannelli O, Zhao Y, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Ozerov D, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c. J Phys Chem Lett 2023; 14:2425-2432. [PMID: 36862109 DOI: 10.1021/acs.jpclett.3c00218] [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: 06/18/2023]
Abstract
We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300 nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723-13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.
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Affiliation(s)
- Camila Bacellar
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jérémy R Rouxel
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- Univ Lyon, UJM-Saint-Etienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien, UMR 5516, Saint-Etienne F-42023, France
| | - Rebecca A Ingle
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Giulia F Mancini
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- 2Laboratory for Ultrafast X-ray and Electron Microscopy, Department of Physics, University of Pavia, Via Agostino Bassi 6, 27100 Pavia PV, Italy
| | - Dominik Kinschel
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Yang Zhao
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Claudio Cirelli
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | | | - Samuel Menzi
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | | | - Wojciech Gawelda
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- IMDEA Nanociencia, Calle Faraday 9, 28049 Madrid, Spain
| | | | - Mykola Biednov
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
| | | | | | | | - Christopher J Milne
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
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9
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Element- and enantiomer-selective visualization of molecular motion in real-time. Nat Commun 2023; 14:386. [PMID: 36693825 PMCID: PMC9873934 DOI: 10.1038/s41467-023-36047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023] Open
Abstract
Ultrafast optical-domain spectroscopies allow to monitor in real time the motion of nuclei in molecules. Achieving element-selectivity had to await the advent of time resolved X-ray spectroscopy, which is now commonly carried at X-ray free electron lasers. However, detecting light element that are commonly encountered in organic molecules, remained elusive due to the need to work under vacuum. Here, we present an impulsive stimulated Raman scattering (ISRS) pump/carbon K-edge absorption probe investigation, which allowed observation of the low-frequency vibrational modes involving specific selected carbon atoms in the Ibuprofen RS dimer. Remarkably, by controlling the probe light polarization we can preferentially access the enantiomer of the dimer to which the carbon atoms belong.
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10
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E J, Kim Y, Bielecki J, Sikorski M, de Wijn R, Fortmann-Grote C, Sztuk-Dambietz J, Koliyadu JCP, Letrun R, Kirkwood HJ, Sato T, Bean R, Mancuso AP, Kim C. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:064101. [PMID: 36411869 PMCID: PMC9675053 DOI: 10.1063/4.0000169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 05/15/2023]
Abstract
The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.
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Affiliation(s)
- Juncheng E
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Bielecki
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Sikorski
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. de Wijn
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - R. Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - T. Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - C. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Author to whom correspondence should be addressed:
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11
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12
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Penfold TJ, Rankine CD. A deep neural network for valence-to-core X-ray emission spectroscopy. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2123406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- T. J. Penfold
- Chemistry–School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - C. D. Rankine
- Chemistry–School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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13
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Chiral control of spin-crossover dynamics in Fe(II) complexes. Nat Chem 2022; 14:739-745. [PMID: 35618767 DOI: 10.1038/s41557-022-00933-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022]
Abstract
Iron-based spin-crossover complexes hold tremendous promise as multifunctional switches in molecular devices. However, real-world technological applications require the excited high-spin state to be kinetically stable-a feature that has been achieved only at cryogenic temperatures. Here we demonstrate high-spin-state trapping by controlling the chiral configuration of the prototypical iron(II)tris(4,4'-dimethyl-2,2'-bipyridine) in solution, associated for stereocontrol with the enantiopure Δ- or Λ-enantiomer of tris(3,4,5,6-tetrachlorobenzene-1,2-diolato-κ2O1,O2)phosphorus(V) (P(O2C6Cl4)3- or TRISPHAT) anions. We characterize the high-spin-state relaxation using broadband ultrafast circular dichroism spectroscopy in the deep ultraviolet in combination with transient absorption and anisotropy measurements. We find that the high-spin-state decay is accompanied by ultrafast changes of its optical activity, reflecting the coupling to a symmetry-breaking torsional twisting mode, contrary to the commonly assumed picture. The diastereoselective ion pairing suppresses the vibrational population of the identified reaction coordinate, thereby achieving a fourfold increase of the high-spin-state lifetime. More generally, our results motivate the synthetic control of the torsional modes of iron(II) complexes as a complementary route to manipulate their spin-crossover dynamics.
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14
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Nikelshparg EI, Baizhumanov AA, Bochkova ZV, Novikov SM, Yakubovsky DI, Arsenin AV, Volkov VS, Goodilin EA, Semenova AA, Sosnovtseva O, Maksimov GV, Brazhe NA. Detection of Hypertension-Induced Changes in Erythrocytes by SERS Nanosensors. BIOSENSORS 2022; 12:32. [PMID: 35049660 PMCID: PMC8773528 DOI: 10.3390/bios12010032] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 05/14/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is a promising tool that can be used in the detection of molecular changes triggered by disease development. Cardiovascular diseases (CVDs) are caused by multiple pathologies originating at the cellular level. The identification of these deteriorations can provide a better understanding of CVD mechanisms, and the monitoring of the identified molecular changes can be employed in the development of novel biosensor tools for early diagnostics. We applied plasmonic SERS nanosensors to assess changes in the properties of erythrocytes under normotensive and hypertensive conditions in the animal model. We found that spontaneous hypertension in rats leads (i) to a decrease in the erythrocyte plasma membrane fluidity and (ii) to a decrease in the mobility of the heme of the membrane-bound hemoglobin. We identified SERS parameters that can be used to detect pathological changes in the plasma membrane and submembrane region of erythrocytes.
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Affiliation(s)
- Evelina I. Nikelshparg
- Department of Biophysics, Biological Faculty, Moscow State University, 119991 Moscow, Russia; (A.A.B.); (Z.V.B.); (G.V.M.)
| | - Adil A. Baizhumanov
- Department of Biophysics, Biological Faculty, Moscow State University, 119991 Moscow, Russia; (A.A.B.); (Z.V.B.); (G.V.M.)
| | - Zhanna V. Bochkova
- Department of Biophysics, Biological Faculty, Moscow State University, 119991 Moscow, Russia; (A.A.B.); (Z.V.B.); (G.V.M.)
| | - Sergey M. Novikov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (MIPT), 141700 Dolgoprudny, Russia; (S.M.N.); (D.I.Y.); (A.V.A.); (V.S.V.)
| | - Dmitry I. Yakubovsky
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (MIPT), 141700 Dolgoprudny, Russia; (S.M.N.); (D.I.Y.); (A.V.A.); (V.S.V.)
| | - Aleksey V. Arsenin
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (MIPT), 141700 Dolgoprudny, Russia; (S.M.N.); (D.I.Y.); (A.V.A.); (V.S.V.)
| | - Valentyn S. Volkov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (MIPT), 141700 Dolgoprudny, Russia; (S.M.N.); (D.I.Y.); (A.V.A.); (V.S.V.)
| | - Eugene A. Goodilin
- Faculty of Materials Sciences, Moscow State University, 119991 Moscow, Russia; (E.A.G.); (A.A.S.)
- Department of Chemistry, Moscow State University, 119991 Moscow, Russia
| | - Anna A. Semenova
- Faculty of Materials Sciences, Moscow State University, 119991 Moscow, Russia; (E.A.G.); (A.A.S.)
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Georgy V. Maksimov
- Department of Biophysics, Biological Faculty, Moscow State University, 119991 Moscow, Russia; (A.A.B.); (Z.V.B.); (G.V.M.)
- Department of Physical Material Engineering, Federal State Autonomous Educational Institution of Higher Education “National Research Technological University “MISiS”, 119049 Moscow, Russia
| | - Nadezda A. Brazhe
- Department of Biophysics, Biological Faculty, Moscow State University, 119991 Moscow, Russia; (A.A.B.); (Z.V.B.); (G.V.M.)
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15
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Sension RJ, Chung T, Dewan P, McClain TP, Lamb RM, Penner-Hahn JE. Time-resolved spectroscopy: Advances in understanding the electronic structure and dynamics of cobalamins. Methods Enzymol 2022; 669:303-331. [DOI: 10.1016/bs.mie.2022.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Gaffney KJ. Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering. Chem Sci 2021; 12:8010-8025. [PMID: 34194691 PMCID: PMC8208315 DOI: 10.1039/d1sc01864g] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.
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Affiliation(s)
- Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University Menlo Park California 94025 USA
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17
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Bacellar C, Kinschel D, Cannelli O, Sorokin B, Katayama T, Mancini GF, Rouxel JR, Obara Y, Nishitani J, Ito H, Ito T, Kurahashi N, Higashimura C, Kudo S, Cirelli C, Knopp G, Nass K, Johnson PJM, Wach A, Szlachetko J, Lima FA, Milne CJ, Yabashi M, Suzuki T, Misawa K, Chergui M. Femtosecond X-ray spectroscopy of haem proteins. Faraday Discuss 2021; 228:312-328. [PMID: 33565544 DOI: 10.1039/d0fd00131g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss our recently reported femtosecond (fs) X-ray emission spectroscopy results on the ligand dissociation and recombination in nitrosylmyoglobin (MbNO) in the context of previous studies on ferrous haem proteins. We also present a preliminary account of femtosecond X-ray absorption studies on MbNO, pointing to the presence of more than one species formed upon photolysis.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Boris Sorokin
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jeremy R Rouxel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Yuki Obara
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Junichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hironori Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Terumasa Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Naoya Kurahashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, 7-1, Chiyoda, 102-8554 Tokyo, Japan
| | - Chika Higashimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shotaro Kudo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Claudio Cirelli
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | | | - Anna Wach
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | | | | | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kazuhiko Misawa
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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18
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Shelby ML, Wildman A, Hayes D, Mara MW, Lestrange PJ, Cammarata M, Balducci L, Artamonov M, Lemke HT, Zhu D, Seideman T, Hoffman BM, Li X, Chen LX. Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations. Proc Natl Acad Sci U S A 2021; 118:e2018966118. [PMID: 33782122 PMCID: PMC8040624 DOI: 10.1073/pnas.2018966118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.
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Affiliation(s)
- Megan L Shelby
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Dugan Hayes
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
| | - Michael W Mara
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Marco Cammarata
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Lodovico Balducci
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Maxim Artamonov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Tamar Seideman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195;
| | - Lin X Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
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19
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Bergmann U, Kern J, Schoenlein RW, Wernet P, Yachandra VK, Yano J. Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes. NATURE REVIEWS. PHYSICS 2021; 3:264-282. [PMID: 34212130 PMCID: PMC8245202 DOI: 10.1038/s42254-021-00289-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 05/14/2023]
Abstract
The metal centres in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.
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Affiliation(s)
- Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Physics, University of Wisconsin–Madison, Madison, WI, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert W. Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Philippe Wernet
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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20
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Rankine CD, Penfold TJ. Progress in the Theory of X-ray Spectroscopy: From Quantum Chemistry to Machine Learning and Ultrafast Dynamics. J Phys Chem A 2021; 125:4276-4293. [DOI: 10.1021/acs.jpca.0c11267] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- C. D. Rankine
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - T. J. Penfold
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
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21
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Panman MR, Biasin E, Berntsson O, Hermann M, Niebling S, Hughes AJ, Kübel J, Atkovska K, Gustavsson E, Nimmrich A, Dohn AO, Laursen M, Zederkof DB, Honarfar A, Tono K, Katayama T, Owada S, van Driel TB, Kjaer K, Nielsen MM, Davidsson J, Uhlig J, Haldrup K, Hub JS, Westenhoff S. Observing the Structural Evolution in the Photodissociation of Diiodomethane with Femtosecond Solution X-Ray Scattering. PHYSICAL REVIEW LETTERS 2020; 125:226001. [PMID: 33315438 DOI: 10.1103/physrevlett.125.226001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/25/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
Resolving the structural dynamics of the initial steps of chemical reactions is challenging. We report the femtosecond time-resolved wide-angle x-ray scattering of the photodissociation of diiodomethane in cyclohexane. The data reveal with structural detail how the molecule dissociates into radicals, how the radicals collide with the solvent, and how they form the photoisomer. We extract how translational and rotational kinetic energy is dispersed into the solvent. We also find that 85% of the primary radical pairs are confined to their original solvent cage and discuss how this influences the downstream recombination reactions.
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Affiliation(s)
- Matthijs R Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Elisa Biasin
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Markus Hermann
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Stephan Niebling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Ashley J Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Kalina Atkovska
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Asmus O Dohn
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Mads Laursen
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Diana B Zederkof
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Alireza Honarfar
- Department of Chemical Physics, Lund University, Box 124, S-2210, Lund, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tim B van Driel
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Kasper Kjaer
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Martin M Nielsen
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Jan Davidsson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE75120 Uppsala, Sweden
| | - Jens Uhlig
- Department of Chemical Physics, Lund University, Box 124, S-2210, Lund, Sweden
| | - Kristoffer Haldrup
- Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Jochen S Hub
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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22
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Femtosecond Optical Laser System with Spatiotemporal Stabilization for Pump-Probe Experiments at SACLA. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10217934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We constructed a synchronized femtosecond optical laser system with spatiotemporal stabilization for pump-probe experiments at SPring-8 Angstrom Compact Free Electron Laser (SACLA). Stabilization of output power and pointing has been achieved with a small fluctuation level of a few percent by controlling conditions of temperature and air-flow in the optical paths. A feedback system using a balanced optical-microwave phase detector (BOMPD) has been successfully realized to reduce jitter down to 50 fs. We demonstrated the temporal stability with a time-resolved X-ray diffraction measurement and observed the coherent phonon oscillation of the photo-excited Bi without the post-processing using the timing monitor.
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