1
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Detlefs B, Graziano S, Glatzel P. Fast Chemical Contrast by X-ray Fluorescence Intensity Ratio Detection. Anal Chem 2023. [PMID: 37235752 DOI: 10.1021/acs.analchem.3c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a protocol for efficient detection of the chemical state of an element based on X-ray emission (fluorescence) spectroscopy using a Bragg optics spectrometer. The ratio of intensities at two appropriately chosen X-ray emission energies is a self-normalized quantity largely free of experimental artifacts and can thus be recorded with high accuracy. As the X-ray fluorescence lines are chemically sensitive, the intensity ratio identifies the chemical state. Differences between chemical states in spatially inhomogeneous or temporally evolving samples can be identified already with low numbers of photon events. This reduces the time required for data acquisition by 2 orders of magnitude as compared to recording a full spectrum.
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Affiliation(s)
- Blanka Detlefs
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Serena Graziano
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Pieter Glatzel
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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2
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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3
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Glatzel P, Harris A, Marion P, Sikora M, Weng TC, Guilloud C, Lafuerza S, Rovezzi M, Detlefs B, Ducotté L. The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:362-371. [PMID: 33399588 DOI: 10.1107/s1600577520015416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/20/2020] [Indexed: 05/25/2023]
Abstract
X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.
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Affiliation(s)
- Pieter Glatzel
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | | | - Philippe Marion
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Marcin Sikora
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Tsu Chien Weng
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Cyril Guilloud
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Sara Lafuerza
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Mauro Rovezzi
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Blanka Detlefs
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
| | - Ludovic Ducotté
- ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France
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4
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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5
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Alonso-Mori R, Sokaras D, Cammarata M, Ding Y, Feng Y, Fritz D, Gaffney KJ, Hastings J, Kao CC, Lemke HT, Maxwell T, Robert A, Schropp A, Seiboth F, Sikorski M, Song S, Weng TC, Zhang W, Glenzer S, Bergmann U, Zhu D. Femtosecond electronic structure response to high intensity XFEL pulses probed by iron X-ray emission spectroscopy. Sci Rep 2020; 10:16837. [PMID: 33033373 PMCID: PMC7545180 DOI: 10.1038/s41598-020-74003-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/24/2020] [Indexed: 11/17/2022] Open
Abstract
We report the time-resolved femtosecond evolution of the K-shell X-ray emission spectra of iron during high intensity illumination of X-rays in a micron-sized focused hard X-ray free electron laser (XFEL) beam. Detailed pulse length dependent measurements revealed that rapid spectral energy shift and broadening started within the first 10 fs of the X-ray illumination at intensity levels between 1017 and 1018 W cm-2. We attribute these spectral changes to the rapid evolution of high-density photoelectron mediated secondary collisional ionization processes upon the absorption of the incident XFEL radiation. These fast electronic processes, occurring at timescales well within the typical XFEL pulse durations (i.e., tens of fs), set the boundary conditions of the pulse intensity and sample parameters where the widely-accepted ‘probe-before-destroy’ measurement strategy can be adopted for electronic-structure related XFEL experiments.
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Affiliation(s)
| | | | - Marco Cammarata
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes), UMR 6251, 35000, Rennes, France
| | - Yuantao Ding
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Yiping Feng
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - David Fritz
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Kelly J Gaffney
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Jerome Hastings
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Chi-Chang Kao
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Henrik T Lemke
- SwissFEL, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Timothy Maxwell
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Aymeric Robert
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Andreas Schropp
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
| | - Frank Seiboth
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
| | | | - Sanghoon Song
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Tsu-Chien Weng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing, 100875, China
| | | | - Uwe Bergmann
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Diling Zhu
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.
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6
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Nowak SH, Armenta R, Schwartz CP, Gallo A, Abraham B, Garcia-Esparza AT, Biasin E, Prado A, Maciel A, Zhang D, Day D, Christensen S, Kroll T, Alonso-Mori R, Nordlund D, Weng TC, Sokaras D. A versatile Johansson-type tender x-ray emission spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:033101. [PMID: 32259983 DOI: 10.1063/1.5121853] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/13/2020] [Indexed: 05/23/2023]
Abstract
We present a high energy resolution x-ray spectrometer for the tender x-ray regime (1.6-5.0 keV) that was designed and operated at Stanford Synchrotron Radiation Lightsource. The instrument is developed on a Rowland geometry (500 mm of radius) using cylindrically bent Johansson analyzers and a position sensitive detector. By placing the sample inside the Rowland circle, the spectrometer operates in an energy-dispersive mode with a subnatural line-width energy resolution (∼0.32 eV at 2400 eV), even when an extended incident x-ray beam is used across a wide range of diffraction angles (∼30° to 65°). The spectrometer is enclosed in a vacuum chamber, and a sample chamber with independent ambient conditions is introduced to enable a versatile and fast-access sample environment (e.g., solid/gas/liquid samples, in situ cells, and radioactive materials). The design, capabilities, and performance are presented and discussed.
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Affiliation(s)
- S H Nowak
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - R Armenta
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - C P Schwartz
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - A Gallo
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - B Abraham
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - A T Garcia-Esparza
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - E Biasin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - A Prado
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - A Maciel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - D Zhang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - D Day
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - S Christensen
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - T Kroll
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - R Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - D Nordlund
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - T-C Weng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - D Sokaras
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
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7
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Galler A, Gawelda W, Biednov M, Bomer C, Britz A, Brockhauser S, Choi TK, Diez M, Frankenberger P, French M, Görries D, Hart M, Hauf S, Khakhulin D, Knoll M, Korsch T, Kubicek K, Kuster M, Lang P, Alves Lima F, Otte F, Schulz S, Zalden P, Bressler C. Scientific instrument Femtosecond X-ray Experiments (FXE): instrumentation and baseline experimental capabilities. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1432-1447. [PMID: 31490131 PMCID: PMC6730617 DOI: 10.1107/s1600577519006647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/08/2019] [Indexed: 05/15/2023]
Abstract
The European X-ray Free-Electron Laser (EuXFEL) delivers extremely intense (>1012 photons pulse-1 and up to 27000 pulses s-1), ultrashort (<100 fs) and transversely coherent X-ray radiation, at a repetition rate of up to 4.5 MHz. Its unique X-ray beam parameters enable novel and groundbreaking experiments in ultrafast photochemistry and material sciences at the Femtosecond X-ray Experiments (FXE) scientific instrument. This paper provides an overview of the currently implemented experimental baseline instrumentation and its performance during the commissioning phase, and a preview of planned improvements. FXE's versatile instrumentation combines the simultaneous application of forward X-ray scattering and X-ray spectroscopy techniques with femtosecond time resolution. These methods will eventually permit exploitation of wide-angle X-ray scattering studies and X-ray emission spectroscopy, along with X-ray absorption spectroscopy, including resonant inelastic X-ray scattering and X-ray Raman scattering. A suite of ultrafast optical lasers throughout the UV-visible and near-IR ranges (extending up to mid-IR in the near future) with pulse length down to 15 fs, synchronized to the X-ray source, serve to initiate dynamic changes in the sample. Time-delayed hard X-ray pulses in the 5-20 keV range are used to probe the ensuing dynamic processes using the suite of X-ray probe tools. FXE is equipped with a primary monochromator, a primary and secondary single-shot spectrometer, and a timing tool to correct the residual timing jitter between laser and X-ray pulses.
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Affiliation(s)
- Andreas Galler
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Wojciech Gawelda
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Mykola Biednov
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Christina Bomer
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
| | - Alexander Britz
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Sandor Brockhauser
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt 62, H-6726 Szeged, Hungary
| | - Tae-Kyu Choi
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Diez
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
| | - Paul Frankenberger
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marcus French
- STFC Technology, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK
| | - Dennis Görries
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthiew Hart
- STFC Technology, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK
| | - Steffen Hauf
- 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
| | - Martin Knoll
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Timo Korsch
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Katharina Kubicek
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Markus Kuster
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Philipp Lang
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Frederico Alves Lima
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Florian Otte
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Sebastian Schulz
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Peter Zalden
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Christian Bressler
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
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8
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Chatterjee R, Weninger C, Loukianov A, Gul S, Fuller FD, Cheah MH, Fransson T, Pham CC, Nelson S, Song S, Britz A, Messinger J, Bergmann U, Alonso-Mori R, Yachandra VK, Kern J, Yano J. XANES and EXAFS of dilute solutions of transition metals at XFELs. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1716-1724. [PMID: 31490163 PMCID: PMC6730626 DOI: 10.1107/s1600577519007550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/23/2019] [Indexed: 05/27/2023]
Abstract
This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anton Loukianov
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Cindy C. Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johannes Messinger
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
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9
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Zalden P, Quirin F, Schumacher M, Siegel J, Wei S, Koc A, Nicoul M, Trigo M, Andreasson P, Enquist H, Shu MJ, Pardini T, Chollet M, Zhu D, Lemke H, Ronneberger I, Larsson J, Lindenberg AM, Fischer HE, Hau-Riege S, Reis DA, Mazzarello R, Wuttig M, Sokolowski-Tinten K. Femtosecond x-ray diffraction reveals a liquid–liquid phase transition in phase-change materials. Science 2019; 364:1062-1067. [DOI: 10.1126/science.aaw1773] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/29/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Peter Zalden
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Florian Quirin
- Faculty of Physics and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Lotharstrasse 1, 47048 Duisburg, Germany
| | - Mathias Schumacher
- Institut für Theoretische Festkörperphysik, JARA-FIT and JARA-HPC, RWTH Aachen University, Germany
| | - Jan Siegel
- Instituto de Optica, CSIC, C/Serrano 121, 28006 Madrid, Spain
| | - Shuai Wei
- I. Physikalisches Institut and JARA-FIT, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | - Azize Koc
- Faculty of Physics and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Lotharstrasse 1, 47048 Duisburg, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Matthieu Nicoul
- Faculty of Physics and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Lotharstrasse 1, 47048 Duisburg, Germany
| | - Mariano Trigo
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Pererik Andreasson
- Department of Physics, Lund University, Professorsgatan 1, 223 62 Lund, Sweden
| | - Henrik Enquist
- Department of Physics, Lund University, Professorsgatan 1, 223 62 Lund, Sweden
| | - Michael J. Shu
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Tommaso Pardini
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Henrik Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ider Ronneberger
- Institut für Theoretische Festkörperphysik, JARA-FIT and JARA-HPC, RWTH Aachen University, Germany
| | - Jörgen Larsson
- Department of Physics, Lund University, Professorsgatan 1, 223 62 Lund, Sweden
| | - Aaron M. Lindenberg
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Henry E. Fischer
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Stefan Hau-Riege
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - David A. Reis
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Riccardo Mazzarello
- Institut für Theoretische Festkörperphysik, JARA-FIT and JARA-HPC, RWTH Aachen University, Germany
| | - Matthias Wuttig
- I. Physikalisches Institut and JARA-FIT, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
- PGI 10 (Green IT), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Klaus Sokolowski-Tinten
- Faculty of Physics and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Lotharstrasse 1, 47048 Duisburg, Germany
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10
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Abraham B, Nowak S, Weninger C, Armenta R, Defever J, Day D, Carini G, Nakahara K, Gallo A, Nelson S, Nordlund D, Kroll T, Hunter MS, van Driel T, Zhu D, Weng TC, Alonso-Mori R, Sokaras D. A high-throughput energy-dispersive tender X-ray spectrometer for shot-to-shot sulfur measurements. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:629-634. [PMID: 31074425 PMCID: PMC6510194 DOI: 10.1107/s1600577519002431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/16/2019] [Indexed: 05/23/2023]
Abstract
An X-ray emission spectrometer that can detect the sulfur Kα emission lines with large throughput and a high energy resolution is presented. The instrument is based on a large d-spacing perfect Bragg analyzer that diffracts the sulfur Kα emission at close to backscattering angles. This facilitates the application of efficient concepts routinely employed in hard X-ray spectrometers towards the tender X-ray regime. The instrument described in this work is based on an energy-dispersive von Hamos geometry that is well suited for photon-in photon-out spectroscopy at X-ray free-electron laser and synchrotron sources. Comparison of its performance with previously used instrumentation is presented through measurements using sulfur-containing species performed at the LCLS. It is shown that the overall signal intensity is increased by a factor of ∼15. Implementation of this approach in the design of a tender X-ray spectroscopy endstation for LCLS-II is also discussed.
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Affiliation(s)
- Baxter Abraham
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stanislaw Nowak
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Clemens Weninger
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Rebecca Armenta
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jim Defever
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - David Day
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Kazutaka Nakahara
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alessandro Gallo
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Tim van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Tsu-Chien Weng
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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11
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Fransson T, Chatterjee R, Fuller FD, Gul S, Weninger C, Sokaras D, Kroll T, Alonso-Mori R, Bergmann U, Kern J, Yachandra VK, Yano J. X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry 2018; 57:4629-4637. [PMID: 29906115 DOI: 10.1021/acs.biochem.8b00325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kβ1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.
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Affiliation(s)
- Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
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12
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Rodriguez-Fernandez A, Esposito V, Sanchez DF, Finkelstein KD, Juranic P, Staub U, Grolimund D, Reiche S, Pedrini B. Spatial displacement of forward-diffracted X-ray beams by perfect crystals. Acta Crystallogr A Found Adv 2018; 74:75-87. [PMID: 29493536 PMCID: PMC5831586 DOI: 10.1107/s2053273318001419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/22/2018] [Indexed: 11/11/2022] Open
Abstract
Time-delayed, narrow-band echoes generated by forward Bragg diffraction of an X-ray pulse by a perfect thin crystal are exploited for self-seeding at hard X-ray free-electron lasers. Theoretical predictions indicate that the retardation is strictly correlated to a transverse displacement of the echo pulses. This article reports the first experimental observation of the displaced echoes. The displacements are in good agreement with simulations relying on the dynamical diffraction theory. The echo signals are characteristic for a given Bragg reflection, the structure factor and the probed interplane distance. The reported results pave the way to exploiting the signals as an online diagnostic tool for hard X-ray free-electron laser seeding and for dynamical diffraction investigations of strain at the femtosecond timescale.
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Affiliation(s)
| | - V. Esposito
- Paul Scherrer Institut, Villigen, Switzerland
| | | | | | - P. Juranic
- Paul Scherrer Institut, Villigen, Switzerland
| | - U. Staub
- Paul Scherrer Institut, Villigen, Switzerland
| | | | - S. Reiche
- Paul Scherrer Institut, Villigen, Switzerland
| | - B. Pedrini
- Paul Scherrer Institut, Villigen, Switzerland
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13
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Kjær KS, Kunnus K, Harlang TCB, Van Driel TB, Ledbetter K, Hartsock RW, Reinhard ME, Koroidov S, Li L, Laursen MG, Biasin E, Hansen FB, Vester P, Christensen M, Haldrup K, Nielsen MM, Chabera P, Liu Y, Tatsuno H, Timm C, Uhlig J, Sundstöm V, Németh Z, Szemes DS, Bajnóczi É, Vankó G, Alonso-Mori R, Glownia JM, Nelson S, Sikorski M, Sokaras D, Lemke HT, Canton SE, Wärnmark K, Persson P, Cordones AA, Gaffney KJ. Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4] 2. Phys Chem Chem Phys 2018; 20:4238-4249. [PMID: 29364300 DOI: 10.1039/c7cp07838b] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The excited state dynamics of solvated [Fe(bpy)(CN)4]2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN)4]2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile.1,2 In the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN)4]2- in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet (3MC) character, unlike other reported six-coordinate Fe(ii)-centered coordination compounds, which form MC quintet (5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN)4]2- allows us to infer the influence of the solvent on the electronic structure of the complex. Furthermore, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.
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Affiliation(s)
- Kasper S Kjær
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA.
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14
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Lassalle-Kaiser B, Gul S, Kern J, Yachandra VK, Yano J. In situ/Operando studies of electrocatalysts using hard X-ray spectroscopy. JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA 2017; 221:18-27. [PMID: 29515287 PMCID: PMC5836735 DOI: 10.1016/j.elspec.2017.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This review focuses on the use of X-ray absorption and emission spectroscopy techniques using hard X-rays to study electrocatalysts under in situ/operando conditions. We describe the importance and the versatility of methods in the study of electrodes in contact with the electrolytes, when being cycled through the catalytic potentials during the progress of the oxygen-evolution, oxygen reduction and hydrogen evolution reactions. The catalytic oxygen evolution reaction is illustrated with examples using Co, Ni and Mn oxides, and Mo and Co sulfides are used as an example for the hydrogen evolution reaction. A bimetallic, bifunctional oxygen evolving and oxygen reducing Ni/Mn oxide is also presented. The various advantages and constraints in the use of these techniques and the future outlook are discussed.
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Affiliation(s)
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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15
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Kubin M, Kern J, Gul S, Kroll T, Chatterjee R, Löchel H, Fuller FD, Sierra RG, Quevedo W, Weniger C, Rehanek J, Firsov A, Laksmono H, Weninger C, Alonso-Mori R, Nordlund DL, Lassalle-Kaiser B, Glownia JM, Krzywinski J, Moeller S, Turner JJ, Minitti MP, Dakovski GL, Koroidov S, Kawde A, Kanady JS, Tsui EY, Suseno S, Han Z, Hill E, Taguchi T, Borovik AS, Agapie T, Messinger J, Erko A, Föhlisch A, Bergmann U, Mitzner R, Yachandra VK, Yano J, Wernet P. Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054307. [PMID: 28944255 PMCID: PMC5586166 DOI: 10.1063/1.4986627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/15/2017] [Indexed: 05/19/2023]
Abstract
X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | | | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Heike Löchel
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Wilson Quevedo
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Christian Weniger
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Jens Rehanek
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Anatoly Firsov
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dennis L Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Joshua J Turner
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Michael P Minitti
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Georgi L Dakovski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Anurag Kawde
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jacob S Kanady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Emily Y Tsui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sandy Suseno
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zhiji Han
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ethan Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Taketo Taguchi
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Andrew S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Alexei Erko
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | | | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Rolf Mitzner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
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16
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 PMCID: PMC5376230 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ernest S. Burgie
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Christopher J. Pollock
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation
Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, 12489
Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
- Department of Biochemistry, University of Oxford, South Parks Road,
Oxford OX1 3QU, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Christian G. Roessler
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raymond G. Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Peter T. Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - James M. Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Department of Chemistry – Ångström,
Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
- Department of Chemistry, Stanford University, Stanford, CA 94305,
USA
| | - George N. Phillips
- Department of BioSciences, Rice Univ. Houston, TX 77005, USA
- Department of Chemistry, Rice Univ. Houston, TX 77005, USA
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
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17
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Alonso-Mori R, Asa K, Bergmann U, Brewster AS, Chatterjee R, Cooper JK, Frei HM, Fuller FD, Goggins E, Gul S, Fukuzawa H, Iablonskyi D, Ibrahim M, Katayama T, Kroll T, Kumagai Y, McClure BA, Messinger J, Motomura K, Nagaya K, Nishiyama T, Saracini C, Sato Y, Sauter NK, Sokaras D, Takanashi T, Togashi T, Ueda K, Weare WW, Weng TC, Yabashi M, Yachandra VK, Young ID, Zouni A, Kern JF, Yano J. Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs. Faraday Discuss 2016; 194:621-638. [PMID: 27711803 PMCID: PMC5177497 DOI: 10.1039/c6fd00084c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.
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Affiliation(s)
- R Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - K Asa
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - U Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - A S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - R Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J K Cooper
- Joint Center for Artificial Photosynthesis (JCAP), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - H M Frei
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - F D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - E Goggins
- Dept. of Chemistry, North Carolina State University, 2620 Yarborough Rd., Raleigh, NC 27695-8204, USA
| | - S Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - H Fukuzawa
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - M Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - T Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - T Kroll
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Y Kumagai
- IMRAM, Tohoku U., Sendai 980-8577, Japan
| | - B A McClure
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - K Motomura
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - K Nagaya
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - T Nishiyama
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - C Saracini
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - Y Sato
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - N K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - D Sokaras
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - T Togashi
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - K Ueda
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - W W Weare
- Dept. of Chemistry, North Carolina State University, 2620 Yarborough Rd., Raleigh, NC 27695-8204, USA
| | - T-C Weng
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | - M Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - V K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - I D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - A Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - J F Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA. and Joint Center for Artificial Photosynthesis (JCAP), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA and IMRAM, Tohoku U., Sendai 980-8577, Japan
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18
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Lima FA, Saleta ME, Pagliuca RJS, Eleotério MA, Reis RD, Fonseca Júnior J, Meyer B, Bittar EM, Souza-Neto NM, Granado E. XDS: a flexible beamline for X-ray diffraction and spectroscopy at the Brazilian synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1538-1549. [PMID: 27787261 DOI: 10.1107/s160057751601403x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
The majority of the beamlines at the Brazilian Synchrotron Light Source Laboratory (LNLS) use radiation produced in the storage-ring bending magnets and are therefore currently limited in the flux that can be used in the harder part of the X-ray spectrum (above ∼10 keV). A 4 T superconducting multipolar wiggler (SCW) was recently installed at LNLS in order to improve the photon flux above 10 keV and fulfill the demands set by the materials science community. A new multi-purpose beamline was then installed at the LNLS using the SCW as a photon source. The XDS is a flexible beamline operating in the energy range between 5 and 30 keV, designed to perform experiments using absorption, diffraction and scattering techniques. Most of the work performed at the XDS beamline concentrates on X-ray absorption spectroscopy at energies above 18 keV and high-resolution diffraction experiments. More recently, new setups and photon-hungry experiments such as total X-ray scattering, X-ray diffraction under high pressures, resonant X-ray emission spectroscopy, among others, have started to become routine at XDS. Here, the XDS beamline characteristics, performance and a few new experimental possibilities are described.
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Affiliation(s)
- F A Lima
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - M E Saleta
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - R J S Pagliuca
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - M A Eleotério
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - R D Reis
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - J Fonseca Júnior
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - B Meyer
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - E M Bittar
- Centro Brasileiro de Pesquisas Físicas, Rua Doutor Xavier Sigaud 150, CEP 22290-180, Rio de Janeiro (RJ), Brazil
| | - N M Souza-Neto
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - E Granado
- Instituto de Física `Gleb Wataghin', Universidade de Campinas, CEP 13083-859, Campinas (SP), Brazil
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19
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A Practical Guide to High-resolution X-ray Spectroscopic Measurements and their Applications in Bioinorganic Chemistry. Isr J Chem 2016. [DOI: 10.1002/ijch.201600037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Honkanen AP, Monaco G, Huotari S. A computationally efficient method to solve the Takagi–Taupin equations for a large deformed crystal. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716010402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A treatise is presented on solving the Takagi–Taupin equations in the case of a strain field with an additional, spatially slowly varying component (owing to, for example, heat expansion or angular compression). It is shown that such a component typically has a negligible effect on the shape of the reflectivity curve when considering the reflectivity of a microscopic surface area of the crystal. However, it makes the centroid of that curve shift in terms of the wavelength (or the incidence angle) as a function of the position of the mentioned area, which alters the shape of the overall reflectivity curve integrated over the crystal's macroscopic surface. The validity of the method is demonstrated by comparing computed reflectivity curves with experimental ones for bent silicon wafers. A good agreement is observed.
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21
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Petric M, Bohinc R, Bučar K, Nowak SH, Žitnik M, Kavčič M. Electronic Structure of Third-Row Elements in Different Local Symmetries Studied by Valence-to-Core X-ray Emission Spectroscopy. Inorg Chem 2016; 55:5328-36. [PMID: 27176734 DOI: 10.1021/acs.inorgchem.6b00237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marko Petric
- J. Stefan Institute , Jamova 39, SI-1000 Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School , Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Rok Bohinc
- J. Stefan Institute , Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Klemen Bučar
- J. Stefan Institute , Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Stanisław H Nowak
- Institute for Scientific Instruments GmbH , 12489 Berlin, Germany.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Matjaž Žitnik
- J. Stefan Institute , Jamova 39, SI-1000 Ljubljana, Slovenia.,Faculty of Mathematics and Physics, University of Ljubljana , Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
| | - Matjaž Kavčič
- J. Stefan Institute , Jamova 39, SI-1000 Ljubljana, Slovenia
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22
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White WE, Robert A, Dunne M. The Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:472-6. [PMID: 25931055 PMCID: PMC4416663 DOI: 10.1107/s1600577515005196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
The Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory was the first hard X-ray free-electron laser (FEL) to operate as a user facility. After five years of operation, LCLS is now a mature FEL user facility. Our personal views about opportunities and challenges inherent to these unique light sources are discussed.
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Affiliation(s)
- William E. White
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Aymeric Robert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mike Dunne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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