Publications by authors named "Tokushi Sato"

33 Publications

A self-referenced in-situ arrival time monitor for X-ray free-electron lasers.

Sci Rep 2021 Feb 11;11(1):3562. Epub 2021 Feb 11.

European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.

We present a novel, highly versatile, and self-referenced arrival time monitor for measuring the femtosecond time delay between a hard X-ray pulse from a free-electron laser and an optical laser pulse, measured directly on the same sample used for pump-probe experiments. Two chirped and picosecond long optical supercontinuum pulses traverse the sample with a mutually fixed time delay of 970 fs, while a femtosecond X-ray pulse arrives at an instant in between both pulses. Behind the sample the supercontinuum pulses are temporally overlapped to yield near-perfect destructive interference in the absence of the X-ray pulse. Stimulation of the sample with an X-ray pulse delivers non-zero contributions at certain optical wavelengths, which serve as a measure of the relative arrival time of the X-ray pulse with an accuracy of better than 25 fs. We find an excellent agreement of our monitor with the existing timing diagnostics at the SACLA XFEL with a Pearson correlation value of 0.98. We demonstrate a high sensitivity to measure X-ray pulses with pulse energies as low as 30 [Formula: see text]J. Using a free-flowing liquid jet as interaction sample ensures the full replacement of the sample volume for each X-ray/optical event, thus enabling its utility even at MHz repetition rate XFEL sources.
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http://dx.doi.org/10.1038/s41598-021-82597-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878505PMC
February 2021

Mapping the emergence of molecular vibrations mediating bond formation.

Nature 2020 06 24;582(7813):520-524. Epub 2020 Jun 24.

Department of Chemistry, KAIST, Daejeon, Republic of Korea.

Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction: A-B + C → A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)] in an aqueous monomer solution, using femtosecond X-ray liquidography with X-ray free-electron lasers. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.
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http://dx.doi.org/10.1038/s41586-020-2417-3DOI Listing
June 2020

Author Correction: Membrane protein megahertz crystallography at the European XFEL.

Nat Commun 2020 Jan 30;11(1):703. Epub 2020 Jan 30.

Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41467-020-14436-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6992783PMC
January 2020

Time-resolved serial femtosecond crystallography at the European XFEL.

Nat Methods 2020 01 18;17(1):73-78. Epub 2019 Nov 18.

Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.

The European XFEL (EuXFEL) is a 3.4-km long X-ray source, which produces femtosecond, ultrabrilliant and spatially coherent X-ray pulses at megahertz (MHz) repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological macromolecules belong to an important class of experiments that explore fundamental and functional structural displacements in these molecules. Due to the unusual MHz X-ray pulse structure at the EuXFEL, these experiments are challenging. Here, we demonstrate how a biological reaction can be followed on ultrafast timescales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. The results connect the previously explored femtosecond PYP dynamics to timescales accessible at synchrotrons. This opens the door to a wide range of time-resolved studies at the EuXFEL.
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http://dx.doi.org/10.1038/s41592-019-0628-zDOI Listing
January 2020

Membrane protein megahertz crystallography at the European XFEL.

Nat Commun 2019 11 4;10(1):5021. Epub 2019 Nov 4.

Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.

The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.
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http://dx.doi.org/10.1038/s41467-019-12955-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6828683PMC
November 2019

Tracking multiple components of a nuclear wavepacket in photoexcited Cu(I)-phenanthroline complex using ultrafast X-ray spectroscopy.

Nat Commun 2019 Aug 9;10(1):3606. Epub 2019 Aug 9.

Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon-Tyne, NE1 7RU, UK.

Disentangling the strong interplay between electronic and nuclear degrees of freedom is essential to achieve a full understanding of excited state processes during ultrafast nonadiabatic chemical reactions. However, the complexity of multi-dimensional potential energy surfaces means that this remains challenging. The energy flow during vibrational and electronic relaxation processes can be explored with structural sensitivity by probing a nuclear wavepacket using femtosecond time-resolved X-ray Absorption Near Edge Structure (TR-XANES). However, it remains unknown to what level of detail vibrational motions are observable in this X-ray technique. Herein we track the wavepacket dynamics of a prototypical [Cu(2,9-dimethyl-1,10-phenanthroline)] complex using TR-XANES. We demonstrate that sensitivity to individual wavepacket components can be modulated by the probe energy and that the bond length change associated with molecular breathing mode can be tracked with a sub-Angstrom resolution beyond optical-domain observables. Importantly, our results reveal how state-of-the-art TR-XANES provides deeper insights of ultrafast nonadiabatic chemical reactions.
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http://dx.doi.org/10.1038/s41467-019-11499-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689108PMC
August 2019

Fate of transient isomer of CHI: Mechanism and origin of ionic photoproducts formation unveiled by time-resolved x-ray liquidography.

J Chem Phys 2019 Jun;150(22):224201

Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea.

Diiodomethane, CHI, in a polar solvent undergoes a unique photoinduced reaction whereby I and I are produced from its photodissociation, unlike for other iodine-containing haloalkanes. While previous studies proposed that homolysis, heterolysis, or solvolysis of iso-CHI-I, which is a major intermediate of the photodissociation, can account for the formation of I and I, there has been no consensus on its mechanism and no clue for the reason why those negative ionic species are not observed in the photodissociation of other iodine-containing chemicals in the same polar solvent, for example, CHI, CHI, CFI, I, and I. Here, using time-resolved X-ray liquidography, we revisit the photodissociation mechanism of CHI in methanol and determine the structures of all transient species and photoproducts involved in its photodissociation and reveal that I and I are formed via heterolysis of iso-CHI-I in the photodissociation of CHI in methanol. In addition, we demonstrate that the high polarity of iso-CHI-I is responsible for the unique photochemistry of CHI.
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http://dx.doi.org/10.1063/1.5099002DOI Listing
June 2019

The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation.

J Synchrotron Radiat 2019 May 12;26(Pt 3):660-676. Epub 2019 Apr 12.

European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany.

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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http://dx.doi.org/10.1107/S1600577519003308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510195PMC
May 2019

MHz data collection of a microcrystalline mixture of different jack bean proteins.

Sci Data 2019 04 3;6(1):18. Epub 2019 Apr 3.

Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.

We provide a detailed description of a serial femtosecond crystallography (SFX) dataset collected at the European X-ray free-electron laser facility (EuXFEL). The EuXFEL is the first high repetition rate XFEL delivering MHz X-ray pulse trains at 10 Hz. The short spacing (<1 µs) between pulses requires fast flowing microjets for sample injection and high frame rate detectors. A data set was recorded of a microcrystalline mixture of at least three different jack bean proteins (urease, concanavalin A, concanavalin B). A one megapixel Adaptive Gain Integrating Pixel Detector (AGIPD) was used which has not only a high frame rate but also a large dynamic range. This dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development and for data analysis training for prospective XFEL users.
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http://dx.doi.org/10.1038/s41597-019-0010-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472352PMC
April 2019

Initial observations of the femtosecond timing jitter at the European XFEL.

Opt Lett 2019 Apr;44(7):1650-1653

Intense, ultrashort, and high-repetition-rate X-ray pulses, combined with a femtosecond optical laser, allow pump-probe experiments with fast data acquisition and femtosecond time resolution. However, the relative timing of the X-ray pulses and the optical laser pulses can be controlled only to a level of the intrinsic error of the instrument which, without characterization, limits the time resolution of experiments. This limitation inevitably calls for a precise determination of the relative arrival time, which can be used after measurement for sorting and tagging the experimental data to a much finer resolution than it can be controlled to. The observed root-mean-square timing jitter between the X-ray and the optical laser at the SPB/SFX instrument at European XFEL was 308 fs. This first measurement of timing jitter at the European XFEL provides an important step in realizing ultrafast experiments at this novel X-ray source. A method for determining the change in the complex refractive index of samples is also presented.
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http://dx.doi.org/10.1364/OL.44.001650DOI Listing
April 2019

Megahertz serial crystallography.

Authors:
Max O Wiedorn Dominik Oberthür Richard Bean Robin Schubert Nadine Werner Brian Abbey Martin Aepfelbacher Luigi Adriano Aschkan Allahgholi Nasser Al-Qudami Jakob Andreasson Steve Aplin Salah Awel Kartik Ayyer Saša Bajt Imrich Barák Sadia Bari Johan Bielecki Sabine Botha Djelloul Boukhelef Wolfgang Brehm Sandor Brockhauser Igor Cheviakov Matthew A Coleman Francisco Cruz-Mazo Cyril Danilevski Connie Darmanin R Bruce Doak Martin Domaracky Katerina Dörner Yang Du Hans Fangohr Holger Fleckenstein Matthias Frank Petra Fromme Alfonso M Gañán-Calvo Yaroslav Gevorkov Klaus Giewekemeyer Helen Mary Ginn Heinz Graafsma Rita Graceffa Dominic Greiffenberg Lars Gumprecht Peter Göttlicher Janos Hajdu Steffen Hauf Michael Heymann Susannah Holmes Daniel A Horke Mark S Hunter Siegfried Imlau Alexander Kaukher Yoonhee Kim Alexander Klyuev Juraj Knoška Bostjan Kobe Manuela Kuhn Christopher Kupitz Jochen Küpper Janine Mia Lahey-Rudolph Torsten Laurus Karoline Le Cong Romain Letrun P Lourdu Xavier Luis Maia Filipe R N C Maia Valerio Mariani Marc Messerschmidt Markus Metz Davide Mezza Thomas Michelat Grant Mills Diana C F Monteiro Andrew Morgan Kerstin Mühlig Anna Munke Astrid Münnich Julia Nette Keith A Nugent Theresa Nuguid Allen M Orville Suraj Pandey Gisel Pena Pablo Villanueva-Perez Jennifer Poehlsen Gianpietro Previtali Lars Redecke Winnie Maria Riekehr Holger Rohde Adam Round Tatiana Safenreiter Iosifina Sarrou Tokushi Sato Marius Schmidt Bernd Schmitt Robert Schönherr Joachim Schulz Jonas A Sellberg M Marvin Seibert Carolin Seuring Megan L Shelby Robert L Shoeman Marcin Sikorski Alessandro Silenzi Claudiu A Stan Xintian Shi Stephan Stern Jola Sztuk-Dambietz Janusz Szuba Aleksandra Tolstikova Martin Trebbin Ulrich Trunk Patrik Vagovic Thomas Ve Britta Weinhausen Thomas A White Krzysztof Wrona Chen Xu Oleksandr Yefanov Nadia Zatsepin Jiaguo Zhang Markus Perbandt Adrian P Mancuso Christian Betzel Henry Chapman Anton Barty

Nat Commun 2018 10 2;9(1):4025. Epub 2018 Oct 2.

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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http://dx.doi.org/10.1038/s41467-018-06156-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168542PMC
October 2018

Megahertz data collection from protein microcrystals at an X-ray free-electron laser.

Nat Commun 2018 08 28;9(1):3487. Epub 2018 Aug 28.

Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.

X-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10-120 Hz, placing significant demands on beam time and sample consumption. We describe serial femtosecond crystallography experiments performed at the European XFEL, the first MHz repetition rate XFEL, delivering 1.128 MHz X-ray pulse trains at 10 Hz. Given the short spacing between pulses, damage caused by shock waves launched by one XFEL pulse on sample probed by subsequent pulses is a concern. To investigate this issue, we collected data from lysozyme microcrystals, exposed to a ~15 μm XFEL beam. Under these conditions, data quality is independent of whether the first or subsequent pulses of the train were used for data collection. We also analyzed a mixture of microcrystals of jack bean proteins, from which the structure of native, magnesium-containing concanavalin A was determined.
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http://dx.doi.org/10.1038/s41467-018-05953-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113309PMC
August 2018

MHz frame rate hard X-ray phase-contrast imaging using synchrotron radiation.

Opt Express 2017 Jun;25(12):13857-13871

Third generation synchrotron light sources offer high photon flux, partial spatial coherence, and ~10 s pulse widths. These enable hard X-ray phase-contrast imaging (XPCI) with single-bunch temporal resolutions. In this work, we exploited the MHz repetition rates of synchrotron X-ray pulses combined with indirect X-ray detection to demonstrate the potential of XPCI with millions of frames per second multiple-frame recording. This allows for the visualization of aperiodic or stochastic transient processes which are impossible to be realized using single-shot or stroboscopic XPCI. We present observations of various phenomena, such as crack tip propagation in glass, shock wave propagation in water and explosion during electric arc ignition, which evolve in the order of km/s (µm/ns).
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http://dx.doi.org/10.1364/OE.25.013857DOI Listing
June 2017

Femtosecond X-ray solution scattering reveals that bond formation mechanism of a gold trimer complex is independent of excitation wavelength.

Struct Dyn 2016 Jul 29;3(4):043209. Epub 2016 Apr 29.

Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) , 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.

The [Au(CN)2 (-)]3 trimer in water experiences a strong van der Waals interaction between the d(10) gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors.
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http://dx.doi.org/10.1063/1.4948516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851617PMC
July 2016

Dynamics of Photoelectrons and Structural Changes of Tungsten Trioxide Observed by Femtosecond Transient XAFS.

Angew Chem Int Ed Engl 2016 Jan 10;55(4):1364-7. Epub 2015 Dec 10.

Institute for Catalysis Hokkaido University, Sapporo, 001-0021, Japan.

The dynamics of the local electronic and geometric structures of WO3 following photoexcitation were studied by femtosecond time-resolved X-ray absorption fine structure (XAFS) spectroscopy using an X-ray free electron laser (XFEL). We found that the electronic state was the first to change followed by the local structure, which was affected within 200 ps of photoexcitation.
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http://dx.doi.org/10.1002/anie.201509252DOI Listing
January 2016

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses.

Nat Commun 2015 Mar 2;6:6359. Epub 2015 Mar 2.

Centre for Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor-acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.
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http://dx.doi.org/10.1038/ncomms7359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366532PMC
March 2015

Direct observation of bond formation in solution with femtosecond X-ray scattering.

Nature 2015 Feb;518(7539):385-9

1] Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan [2] Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.
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http://dx.doi.org/10.1038/nature14163DOI Listing
February 2015

Cooling dynamics of self-assembled monolayer coating for integrated gold nanocrystals on a glass substrate.

J Synchrotron Radiat 2015 Jan 1;22(1):29-33. Epub 2015 Jan 1.

Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.

Picosecond time-resolved X-ray diffraction has been used to study the nanoscale thermal transportation dynamics of bare gold nanocrystals and thiol-based self-assembled monolayer (SAM)-coated integrated gold nanocrystals on a SiO2 glass substrate. A temporal lattice expansion of 0.30-0.33% was observed in the bare and SAM-coated nanocrystals on the glass substrate; the thermal energy inside the gold nanocrystals was transported to the contacted substrate through the gold-SiO2 interface. The interfacial thermal conductivity between the single-layered gold nanocrystal film and the SiO2 substrate is estimated to be 45 MW m(-2) K(-1) from the decay of the Au 111 peak shift, which was linearly dependent on the transient temperature. For the SAM-coated gold nanocrystals, the thermal dissipation was faster than that of the bare gold nanocrystal film. The thermal flow from the nanocrystals to the SAM-coated molecules promotes heat dissipation from the laser-heated SAM-coated gold nanocrystals. The thermal transportation of the laser-heated SAM-coated gold nanocrystal film was analyzed using the bidirectional thermal dissipation model.
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http://dx.doi.org/10.1107/S1600577514019730DOI Listing
January 2015

Crystal melting by light: X-ray crystal structure analysis of an azo crystal showing photoinduced crystal-melt transition.

J Am Chem Soc 2014 Jun 11;136(25):9158-64. Epub 2014 Jun 11.

Department of Chemistry and Materials Science, Tokyo Institute of Technology , Meguro-ku, Tokyo 152-8551, Japan.

Trans-cis photoisomerization in an azo compound containing azobenzene chromophores and long alkyl chains leads to a photoinduced crystal-melt transition (PCMT). X-ray structure analysis of this crystal clarifies the characteristic coexistence of the structurally ordered chromophores through their π···π interactions and disordered alkyl chains around room temperature. These structural features reveal that the PCMT starts near the surface of the crystal and propagates into the depth, sacrificing the π···π interactions. A temporal change of the powder X-ray diffraction pattern under light irradiation and a two-component phase diagram allow qualitative analysis of the PCMT and the following reconstructive crystallization of the cis isomer as a function of product accumulation. This is the first structural characterization of a compound showing the PCMT, overcoming the low periodicity that makes X-ray crystal structure analysis difficult.
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http://dx.doi.org/10.1021/ja503652cDOI Listing
June 2014

Application of singular value decomposition analysis to time-dependent powder diffraction data of an in-situ photodimerization reaction.

J Synchrotron Radiat 2014 May 2;21(Pt 3):554-60. Epub 2014 Apr 2.

Photon Factory, High Energy Accelerator Research Organization, KEK, Tsukuba 305-0801, Japan.

Singular value decomposition (SVD) analysis has important applications for time-dependent crystallographic data, extracting significant information. Herein, a successful application of SVD analysis of time-resolved powder diffraction data over the course of an in-situ photodimerization reaction of anthracene derivatives is introduced. SVD revealed significant results in the case of 9-methylanthracene and 1-chloroanthracene. The results support the formation of the 9-methylanthracene stable dimer phase and suggest the existence of an excimer state.
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http://dx.doi.org/10.1107/S1600577514004366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333817PMC
May 2014

Global reaction pathways in the photodissociation of I3 (-) ions in solution at 267 and 400 nm studied by picosecond X-ray liquidography.

Chemphyschem 2013 Nov 2;14(16):3687-97. Epub 2013 Oct 2.

Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701 (Republic of Korea), Fax: (+82) 42-350-2810; Department of Chemistry, KAIST, Daejeon 305-701 (Republic of Korea).

The mechanism of a photochemical reaction involves the formation and dissociation of various short-lived species on ultrafast timescales and therefore its characterization requires detailed structural information on the transient species. By making use of a structurally sensitive X-ray probe, time-resolved X-ray liquidography (TRXL) can directly elucidate the structures of reacting molecules in the solution phase and thus determine the comprehensive reaction mechanism with high accuracy. In this work, by performing TRXL measurements at two different wavelengths (400 and 267 nm), the reaction mechanism of I3 (-) photolysis, which changes subtly depending on the excitation wavelength, is elucidated. Upon 400 nm photoexcitation, the I3 (-) ion dissociates into I2 (-) and I. By contrast, upon 267 nm photoexcitation, the I3 (-) ion undergoes both two-body dissociation (I2 (-) +I) and three-body dissociation (I(-) +2I) with 7:3 molar ratio. At both excitation wavelengths, all the transient species ultimately disappear in 80 ns by recombining to form the I3 (-) ion nongeminately. In addition to the reaction dynamics of solute species, the results reveal the transient structure of the solute/solvent cage and the changes in solvent density and temperature as a function of time.
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http://dx.doi.org/10.1002/cphc.201300713DOI Listing
November 2013

ATP dependent rotational motion of group II chaperonin observed by X-ray single molecule tracking.

PLoS One 2013 29;8(5):e64176. Epub 2013 May 29.

CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, Kashiwa city, Chiba, Japan.

Group II chaperonins play important roles in protein homeostasis in the eukaryotic cytosol and in Archaea. These proteins assist in the folding of nascent polypeptides and also refold unfolded proteins in an ATP-dependent manner. Chaperonin-mediated protein folding is dependent on the closure and opening of a built-in lid, which is controlled by the ATP hydrolysis cycle. Recent structural studies suggest that the ring structure of the chaperonin twists to seal off the central cavity. In this study, we demonstrate ATP-dependent dynamics of a group II chaperonin at the single-molecule level with highly accurate rotational axes views by diffracted X-ray tracking (DXT). A UV light-triggered DXT study with caged-ATP and stopped-flow fluorometry revealed that the lid partially closed within 1 s of ATP binding, the closed ring subsequently twisted counterclockwise within 2-6 s, as viewed from the top to bottom of the chaperonin, and the twisted ring reverted to the original open-state with a clockwise motion. Our analyses clearly demonstrate that the biphasic lid-closure process occurs with unsynchronized closure and a synchronized counterclockwise twisting motion.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064176PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666759PMC
January 2014

Solvent-dependent molecular structure of ionic species directly measured by ultrafast x-ray solution scattering.

Phys Rev Lett 2013 Apr 18;110(16):165505. Epub 2013 Apr 18.

Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, Republic of Korea.

Ionic species often play important roles in chemical reactions occurring in water and other solvents, but it has been elusive to determine the solvent-dependent molecular structure with atomic resolution. The triiodide ion has a molecular structure that sensitively changes depending on the type of solvent and its symmetry can be broken by strong solute-solvent interaction. Here, by applying pump-probe x-ray solution scattering, we characterize the exact molecular structure of I(3)(-) ion in water, methanol, and acetonitrile with subangstrom accuracy. The data reveal that I(3)(-) ion has an asymmetric and bent structure in water. In contrast, the ion keeps its symmetry in acetonitrile, while the symmetry breaking occurs to a lesser extent in methanol than in water. The symmetry breaking of I(3)(-) ion is reproduced by density functional theory calculations using 34 explicit water molecules, confirming that the origin of the symmetry breaking is the hydrogen-bonding interaction between the solute and solvent molecules.
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http://dx.doi.org/10.1103/PhysRevLett.110.165505DOI Listing
April 2013

A time-resolved powder diffraction study of in-situ photodimerization kinetics of 9-methylanthracene using a CCD area detector and parametric Rietveld refinement.

Acta Crystallogr B 2012 Aug 17;68(Pt 4):424-30. Epub 2012 Jul 17.

Department of Materials Structure Science, School of High Energy Accelerator Science (KEK), The Graduate University for Advanced Studies (Sokendai), Tsukuba 305-0801, Japan.

The [4π + 4π] photodimerization process of the 9-substituted anthracene derivative crystalline 9-methylanthracene (9-MA) was investigated using time-resolved X-ray powder diffraction. The study was carried out in-situ using a CCD area detector. Sequential and parametric Rietveld refinement was applied for quantitative phase analysis. The results of traditional sequential Rietveld refinement showed that the evolution of the dimerization process can be described using the Johnson-Mehl-Avrami-Kolmogorov (JMAK) model. The parameters of the JMAK equation were obtained successfully by parametric Rietveld refinement and suggest that the reaction follows heterogeneous nucleation and one-dimensional growth with a decreasing nucleation rate.
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http://dx.doi.org/10.1107/S0108768112027450DOI Listing
August 2012

Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering.

J Am Chem Soc 2012 Apr 12;134(16):7001-8. Epub 2012 Apr 12.

Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon, 305-701, Republic of Korea.

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I(1), I(2), and I(3)) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I(1) intermediate is generated within 100 ps and transforms to the R-like I(2) intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I(3) intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I(3) intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.
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http://dx.doi.org/10.1021/ja210856vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337689PMC
April 2012

Determination of the structural features of a long-lived electron-transfer state of 9-mesityl-10-methylacridinium ion.

J Am Chem Soc 2012 Mar 1;134(10):4569-72. Epub 2012 Mar 1.

Department of Chemistry and Materials Science, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan.

Extensive efforts have been devoted to developing electron donor-acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor-acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr(+)-Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The N-methyl group in Acr(+) was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO(4)) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr(+)-Mes for mimicking photosynthesis efficiently.
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http://dx.doi.org/10.1021/ja300602hDOI Listing
March 2012

Transient photoinduced 'hidden' phase in a manganite.

Nat Mater 2011 Feb 16;10(2):101-5. Epub 2011 Jan 16.

JST, ERATO, Tsukuba 305-0801, Japan.

Photoinduced phase transitions are of special interest in condensed matter physics because they can be used to change complex macroscopic material properties on the ultrafast timescale. Cooperative interactions between microscopic degrees of freedom greatly enhance the number and nature of accessible states, making it possible to switch electronic, magnetic or structural properties in new ways. Photons with high energies, of the order of electron volts, in particular are able to access electronic states that may differ greatly from states produced with stimuli close to equilibrium. In this study we report the photoinduced change in the lattice structure of a charge and orbitally ordered Nd(0.5)Sr(0.5)MnO(3) thin film using picosecond time-resolved X-ray diffraction. The photoinduced state is structurally ordered, homogeneous, metastable and has crystallographic parameters different from any thermodynamically accessible state. A femtosecond time-resolved spectroscopic study shows the formation of an electronic gap in this state. In addition, the threshold-like behaviour and high efficiency in photo-generation yield of this gapped state highlight the important role of cooperative interactions in the formation process. These combined observations point towards a 'hidden insulating phase' distinct from that found in the hitherto known phase diagram.
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http://dx.doi.org/10.1038/nmat2929DOI Listing
February 2011

Tracking ligand-migration pathways of carbonmonoxy myoglobin in crystals at cryogenic temperatures.

Acta Crystallogr A 2010 Mar 9;66(Pt 2):220-8. Epub 2010 Feb 9.

Department of Materials Science, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan.

In order to explore the ligand-migration dynamics in myoglobin induced by photodissociation, cryogenic X-ray crystallographic investigations of carbonmonoxy myoglobin crystals illuminated by continuous wave and pulsed lasers at 1-15 kHz repetition rate have been carried out. Here it is shown that this novel method, extended pulsed-laser pumping of carbonmonoxy myoglobin, promotes ligand migration in the protein matrix by crossing the glass transition temperature repeatedly, and enables the visualization of the migration pathway of the photodissociated ligands in native Mb at cryogenic temperatures. It has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino-acid residues around the cavity which result in the expansion of the cavity. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand-migration channel arising by induced fit.
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http://dx.doi.org/10.1107/S0108767309050752DOI Listing
March 2010

Direct probing of spin state dynamics coupled with electronic and structural modifications by picosecond time-resolved XAFS.

J Am Chem Soc 2010 Jan;132(1):61-3

ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.

The first direct observation of the transient spin-state in a disordered magnetic system with time-resolved XAFS is reported. By observing the evolution of the Fe(II) 1s-3d transition, the spin crossover transition from the (1)A(1) low spin state to (5)T(2) high spin state has been directly observed on a picosecond time scale. Moreover, observation of the transient spin state with time-resolved XAFS allows for the investigation of the variations in the electronic state and molecular structure. This unique experimental technique probes the excited states involved in the ultrafast photoinduced reactions in disordered magnetic systems.
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http://dx.doi.org/10.1021/ja907460bDOI Listing
January 2010

The RATIO method for time-resolved Laue crystallography.

J Synchrotron Radiat 2009 Mar 10;16(Pt 2):226-30. Epub 2009 Jan 10.

Chemistry Department, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA.

A RATIO method for analysis of intensity changes in time-resolved pump-probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.
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http://dx.doi.org/10.1107/S0909049508040892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651764PMC
March 2009