Junko Yano

Lawrence Berkeley National Laboratory, Berkeley, California, United States

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Publications (126)947.56 Total impact

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    ABSTRACT: Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice / DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.
    Full-text · Article · Jan 2016
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    ABSTRACT: The co-existence of "axial" and "rhombic" coordination environments has been demonstrated in a "Type 1" copper site of Pseudoazurin. This observation opens up previously not considered interpretations for the relationship between geometry and electronic structure of the four coordinate copper site. The Met16 variants of pseudoazurin were considered as model systems for investigating the effect of weak interactions from the second coordination sphere. The correlation between geometric and electronic structures of "Type 1" copper site was evaluated by the multi-edge (Cu K-edge and S K-edge) X-ray absorption spectroscopy (XAS) of Met16 variants of pseudoazurin. The co-existing axial and rhombic sites in pseudoazurin were characterized by Cu ligand distances, effective nuclear charge, and Cu S(Cys) covalency from XAS. The XAS results were correlated with DFT calculations for investigating the effect of protein environment from the inner-sphere and beyond around the Cu site. The combined experimental and theoretical results support the presence of a close correlation between outer sphere environment and inner sphere coordination environment. This is achieved in pseudoazurin by a previously undisclosed allosteric effect that involves a rearrangement of the protein tertiary structure.
    No preview · Article · Dec 2015 · Bulletin of the Chemical Society of Japan
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    Full-text · Dataset · Dec 2015
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    ABSTRACT: We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).
    Full-text · Article · Nov 2015 · Nature Methods
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    Bo You · Nan Jiang · Meili Sheng · Sheraz Gul · Junko Yano · Yujie Sun

    Full-text · Dataset · Nov 2015
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    Bo You · Nan Jiang · Meili Sheng · Sheraz Gul · Junko Yano · Yujie Sun
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    ABSTRACT: The design of active, robust, and nonprecious electrocatalysts with both H 2 and O 2 evolution reaction (HER and OER) activities for overall water splitting is highly desirable but remains a grand challenge. Herein, we report a facile two-step method to synthesize porous Co-P/NC nano-polyhedrons composed of CoP x (a mixture of CoP and Co 2 P) nanoparticles embedded in N-doped carbon matrices as electrocatalysts for overall water splitting. The Co-P/NC catalysts were prepared by direct carbonization of Co-based zeolitic imidazolate framework (ZIF-67) followed by phosphidation. Benefiting from the large specific surface area, controllable pore texture, and high nitrogen content of ZIF (a subclass of metal−organic frameworks), the optimal Co-P/NC showed high specific surface area of 183 m 2 g −1 and large mesopores, and exhibited remarkable catalytic performance for both HER and OER in 1.0 M KOH, affording a current density of 10 mA cm −2 at low overpotentials of −154 mV for HER and 319 mV for OER, respectively. Furthermore, a Co-P/NC-based alkaline electrolyzer approached 165 mA cm −2 at 2.0 V, superior to that of Pt/IrO 2 couple, along with strong stability. Various characterization techniques including X-ray absorption spectroscopy (XAS) revealed that the superior activity and strong stability of Co-P/NC originated from its 3D interconnected mesoporosity with high specific surface area, high conductivity, and synergistic effect of CoP x encapsulated within N-doped carbon matrices.
    Full-text · Article · Nov 2015 · Chemistry of Materials
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    Full-text · Dataset · Oct 2015
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    ABSTRACT: The development of low-cost catalysts with oxygen reduction reaction (ORR) activity superior to that of Pt for fuel cells is highly desirable but remains challenging. Herein, we report a bimetal-organic framework (bi-MOF) self-adjusted synthesis of support-free porous Co-N-C nanopolyhedron electrocatalysts by pyrolysis of a Zn/Co bi-MOF without any post-treatments. The presence of initial Zn forms a spatial isolation of Co that suppresses its sintering during pyrolysis, and Zn evaporation also promotes the surface area of the resultant catalysts. The composition, morphology, and hence ORR activity of Co-N-C could be tuned by the Zn/Co ratio. The optimal Co-N-C exhibited remarkable ORR activity with a half-wave potential of 0.871 V versus the reversible hydrogen electrode (RHE) (30 mV more positive than that of commercial 20 wt % Pt/C) and a kinetic current density of 39.3 mA cm-2 at 0.80 V versus RHE (3.1 times that of Pt/C) in 0.1 M KOH, and excellent stability and methanol tolerance. It also demonstrated ORR activity comparable to and stability much higher than those of Pt/C in acidic and neutral electrolytes. Various characterization techniques, including X-ray absorption spectroscopy, revealed that the superior activity and strong stability of Co-N-C originated from the intense interaction between Co and N, the high content of ORR active pyridinic and pyrrolic N, and the large specific surface area.
    Full-text · Article · Oct 2015 · ACS Catalysis
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    Full-text · Dataset · Oct 2015
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    ABSTRACT: The challenge of fine compositional tuning and microstructure control in complex oxides is overcome by developing a general two-step synthetic approach. Antimony-alloyed bismuth vanadate, which is identified as a novel light absorber for solar fuel applications, is prepared in a wide compositional range. The bandgap of this quaternary oxide linearly decreases with the Sb content, in agreement with first-principles calculations.
    No preview · Article · Sep 2015 · Advanced Materials
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    ABSTRACT: First principle calculations of extended x-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically-defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S02 and Debye-Waller values, as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.
    No preview · Article · Sep 2015 · Journal of the American Chemical Society
  • Jan Kern · Vittal K Yachandra · Junko Yano
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    ABSTRACT: Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism. Copyright © 2015 Elsevier Ltd. All rights reserved.
    No preview · Article · Sep 2015 · Current Opinion in Structural Biology
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    ABSTRACT: Condensation of ortho-phenylenediamine derivatives with ortho-quinone moieties at edge planes of graphitic carbon generates graphite-conjugated pyrazines (GCPs) that are active for oxygen reduction electrocatalysis in alkaline aqueous electrolyte. Catalytic rates of oxygen reduction are positively correlated with the electrophilicity of the active site pyrazine unit and can be tuned by over 70-fold by appending electron-withdrawing substituents to the phenylenediamine precursors. Discrete molecular analogs containing pyrazine moieties display no activity above background under identical conditions. This simple bottom up method for constructing molecularly well-defined active sites on ubiquitous graphitic solids enables the rational design of tunable heterogeneous catalysts.
    No preview · Article · Aug 2015 · Journal of the American Chemical Society
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    ABSTRACT: Well-defined mixed-metal [CoMn3 O4 ] and [NiMn3 O4 ] cubane complexes were synthesized and used as precursors for heterogeneous oxygen evolution reaction (OER) electrocatalysts. The discrete clusters were dropcasted onto glassy carbon (GC) and indium tin oxide (ITO) electrodes, and the OER activities of the resulting films were evaluated. The catalytic surfaces were analyzed by various techniques to gain insight into the structure-function relationships of the electrocatalysts' heterometallic composition. Depending on preparation conditions, the Co-Mn oxide was found to change metal composition during catalysis, while the Ni-Mn oxides maintained the NiMn3 ratio. XAS studies provided structural insights indicating that the electrocatalysts are different from the molecular precursors, but that the original NiMn3 O4 cubane-like geometry was maintained in the absence of thermal treatment (2-Ni). In contrast, the thermally generated 3-Ni develops an oxide-like extended structure. Both 2-Ni and 3-Ni undergo structural changes upon electrolysis, but they do not convert into the same material. The observed structural motifs in these heterogeneous electrocatalysts are reminiscent of the biological oxygen-evolving complex in Photosystem II, including the MMn3 O4 cubane moiety. The reported studies demonstrate the use of discrete heterometallic oxide clusters as precursors for heterogeneous water oxidation catalysts of novel composition and the distinct behavior of two sets of mixed metal oxides. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    No preview · Article · Aug 2015 · Chemistry - A European Journal
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    ABSTRACT: In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup that requires microcrystals less than 40 μm in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5 Å, using crystals grown without the micro seeding approach, to 4.5 Å using crystals generated with the new method.
    Full-text · Article · Jul 2015 · Structural Dynamics
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    Full-text · Technical Report · Jun 2015
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    ABSTRACT: Ca2+-depleted and Ca2+-reconstituted spinach photosystem II was studied using polarized X-ray absorption spectroscopy of oriented PS II preparations to investigate the structural and functional role of the Ca2+ ion in the Mn4O5Ca cluster of the oxygen-evolving complex (OEC). Samples were prepared by low pH/citrate treatment as one-dimensionally ordered membrane layers, and poised in the Ca2+-depleted S1 (S1'), S2 (S2') and S2'YZ• states, at which point the catalytic cycle of water oxidation is inhibited, and the Ca2+-reconstituted S1 state. Polarized Mn K-edge XANES and EXAFS spectra exhibit pronounced dichroism. Polarized EXAFS data of all states of Ca2+-depleted PS II investigated show only minor changes in distances and orientations of the Mn-Mn vectors compared to the Ca2+-containing OEC, which may be attributed to some loss of rigidity of the core structure. Thus, removal of the Ca2+ ion does not lead to fundamental distortion or rearrangement of the tetranuclear Mn cluster, which indicates that the Ca2+ ion in the OEC is not critical for structural maintenance of the cluster at least in the S1 and S2 states, but fulfills a crucial catalytic function in the mechanism of the water oxidation reaction. On the basis of this structural information, reasons for the inhibitory effect of Ca2+ removal are discussed, attributing to the Ca2+ ion a fundamental role in organizing the surrounding (substrate) water framework and in proton-coupled electron transfer to YZ• (D1-Tyr161).
    No preview · Article · May 2015 · The Journal of Physical Chemistry B
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    ABSTRACT: Semiconductor quantum dots (QDs) with stable, oxidation resistant, and tunable photoluminescence (PL) are highly desired for various applications including solid-state lighting and biological labeling. However, many current systems for visible light emission involve the use of toxic Cd. Here, we report the synthesis and characterization of a series of codoped core/shell ZnSe/ZnS quantum dots (QDs) with tunable PL maxima spanning 430 nm to 570 nm (FWHM = 80 nm), with broad emission extending to 700 nm, through the use of Cu+ as the primary dopant and trivalent cations (Al3+, Ga3+, and In3+) as codopants. Furthermore, we developed a unique thiol-based bidentate ligand that significantly improved PL intensity, long term stability, and resilience to post-synthetic processing. Through comprehensive experimental and computational studies based on steady state and time-resolved spectroscopy, electron microscopy, and density functional theory (DFT), we show that the tunable PL of this system is the result of energy level modification to donor and/or acceptor recombination pathways. By incorporating these findings with local structure information obtained from extended X-ray absorption fine structure (EXAFS) studies, we generate a complete energetic model accounting for the photophysical processes in these unique QDs. With the understanding of optical, structural, and electronic properties we gain in this study, this successful codoping strategy may be applied to other QD or related systems to tune the optical properties of semiconductors while maintaining low toxicity.
    No preview · Article · Apr 2015 · ACS Applied Materials & Interfaces
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    ABSTRACT: The structural and electronic properties of a series of manganese complexes with terminal oxido ligands are described. The complexes span three different oxidation states at the manganese center (III-V), have similar molecular structures, and contain intramolecular hydrogen-bonding networks surrounding the Mn-oxo unit. Structural studies using X-ray absorption methods indicated that each complex is mononuclear and that oxidation occurs at the manganese centers, which is also supported by electron paramagnetic resonance (EPR) studies. This gives a high-spin Mn(V)-oxo complex and not a Mn(IV)-oxy radical as the most oxidized species. In addition, the EPR findings demonstrated that the Fermi contact term could experimentally substantiate the oxidation states at the manganese centers and the covalency in the metal-ligand bonding. Oxygen-17-labeled samples were used to determine spin density within the Mn-oxo unit, with the greatest delocalization occurring within the Mn(V)-oxo species (0.45 spins on the oxido ligand). The experimental results coupled with density functional theory studies show a large amount of covalency within the Mn-oxo bonds. Finally, these results are examined within the context of possible mechanisms associated with photosynthetic water oxidation; specifically, the possible identity of the proposed high valent Mn-oxo species that is postulated to form during turnover is discussed.
    No preview · Article · Apr 2015 · Proceedings of the National Academy of Sciences
  • Hyun S. Ahn · Junko Yano · T. Don Tilley
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    ABSTRACT: Single-atom cobalt centers on various oxide surfaces (TiO2, MgO, SBA-15, AlPO, and Y-Zeolite) were prepared and evaluated as water oxidation catalysts by photochemical water oxidation experiments. Superior catalytic rates were observed for cobalt sites on basic supporting oxides (TiO2 and MgO) relative to those on acidic oxides (Y-Zeolite, AlPO, and SiO2). Per-atom turnover frequencies of ca. 0.04 s-1 were achieved, giving initial rates 100 times greater than that of a surface atom of a Co3O4 nanoparticle. Contrary to expectations based on theoretical work, no apparent correlation was observed between the catalytic rates and the oxygen atom affinities of the supporting oxides.
    No preview · Article · Mar 2015 · ACS Catalysis

Publication Stats

4k Citations
947.56 Total Impact Points

Institutions

  • 2005-2015
    • Lawrence Berkeley National Laboratory
      • Physical Biosciences Division
      Berkeley, California, United States
  • 2002-2015
    • University of California, Berkeley
      • Department of Chemistry
      Berkeley, California, United States
  • 2010
    • Massachusetts Institute of Technology
      • Department of Chemistry
      Cambridge, Massachusetts, United States
  • 2007
    • University of Bonn
      • Institute of Physical and Theoretical Chemistry
      Bonn, North Rhine-Westphalia, Germany