Junko Yano

Lawrence Berkeley National Laboratory, Berkeley, California, United States

Are you Junko Yano?

Claim your profile

Publications (80)607.94 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The structure of photosystem II and the catalytic intermediate states of the Mn4CaO5 cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 07/2014; 369(1647).
  • [Show abstract] [Hide abstract]
    ABSTRACT: Silicon(111) surfaces have been functionalized with mixed monolayers consisting of submonolayer coverages of immobilized 4-vinyl-2,2'-bipyridyl (, vbpy) moieties, with the remaining atop sites of the silicon surface passivated by methyl groups. As the immobilized bipyridyl ligands bind transition metal ions, metal complexes can be assembled on the silicon surface. X-ray photoelectron spectroscopy (XPS) demonstrates that bipyridyl complexes of [Cp*Rh], [Cp*Ir], and [Ru(acac)2] were formed on the surface (Cp* is pentamethylcyclopentadienyl, acac is acetylacetonate). For the surface prepared with Ir, X-ray absorption spectroscopy at the Ir LIII edge showed an edge energy as well as post-edge features that were essentially identical with those observed on a powder sample of [Cp*Ir(bpy)Cl]Cl (bpy is 2,2'-bipyridyl). Charge-carrier lifetime measurements confirmed that the silicon surfaces retain their highly favorable photoelectronic properties upon assembly of the metal complexes. Electrochemical data for surfaces prepared on highly doped, n-type Si(111) electrodes showed that the assembled molecular complexes were redox active. However the stability of the molecular complexes on the surfaces was limited to several cycles of voltammetry.
    Dalton Transactions 07/2014; · 3.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 07/2014; 369(1647).
  • [Show abstract] [Hide abstract]
    ABSTRACT: Supplementary information available for this article at http://www.nature.com/ncomms/2014/140709/ncomms5371/suppinfo/ncomms5371_S1.html
    Nat Commun. 07/2014; 5.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Enzymatic haem and non-haem high-valent iron-oxo species are known to activate strong C-H bonds, yet duplicating this reactivity in a synthetic system remains a formidable challenge. Although instability of the terminal iron-oxo moiety is perhaps the foremost obstacle, steric and electronic factors also limit the activity of previously reported mononuclear iron(IV)-oxo compounds. In particular, although nature's non-haem iron(IV)-oxo compounds possess high-spin S = 2 ground states, this electronic configuration has proved difficult to achieve in a molecular species. These challenges may be mitigated within metal-organic frameworks that feature site-isolated iron centres in a constrained, weak-field ligand environment. Here, we show that the metal-organic framework Fe2(dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate) and its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc), are able to activate the C-H bonds of ethane and convert it into ethanol and acetaldehyde using nitrous oxide as the terminal oxidant. Electronic structure calculations indicate that the active oxidant is likely to be a high-spin S = 2 iron(IV)-oxo species.
    Nature Chemistry 07/2014; 6(7):590-5. · 21.76 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Plasma-enhanced atomic layer deposition of cobalt oxide onto nanotextured p+n-Si devices enables efficient photoelectrochemical water oxidation and effective protection of Si from corrosion at high pH (pH 13.6). A photocurrent density of 17 mA/cm2 at 1.23 V vs. RHE, saturation current density of 30 mA/cm2, and photovoltage of greater than 600 mV were achieved under simulated solar illumination. Sustained photocatalytic activities were observed at a constant current density of 10 mA/cm2, with no detectable degradation after 24 h. The as-deposited catalyst is composed of Co3O4, with an underlying CoO interfacial layer, while the surface of the catalyst undergoes progressive oxidation to CoO(OH) during the oxygen evolution reaction. Enhanced stability and performance of the nanotextured structure, compared to planar Si, is attributed to the larger interfacial area (semiconductor/catalyst) and higher surface area (catalyst/electrolyte), which reduces the interfacial resistance to charge transfer and increases the surface concentration of active Co sites for oxygen evolution, respectively. This work highlights a general approach that may be used to improve the performance and stability of Si photoelectrodes by directly engineering the catalyst/semiconductor interface.
    Journal of the American Chemical Society 04/2014; · 10.68 Impact Factor
  • Junko Yano, Vittal Yachandra
    Chemical Reviews 03/2014; · 41.30 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
    Nature Methods 03/2014; · 23.57 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Unsaturated metal sites within the nodes of metal-organic frameworks (MOFs) can be interrogated by redox reagents common to small molecule chemistry. We show, for the first time, that an analogue of the iconic M2(2,5-dioxidoterephthalate) (M2DOBDC, MOF-74) class of materials can be stoichiometrically oxidized by one electron per metal center. The reaction of Mn2DOBDC with C6H5ICl2, produces the oxidized material Cl2Mn2DOBDC, which retains crystallinity and porosity. Surprisingly, magnetic measurements, X-ray absorption and infrared spectroscopic data indicate that the Mn ions maintain a formal oxidation state of +2, suggesting instead the oxidation of the DOBDC(4-) ligand to the quinone DOBDC(2-). These results describe the first example of ligand redox non-innocence in a MOF and a rare instance of stoichiometric electron transfer involving the metal nodes. The methods described herein offer a synthetic toolkit that will be of general use for further explorations of the redox reactivity of MOF nodes.
    Journal of the American Chemical Society 02/2014; · 10.68 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: ZnSn1-x Gex N2 direct bandgap semiconductor alloys, with a crystal structure and electronic structure similar to InGaN, are earth-abundant alternatives for efficient, high-quality optoelectronic devices and solar energy conversion. The bandgap is tunable almost monotonically from 2 eV (ZnSnN2 ) to 3.1 eV (ZnGeN2 ) by control of the Sn/Ge ratio.
    Advanced Materials 12/2013; · 14.83 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A cobalt-sulfide (Co-S) film prepared via electrochemical deposition on conductive substrates is shown to behave as an efficient and robust catalyst for electrochemical and photoelectrochemical hydrogen generation from neutral pH water. Electrochemical experiments demonstrate that the film exhibits a low catalytic onset overpotential (η) of 43 mV, a Tafel slope of 93 mV/dec, and near 100% Faradaic efficiency in pH 7 phosphate buffer. Catalytic current densities can approach 50 mA/cm(2) and activity is maintained for at least 40 h. The catalyst can also be electrochemically coated on silicon, rendering a water-compatible photoelectrochemical system for hydrogen production under simulated 1 sun illumination. The facile preparation of this Co-S film, along with its low overpotential, high activity, and long-term aqueous stability, offer promising features for potential use in solar energy applications.
    Journal of the American Chemical Society 11/2013; · 10.68 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In the 1.9 Å structural model of photosystem II (3arc.pdb), the amino acid residue Glu333 of the D1 polypeptide coordinates to the oxygen-evolving Mn4CaO5 cluster. This residue appears to be highly significant in that it bridges the two Mn ions (MnB3 and the "dangling" MnA4) that are also bridged by the oxygen atom O5. This oxygen atom has been proposed to be derived from one of two substrate water molecules and to become incorporated into the product dioxygen molecule during the final step in the catalytic cycle. In addition, the backbone nitrogen of D1-Glu333 interacts directly with a nearby Cl- atom. To further explore the influence of this structurally unique residue on the properties of the Mn4CaO5 cluster, the D1-E333Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray Absorption, and FTIR difference spectroscopy. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild-type. In addition, the oxygen flash-yields exhibited normal period-four oscillations having normal S state parameters, although the yields were lower, indicative of the mutant's lower steady-state dioxygen evolution rate of approx. 30% compared to wild-type. The S1 state Mn-XANES and Mn-EXAFS and S2 state multiline EPR signals of purified D1-E333Q PSII core complexes closely resembled those of wild-type, aside from having lower amplitudes. The Sn+1-minus-Sn FTIR difference spectra showed only minor alterations to the carbonyl, amide, and carboxylate stretching regions. However, the mutation eliminated a negative peak at 3663 cm-1 in the weakly H-bonding OH stretching region of the S2-minus-S1 FTIR difference spectrum and caused a 9 cm-1 downshift of the negative feature in this region of the S1-minus-S0 FTIR difference spectrum. We conclude that fully functional Mn4CaO5 clusters assemble in the presence of the D1-E333Q mutation, but that the mutation decreases the yield of assembled clusters and alters the H-bonding properties of one or more water molecules or hydroxide groups that are located on or near the Mn4CaO5 cluster and that either deprotonate or form stronger hydrogen bonds during the S0 to S1 and S1 to S2 transitions.
    Biochemistry 10/2013; · 3.38 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local eg character (dz(2) and dxy based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.
    Inorganic Chemistry 10/2013; · 4.59 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-μ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kβ emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kβ2,5 peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kβ″ peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated μ-oxo bridges dominate this spectral region. The energies of the Kβ″ features differ by ∼3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (μ-O)(μ-OH2) motif can be distinguished from a symmetric (μ-OH)2 one. The results reported here highlight the sensitivity of Kβ valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.
    Inorganic Chemistry 10/2013; · 4.59 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Photosystem II supports four manganese centers through nine oxidation states from manganese(II) during assembly through to the most oxidized state before O2 formation and release. The protein-based carboxylate and imidazole ligands allow for significant changes of the coordination environment during the incorporation of hydroxido and oxido ligands upon oxidation of the metal centers. We report the synthesis and characterization of a series of tetramanganese complexes in four of the six oxidation states from Mn(II) 3Mn(III) to Mn(III) 2 Mn(IV) 2 with the same ligand framework (L) by incorporating four oxido ligands. A 1,3,5-triarylbenzene framework appended with six pyridyl and three alkoxy groups was utilized along with three acetate anions to access tetramanganese complexes, Mn4O x , with x = 1, 2, 3, and 4. Alongside two previously reported complexes, four new clusters in various states were isolated and characterized by crystallography, and four were observed electrochemically, thus accessing the eight oxidation states from Mn(II) 4 to Mn(III)Mn(IV) 3. This structurally related series of compounds was characterized by EXAFS, XANES, EPR, magnetism, and cyclic voltammetry. Similar to the ligands in the active site of the protein, the ancillary ligand (L) is preserved throughout the series and changes its binding mode between the low and high oxido-content clusters. Implications for the rational assembly and properties of high oxidation state metal-oxido clusters are presented.
    Chemical Science 10/2013; 4(10):3986-3996. · 8.31 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.
    Journal of Physical Chemistry Letters 10/2013; 4(21):3641-3647. · 6.59 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The dopant local structureand optical properties of Cu-doped ZnSe (ZnSe:Cu) and Cu and Al co-doped ZnSe (ZnSe:Cu,Al) nanocrystals (NCs) were studied with an emphasis on understanding the impact of introducing Al as a co-dopant. Quantum confined NCs with zinc blende crystal structure and particle size of 6±0.6 Å, were synthesized using a wet chemical route. The local structure of the Cu dopant studied by extended X-ray absorption fine structure (EXAFS) indicated that Cu in ZnSe:Cu NCs occupies a site that is neither substitutional nor interstitial and is adjacent to a Se vacancy. Additionally, we estimated that approximately 25±8% of Cu was locatedon the surface of the NC. Al3+ co-doping aids in Cu doping by accounting for the charge imbalance originated by Cu+ doping and consequently reduces surface Cu doping. The Cu ions remain distorted from the center of the tetrahedron to one of the triangular faces. The lifetime of the dopant related PL was found to increase from 550±60 to 700±60 ns after Al co-doping. DFT calculations were used to obtain the density of states of a model system to help explain the optical properties and dynamics processes observed. This study demonstrates that co-doping using different cations with complementary oxidation states is an effective method to enhance optical properties of doped semiconductor NCs of interest for various photonics applications.
    ACS Nano 09/2013; · 12.03 Impact Factor
  • Source
    Journal of the American Chemical Society 07/2013; · 10.68 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Molecular cobalt-containing hydrogen produc-tion catalysts are grafted to a visible-light-absorbing semi-conductor. The attachment procedure exploits the UV-induced immobilization chemistry of vinylpyridine to p-type (100) gallium phosphide (GaP). Single step surface-initiated photopolymerization yields a covalently attached polymer with pendent pyridyl groups that provide attachment points for assembling cobaloxime catalysts. Successful attachment is characterized by grazing angle attenuated total reflection Fourier transform infrared spectroscopy (GATR-FTIR), which shows distinct vibrational modes associated with the catalyst, as well as X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure spectroscopy (XANES) that confirm the presence of intact Co III complex on the surface. The Co-functionalized photocathode shows significantly enhanced photoelectrochemical (PEC) performance in aqueous conditions at neutral pH, compared to results obtained on GaP without attached cobalt complex. PEC measurements, at 100 mW cm^−2 illumination, yield a 2.4 mA cm^−2 current density at a 310 mV underpotential.
    Journal of the American Chemical Society 07/2013; 135(32):11861. · 10.68 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The oxygen-evolving complex (OEC) in the membrane-bound protein complex Photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn4CaO5 cluster in the OEC during the S state transitions using X-ray absorption spectroscopy (XAS). Overall structural changes of the Mn4CaO5 cluster, based on the Mn-ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn4CaO5 cluster in the OEC obtained from polarized XAS model and the 1.9 Å high-resolution crystal structure. Additionally, we compared the S1 state XAS of the dimeric and monomeric form of PSII from T. elongatus and spinach PSII. While the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the Mn K-edge XAS between T. elongatus PSII and spinach PSII are found, and may originate from differences in the 2nd sphere ligand atom geometry.
    Journal of Biological Chemistry 06/2013; · 4.65 Impact Factor

Publication Stats

1k Citations
607.94 Total Impact Points

Institutions

  • 2002–2014
    • Lawrence Berkeley National Laboratory
      • Physical Biosciences Division
      Berkeley, California, United States
  • 2013
    • Technische Universität Berlin
      • Department of Chemistry
      Berlin, Land Berlin, Germany
  • 2009–2013
    • European Synchrotron Radiation Facility
      Grenoble, Rhône-Alpes, France
  • 2007–2012
    • University of Florida
      • Department of Chemistry
      Gainesville, FL, United States
  • 2008–2010
    • University of California, Riverside
      • Department of Biochemistry
      Riverside, CA, United States
    • CSU Mentor
      Long Beach, California, United States
  • 2005–2008
    • University of California, Berkeley
      • Department of Chemistry
      Berkeley, MO, United States
  • 2004
    • University of California, Davis
      • Department of Chemistry
      Davis, California, United States