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Yano, Junko

Publications and source records attributed to Yano, Junko.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Phase Transformation and Water Adsorption Behavior of As‐Deposited and Annealed Ru Metal Thin Films Prepared by Atomic Layer Deposition

ABSTRACT Surfaces play a central role in catalytic processes, and understanding the transformation of ruthenium metal into ruthenium oxide during annealing is essential for tailoring functional catalytic interfaces. In this study, we systematically investigate ≈22 nm thick Ru metal films deposited by atomic layer deposition (ALD) at 300°C, focusing on their chemical composition, structural evolution, and surface hydration behavior following post‐deposition annealing in air from 400 to 600°C. Lab‐based and synchrotron X‐ray photoelectron spectroscopy (XPS) reveal a gradual conversion from metallic Ru to fully oxidized Ru 4+ with increasing annealing temperature, accompanied by a corresponding increase in lattice oxygen. X‐ray diffraction (XRD) shows amorphous Ru oxide phases at 400°C and 500°C that evolve into crystalline RuO 2 at 600°C, while atomic force microscopy (AFM) indicates enhanced grain growth and surface roughening upon annealing. Ambient‐pressure XPS (AP‐XPS) under controlled H 2 O vapor environments (1–17 Torr) demonstrates that samples annealed at 400°C and 500°C exhibit initially high hydroxyl coverage that decreases with increasing water vapor pressure, concurrent with a rise in molecular H 2 O adsorption. In contrast, the crystalline RuO 2 surface formed at 600°C maintains stable hydroxylation and supports increased water uptake. Overall, this work provides fundamental insight into Ru oxide–H 2 O interactions and establishes design principles for engineering oxide surfaces optimized for electrocatalytic applications.

APXPS↗
DOE OSTI2025

Insights from designing an artificial cascade catalysis system using principles from substrate channeling in enzymes

Generalizing the key requirements of highly-selective, multi-step chemical conversions involving spatially separated reaction centers remains one of the grand challenges of chemistry. Much work towards this effort has focused on decomposing multi-step conversions into their constituent reactions, whose intermediates are successively upgraded in a chemical cascade via diffusion from center to center. This approach for synthesizing more complex molecules takes its cues from biochemical networks, where near-unit conversion of even complex carbohydrates is achieved by upgrading chemical precursors via enzymatic cascades. In this computational study we examine a simple cascade involving coupled Ag and Cu catalysts that sequentially converts CO2 to CO and then CO2 and CO to reduced products, generically named CO2Product and COProduct. The system architecture is inspired by the phenomenon of biological substrate channeling, and components are examined to evaluate their effects on conversion efficiency in the cascade. Aside from a substrate channel linking two reaction centers, we find efficient cascades must also incorporate directional substrate diffusion, compartmentalization of the reaction centers, and proper timing of substrate arrival at the active center. We make explicit linkages between these requirements and chemical conversion in known biological systems, revealing additional control elements that could be incorporated.

CO 2 reduction↗
DOE OSTI2025

The electrode–electrolyte interface of Cu via modulation excitation X-ray absorption spectroscopy

The development and application of modulation excitation X-ray absorption spectroscopy with sub-second resolution and better than 0.02% detection sensitivity unveils the kinetics of the anodic oxidation of Cu in bicarbonate electrolytes. Accessing the electrode–electrolyte interface under operating conditions and capturing time-resolved kinetics remain challenging in electrochemical studies. Copper's interfacial oxidation dynamics remain unclear despite extensive research. Modulation excitation X-ray absorption spectroscopy (ME-XAS) was used to probe Cu in 100 mM KHCO 3 with sub-second sensitivity, revealing that hydroxide forms 30 ± 10 ms before the appearance of Cu 2 O at positive potentials (0 to 0.5 V vs. RHE) near open-circuit conditions. From −0.4 to 0.8 V vs. RHE, hydroxide coverage reaches 49%, accompanied by a balanced presence of Cu( i ) and Cu( ii ) oxides. These insights into Cu interfacial redox behavior under intermittent renewable energy operation—relevant to CO 2 electrolyzer durability—enhance our fundamental understanding of electrochemical interfaces.

Garcia-Esparza, Angel T↗
DOE OSTI2025

Transformation of TiN to TiNO Films via In-Situ Temperature-Dependent Oxygen Diffusion Process and Their Electrochemical Behavior

Titanium oxynitride (TiNO) thin films represent a multifaceted material system applicable in diverse fields, including energy storage, solar cells, sensors, protective coatings, and electrocatalysis. This study reports the synthesis of TiNO thin films grown at different substrate temperatures using pulsed laser deposition. A comprehensive structural investigation was conducted by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Non-Rutherford backscattering spectrometry (N-RBS), and X-ray absorption spectroscopy (XAS), which facilitated a detailed analysis that determined the phase, composition, and crystallinity of the films. Structural control was achieved via temperature-dependent oxygen in-diffusion, nitrogen out-diffusion, and the nucleation growth process related to adatom mobility. The XPS analysis indicates that the TiNO films consist of heterogeneous mixtures of TiN, TiNO, and TiO2 phases with temperature-dependent relative abundances. The correlation between the structure and electrochemical behavior of the thin films was examined. The TiNO films with relatively higher N/O ratio, meaning less oxidized, were more electrochemically active than the films with lower N/O ratio, i.e., more oxidized films. Films with higher oxidation levels demonstrated enhanced crystallinity and greater stability under electrochemical polarization. These findings demonstrate the importance of substrate temperature control in tailoring the properties of TiNO film, which is a fundamental part of designing and optimizing an efficient electrode material.

Cherono, Sheilah↗
DOE OSTI2024

Tribute to Kenneth Sauer (1931–2022): a mentor, a role-model, and an inspiration to all in the field of photosynthesis

Abstract Kenneth (Ken) Sauer was a mainstay of research in photosynthesis at the University of California, Berkeley and the Lawrence Berkeley National Laboratory (LBNL) for more than 50 years. Ken will be remembered by his colleagues, and other workers in the field of photosynthesis as well, for his pioneering work that introduced the physical techniques whose application have enriched our understanding of the basic reactions of oxygenic photosynthesis. His laboratory was a training ground for many students and postdocs who went on to success in the field of photosynthesis and many others. Trained as a physical chemist, he always brought that quantitative approach to research questions and used several spectroscopic methods in his research. His broad scientific interests concerned the role of manganese in oxygen evolution, electronic properties of chlorophylls, energy transport in antenna complexes, and electron transport reactions. He was also an enthusiastic teacher, an enormously successful mentor who leaves behind a legion of scientists as his abiding legacy, a lover of music and the outdoors with many interests beyond science, and a dedicated family man with a great sense of humility. In this tribute, we summarize some aspects of Ken Sauer’s life and career, illustrated with selected research achievements, and describe his approach to research and life as we perceived it, which is complemented by reminiscences of several current researchers in photosynthesis and other fields. The supporting material includes Ken Sauers’s CV and publication list, as well as a list of the graduate students and postdocs he trained and of researchers that spent a sabbatical in his lab.

Plant Sciences↗
DOE OSTI2024

The physical chemistry of solar fuels catalysis

The demonstration of effective light-driven electrochemical water splitting at the surface of a TiO 2 electrode in the seminal 1972 Honda–Fujishima publication spurred global research efforts to understand this effect and design advanced systems for solar H 2 generation from water as a carbon-free and sustainable fuel. In the 50+ years since that discovery, research investigating approaches toward the catalytic generation of the so-called “solar fuels,” i.e., not only H 2 from water but also CO 2 reduction products and NH 3 from N 2 , has expanded dramatically in scope and scale. The development of new experimental and computational methods and construction and commissioning of large-scale facilities have paved the way for important insights into the machinery of natural photosynthesis, leading to a greater understanding of the complexity of light-to-chemical energy conversion with an exquisite temporal and spatial resolution. Finally, these studies have provided the foundation for biologically inspired molecular and hybrid designs with the goal to promote the photochemical steps critical to solar fuels generation while avoiding unproductive or unnecessary pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers

The structure and mechanism of the water-oxidation chemistry that occurs in photosystem II have been subjects of great interest. The advent of X-ray free electron lasers allowed the determination of structures of the stable intermediate states and of steps in the transitions between these intermediate states, bringing a new perspective to this field. The room-temperature structures collected as the photosynthetic water oxidation reaction proceeds in real time have provided important novel insights into the structural changes and the mechanism of the water oxidation reaction. The time-resolved measurements have also given us a view of how this reaction—which involves multielectron, multiproton processes—is facilitated by the interaction of the ligands and the protein residues in the oxygen-evolving complex. These structures have also provided a picture of the dynamics occurring in the channels within photosystem II that are involved in the transport of the substrate water to the catalytic center and protons to the bulk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Deciphering Photoinduced Catalytic Reaction Mechanisms in Natural and Artificial Photosynthetic Systems on Multiple Temporal and Spatial Scales Using X-ray Probes

Utilization of renewable energies for catalytically generating value-added chemicals is highly desirable in this era of rising energy demands and climate change impacts. Artificial photosynthetic systems or photocatalysts utilize light to convert abundant CO 2 , H 2 O, and O 2 to fuels, such as carbohydrates and hydrogen, thus converting light energy to storable chemical resources. Here, the emergence of intense X-ray pulses from synchrotrons, ultrafast X-ray pulses from X-ray free electron lasers, and table-top laser-driven sources over the past decades opens new frontiers in deciphering photoinduced catalytic reaction mechanisms on the multiple temporal and spatial scales. Operando X-ray spectroscopic methods offer a new set of electronic transitions in probing the oxidation states, coordinating geometry, and spin states of the metal catalytic center and photosensitizers with unprecedented energy and time resolution. Operando X-ray scattering methods enable previously elusive reaction steps to be characterized on different length scales and time scales. The methodological progress and their application examples collected in this review will offer a glimpse into the accomplishments and current state in deciphering reaction mechanisms for both natural and synthetic systems. Looking forward, there are still many challenges and opportunities at the frontier of catalytic research that will require further advancement of the characterization techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Seeded stimulated x-ray emission at 5.9 keV: erratum

We recently identified two labeling-related mistakes in Optica 10 , 513 ( 2023 ) OPTIC8 2334-2536 10.1364/OPTICA.485989 . The first mistake concerns the labeling of the focus used during one scan. The second mistake concerns the labeling of a filter used in some runs to protect the detector. These mistakes do not affect the overall findings and conclusions in our paper, but some numbers, text, and figures are slightly affected by it. These items have been corrected and are listed below. Finally, a missing DOE award number (DE-SC0023270) has been added below.

Doyle, Margaret D.↗
DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

High‐Spin and Reactive Fe 13 Cluster with Exposed Metal Sites

Abstract Atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp* 4 W 4 Fe 13 S 12 , displaying a Fe 13 core with M−M bonds that has precedent only in main group and late metal chemistry. M 13 clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp* 4 W 4 Fe 13 S 12 displays a large spin ground state of S =13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.

Scott, Anna G.↗
DOE OSTI2023

High-Spin and Reactive Fe 13 Cluster with Exposed Metal Sites

We report atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp* 4 W 4 Fe 13 S 12 , displaying a Fe 13 core with M-M bonds that has precedent only in main group and late metal chemistry. M 13 clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp* 4 W 4 Fe 13 S 12 displays a large spin ground state of S=13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

59 BASIC BIOLOGICAL SCIENCES↗