32 results on '"Shibata N"'
Search Results
2. Direct observation of space-charge-induced electric fields at oxide grain boundaries.
- Author
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Toyama S, Seki T, Feng B, Ikuhara Y, and Shibata N
- Abstract
Space charge layers (SCLs) formed at grain boundaries (GBs) are considered to critically influence the properties of polycrystalline materials such as ion conductivities. Despite the extensive researches on this issue, the presence of GB SCLs and their relationship with GB orientations, atomic-scale structures and impurity/solute segregation behaviors remain controversial, primarily due to the difficulties in directly observing charge distribution at GBs. In this study, we directly observe electric field distribution across the well-defined yttria-stabilized zirconia (YSZ) GBs by tilt-scan averaged differential phase contrast scanning transmission electron microscopy. Our observation clearly reveals the existence of SCLs across the YSZ GBs with nanometer precision, which are significantly varied depending on the GB orientations and the resultant core atomic structures. Moreover, the magnitude of SCLs show a strong correlation with yttrium segregation amounts. This study provides critical insights into the complex interplay between SCLs, orientations, atomic structures and segregation of GBs in ionic crystals., (© 2024. The Author(s).)
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- 2024
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3. Author Correction: Efficient and stable visible-light-driven Z-scheme overall water splitting using an oxysulfide H 2 evolution photocatalyst.
- Author
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Lin L, Ma Y, Vequizo JJM, Nakabayashi M, Gu C, Tao X, Yoshida H, Pihosh Y, Nishina Y, Yamakata A, Shibata N, Hisatomi T, Takata T, and Domen K
- Published
- 2024
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4. Ultra-stable and highly reactive colloidal gold nanoparticle catalysts protected using multi-dentate metal oxide nanoclusters.
- Author
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Xia K, Yatabe T, Yonesato K, Kikkawa S, Yamazoe S, Nakata A, Ishikawa R, Shibata N, Ikuhara Y, Yamaguchi K, and Suzuki K
- Abstract
Owing to their remarkable properties, gold nanoparticles are applied in diverse fields, including catalysis, electronics, energy conversion and sensors. However, for catalytic applications of colloidal gold nanoparticles, the trade-off between their reactivity and stability is a significant concern. Here we report a universal approach for preparing stable and reactive colloidal small (~3 nm) gold nanoparticles by using multi-dentate polyoxometalates as protecting agents in non-polar solvents. These nanoparticles exhibit exceptional stability even under conditions of high concentration, long-term storage, heating and addition of bases. Moreover, they display excellent catalytic performance in various oxidation reactions of organic substrates using molecular oxygen as the sole oxidant. Our findings highlight the ability of inorganic multi-dentate ligands with structural stability and robust steric and electronic effects to confer stability and reactivity upon gold nanoparticles. This approach can be extended to prepare metal nanoparticles other than gold, enabling the design of novel nanomaterials with promising applications., (© 2024. The Author(s).)
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- 2024
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5. Efficient and stable visible-light-driven Z-scheme overall water splitting using an oxysulfide H 2 evolution photocatalyst.
- Author
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Lin L, Ma Y, Vequizo JJM, Nakabayashi M, Gu C, Tao X, Yoshida H, Pihosh Y, Nishina Y, Yamakata A, Shibata N, Hisatomi T, Takata T, and Domen K
- Abstract
So-called Z-scheme systems permit overall water splitting using narrow-bandgap photocatalysts. To boost the performance of such systems, it is necessary to enhance the intrinsic activities of the hydrogen evolution photocatalyst and oxygen evolution photocatalyst, promote electron transfer from the oxygen evolution photocatalyst to the hydrogen evolution photocatalyst, and suppress back reactions. The present work develop a high-performance oxysulfide photocatalyst, Sm
2 Ti2 O5 S2 , as an hydrogen evolution photocatalyst for use in a Z-scheme overall water splitting system in combination with BiVO4 as the oxygen evolution photocatalyst and reduced graphene oxide as the solid-state electron mediator. After surface modifications of the photocatalysts to promote charge separation and redox reactions, this system is able to split water into hydrogen and oxygen for more than 100 hours with a solar-to-hydrogen energy conversion efficiency of 0.22%. In contrast to many existing photocatalytic systems, the water splitting activity of the present system is only minimally reduced by increasing the background pressure to 90 kPa. These results suggest characteristics suitable for applications under practical operating conditions., (© 2024. The Author(s).)- Published
- 2024
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6. Incommensurate grain-boundary atomic structure.
- Author
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Seki T, Futazuka T, Morishige N, Matsubara R, Ikuhara Y, and Shibata N
- Abstract
Grain-boundary atomic structures of crystalline materials have long been believed to be commensurate with the crystal periodicity of the adjacent crystals. In the present study, we experimentally observed a Σ9 grain-boundary atomic structure of a bcc crystal (Fe-3%Si). It is found that the Σ9 grain-boundary structure is largely reconstructed and forms a dense packing of icosahedral clusters in its core. Combining with the detailed theoretical calculations, the Σ9 grain-boundary atomic structure is discovered to be incommensurate with the adjacent crystal structures. The present findings shed new light on the study of stable grain-boundary atomic structures in crystalline materials., (© 2023. The Author(s).)
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- 2023
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7. Sub-50 nm perovskite-type tantalum-based oxynitride single crystals with enhanced photoactivity for water splitting.
- Author
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Xiao J, Nakabayashi M, Hisatomi T, Vequizo JJM, Li W, Chen K, Tao X, Yamakata A, Shibata N, Takata T, Inoue Y, and Domen K
- Abstract
A long-standing trade-off exists between improving crystallinity and minimizing particle size in the synthesis of perovskite-type transition-metal oxynitride photocatalysts via the thermal nitridation of commonly used metal oxide and carbonate precursors. Here, we overcome this limitation to fabricate ATaO
2 N (A = Sr, Ca, Ba) single nanocrystals with particle sizes of several tens of nanometers, excellent crystallinity and tunable long-wavelength response via thermal nitridation of mixtures of tantalum disulfide, metal hydroxides (A(OH)2 ), and molten-salt fluxes (e.g., SrCl2 ) as precursors. The SrTaO2 N nanocrystals modified with a tailored Ir-Pt alloy@Cr2 O3 cocatalyst evolved H2 around two orders of magnitude more efficiently than the previously reported SrTaO2 N photocatalysts, with a record solar-to-hydrogen energy conversion efficiency of 0.15% for SrTaO2 N in Z-scheme water splitting. Our findings enable the synthesis of perovskite-type transition-metal oxynitride nanocrystals by thermal nitridation and pave the way for manufacturing advanced long-wavelength-responsive particulate photocatalysts for efficient solar energy conversion., (© 2023. The Author(s).)- Published
- 2023
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8. Lenalidomide derivatives and proteolysis-targeting chimeras for controlling neosubstrate degradation.
- Author
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Yamanaka S, Furihata H, Yanagihara Y, Taya A, Nagasaka T, Usui M, Nagaoka K, Shoya Y, Nishino K, Yoshida S, Kosako H, Tanokura M, Miyakawa T, Imai Y, Shibata N, and Sawasaki T
- Subjects
- Female, Pregnancy, Humans, Lenalidomide pharmacology, Proteolysis, Immunomodulating Agents, Chromosome Aberrations, Proteolysis Targeting Chimera, Multiple Myeloma drug therapy, Myelodysplastic Syndromes drug therapy, Hematologic Neoplasms
- Abstract
Lenalidomide, an immunomodulatory drug (IMiD), is commonly used as a first-line therapy in many haematological cancers, such as multiple myeloma (MM) and 5q myelodysplastic syndromes (5q MDS), and it functions as a molecular glue for the protein degradation of neosubstrates by CRL4
CRBN . Proteolysis-targeting chimeras (PROTACs) using IMiDs with a target protein binder also induce the degradation of target proteins. The targeted protein degradation (TPD) of neosubstrates is crucial for IMiD therapy. However, current IMiDs and IMiD-based PROTACs also break down neosubstrates involved in embryonic development and disease progression. Here, we show that 6-position modifications of lenalidomide are essential for controlling neosubstrate selectivity; 6-fluoro lenalidomide induced the selective degradation of IKZF1, IKZF3, and CK1α, which are involved in anti-haematological cancer activity, and showed stronger anti-proliferative effects on MM and 5q MDS cell lines than lenalidomide. PROTACs using these lenalidomide derivatives for BET proteins induce the selective degradation of BET proteins with the same neosubstrate selectivity. PROTACs also exert anti-proliferative effects in all examined cell lines. Thus, 6-position-modified lenalidomide is a key molecule for selective TPD using thalidomide derivatives and PROTACs., (© 2023. Springer Nature Limited.)- Published
- 2023
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9. Transition-metal-free silylboronate-mediated cross-couplings of organic fluorides with amines.
- Author
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Zhou J, Zhao Z, and Shibata N
- Abstract
C-N bond cross-couplings are fundamental in the field of organic chemistry. Herein, silylboronate-mediated selective defluorinative cross-coupling of organic fluorides with secondary amines via a transition-metal-free strategy is disclosed. The cooperation of silylboronate and potassium tert-butoxide enables the room-temperature cross-coupling of C-F and N-H bonds, effectively avoiding the high barriers associated with thermally induced S
N 2 or SN 1 amination. The significant advantage of this transformation is the selective activation of the C-F bond of the organic fluoride by silylboronate without affecting potentially cleavable C-O, C-Cl, heteroaryl C-H, or C-N bonds and CF3 groups. Tertiary amines with aromatic, heteroaromatic, and/or aliphatic groups were efficiently synthesized in a single step using electronically and sterically varying organic fluorides and N-alkylanilines or secondary amines. The protocol is extended to the late-stage syntheses of drug candidates, including their deuterium-labeled analogs., (© 2023. The Author(s).)- Published
- 2023
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10. Decoupling light absorption and carrier transport via heterogeneous doping in Ta 3 N 5 thin film photoanode.
- Author
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Xiao Y, Fan Z, Nakabayashi M, Li Q, Zhou L, Wang Q, Li C, Shibata N, Domen K, and Li Y
- Abstract
The trade-off between light absorption and carrier transport in semiconductor thin film photoelectrodes is a major limiting factor of their solar-to-hydrogen efficiency for photoelectrochemical water splitting. Herein, we develop a heterogeneous doping strategy that combines surface doping with bulk gradient doping to decouple light absorption and carrier transport in a thin film photoelectrode. Taking La and Mg doped Ta
3 N5 thin film photoanode as an example, enhanced light absorption is achieved by surface La doping through alleviating anisotropic optical absorption, while efficient carrier transport in the bulk is maintained by the gradient band structure induced by gradient Mg doping. Moreover, the homojunction formed between the La-doped layer and the gradient Mg-doped layer further promotes charge separation. As a result, the heterogeneously doped photoanode yields a half-cell solar-to-hydrogen conversion efficiency of 4.07%, which establishes Ta3 N5 as a leading performer among visible-light-responsive photoanodes. The heterogeneous doping strategy could be extended to other semiconductor thin film light absorbers to break performance trade-offs by decoupling light absorption and carrier transport., (© 2022. The Author(s).)- Published
- 2022
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11. A hygroscopic nano-membrane coating achieves efficient vapor-fed photocatalytic water splitting.
- Author
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Suguro T, Kishimoto F, Kariya N, Fukui T, Nakabayashi M, Shibata N, Takata T, Domen K, and Takanabe K
- Abstract
Efficient water vapor splitting opens a new strategy to develop scalable and corrosion-free solar-energy-harvesting systems. This study demonstrates highly efficient overall water splitting under vapor feeding using Al-doped SrTiO
3 (SrTiO3 :Al)-based photocatalyst decorated homogeneously with nano-membrane TiOx or TaOx thin layers (<3 nm). Here, we show the hygroscopic nature of the metal (hydr)oxide layer provides liquid water reaction environment under vapor, thus achieving an AQY of 54 ± 4%, which is comparable to a liquid reaction. TiOx coated, CoOOH/Rh loaded SrTiO3 :Al photocatalyst works for over 100 h, under high pressure (0.3 MPa), and with no problems using simulated seawater as the water vapor supply source. This vapor feeding concept is innovative as a high-pressure-tolerant photoreactor and may have value for large-scale applications. It allows uniform distribution of the water reactant into the reactor system without the potential risk of removing photocatalyst powders and eluting some dissolved ions from the reactor., (© 2022. The Author(s).)- Published
- 2022
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12. Grain boundary structural transformation induced by co-segregation of aliovalent dopants.
- Author
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Futazuka T, Ishikawa R, Shibata N, and Ikuhara Y
- Abstract
Impurity doping is a conventional but one of the most effective ways to control the functional properties of materials. In insulating materials, the dopant solubility limit is considerably low in general, and the dopants often segregate to grain boundaries (GBs) in polycrystals, which significantly alter their entire properties. However, detailed mechanisms on how dopant atoms form structures at GBs and change their properties remain a matter of conjecture. Here, we show GB structural transformation in α-Al
2 O3 induced by co-segregation of Ca and Si aliovalent dopants using atomic-resolution scanning transmission electron microscopy combined with density functional theory calculations. To accommodate large-sized Ca ions at the GB core, the pristine GB atomic structure is transformed into a new GB structure with larger free volumes. Moreover, the Si and Ca dopants form a chemically ordered structure, and the charge compensation is achieved within the narrow GB core region rather than forming broader space charge layers. Our findings give an insight into GB engineering by utilizing aliovalent co-segregation., (© 2022. The Author(s).)- Published
- 2022
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13. Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota.
- Author
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Hosomi K, Saito M, Park J, Murakami H, Shibata N, Ando M, Nagatake T, Konishi K, Ohno H, Tanisawa K, Mohsen A, Chen YA, Kawashima H, Natsume-Kitatani Y, Oka Y, Shimizu H, Furuta M, Tojima Y, Sawane K, Saika A, Kondo S, Yonejima Y, Takeyama H, Matsutani A, Mizuguchi K, Miyachi M, and Kunisawa J
- Subjects
- Acetylcholine, Administration, Oral, Adult, Amylopectin, Animals, Cross-Sectional Studies, Diet, High-Fat adverse effects, Humans, Japan, Mice, Mice, Inbred C57BL, Ornithine, Symbiosis, Carbohydrate Metabolism, Clostridiales metabolism, Diabetes Mellitus, Type 2 microbiology, Diabetes Mellitus, Type 2 therapy, Gastrointestinal Microbiome physiology, Obesity microbiology, Obesity therapy
- Abstract
The gut microbiome is an important determinant in various diseases. Here we perform a cross-sectional study of Japanese adults and identify the Blautia genus, especially B. wexlerae, as a commensal bacterium that is inversely correlated with obesity and type 2 diabetes mellitus. Oral administration of B. wexlerae to mice induce metabolic changes and anti-inflammatory effects that decrease both high-fat diet-induced obesity and diabetes. The beneficial effects of B. wexlerae are correlated with unique amino-acid metabolism to produce S-adenosylmethionine, acetylcholine, and L-ornithine and carbohydrate metabolism resulting in the accumulation of amylopectin and production of succinate, lactate, and acetate, with simultaneous modification of the gut bacterial composition. These findings reveal unique regulatory pathways of host and microbial metabolism that may provide novel strategies in preventive and therapeutic approaches for metabolic disorders., (© 2022. The Author(s).)
- Published
- 2022
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14. Direct imaging of the disconnection climb mediated point defects absorption by a grain boundary.
- Author
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Wei J, Feng B, Tochigi E, Shibata N, and Ikuhara Y
- Abstract
Grain boundaries (GBs) are considered as the effective sinks for point defects, which improve the radiation resistance of materials. However, the fundamental mechanisms of how the GBs absorb and annihilate point defects under irradiation are still not well understood at atomic scale. With the aid of the atomic resolution scanning transmission electron microscope, we experimentally investigate the atomistic mechanism of point defects absorption by a ∑31 GB in α-Al
2 O3 under high energy electron beam irradiation. It is shown that a disconnection pair is formed, during which all the Al atomic columns are tracked. We demonstrate that the formation of the disconnection pair is proceeded with disappearing of atomic columns in the GB core, which suggests that the GB absorbs vacancies. Such point defect absorption is attributed to the nucleation and climb motion of disconnections. These experimental results provide an atomistic understanding of how GBs improve the radiation resistance of materials., (© 2022. The Author(s).)- Published
- 2022
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15. Interface engineering of Ta 3 N 5 thin film photoanode for highly efficient photoelectrochemical water splitting.
- Author
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Fu J, Fan Z, Nakabayashi M, Ju H, Pastukhova N, Xiao Y, Feng C, Shibata N, Domen K, and Li Y
- Abstract
Interface engineering is a proven strategy to improve the efficiency of thin film semiconductor based solar energy conversion devices. Ta
3 N5 thin film photoanode is a promising candidate for photoelectrochemical (PEC) water splitting. Yet, a concerted effort to engineer both the bottom and top interfaces of Ta3 N5 thin film photoanode is still lacking. Here, we employ n-type In:GaN and p-type Mg:GaN to modify the bottom and top interfaces of Ta3 N5 thin film photoanode, respectively. The obtained In:GaN/Ta3 N5 /Mg:GaN heterojunction photoanode shows enhanced bulk carrier separation capability and better injection efficiency at photoanode/electrolyte interface, which lead to a record-high applied bias photon-to-current efficiency of 3.46% for Ta3 N5 -based photoanode. Furthermore, the roles of the In:GaN and Mg:GaN layers are distinguished through mechanistic studies. While the In:GaN layer contributes mainly to the enhanced bulk charge separation efficiency, the Mg:GaN layer improves the surface charge inject efficiency. This work demonstrates the crucial role of proper interface engineering for thin film-based photoanode in achieving efficient PEC water splitting., (© 2022. The Author(s).)- Published
- 2022
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16. A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues.
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Yamanaka S, Horiuchi Y, Matsuoka S, Kido K, Nishino K, Maeno M, Shibata N, Kosako H, and Sawasaki T
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- Adaptor Proteins, Signal Transducing metabolism, Biotinylation, Cell Line, Tumor, DNA-Binding Proteins metabolism, Gene Expression Regulation, HEK293 Cells, Hepatocytes cytology, Hepatocytes drug effects, Humans, Immunologic Factors pharmacology, Intracellular Signaling Peptides and Proteins genetics, Intracellular Signaling Peptides and Proteins metabolism, Lymphocytes cytology, Lymphocytes drug effects, Neurons cytology, Neurons drug effects, Neurons metabolism, Protein Binding, Protein Interaction Mapping, Proteolysis drug effects, Receptor, Fibroblast Growth Factor, Type 1 genetics, Receptor, Fibroblast Growth Factor, Type 1 metabolism, Substrate Specificity, Sulfonamides pharmacology, Transcription Factors metabolism, Ubiquitin-Protein Ligases metabolism, Adaptor Proteins, Signal Transducing genetics, Biological Assay, DNA-Binding Proteins genetics, Hepatocytes metabolism, Lymphocytes metabolism, Transcription Factors genetics, Ubiquitin-Protein Ligases genetics
- Abstract
Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells., (© 2022. The Author(s).)
- Published
- 2022
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17. A self-healing catalyst for electrocatalytic and photoelectrochemical oxygen evolution in highly alkaline conditions.
- Author
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Feng C, Wang F, Liu Z, Nakabayashi M, Xiao Y, Zeng Q, Fu J, Wu Q, Cui C, Han Y, Shibata N, Domen K, Sharp ID, and Li Y
- Abstract
While self-healing is considered a promising strategy to achieve long-term stability for oxygen evolution reaction (OER) catalysts, this strategy remains a challenge for OER catalysts working in highly alkaline conditions. The self-healing of the OER-active nickel iron layered double hydroxides (NiFe-LDH) has not been successful due to irreversible leaching of Fe catalytic centers. Here, we investigate the introduction of cobalt (Co) into the NiFe-LDH as a promoter for in situ Fe redeposition. An active borate-intercalated NiCoFe-LDH catalyst is synthesized using electrodeposition and shows no degradation after OER tests at 10 mA cm
-2 at pH 14 for 1000 h, demonstrating its self-healing ability under harsh OER conditions. Importantly, the presence of both ferrous ions and borate ions in the electrolyte is found to be crucial to the catalyst's self-healing. Furthermore, the implementation of this catalyst in photoelectrochemical devices is demonstrated with an integrated silicon photoanode. The self-healing mechanism leads to a self-limiting catalyst thickness, which is ideal for integration with photoelectrodes since redeposition is not accompanied by increased parasitic light absorption., (© 2021. The Author(s).)- Published
- 2021
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18. Catalyst-free carbosilylation of alkenes using silyl boronates and organic fluorides via selective C-F bond activation.
- Author
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Zhou J, Jiang B, Fujihira Y, Zhao Z, Imai T, and Shibata N
- Abstract
A regioselective carbosilylation of alkenes has emerged as a powerful strategy to access molecules with functionalized silylated alkanes, by incorporating silyl and carbon groups across an alkene double bond. However, to the best of our knowledge, organic fluorides have never been used in this protocol. Here we disclose the catalyst-free carbosilylation of alkenes using silyl boronates and organic fluorides mediated by
t BuOK. The main feature of this transformation is the selective activation of the C-F bond of an organic fluoride by the silyl boronate without undergoing potential side-reactions involving C-O, C-Cl, heteroaryl-CH, and even CF3 groups. Various silylated alkanes with tertiary or quaternary carbon centers that have aromatic, hetero-aromatic, and/or aliphatic groups at the β-position are synthesized in a single step from substituted or non-substituted aryl alkenes. An intramolecular variant of this carbosilylation is also achieved via the reaction of a fluoroarene with a ω-alkenyl side chain and a silyl boronate.- Published
- 2021
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19. Sequential cocatalyst decoration on BaTaO 2 N towards highly-active Z-scheme water splitting.
- Author
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Wang Z, Luo Y, Hisatomi T, Vequizo JJM, Suzuki S, Chen S, Nakabayashi M, Lin L, Pan Z, Kariya N, Yamakata A, Shibata N, Takata T, Teshima K, and Domen K
- Abstract
Oxynitride photocatalysts hold promise for renewable solar hydrogen production via water splitting owing to their intense visible light absorption. Cocatalyst loading is essential for activation of such oxynitride photocatalysts. However, cocatalyst nanoparticles form aggregates and exhibit weak interaction with photocatalysts, which prevents eliciting their intrinsic photocatalytic performance. Here, we demonstrate efficient utilization of photoexcited electrons in a single-crystalline particulate BaTaO
2 N photocatalyst prepared with the assistance of RbCl flux for H2 evolution reactions via sequential decoration of Pt cocatalyst by impregnation-reduction followed by site-selective photodeposition. The Pt-loaded BaTaO2 N photocatalyst evolves H2 over 100 times more efficiently than before, with an apparent quantum yield of 6.8% at the wavelength of 420 nm, from a methanol aqueous solution, and a solar-to-hydrogen energy conversion efficiency of 0.24% in Z-scheme water splitting. Enabling uniform dispersion and intimate contact of cocatalyst nanoparticles on single-crystalline narrow-bandgap particulate photocatalysts is a key to efficient solar-to-chemical energy conversion.- Published
- 2021
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20. Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide.
- Author
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Furihata H, Yamanaka S, Honda T, Miyauchi Y, Asano A, Shibata N, Tanokura M, Sawasaki T, and Miyakawa T
- Subjects
- Adaptor Proteins, Signal Transducing chemistry, Adaptor Proteins, Signal Transducing metabolism, Amino Acid Sequence, HEK293 Cells, Humans, Protein Binding drug effects, Protein Domains, Stereoisomerism, Structural Homology, Protein, Substrate Specificity, Thalidomide chemistry, Thalidomide pharmacology, Transcription Factors chemistry, Transcription Factors metabolism, Ubiquitin-Protein Ligases, Immunologic Factors chemistry, Immunologic Factors pharmacology, Thalidomide analogs & derivatives
- Abstract
Thalidomide and its derivatives exert not only therapeutic effects as immunomodulatory drugs (IMiDs) but also adverse effects such as teratogenicity, which are due in part to different C2H2 zinc-finger (ZF) transcription factors, IKZF1 (or IKZF3) and SALL4, respectively. Here, we report the structural bases for the SALL4-specific proteasomal degradation induced by 5-hydroxythalidomide, a primary thalidomide metabolite generated by the enzymatic activity of cytochrome P450 isozymes, through the interaction with cereblon (CRBN). The crystal structure of the metabolite-mediated human SALL4-CRBN complex and mutagenesis studies elucidate the complex formation enhanced by the interaction between CRBN and an additional hydroxy group of (S)-5-hydroxythalidomide and the variation in the second residue of β-hairpin structure that underlies the C2H2 ZF-type neo-morphic substrate (neosubstrate) selectivity of 5-hydroxythalidomide. These findings deepen our understanding of the pharmaceutical action of IMiDs and provide structural evidence that the glue-type E3 ligase modulators cause altered neosubstrate specificities through their metabolism.
- Published
- 2020
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21. Dislocation and oxygen-release driven delithiation in Li 2 MnO 3 .
- Author
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Nakayama K, Ishikawa R, Kobayashi S, Shibata N, and Ikuhara Y
- Abstract
Lithium-excess layered cathode materials such as Li
2 MnO3 have attracted much attention owing to their high energy densities. It has been proposed that oxygen-release and cation-mixing might be induced by delithiation. However, it is still unclear as to how the delithiated-region grows. Here, by using atomic-resolution scanning transmission electron microscopy combined with electron energy-loss spectroscopy, we directly observe the atomic structures at the interface between pristine and delithiated regions in the partially delithiated Li2 MnO3 single crystal. We elucidate that the delithiated regions have extensive amounts of irreversible defects such as oxygen-release and Mn/Li cation-mixing. At the interface, a partially cation disordered structure is formed, where Mn migration occurred only in the specific Mn/Li layers. Besides, a number of dislocations are formed at the interface to compensate the lattice mismatch between the pristine and delithiated regions. The observed oxygen-release and dislocations could govern the growth of delithiated-regions and performance degradation in Li2 MnO3 .- Published
- 2020
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22. Direct observation of atomic-scale fracture path within ceramic grain boundary core.
- Author
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Kondo S, Ishihara A, Tochigi E, Shibata N, and Ikuhara Y
- Abstract
In fracture processes, grain boundaries behave as preferential paths for crack propagation. These grain boundary fractures proceed by the atomic-bond rupture within the grain boundary cores, and thus grain boundary structures have crucial influence on the fracture properties. However, the relationship between grain boundary structures and atomic fracture processes has been a matter of conjecture, especially in the case of dopant-segregated grain boundaries which have complicated local structures and chemistries. Here, we determine the atomic-bond breaking path within a dopant-segregated Al
2 O3 grain boundary core, via atomic-scale observations of the as-fractured surface and the crack tip introduced by in situ nanoindentation experiments inside a transmission electron microscope. Our observations show that the atomic fracture path is selected to produce less coordination-deficient oxygen polyhedra of dopant cations, which is rationalised using first-principles calculations. The present findings indicate that the atomic coordination geometry at the grain boundary core affects the fracture processes.- Published
- 2019
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23. Defluorosilylation of fluoroarenes and fluoroalkanes.
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Cui B, Jia S, Tokunaga E, and Shibata N
- Abstract
Direct activation of carbon-fluorine bonds (C-F) to introduce the silyl or boryl groups and generate valuable carbon-silicon (C-Si) or carbon-boron (C-B) bonds is important in the development of synthetically useful reactions, owing to the unique opportunities for further derivatization to achieve more complex molecules. Despite considerable progress of C-F bond activation to construct carbon-carbon (C-C) and carbon-heteroatom (C-X) bond formation, the defluorosilylation via C-F cleavage has been rarely demonstrated. Here, we report an ipso-silylation of aryl fluorides via cleavage of unactivated C-F bonds by a Ni catalyst under mild conditions and without the addition of any external ligand. Alkyl fluorides are also directly converted into the corresponding alkyl silanes under similar conditions, even in the absence of the Ni catalyst. Applications of this protocol in late-stage defluorosilylation of potentially bioactive pharmaceuticals and in further derivatizations are also carried out.
- Published
- 2018
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24. Direct electric field imaging of graphene defects.
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Ishikawa R, Findlay SD, Seki T, Sánchez-Santolino G, Kohno Y, Ikuhara Y, and Shibata N
- Abstract
Material properties are sensitive to atomistic structure defects such as vacancies or impurities, and it is therefore important to determine not only the local atomic configuration but also their chemical bonding state. Annular dark-field scanning transmission electron microscopy (STEM) combined with electron energy-loss spectroscopy has been utilized to investigate the local electronic structures of such defects down to the level of single atoms. However, it is still challenging to two-dimensionally map the local bonding states, because the electronic fine-structure signal from a single atom is extremely weak. Here, we show that atomic-resolution differential phase-contrast STEM imaging can directly visualize the anisotropy of single Si atomic electric fields in monolayer graphene. We also visualize the atomic electric fields of Stone-Wales defects and nanopores in graphene. Our results open the way to directly examine the local chemistry of the defective structures in materials at atomistic dimensions.
- Published
- 2018
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25. A small-molecule inhibitor of SOD1-Derlin-1 interaction ameliorates pathology in an ALS mouse model.
- Author
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Tsuburaya N, Homma K, Higuchi T, Balia A, Yamakoshi H, Shibata N, Nakamura S, Nakagawa H, Ikeda SI, Umezawa N, Kato N, Yokoshima S, Shibuya M, Shimonishi M, Kojima H, Okabe T, Nagano T, Naguro I, Imamura K, Inoue H, Fujisawa T, and Ichijo H
- Subjects
- Amyotrophic Lateral Sclerosis genetics, Amyotrophic Lateral Sclerosis metabolism, Animals, Brain drug effects, Brain metabolism, HEK293 Cells, Humans, Male, Membrane Proteins genetics, Mice, Inbred C57BL, Mice, Transgenic, Protein Binding drug effects, Spinal Cord drug effects, Spinal Cord metabolism, Superoxide Dismutase-1 genetics, Amyotrophic Lateral Sclerosis prevention & control, Disease Models, Animal, Membrane Proteins metabolism, Small Molecule Libraries pharmacology, Superoxide Dismutase-1 metabolism
- Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder. Despite its severity, there are no effective treatments because of the complexity of its pathogenesis. As one of the underlying mechanisms of Cu, Zn superoxide dismutase (SOD1) gene mutation-induced ALS, SOD1 mutants (SOD1
mut ) commonly interact with an endoplasmic reticulum-resident membrane protein Derlin-1, triggering motoneuron death. However, the importance of SOD1-Derlin-1 interaction in in vitro human model and in vivo mouse model remains to be elucidated. Here, we identify small-molecular-weight compounds that inhibit the SOD1-Derlin-1 interaction by screening approximately 160,000 compounds. The inhibitor prevents 122 types of SOD1mut from interacting with Derlin-1, and significantly ameliorates the ALS pathology both in motoneurons derived from patient induced pluripotent stem cells and in model mice. Our data suggest that the SOD1-Derlin-1 interaction contributes to the pathogenesis of ALS and is a promising drug target for ALS treatment.- Published
- 2018
- Full Text
- View/download PDF
26. Possible absence of critical thickness and size effect in ultrathin perovskite ferroelectric films.
- Author
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Gao P, Zhang Z, Li M, Ishikawa R, Feng B, Liu HJ, Huang YL, Shibata N, Ma X, Chen S, Zhang J, Liu K, Wang EG, Yu D, Liao L, Chu YH, and Ikuhara Y
- Abstract
Although the size effect in ferroelectric thin films has been known for long time, the underlying mechanism is not yet fully understood and whether or not there is a critical thickness below which the ferroelectricity vanishes is still under debate. Here, we directly measure the thickness-dependent polarization in ultrathin PbZr
0.2 Ti0.8 O3 films via quantitative annular bright field imaging. We find that the polarization is significantly suppressed for films <10-unit cells thick (∼4 nm). However, approximately the polarization never vanishes. The residual polarization is ∼16 μCcm-2 (∼17%) at 1.5-unit cells (∼0.6 nm) thick film on bare SrTiO3 and ∼22 μCcm-2 at 2-unit cells thick film on SrTiO3 with SrRuO3 electrode. The residual polarization in these ultrathin films is mainly attributed to the robust covalent Pb-O bond. Our atomic study provides new insights into mechanistic understanding of nanoscale ferroelectricity and the size effects.- Published
- 2017
- Full Text
- View/download PDF
27. Electric field imaging of single atoms.
- Author
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Shibata N, Seki T, Sánchez-Santolino G, Findlay SD, Kohno Y, Matsumoto T, Ishikawa R, and Ikuhara Y
- Abstract
In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures.
- Published
- 2017
- Full Text
- View/download PDF
28. Atomic mechanism of polarization-controlled surface reconstruction in ferroelectric thin films.
- Author
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Gao P, Liu HJ, Huang YL, Chu YH, Ishikawa R, Feng B, Jiang Y, Shibata N, Wang EG, and Ikuhara Y
- Abstract
At the ferroelectric surface, the broken translational symmetry induced bound charge should significantly alter the local atomic configurations. Experimentally revealing the atomic structure of ferroelectric surface, however, is very challenging due to the strong spatial variety between nano-sized domains, and strong interactions between the polarization and other structural parameters. Here, we study surface structures of Pb(Zr0.2Ti0.8)O3 thin film by using the annular bright-field imaging. We find that six atomic layers with suppressed polarization and a charged 180° domain wall are at negatively poled surfaces, no reconstruction exists at positively poled surfaces, and seven atomic layers with suppressed polarization and a charged 90° domain wall exist at nominally neutral surfaces in ferroelastic domains. Our results provide critical insights into engineering ferroelectric thin films, fine grain ceramics and surface chemistry devices. The state-of-the-art methodology demonstrated here can greatly advance our understanding of surface science for oxides.
- Published
- 2016
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- View/download PDF
29. Atomically ordered solute segregation behaviour in an oxide grain boundary.
- Author
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Feng B, Yokoi T, Kumamoto A, Yoshiya M, Ikuhara Y, and Shibata N
- Abstract
Grain boundary segregation is a critical issue in materials science because it determines the properties of individual grain boundaries and thus governs the macroscopic properties of materials. Recent progress in electron microscopy has greatly improved our understanding of grain boundary segregation phenomena down to atomistic dimensions, but solute segregation is still extremely challenging to experimentally identify at the atomic scale. Here, we report direct observations of atomic-scale yttrium solute segregation behaviours in an yttria-stabilized-zirconia grain boundary using atomic-resolution energy-dispersive X-ray spectroscopy analysis. We found that yttrium solute atoms preferentially segregate to specific atomic sites at the core of the grain boundary, forming a unique chemically-ordered structure across the grain boundary.
- Published
- 2016
- Full Text
- View/download PDF
30. Atomistic mechanisms of nonstoichiometry-induced twin boundary structural transformation in titanium dioxide.
- Author
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Sun R, Wang Z, Saito M, Shibata N, and Ikuhara Y
- Abstract
Grain boundary (GB) phase transformations often occur in polycrystalline materials while exposed to external stimuli and are universally implicated in substantially affecting their properties, yet atomic-scale knowledge on the transformation process is far from developed. In particular, whether GBs loaded with defects due to treatments can still be conventionally considered as disordered areas with kinetically trapped structure or turn ordered is debated. Here we combine advanced electron microscopy, spectroscopy and first-principles calculations to probe individual TiO2 GB subject to different atmosphere, and to demonstrate that stimulated structural defects can self-assemble at GB, forming an ordered structure, which results in GB nonstoichiometry and structural transformations at the atomic scale. Such structural transformation is accompanied with electronic transition at GB. The three-dimensional transformations afford new perspectives on the structural defects at GBs and on the development of strategies to manipulate practically significant GB transformations.
- Published
- 2015
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31. Misfit accommodation mechanism at the heterointerface between diamond and cubic boron nitride.
- Author
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Chen C, Wang Z, Kato T, Shibata N, Taniguchi T, and Ikuhara Y
- Abstract
Diamond and cubic boron nitride (c-BN) are the top two hardest materials on the Earth. Clarifying how the two seemingly incompressible materials can actually join represents one of the most challenging issues in materials science. Here we apply the temperature gradient method to grow the c-BN single crystals on diamond and report a successful epitaxial growth. By transmission electron microscopy, we reveal a novel misfit accommodation mechanism for a {111} diamond/c-BN heterointerface, that is, lattice misfit can be accommodated by continuous stacking fault networks, which are connected by periodically arranged hexagonal dislocation loops. The loops are found to comprise six 60° Shockley partial dislocations. Atomically, the carbon in diamond bonds directly to boron in c-BN at the interface, which electronically induces a two-dimensional electron gas and a quasi-1D electrical conductivity. Our findings point to the existence of a novel misfit accommodation mechanism associated with the superhard materials.
- Published
- 2015
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- View/download PDF
32. Controlling frustrated liquids and solids with an applied field in a kagome Heisenberg antiferromagnet.
- Author
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Nishimoto S, Shibata N, and Hotta C
- Abstract
Quantum spin-1/2 kagome Heisenberg antiferromagnet is the representative frustrated system possibly hosting a spin liquid. Clarifying the nature of this elusive topological phase is a key challenge in condensed matter; however, even identifying it still remains unsettled. Here we apply a magnetic field and discover a series of spin-gapped phases appearing at five different fractions of magnetization by means of a grand canonical density matrix renormalization group, an unbiased state-of-the-art numerical technique. The magnetic field dopes magnons and first gives rise to a possible Z₃ spin liquid plateau at 1/9 magnetization. Higher field induces a self-organized super-lattice unit, a six-membered ring of quantum spins, resembling an atomic orbital structure. Putting magnons into this unit one by one yields three quantum solid plateaus. We thus find that the magnetic field could control the transition between various emergent phases by continuously releasing the frustration.
- Published
- 2013
- Full Text
- View/download PDF
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