SPring-8

Core level spectroscopy has become a powerful tool in the study of electronic states in solids. From fundamental aspects to the most recent developments, Core Level Spectroscopy of Solids presents the theoretical calculations, experimental data, and underlying physics of x-ray photoemission spectroscopy (XPS), x-ray absorption spectroscopy (XAS), x

Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobacterium Thermosynechococcus elongatus was reported recently [Zouni, A., Witt, H. T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature 409, 739-743)] at 3.8-A resolution. To analyze the PSII structure in more detail, we have obtained the crystal structure of PSII from another thermophilic cyanobacterium, Thermosynechococcus vulcanus, at 3.7-A resolution. The present structure was built on the basis of the sequences of PSII large subunits D1, D2, CP47, and CP43; extrinsic 33- and 12-kDa proteins and cytochrome c550; and several low molecular mass subunits, among which the structure of the 12-kDa protein was not reported previously. This yielded much information concerning the molecular interactions within this large protein complex. We also show the arrangement of chlorophylls and cofactors, including two beta-carotenes recently identified in a region close to the reaction center, which provided important clues to the secondary electron transfer pathways around the reaction center. Furthermore, possible ligands for the Mn-cluster were determined. In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions.

Measurement of the quantum-mechanical phase in quantum matter provides the most direct manifestation of the underlying abstract physics. We used resonant x-ray scattering to probe the relative phases of constituent atomic orbitals in an electronic wave function, which uncovers the unconventional Mott insulating state induced by relativistic spin-orbit coupling in the layered 5d transition metal oxide Sr2IrO4. A selection rule based on intra-atomic interference effects establishes a complex spin-orbital state represented by an effective total angular momentum = 1/2 quantum number, the phase of which can lead to a quantum topological state of matter.

First Talbot interferometry in the hard X-ray region was demonstrated using a pair of transmission gratings made by forming gold stripes on glass plates. By aligning the gratings on the optical axis of X-rays with a separation that caused the Talbot effect by the first grating, moiré fringes were produced inclining one grating slightly against the other around the optical axis. A phase object placed in front of the first grating was detected by moiré-fringe bending. Using the technique of phase-shifting interferometry, the differential phase corresponding to the phase object could also be measured. This result suggests that X-ray Talbot interferometry is a novel and simple method for phase-sensitive X-ray radiography.

A π-conjugated nanosheet comprising planar nickel bis(dithiolene) complexes was synthesized by a bottom-up method. A liquid-liquid interfacial reaction using benzenehexathiol in the organic phase and nickel(II) acetate in the aqueous phase produced a semiconducting bulk material with a thickness of several micrometers. Powder X-ray diffraction analysis revealed that the crystalline portion of the bulk material comprised a staggered stack of nanosheets. A single-layer nanosheet was successfully realized using a gas-liquid interfacial reaction. Atomic force microscopy and scanning tunneling microscopy confirmed that the π-conjugated nanosheet was single-layered. Modulation of the oxidation state of the nanosheet was possible using chemical redox reactions.

Several novel UDP glycosyltransferase (UGT) genes, mainly UDP glucuronosyltransferases, have been identified in the human, mouse and rat genomes and in other mammalian species. This review provides an update of the UGT nomenclature to include these new genes and prevent the confusion that arises when the same gene is given different names. The new genes are named following previously established recommendations, taking into consideration evolutionary relatedness and the names already in general usage in the literature. The mammalian UGT gene superfamily currently has 117 members that can be divided into four families, UGT1, UGT2, UGT3 and UGT8. The 5-exon genes of the UGT1 family each contain a unique first exon, plus four exons that are shared between the genes; the exons 1 appear to have evolved by a process of duplication, leading to the synthesis of proteins with identical carboxyl-terminal and variable amino-terminal domains. Exon-sharing is also seen with the 6-exon UGT2A1 and UGT2A2 genes. However, UGT2A3 and those of the UGT2B (six exons), UGT3 (seven exons) and UGT8 gene families (five or six exons) do not share exons and most likely were derived by a process of duplication of all exons in the gene. Most UGT1 and UGT8 enzymes have been characterized in detail; however, the catalytic functions of the UGT3A enzymes and several UGT2 enzymes remain to be characterized.

X-ray crystallography has been central to the development of many fields of science over the past century. It has now matured to a point that as long as good-quality crystals are available, their atomic structure can be routinely determined in three dimensions. However, many samples in physics, chemistry, materials science, nanoscience, geology, and biology are noncrystalline, and thus their three-dimensional structures are not accessible by traditional x-ray crystallography. Overcoming this hurdle has required the development of new coherent imaging methods to harness new coherent x-ray light sources. Here we review the revolutionary advances that are transforming x-ray sources and imaging in the 21st century.

We have observed an unconventional, likely topological, Hall effect over a wide temperature region in the magnetization process of a chiral-lattice helimagnet MnGe. The magnitude of the topological Hall resistivity is nearly temperature-independent below 70 K, which reflects the real-space fictitious magnetic field proportional to a geometric quantity (scalar spin chirality) of the underlying spin texture. From the neutron diffraction study, it is anticipated that a relatively short-period (3-6 nm) noncoplanar spin structure is stabilized from the proper screw state in a magnetic field to produce the largest topological Hall response among the B20-type (FeSi-type) chiral magnets.

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).

Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of approximately 1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl(4), exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.

$\ensuremath{\alpha}\text{-FeSe}$ with the PbO structure is a key member of the family of high-${T}_{c}$ iron pnictide and chalcogenide superconductors, as while it possesses the basic layered structural motif of edge-sharing distorted ${\text{FeSe}}_{4}$ tetrahedra, it lacks interleaved ion spacers or charge-reservoir layers. We find that the application of hydrostatic pressure first rapidly increases ${T}_{c}$ which attains a broad maximum of 37 K at $\ensuremath{\sim}7\text{ }\text{GPa}$ before decreasing to 6 K upon further compression to $\ensuremath{\sim}14\text{ }\text{GPa}$. Complementary synchrotron x-ray diffraction at 16 K was used to measure the low-temperature isothermal compressibility of $\ensuremath{\alpha}\text{-FeSe}$, revealing an extremely soft solid with a bulk modulus, ${K}_{0}=30.7(1.1)\text{ }\text{GPa}$ and strong bonding anisotropy between interlayer and intralayer directions that transforms to the more densely packed $\ensuremath{\beta}$ polymorph above $\ensuremath{\sim}9\text{ }\text{GPa}$. The nonmonotonic ${T}_{c}(P)$ behavior of FeSe coincides with drastic anomalies in the pressure evolution of the interlayer spacing, pointing to the key role of this structural feature in modulating the electronic properties.

Flexible porous coordination polymers change their structure in response to molecular incorporation but recover their original configuration after the guest has been removed. We demonstrated that the crystal downsizing of twofold interpenetrated frameworks of [Cu(2)(dicarboxylate)(2)(amine)](n) regulates the structural flexibility and induces a shape-memory effect in the coordination frameworks. In addition to the two structures that contribute to the sorption process (that is, a nonporous closed phase and a guest-included open phase), we isolated an unusual, metastable open dried phase when downsizing the crystals to the mesoscale, and the closed phase was recovered by thermal treatment. Crystal downsizing suppressed the structural mobility and stabilized the open dried phase. The successful isolation of two interconvertible empty phases, the closed phase and the open dried phase, provided switchable sorption properties with or without gate-opening behavior.

The ferroelectric properties and crystal structure of doped HfO2 thin films were investigated for different thicknesses, electrode materials, and annealing conditions. Metal-ferroelectric-metal capacitors containing Gd:HfO2 showed no reduction of the polarization within the studied thickness range, in contrast to hafnia films with other dopants. A qualitative model describing the influence of basic process parameters on the crystal structure of HfO2 was proposed. The influence of different structural parameters on the field cycling behavior was examined. This revealed the wake-up effect in doped HfO2 to be dominated by interface induced effects, rather than a field induced phase transition. TaN electrodes were shown to considerably enhance the stabilization of the ferroelectric phase in HfO2 compared to TiN electrodes, yielding a Pr of up to 35 μC/cm2. This effect was attributed to the interface oxidation of the electrodes during annealing, resulting in a different density of oxygen vacancies in the Gd:HfO2 films. Ab initio simulations confirmed the influence of oxygen vacancies on the phase stability of ferroelectric HfO2.

Synthetic two-dimensional polymers, or bottom-up nanosheets, are ultrathin polymeric frameworks with in-plane periodicity. They can be synthesized in a direct, bottom-up fashion using atomic, ionic, or molecular components. However, few are based on carbon-carbon bond formation, which means that there is a potential new field of investigation into these fundamentally important chemical bonds. Here, we describe the bottom-up synthesis of all-carbon, π-conjugated graphdiyne nanosheets. A liquid/liquid interfacial protocol involves layering a dichloromethane solution of hexaethynylbenzene on an aqueous layer containing a copper catalyst at room temperature. A multilayer graphdiyne (thickness, 24 nm; domain size, >25 μm) emerges through a successive alkyne-alkyne homocoupling reaction at the interface. A gas/liquid interfacial synthesis is more successful. Sprinkling a very small amount of hexaethynylbenzene in a mixture of dichloromethane and toluene onto the surface of the aqueous phase at room temperature generated single-crystalline graphdiyne nanosheets, which feature regular hexagonal domains, a lower degree of oxygenation, and uniform thickness (3.0 nm) and lateral size (1.5 μm).

Homogeneous catalysts generally possess superior catalytic performance compared to heterogeneous catalysts. However, the issue of catalyst separation and recycling severely limits their use in practical applications. Single-atom catalysts have the advantages of both homogeneous catalysts, such as "isolated sites", and heterogeneous catalysts, such as stability and reusability, and thus would be a promising alternative to traditional homogeneous catalysts. In the hydroformylation of olefins, single-atom Rh catalysts supported on ZnO nanowires demonstrate similar efficiency (TON≈40000) compared to that of homogeneous Wilkinson's catalyst (TON≈19000). HAADF-STEM and infrared CO chemisorption experiments identified isolated Rh atoms on the support. XPS and XANES spectra indicate that the electronic state of Rh is almost metallic. The catalysts are about one or two orders of magnitude more active than most reported heterogeneous catalysts and can be reused four times without an obvious decline in activity.

The ins and outs of spin: Using the microporous coordination polymer {Fe(pz)[Pt(CN)(4)]} (1, pz=pyrazine), incorporating spin-crossover subunits, two-directional magnetic chemo-switching is achieved at room temperature. In situ magnetic measurements following guest vapor injection show that most guest molecules transform 1 from the low-spin (LS) state to the high-spin (HS) state, whereas CS(2) uniquely causes the reverse HS-to-LS transition.

Carbon monoxide (CO) produced in many large-scale industrial oxidation processes is difficult to separate from nitrogen (N2), and afterward, CO is further oxidized to carbon dioxide. Here, we report a soft nanoporous crystalline material that selectively adsorbs CO with adaptable pores, and we present crystallographic evidence that CO molecules can coordinate with copper(II) ions. The unprecedented high selectivity was achieved by the synergetic effect of the local interaction between CO and accessible metal sites and a global transformation of the framework. This transformable crystalline material realized the separation of CO from mixtures with N2, a gas that is the most competitive to CO. The dynamic and efficient molecular trapping and releasing system is reminiscent of sophisticated biological systems such as heme proteins.

Endocytic proteins such as epsin, AP180, and Hip1R (Sla2p) share a conserved modular region termed the epsin NH2-terminal homology (ENTH) domain, which plays a crucial role in clathrin-mediated endocytosis through an unknown target. Here, we demonstrate a strong affinity of the ENTH domain for phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2]. With nuclear magnetic resonance analysis of the epsin ENTH domain, we determined that a cleft formed with positively charged residues contributed to phosphoinositide binding. Overexpression of a mutant, epsin Lys76 --> Ala76, with an ENTH domain defective in phosphoinositide binding, blocked epidermal growth factor internalization in COS-7 cells. Thus, interaction between the ENTH domain and PtdIns(4,5)P2 is essential for endocytosis mediated by clathrin-coated pits.

The platinum-group metals (PGMs) are six neighboring elements in the periodic table of the elements. Each PGM can efficiently promote unique reactions, and therefore, alloying PGMs would create ideal catalysts for complex or multistep reactions that involve several reactants and intermediates. Thus, high-entropy-alloy (HEA) nanoparticles (NPs) of all six PGMs (denoted as PGM-HEA) having a great variety of adsorption sites on their surfaces could be ideal candidates to catalyze complex reactions. Here, we report for the first time PGM-HEA and demonstrate that PGM-HEA efficiently promotes the ethanol oxidation reaction (EOR) with complex 12-electron/12-proton transfer processes. PGM-HEA shows 2.5 (3.2), 6.1 (9.7), and 12.8 (3.4) times higher activity than the commercial Pd/C, Pd black and Pt/C catalysts in terms of intrinsic (mass) activity, respectively. Remarkably, it records more than 1.5 times higher mass activity than the most active catalyst to date. Our findings pave the way for promoting complex or multistep reactions that are seldom realized by mono- or bimetallic catalysts.

We have determined the postspinel transformation boundary in Mg 2 SiO 4 by combining quench technique with in situ pressure measurements, using multiple internal pressure standards including Au, MgO, and Pt. The experimentally determined boundary is in general agreement with previous in situ measurements in which the Au scale of Anderson et al. [1989] was used to calculate pressure: Using this pressure scale, it occurs at significantly lower pressures compared to that corresponding to the 660‐km seismic discontinuity. In this study, we also report new experimental data on the transformation boundary determined using MgO as an internal standard. The results show that the transition boundary is located at pressures close to the 660‐km discontinuity using the MgO pressure scale of Speziale et al. [2001] and can be represented by a linear equation, P (GPa) = 25.12 − 0.0013 T (°C). The Clapeyron slope for the postspinel transition boundary is precisely determined and is significantly less negative than previous estimates. Our results, based on the MgO pressure scale, support the conventional hypothesis that the postspinel transformation is responsible for the observed 660‐km seismic discontinuity.