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It is shown that the locus of the f' + if'' plot in the complex plane, f' being determined from measured f'' by using the dispersion relation, looks like a semicircle very near the absorption edge of Ge. The semicircular locus is derived from a quantum theory of X-ray resonant scattering when there is a sharp isolated peak in f'' just above the K-absorption edge. Using the semicircular behavior, an approach is proposed to determine the anomalous scattering factors in a crystal by fitting known calculated values based on an isolated-atom model to a semicircular focus. The determined anomalous scattering factors f' show excellent agreement with the measured values just below the absorption edge. In addition, the phase determination of a crystal structure factor has been considered by using the semicircular behavior.

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

It is shown that the locus of the f′ + if′′ plot in the complex plane, f′ being determined from measured f′′ by using the dispersion relation, looks like a semicircle very near the absorption edge of Ge. The semicircular locus is derived from a quantum theory of X-ray resonant scattering when there is a sharp isolated peak in f′′ just above the K-absorption edge. Using the semicircular behavior, an approach is proposed to determine the anomalous scattering factors in a crystal by fitting known calculated values based on an isolated-atom model to a semicircular focus. The determined anomalous scattering factors f′ show excellent agreement with the measured values just below the absorption edge. In addition, the phase determination of a crystal structure factor has been considered by using the semicircular behavior. [ABSTRACT FROM AUTHOR]

AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X‐ray crystallography and cryo‐electron microscopy, are often time‐consuming and resource‐intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post‐translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X‐ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f′′. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions. [ABSTRACT FROM AUTHOR]

The electron-density distribution and the contribution to anomalous scattering factors for Fe ions in magnetite have been analyzed by X-ray resonant scattering at the pre-edge of Fe K absorption. Synchrotron X-ray experiments were carried out using a conventional four-circle diffractometer in the right-handed circular polarization. Difference-Fourier synthesis was applied with a difference in structure factors measured on and off the pre-edge ( Eon = 7.1082 keV, Eoff = 7.1051 keV). Electron-density peaks due to X-ray resonant scattering were clearly observed for both A and B sites. The real part of the anomalous scattering factor f′ has been determined site-independently, based on the crystal-structure refinements, to minimize the squared residuals at the Fe K pre-edge. The f′ values obtained at Eon and Eoff are −7.063 and −6.682 for the A site and −6.971 and −6.709 for the B site, which are significantly smaller than the values of −6.206 and −5.844, respectively, estimated from the Kramers-Kronig transform. The f′ values at Eon are reasonably smaller than those at Eoff. Our results using a symmetry-based consideration suggest that the origin of the pre-edge peak is Fe ions occupying both A and B sites, where p- d mixing is needed with hybridized electrons of Fe in both sites overlapping the neighbouring O atoms. [ABSTRACT FROM AUTHOR]

Spatial distribution of bromobenzene (BrBz) and 4-bromophenol (BrPh) as hydrophobic aromatic compounds incorporated in polymer micelles with vesicular structure consisting of poly(ethylene glycol)-b-poly(tert-butyl methacrylate) (PEG-b-PtBMA) in aqueous solution is investigated by anomalous small-angle X-ray scattering (ASAXS) analyses near Br K edge. Small-angle X-ray scattering (SAXS) intensities from PEG-b-PtBMA micelles containing BrBz and BrPh were decreased as the energy of incident X-ray approached to Br K edge corresponding to the energy dependence of anomalous scattering factor of Br. The analysis for the energy dependence of SAXS profiles from the PEG-b-PtBMA micelles containing BrBz revealed that BrBz molecules were located in hydrophobic layer of PEG-b-PtBMA micelles. On the contrary, it was found by ASAXS that BrPh existed not only in the hydrophobic layer but also in the shell layer. Since ASAXS analysis successfully accomplished to visualize the spatial distribution of hydrophobic molecules in polymer micelles, it should be expected to be a powerful tool for characterization of drug delivery vehicles. [ABSTRACT FROM AUTHOR]

The present review places emphasis on a comprehensive survey of experimental techniques to probe the structural and morphological features at the nanoscale range in thin magnetic films, incorporating those available at in-house laboratories as well as those at state-of-the-art synchrotron radiation facilities. This elucidating the range of available techniques, and the information they can yield represents a step for advancing the understanding of and for unlocking new possibilities in the design and optimization of thin magnetic films across a wide range of applications. [ABSTRACT FROM AUTHOR]

Although high-entropy materials are excellent candidates for a range of functional materials, their formation traditionally requires high-temperature synthetic procedures of over 1,000 °C and complex processing techniques such as hot rolling1–5. One route to address the extreme synthetic requirements for high-entropy materials should involve the design of crystal structures with ionic bonding networks and low cohesive energies. Here we develop room-temperature-solution (20 °C) and low-temperature-solution (80 °C) synthesis procedures for a new class of metal halide perovskite high-entropy semiconductor (HES) single crystals. Due to the soft, ionic lattice nature of metal halide perovskites, these HES single crystals are designed on the cubic Cs2MCl6 (M=Zr4+, Sn4+, Te4+, Hf4+, Re4+, Os4+, Ir4+ or Pt4+) vacancy-ordered double-perovskite structure from the self-assembly of stabilized complexes in multi-element inks, namely free Cs+ cations and five or six different isolated [MCl6]2– anionic octahedral molecules well-mixed in strong hydrochloric acid. The resulting single-phase single crystals span two HES families of five and six elements occupying the M-site as a random alloy in near-equimolar ratios, with the overall Cs2MCl6 crystal structure and stoichiometry maintained. The incorporation of various [MCl6]2– octahedral molecular orbitals disordered across high-entropy five- and six-element Cs2MCl6 single crystals produces complex vibrational and electronic structures with energy transfer interactions between the confined exciton states of the five or six different isolated octahedral molecules.Room-temperature-solution (20 °C) and low-temperature-solution (80 °C) synthesis procedures are developed for a new class of metal halide perovskite high-entropy semiconductor single crystals. [ABSTRACT FROM AUTHOR]

In X-ray macromolecular crystallography (MX), single-wavelength anomalous dispersion (SAD) and multi-wavelength anomalous dispersion (MAD) techniques are commonly used for obtaining experimental phases. For an MX synchrotron beamline to support SAD and MAD techniques it is a prerequisite to have a reliable, fast and well automated energy scan routine. This work reports on a continuous energy scan procedure newly implemented at the BioMAX MX beamline at MAX IV Laboratory. The continuous energy scan is fully automated, capable of measuring accurate fluorescence counts over the absorption edge of interest while minimizing the sample exposure to X-rays, and is about a factor of five faster compared with a conventional step scan previously operational at BioMAX. The implementation of the continuous energy scan facilitates the prompt access to the anomalous scattering data, required for the SAD and MAD experiments. [ABSTRACT FROM AUTHOR]

Ni,Fe‐containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of carbon dioxide to carbon monoxide. CODHs are found in anaerobic microorganisms and can rapidly lose their activity when exposed to air. What causes the loss of activity is unclear. In this study, we analyzed the time‐dependent structural changes induced by the presence of air on the metal centers of CODH‐II. We show that inactivation is a multistep process. In a reversible step, the open coordination site on the Ni ion is blocked by a Ni,Fe‐bridging μ‐sulfido or chlorido ligand. Blocking this open coordination site with a cyanide ligand stabilizes the cluster against O2‐induced decomposition, indicating that O2 attacks at the Ni ion. In the subsequent irreversible phase, nickel is lost, the Fe ions rearrange and the sulfido ligands disappear. Our data are consistent with a reversible reductive reactivation mechanism to protect CODHs from transient over‐oxidation. [ABSTRACT FROM AUTHOR]

The polarization dependence of the cross sections of two-photon transitions including X-ray scattering was analyzed. We developed the regular approach to the derivation of the polarization parameters of photoprocesses. Our approach is based on the tensor representation of the photon density matrix, which is written in terms of the unit vectors directed along the major axis of the polarization ellipse ( ϵ ˆ ) and the photon propagation ( k ˆ ). Explicit expressions for the product of two photon density matrices were derived. As an example, the parametrization of the polarization dependence of the X-ray scattering by closed-shell atoms is given both in terms of (i) scalar products of photon vectors ϵ ˆ 1 , 2 , k ˆ 1 , 2 and (ii) X-ray Stokes parameters. We discuss the applicability of the atomic scattering for the measurement of the polarization of X-rays. [ABSTRACT FROM AUTHOR]

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Superparamagnetic Co–Pt nanoparticles were synthesized in crystal composed of Pyrococcus furiosus virus-like (PfV) particles, a protein with a cage-like structure. Synchrotron X-ray diffraction measurements at the Pt L III edge for the PfV crystal and analysis of Pt anomalous differences revealed that the electron density originated from Pt atom appeared at the 5-fold symmetric site of PfV by soaking Co2+ and PtCl 4 2−, which did not for the PfV crystal without the soaking. Although the change in electron density extracted by the difference in the anomalous scattering factor at the Co K edge was undetected, we confirmed that Co2+ was incorporated into the PfV crystal from the experimental result of the X-ray fluorescence spectrum at the Co K edge. Co–Pt nanoparticles were successfully formed by reducing the PfV crystal soaked by Co2+ and PtCl 4 2−. Transmission electron microscope observation revealed that the average diameter of the synthesized particles was approximately 3.6 nm. Magnetization measurements showed that the synthesized particles were in the superparamagnetic state with a blocking temperature of approximately 50 K at 25 Oe. • Magnetic Co–Pt nanoparticles are synthesized in protein, Pyrococcus furiosus virus-like Particle (PfV) crystal. • Ferromagnetic element (Co) can be incorporated in the PfV by alloying with Pt. • The incorporated nanoparticles exhibit the superparamagnetism at room temperature. [ABSTRACT FROM AUTHOR]

The dynamical theory of diffraction is used to analyse irregular X‐ray mirage interference fringes observed in Si220 X‐ray reflection topography from a weakly bent, thin crystal due to gravity. The origin of the irregular fringes is attributed to the interference between mirage diffracted beams and a reflected beam from the back surface, which is a new type of interference fringe. The irregular fringes are reproduced by calculating the reflected intensities numerically. The effects of absorption and thermal vibration are quite important for the reproduction. The result shows that the interference fringes depend on the strain as well as the thickness of the crystal, which indicates that the fringes should be useful for analysing weak strain in a crystal as an application. [ABSTRACT FROM AUTHOR]

Absolute measurements of small-angle X-ray scattering (SAXS) intensities at the K absorption edge of Mg have been performed using glassy carbon as an intensity standard. Glassy carbon samples polished down to give appropriate transmission have been prepared as a secondary standard to be used at 1.3 keV. Alâ€"Mg binary alloys were used to assess the metastable phase boundary for the Al3Mg metastable precipitation from the absolute scattering intensity. The assessed phase boundary agreed with the previous reports. Glassy carbon was concluded to be an appropriate candidate for an intensity standard sample for transmission measurements of SAXS in the tender X-ray regions. [ABSTRACT FROM AUTHOR]

The anomalous scattering factor (ASF) correction to the relativistic form-factor approximation for Rayleigh scattering is examined in support of its utilization in radiographic imaging. ASF corrected total cross-section data have been generated for a low resolution grid for the Monte Carlo code EGS4 for the biologically important elements, K, Ca, Mn, Fe, Cu and Zn. Points in the fixed energy grid used by EGS4 as well as 8 other points in the vicinity of the K-edge have been chosen to achieve an uncertainty in the ASF component of 20% according to the Thomas–Reiche–Kuhn sum rule and an energy resolution of 20 eV. Such data is useful for analysis of imaging with a quasi-monoenergetic source. Corrections to the sampled distribution of outgoing photons, due to ASF, are given and new total cross-section data including that of the photoelectric effect have been computed using the Slater exchange self-consistent potential with the Latter tail. A measurement of Rayleigh scattering in a dilute aqueous solution of manganese (II) was performed, this system enabling determination of the absolute cross-section, although background subtraction was necessary to remove Kβ fluorescence and resonant Raman scattering occurring within several 100 eV of the edge. Measurements confirm the presence of below edge bound–bound structure and variation in the structure due to the ionic state that are not currently included in tabulations. [Copyright &y& Elsevier]

We review our recent studies on the occurrence of atomic charge localization in magnetite and halfdoped manganites. X-ray resonant scattering experiments at the iron K-edge of magnetite and X-ray absorption spectroscopy at the Mn K-edge of Ca-doped manganites show the lack of charge localization on the transition metal atom, either temporal or spatial. The evolution of the intensity of (002) and (006) forbidden reflections in magnetite across the Verwey transition, as a function of the incoming X-ray beam energy, the azimuthal angle and the polarization of the scattering process, indicates that the atomic anomalous scattering factors for the octahedral iron ions are identical to each other, i.e. all of them show an identical electronic state. High resolution XANES spectra of RE[sub 1-χ]Ca[sub χ]MnO[sub 3] series cannot be reproduced by a linear combination of REMnO[sub 3] and CaMnO[sub 3] spectra. Accordingly, the electronic state of the Mn atom in these intermediate compounds cannot be described as a bimodal distribution of Mn[sup 3+] and Mn[sup 4+] pure ionic states. The claimed experimental evidence of charge ordering in Mn[sup 3+]/Mn[sup 4+] = 1 manganites proposed from X-ray resonant scattering experiments has also been critically re-examined. We show that although these experiments prove the existence of two kinds of Mn atoms, they cannot be identified as Mn[sup 3+] and Mn[sup 4+] ions. Moreover, the so-called chargeordering (CO) and orbital-ordering (OO) resonant scattering reflections are naturally explained due to the presence of local distortions without including any ordering of the Mn d-orbitals. [ABSTRACT FROM AUTHOR]

We performed soft X-ray resonant scattering experiments on poly (3-hexylthiophene) (P3HT):[6,6]-phenyl-C61-buteric acid methyl ester (PCBM) blend thin films to reveal the domain structure and electronic state, where P3HT and PCBM mean regioregular poly (3-hexylthiophene) and [6,6]-phenyl-C61-buteric acid methyl ester, respectively. We measured two films, where chloroform (CF sample) and 1,2-dichlorobenzene (DCB sample) are used as solvents in the fabrication process. There is negligible X-ray incident angle dependence of the X-ray absorption spectra at the S K-absorption edge in the CF sample, whereas the DCB sample exhibits clear incident angle dependence. We obtained the wave-number resolved spectra at Q=(1, 0, 0) for P3HT molecules in both samples. The packing growth of P3HT molecules is revealed to be much more developed in the DCB sample than in the CF sample. In addition, the electronic structure at local sulfur element sites clearly changes for both the samples. [ABSTRACT FROM AUTHOR]

X-ray absorption near edge structure (XANES) analysis is an element-specific method for proving electronic state mostly in the field of applied physics, such as battery and catalysis reactions, where the valence change plays an important role. In particular, many results have been reported for the analysis of positive electrode materials of Li-ion batteries, where multiple transition materials contribute to the reactions. However, XANES analysis has been limited to identifying the valence state simply in comparison with reference materials. When the shape of XANES spectra shows complicated changes, we were not able to identify the valence states or estimate the valence quantitatively, resulting in insufficient reaction analysis. To overcome such issues, we propose a valence state evaluation method using K- and L-edge XANES analysis with first-principles simulations. By using this method, we demonstrated that the complicated reaction mechanism of Li(Ni1/3Co1/3Mn1/3)O2 can be successfully analyzed for distinguishing each contribution of Ni, Co, Mn, and O to the redox reactions during charge operation. In addition to the XANES analysis, we applied resonant photoelectron spectroscopy (RPES) and diffraction anomalous fine structure spectroscopy (DAFS) with first-principles calculations to the reaction analysis of Co and Mn, which shows no or very little contribution to the redox. The combination of RPES and first-principles calculations successfully enables us to confirm the contribution of Co at high potential regions by electively observing Co 3d orbitals. Through the DAFS analysis, we deeply analyzed the spectral features of Mn K-edges and concluded that the observed spectral shape change for Mn does not originate from the valence change but from the change in distribution of wave functions around Mn upon Li extraction. [ABSTRACT FROM AUTHOR]