Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals.

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

Semiconductor-metal transition in Bi2Se3 caused by impurity doping.

Doping a typical topological insulator, Bi2Se3, with Ag impurity causes a semiconductor-metal (S-M) transition at 35 K. To deepen the understanding of this phenomenon, structural and transport properties of Ag-doped Bi2Se3 were studied. Single-crystal X-ray diffraction (SC-XRD) showed no structural transitions but slight shrinkage of the lattice, indicating no structural origin of the transition. To better understand electronic properties of Ag-doped Bi2Se3, extended analyses of Hall effect and electric-field effect were carried out. Hall effect measurements revealed that the reduction of resistance was accompanied by increases in not only carrier density but carrier mobility. The field-effect mobility is different for positive and negative gate voltages, indicating that the EF is located at around the bottom of the bulk conduction band (BCB) and that the carrier mobility in the bulk is larger than that at the bottom surface at all temperatures. The pinning of the EF at the BCB is found to be a key issue to induce the S-M transition, because the transition can be caused by depinning of the EF or the crossover between the bulk and the top surface transport.

X-ray fluorescence holography of biological metal sites: Application to myoglobin.

X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.

Relationship between diffraction peak, network topology, and amorphous-forming ability in silicon and silica.

The network topology in disordered materials is an important structural descriptor for understanding the nature of disorder that is usually hidden in pairwise correlations. Here, we compare the covalent network topology of liquid and solidified silicon (Si) with that of silica (SiO2) on the basis of the analyses of the ring size and cavity distributions and tetrahedral order. We discover that the ring size distributions in amorphous (a)-Si are narrower and the cavity volume ratio is smaller than those in a-SiO2, which is a signature of poor amorphous-forming ability in a-Si. Moreover, a significant difference is found between the liquid topology of Si and that of SiO2. These topological features, which are reflected in diffraction patterns, explain why silica is an amorphous former, whereas it is impossible to prepare bulk a-Si. We conclude that the tetrahedral corner-sharing network of AX2, in which A is a fourfold cation and X is a twofold anion, as indicated by the first sharp diffraction peak, is an important motif for the amorphous-forming ability that can rule out a-Si as an amorphous former. This concept is consistent with the fact that an elemental material cannot form a bulk amorphous phase using melt quenching technique.

A cryostat designed for x-ray fluorescence holography experiments down to 4 K.

A cryostat was designed for x-ray fluorescence holography (XFH) experiments at low temperatures down to 4 K, where many functional materials show characteristic transitions, such as high-temperature superconducting, magnetic, dielectric, and valence transitions. For XFH measurements, changes in two angles of samples with respect to the incident synchrotron x-ray beam, i.e., incident angle θ and azimuthal angle ϕ, are necessary. A low-temperature specialized small piezoelectric motor is installed at the cryostat head for ϕ, and the cryostat itself is rotated by a stepping motor for θ. The heat from the piezoelectric motor for ϕ and the cryostat power determining the total cryostat mass were optimized for the limited working spaces and beamtimes of synchrotron experiments. Some examples of the XFH results at low temperatures, such as a Pb crystal and an YbInCu4 valence transition material, are presented to show the feasibility of this low-temperature equipment.

Emergence of a Pressure-Driven Superconducting Phase in Ba0.77Na0.23Ti2Sb2O.

We investigated the pressure dependence of electric transport in a superconducting sample, Ba0.77Na0.23Ti2Sb2O, to complete the phase diagram of superconducting transition temperature (Tc) against pressure (p). This superconducting sample exhibits a Tc value of 5.8 K at ambient pressure. Here, the superconductivity of the recently reported sample was investigated over a wide pressure range. The Tc value monotonously decreased with pressure below 8 GPa. Interestingly, the Tc value rapidly increased above 8 GPa and slowly declined with pressure above 11 GPa. Thus, a new superconducting phase was discovered above ∼9 GPa. The crystal structure of Ba0.77Na0.23Ti2Sb2O was also elucidated at 0-22.0 GPa with synchrotron X-ray powder diffraction. Consequently, an evident relation between the crystal structure and the superconductivity was revealed, namely, a clear structural phase transition was observed at 8-11 GPa, where the Tc value rapidly increased against pressure. This study provides detailed information on the superconductivity of Ba0.77Na0.23Ti2Sb2O under pressure, which will lead to a comprehensive understanding of pressure-driven superconductivity.

Application of Anomalous X-ray Scattering Method to Liquid Electrolytes Used in a Battery: Local Structural Analysis around a Dilute Metallic Ion.

In liquid electrolytes used for a battery, various metal complexes are formed as a result of ion-solvent and ion-ion interactions, which strongly influence the properties of the electrolyte and thus the performance of the battery. Therefore, the structural characterization of such complexes is of great importance. In this study, the anomalous X-ray scattering (AXS) technique was applied to the potassium hydroxide solution including ∼0.3 mol % zinc, which is widely used in various batteries such as the alkaline battery. In spite of the small amount of the metallic ions, we have successfully extracted a local structure around zinc after careful data analysis. The obtained pair distribution function exhibited not only the short-range correlation corresponding to the Zn-O bond within the zincate anion but also a medium-range correlation above 3.5 Å. The present study demonstrates the capability of the AXS technique to detect local structures around dilute metallic ions in liquid electrolytes, which will largely extend the applicable range of this technique, especially to the field related to batteries.

Development of a half-cell for x-ray structural analysis of liquid electrolytes in rechargeable batteries.

A half-cell of the rechargeable Li-ion battery was developed to characterize an electrolyte structure using high energy x-ray total scattering measurements in combination with a two-dimensional x-ray detector. The scattering pattern consisted of strong Bragg peaks from electrodes and diffuse scatterings from sapphire windows, in addition to a weak halo pattern from the electrolyte. By selectively removing the signals of the electrodes and windows using specific numerical procedures, we could successfully extract the structural information of the electrolyte, which was in reasonable agreement with the reference data obtained from the electrolyte in a glass capillary. The present demonstration with a half-cell is expected to shed new light on operand characterization of the electrolyte structure during charging and discharging.

Individual Atomic Imaging of Multiple Dopant Sites in As-Doped Si Using Spectro-Photoelectron Holography.

The atomic scale characterization of dopant atoms in semiconductor devices to establish correlations with the electrical activation of these atoms is essential to the advancement of contemporary semiconductor process technology. Spectro-photoelectron holography combined with first-principles simulations can determine the local three-dimensional atomic structures of dopant elements, which in turn affect their electronic states. In the work reported herein, this technique was used to examine arsenic (As) atoms doped into a silicon (Si) crystal. As 3d core level photoelectron spectroscopy demonstrated the presence of three types of As atoms at a total concentration of approximately 1020 cm-3, denoted as BEH, BEM, and BEL. On the basis of Hall effect measurements, the BEH atoms corresponded to electrically active As occupying substitutional sites and exhibiting larger thermal fluctuations than the Si atoms, while the BEM atoms corresponded to electrically inactive As embedded in the AsnV (n = 2-4) type clusters. Finally, the BEL atoms were assigned to electrically inactive As in locally disordered structures.

Multiple-wavelength neutron holography with pulsed neutrons.

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Strain Engineering for Anion Arrangement in Perovskite Oxynitrides.

Mixed-anion perovskites such as oxynitrides, oxyfluorides, and oxyhydrides have flexibility in their anion arrangements, which potentially enables functional material design based on coordination chemistry. However, difficulty in the control of the anion arrangement has prevented the realization of this concept. In this study, we demonstrate strain engineering of the anion arrangement in epitaxial thin films of the Ca1-xSrxTaO2N perovskite oxynitrides. Under compressive epitaxial strain, the axial sites in TaO4N2 octahedra tend to be occupied by nitrogen rather than oxygen, which was revealed by N and O K-edge linearly polarized X-ray absorption near-edge structure (LP-XANES) and scanning transmission electron microscopy combined with electron energy loss spectroscopy. Furthermore, detailed analysis of the LP-XANES indicated that the high occupancy of nitrogen at the axial sites is due to the partial formation of a metastable trans-type anion configuration. These results are expected to serve as a guide for the material design of mixed-anion compounds based on their anion arrangements.

Development of an X-ray fluorescence holographic measurement system for protein crystals.

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2ß2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm(3)) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

Atomic resolution holography.

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell.

One-shot spectrometer for several elements using an integrated conical crystal analyzer.

Time-resolved x-ray spectrometry using an ultrastrong x-ray source such as an x-ray free electron laser is one of the new trends in the field of x-ray physics. To achieve such time-resolved measurement, the development of an one-shot spectrometer with a wide wavelength range, high efficiency, and good energy resolution is an essential prerequisite. Here we developed an integrated conical Ge crystal analyzer consisting of several conical rings, which were connected using spline surfaces to form a single body using our previously developed hot deformation technique, which can form a Si or Ge wafer into an arbitrary and accurate shape. We simultaneously focused several characteristic lines from an alloy sample onto different positions on a small x-ray charge-coupled device with very high image brightness (gain relative to planar analyzer: 100) and a good spatial resolution of 9-13 eV. The small radius of curvature of the crystal (28-50 mm) enabled us to realize a very short sample-detector distance of 214.4 mm. The present result shows the possibility of realizing a new focusing x-ray crystal spectrograph that can control the focal position as desired.

X-ray fluorescence holography.

X-ray fluorescence holography (XFH) is a method of atomic resolution holography which utilizes fluorescing atoms as a wave source or a monitor of the interference field within a crystal sample. It provides three-dimensional atomic images around a specified element and has a range of up to a few nm in real space. Because of this feature, XFH is expected to be used for medium-range local structural analysis, which cannot be performed by x-ray diffraction or x-ray absorption fine structure analysis. In this article, we explain the theory of XFH including solutions to the twin-image problem, an advanced measuring system, and data processing for the reconstruction of atomic images. Then, we briefly introduce our recent applications of this technique to the analysis of local lattice distortions in mixed crystals and nanometer-size clusters appearing in the low-temperature phase of a shape-memory alloy.

3D atomic imaging by internal-detector electron holography.

A method of internal-detector electron holography is the time-reversed version of photoelectron holography. Using an energy-dispersive x-ray detector, an electron gun, and a computer-controllable sample stage, we measured a multiple-energy hologram of the atomic arrangement around the Ti atom in SrTiO3 by recording the characteristic Ti Kα x-ray spectra for different electron beam angles and wavelengths. A real-space image was obtained by using a fitting-based reconstruction algorithm. 3D atomic images of the elements Sr, Ti, and O in SrTiO3 were clearly visualized. The present work reveals that internal-detector electron holography has great potential for reproducing 3D atomic arrangements, even for light elements.

Review of the applications of x-ray refraction and the x-ray waveguide phenomenon to estimation of film structures.

Based on our previous work, I review the applications of x-ray refraction and the x-ray waveguide phenomenon to organic and inorganic thin films in the present paper. Under grazing incidence conditions, observations of refracted x-rays and guided x-rays due to the x-ray waveguide phenomenon provide information about thin film structures, and thus have potential as alternative methods to x-ray reflectivity. To date, we have measured the spectra of the refracted x-rays and guided x-rays from end faces of thin films using white incident x-ray beams, and utilized them for the determination of film density and thickness. Some of this work is summarized in the present paper. At the end of this paper, I describe our recent achievement in this field, namely the in situ measurement of guided x-rays during the film degradation process due to strong synchrotron radiation damage. Moreover, I discuss the perspective of the present technique from the viewpoint of micro-characterization and real-time estimation of thin films.