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Three-dimensional (3D) local atomic structure around specific functional atom plays a crucial role in functional materials, but it has not been able to be analyzed by a standard structure analysis method of x-ray diffraction (XRD) because this kind of small amount of atom has no translational symmetry. Recently several atomic-resolution holography methods have been developed, which can directly display the 3D atomic structure around this kind of specific atoms with no translational symmetry. These are the ‘photoelectron holography’, ‘x-ray fluorescence holography’, and ‘CTR holography’. Their accuracy improved dramatically by the development of new analysis codes and sensitive analyzers and detectors. A new technique of direct 3D atomic structure analysis method ‘stereography of atomic arrangement’ has also been developed. These techniques received renewed attention recently, and a project ‘3D Active-Site Science’ of JSPS Grant-in-Aid for Scientific Research on Innovative Areas has been pursued for 5 years. This article reviews principles and some results of atomic-resolution holography methods.

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.

X-ray fluorescence holography was applied to dilute Mg99.2Zn0.2Y0.6 alloy annealed at 520°C for 5 h to obtain atomic images around Zn atom. In spite of the extremely low concentration of the solute-element, clear hologram patterns were obtained. The reconstructed atomic images revealed that the Zn atom in this annealed Mg99.2Zn0.2Y0.6 alloy mainly occupy the hcp Mg site. This finding is consistent with the transmission electron microscope image, where fcc-type stacking faults are hardly observed. These results are in contrast to the previous report that Zn and Y form short-range-ordered solute clusters at the fcc-type stacking fault in MgZnYalloy. The effect of heat treatment on the atomic arrangement of solute-elements in this dilute alloy is discussed in relation to the previously reported mechanical properties. [ABSTRACT FROM AUTHOR]

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 K-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 timeresolved XFH. [ABSTRACT FROM AUTHOR]

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. • X-ray fluorescence holography (XFH) is three-dimensional atomic imaging method. • Atomic imaging using XFH has been applied to protein crystals for the first time. • Atomic image reconstruction of active site in myoglobin was performed using XFH. [ABSTRACT FROM AUTHOR]

Analyses of the local structures around Zr doped in ferroelectric (Ba,Ca)(Zr,Ti)O3 (BCZT) and paraelectric Ca(Zr,Ti)O3 (CZT) are carried out by X‐ray fluorescence holography. The images of the cations at the A and B sites of these ABO3 perovskites are clearly reconstructed from the measured holograms. In the real space images, a 0.2 Å outward displacement of the nearest Ba and Ca is observed in the atomic images of both BCZT and CZT, attributable to the difference in the ionic radius between Zr4+ and Ti4+. In addition, the first‐neighboring Ti in BCZT is displaced inward by 0.5 Å, whereas no such displacement is observed in CZT. This shift of Ti in BCZT appears due to the large strain of the local lattice, and it can affect to the piezoelectric response of BCZT. [ABSTRACT FROM AUTHOR]

The atomic positions and displacements of atoms around the Ta atom in piezoelectric materials Ca3TaGa3Si2O7 (CTGS) and Ca3TaGa1.5Al1.5Si2O7 (CTGAS) were investigated at 100 K by Ta-Lα X-ray fluorescence holography (XFH). The experimental atomic images were compared with the simulated ones using the crystal structures of CTGS and CTGAS, which were determined by single crystal X-ray diffractometry (SC-XRD). The atomic positions agreed between XFH and SC-XRD experiments. With the help of XFH simulation, the displacements of Ta, Ca, Si, and Ga atoms relative to the Ta atom were qualitatively analyzed using experimental atomic image intensities. The relative displacement of the Ca atom was increased by Al substitution, while those of the Ta and Ga atoms were decreased. The first principles calculation based on density-functional theory (DFT) was performed to understand bonding character between constituents. The evaluation of the crystal orbital Hamilton population (COHP) clarified that the Ca-O bond has strong ionic character different with the other bonds, suggesting that the positional shift of the Ca atom is responsible for the piezoelectricity in CTGS. The effect of Al substitution on piezoelectricity was also considered based on the change in the Ca-O bond.

To clarify the mechanism of ferroelectricity in lead zirconate titanate (PZT), the local structure around Ti in a Pb(Zr0.7Ti0.3)O3 single crystal is investigated using X‐ray fluorescence holography. The raw hologram data are contaminated by periodic noise due to the fluctuation of the incident X‐ray intensity. The periodical noise is successfully removed using an inverse Fourier transformation method. From the filtered holograms, the atomic images around Ti can be reconstructed clearly. The reconstructions of B‐site cations demonstrate an outward displacement of the neighboring Ti from the ideal B‐site position, indicating an expansion of the local lattice around Ti. In addition, the splitting of Pb images is found, and the relative displacement between Ti and Pb atoms is deduced. These results contribute to the understanding of the local structure of PZT and can reveal the microscopic origins of very high dielectric and piezoelectric responses, which are essential for designing new and improved ferroelectric materials. [ABSTRACT FROM AUTHOR]

Crystal structures of the multiferroic Eu1−xYxMnO3 (x = 0.2, 0.4) are investigated from the point of view of average and local structure analyses using single‐crystal X‐ray diffraction (XRD) and X‐ray fluorescence holography (XFH). With increasing Y content, the lattice constants decrease and the orthorhombic distortions increase. The differences between the local structures around Eu and Y are observed in the reconstructed atomic images by XFH. x = 0.2 and 0.4 compounds exhibit different local distortions at Mn sites, whereas no characteristic difference is shown in the average structures. In this system, the long‐range structural coherence is likely to be maintained even with significant substitution of Y. [ABSTRACT FROM AUTHOR]

The local structure around the dopant atom in Nd(8 mol%):LaF3 single‐crystal scintillator is analyzed by X‐ray fluorescence holography experiments in combination with a sparse modeling algorithm. The average local environment of Nd is reconstructed up to large distances of about 12 Å and confirms a substitution of La atoms with Nd with only small crystal lattice distortions. The experimental findings are substantiated by comparison with reference data from La holograms and with computationally generated holograms based on a model structure of the dopant site. [ABSTRACT FROM AUTHOR]

We report on the characterization of a thin film of yttrium oxide by X‐ray fluorescence holography. The sample has a layered structure with an YO base layer and an oxidized Y2O3 surface. Both layers are clearly observed in the atomic image reconstructions, and their local structure is analyzed. We show that by using incident energies close to the absorption edge of the fluorescing atom, it becomes possible to observe the thin surface layer clearly, even next to a base layer containing the same fluorescing element. [ABSTRACT FROM AUTHOR]

We performed X‐ray fluorescence holography measurements on an In‐doped Bi2Se3 topological insulator and obtained an in‐plane atomic image in the vicinity of In. We found that atomic images at the positions of the first nearest neighbors (NNs) are very weak whereas those at the positions of the second and the third NNs are relatively strong. On the basis of the fact that In is half of the atomic number of Bi, we attributed the origin of this feature to the clustering of the In atoms in the Bi plane. We calculated the intensity of the atomic images and confirmed that the formation of In cluster results in a decrease by 30% in the first NN atomic image intensity. However, the decrease in the magnitude is not enough to explain the experimental results, suggesting another contribution such as the lattice distortions. The effect of the lattice distortion on the atomic image intensity is discussed on the basis of the simulation including the positional fluctuation of In atoms. [ABSTRACT FROM AUTHOR]

Perovskite-structured NaTaO 3 films were epitaxially deposited on centimeter-sized SrTiO 3 (001) wafers by hydrothermal and solvothermal reactions to examine the surface science for an efficient photocatalytic water-splitting reaction. The addition of Ba cations in the starting solutions afforded Ba-doped NaTaO 3 films. X-ray fluorescence holography was employed to investigate and confirm the heteroepitaxial relationship between the Ba-doped film and substrate. [ABSTRACT FROM AUTHOR]

The first direct valence-selective structure determination by X-ray fluorescence holography is reported. The method is applied to investigate an epitaxial thin film of the rare earth monoxide YO, which has recently been synthesized by pulsed laser deposition. The surface of the sample is easily oxidized to Y2O3. In order to separate the structural information connected with the two different valence states of Y, the X-ray fluorescence holography measurements were performed close to the Y K absorption edge. Using the shift of the absorption edge for the different valence states, very different relative contributions of YO and Y2O3 are obtained. Thus, it is possible to distinguish the crystal structures of YO and Y2O3 in the thin-film sample. [ABSTRACT FROM AUTHOR]

While high-throughput screening for protein crystallization conditions have rapidly evolved in the last few decades, it is also becoming increasingly necessary for the control of crystal size and shape as increasing diversity of protein crystallographic experiments. For example, X-ray crystallography (XRC) combined with photoexcitation and/or spectrophotometry requires optically thin but well diffracting crystals. By contrast, large-volume crystals are needed for weak signal experiments, such as neutron crystallography (NC) or recently developed X-ray fluorescent holography (XFH). In this article, we present, using hemoglobin as an example protein, some techniques for obtaining the crystals of controlled size, shape, and adequate quality. Furthermore, we describe a few case studies of applications of the optimized hemoglobin crystals for implementing the above mentioned crystallographic experiments, providing some hints and tips for the further progress of advanced protein crystallography. [ABSTRACT FROM AUTHOR]

X-ray Fluorescence Holography (XFH) study of Cu(In,Ga)Se2 single crystals has been performed using an inverse mode. Energies of incident X-ray are from 9.2 to 13.2 keV. The Cu-Kα X-ray fluorescence hologram has been constructed, and atomic images were reconstructed using Barton's algorithm. Dependence of fluorescent X-ray, either Cu or Ga, on the reconstructed atomic images of CuIn0.2Ga0.8Se2 was examined. The atomic image of CuIn0.2Ga0.8Se2 was compared with that of CuIn0.8Ga0.2Se2. The reconstructed atomic images of the cation (Cu, Ga, and In) plane and that of the anion (Se) plane are discussed in terms of the alloy composition. [ABSTRACT FROM AUTHOR]

The local structure around Ag atoms in Ag-doped Bi 2 Se 3 (Ag x Bi 2 − y Se 3) was investigated by photoelectron diffraction and X-ray fluorescence holography to understand the manner of Ag atom doping. At a low Ag concentration (x = 0. 05), photoelectron diffraction indicated that Ag atoms occupied Bi substitution sites. However, a mere accumulation of holes via Ag substitution for Bi fails to explain the observed variation previously reported in the transport properties of Ag-doped Bi 2 Se 3 with different x values. In particular, simple Ag substitution for Bi fails to explain the pinning of the Fermi level at the bottom of conduction band, as suggested by the observed transport properties. In the case of a high Ag concentration (x = 0. 2), photoelectron diffraction suggested that the Ag atoms occupied not only the substitutional Bi site but also multiple interstitial sites, namely, the octahedral site in the van der Waals interlayer and the interstitial site in the Se layer. Ag 3d photoelectron spectra revealed that the Ag atoms had the same oxidation state, + 1 , regardless of the type of occupied site. Furthermore, X-ray fluorescence holography was employed for a model-free local structural analysis that refined the exact locations of Ag atoms in the Bi 2 Se 3 crystal lattice. The behavioral crossover documented herein from hole doping at the substitutional site to electron doping at multiple sites reasonably explains the dependence of electronic structures and transport properties of Ag-doped Bi 2 Se 3 on dopant concentration. • The local atomic structure around the Ag dopant in Bi 2 Se 3 was revealed. • Photoelectron and x-ray fluorescence diffraction techniques were used. • Bi atoms were found to be substituted by Ag atoms at low Ag concentration. • Intercalation sites were found in addition at high Ag concentration. • This finding reasonably explains the mystery of transport property of Ag x Bi 2 Se 3. [ABSTRACT FROM AUTHOR]

[Display omitted] • Epitaxial thin film of anatase TiO 2 was fabricated by solvothermal method. • The substrate corrosion was suppressed by acetylacetone as stabilizer for Ti4+ ions. • The growth method has advantages in simpleness, thickness and large-area uniformity. • The grown film has the orientation of (0 0 1) [1 0 0] TiO 2 || (0 0 1) [1 0 0] LaAlO 3. • Dopant atom site was clarified using X-ray fluorescence holography. TiO 2 is one of the most extensively investigated oxides owing to its numerous potential applications. However, most methods reported for the growth of epitaxial thin films of anatase TiO 2 are costly and laborious. In this study, a solvothermal method being simple and inexpensive was used for epitaxial growth of anatase TiO 2 thin films on a LaAlO 3 substrate. Solvothermal methods usually use highly acidic conditions to stabilize Ti ions in water. The acids used tend to corrode the substrate. Hence, acetylacetone was used as a stabilizer to grow epitaxial thin films. The fabricated epitaxial thin film had the orientation of (0 0 1) [1 0 0] TiO 2 || (0 0 1) [1 0 0] LaAlO 3 with 2.5 μm thickness. The fabricated thin film can be used as applications such as photocatalysts, electrodes, and optical devices. Substitution of Ti atom with dopant atom was clarified using X-ray fluorescence holography. [ABSTRACT FROM AUTHOR]

Mg-Y alloys exhibit a good room-temperature ductility even at fairly large grain sizes and a moderately strong basal texture. Since a clarification of this structural origin is contributed for developing high-performance, affordable, lightweighted structural metals, it is desired to reveal the structural origin. The objective of this study is to reveal the structural origin of an enhanced ductility in a Mg 99.7 Y 0.3 single crystal using an x-ray fluorescence holography (XFH) analysis. It was found that a part of Y atoms was located at the ideal positions in pure Mg but others formed Y dimers in the hexagonal close-packed structure of Mg 99.7 Y 0.3. It was considered that the dimer formation plays an important role in activating non-limited the plastic slip in the crystallographic z -direction of Mg-Y alloys although the crystal structure is still hexagonal by close-packed. • Local structure around Y atoms in Mg 99.7 Y 0.3 single crystal was investigated by x-ray fluorescence holography. • The objective of this study is to reveal the structural origin of enhanced ductility in Mg 99.7 Y 0.3 alloy as one of the Mg-rare earth element alloys. • The clear hologram and atomic images were successfully obtained. • Y atoms were not only located at the substitutional sites in pure Mg but also formed Y dimers. • The dimer formation is important to hider the basal slip and to activate non-limited plastic slip in the crystallographic z-direction of Mg-Y alloys. [ABSTRACT FROM AUTHOR]

The influence of matrix effects i.e. beam attenuation (BA) and indirect excitation (IE) on local structure imaging with multiple-energy x-ray fluorescence holography is studied using computer simulations. An analytic formalism is developed which allows for the description of BA and IE when the thickness of the sample is arbitrary. It is shown that beyond the thin-sample approximation, in specific cases, the measured holograms cannot be treated as entirely element sensitive. Consequently, it is demonstrated that due to the reduction of element sensitivity, spurious maxima can arise in the holographic reconstruction which can be misinterpreted as atomic images. The proposed formalism allows one to analyse BA and IE and to correct for them. It opens way for quantitative interpretation of x-ray fluorescence holograms. [ABSTRACT FROM AUTHOR]

A fast calculation algorithm for three-dimensional atomic image reconstruction from X-ray fluorescence holography (Barton's method) is described. This method employs HEALPix, an algorithm that is used to subdivide a spherical surface in which each pixel covers an identical surface area. Using this algorithm, the computing time for atomic image reconstruction is reduced by a factor of 14.5. The time can be reduced further by parallel processing and an optimization of the resolution parameter of HEALPix. [ABSTRACT FROM AUTHOR]

X-ray fluorescence holograms of ZnSe and Zn0.74Mn0.2Be0.06Se single crystals were measured by means of a table-top laboratory setup. Holograms were recorded simultaneously for Zn K, Se K and, in the case of the mixed crystal, for Mn K X-ray fluorescence. Analysis of the holograms was based on a linear regression algorithm preceded by the matrix effects correction. It enabled the determination of real and imaginary parts of the structure factors from which atomic structures around different fluorescing atoms could be reconstructed. In particular, direct imaging of Mn lattice sites in Zn0.74Mn0.2Be0.06Se unambiguously demonstrated that the majority of Mn atoms occupy substitutional Zn positions. However, it was shown that the precise analysis of Mn lattice site distribution can be hindered due to extinction effects which have to be included in the analysis of XFH in the case of non-centrosymmetric samples. [ABSTRACT FROM AUTHOR]

The local atomic structure near an Nb atom in a Ti-20 at. %Nb alloy single crystal, which consists of the β, α′′ and ω Ti phases, was investigated by means of X-ray fluorescence holography (XFH). The atomic images were reconstructed in the vicinity of an Nb atom, which is one of the typical β stabilizing elements in β Ti alloys. Most atoms in the β Ti primary phase were reconstructed clearly. The atoms in the α′′ Ti martensite phase could not be reconstructed, because the α′′ Ti martensite has the crystal structure with low symmetry. Some atoms in the ω Ti fine precipitates were reconstructed successfully, although the amount of the ω Ti phase was much smaller than that of the β phase. An Nb atom and its first nearest neighbors tend to keep the BCC structure even upon the ω Ti phase formation. [ABSTRACT FROM AUTHOR]

To observe the difference of atomic heights between the Se and Te layers with respect to the Fe layer in FeSe0.4Te0.6 single crystal, a Fe Kα fluorescence X-ray holography (XFH) experiment was performed at room temperature. The crystal structure of superconductor FeSe0.4Te0.6 obtained by X-ray diffraction (XRD) at a low temperature has distinct z-coordinates of Se and Te, remarkably different from each other. The reconstructed atomic image around central Fe atoms by XFH, however, reveals the different and complex results. [ABSTRACT FROM AUTHOR]

Recently, it has been shown that atomic structure determination with X-ray fluorescence holography (XFH) can be hindered by matrix effects, i.e. beam attenuation and indirect excitation. The analysis was limited to the monochromatic regime. In this work, the description of matrix effects is extended to the polychromatic case. It is shown that matrix effects affect the element sensitivity of white-beam XFH by introducing distortions in the holographic signal which may lead to spurious maxima in the reconstructed image. For high energies of the X-ray beam it is found that the effect of beam attenuation is very weak and indirect excitation mainly contributes to the distortions. A correction for matrix effects is proposed in the high-energy range, which allows one to remove the distortions and retrieve pure element-sensitive information. Numerical model calculations are performed to visualize the reduction of element sensitivity and its implications on local structure imaging. [ABSTRACT FROM AUTHOR]

X-ray fluorescence holography (XFH) is a method for investigating atomic order up to the medium ranges, and can provide 3D atomic images around specific elements within a radius of nm order. In addition to these characteristics, XFH is sensitive to positional fluctuations of atoms, and therefore it is useful for characterizing the local lattice distortions around specific elements. We have applied XFH to dopants and mixed crystals. We found interesting features in local lattice distortions, such as the displacements of first-neighbor atoms around dopants, far-sighted views of the atomistic fluctuations in mixed crystals, and the coexistence of distorted/undistorted sites in the same material. [ABSTRACT FROM AUTHOR]

Abstract: In this work, the results of numerical simulations of X-ray fluorescence holograms and the reconstructed atomic images for Fe single crystal are given. The influences of the recording angles ranges and the polarization effect on the reconstruction of the atomic images are discussed. The process for removing twin images by multiple energy fluorescence holography and expanding the energy range of the incident X-rays to improve the resolution of the reconstructed images is presented. [Copyright &y& Elsevier]

X-ray fluorescence holography (XFH) is a new technique enabling the determination of the three-dimensional local atomic structure around a certain element. This method has been applied to analyze the local structure around Cu in 300 nm thin films of EuBa2Cu3O7-δ (EBCO) epitaxially grown on MgO (100) substrate, using the newest system for XFH measurement and high-brilliance synchrotron radiation at SPring-8. Here, the results of a study on the irradiation effect on the local atomic structure of EBCO superconductor with XFH measurements are presented. [ABSTRACT FROM AUTHOR]