Frontier of active-site science: new insights on material functions

There is now a range of well-established experimental methods for quantitative determination of the structure of crystalline surfaces with sub-ångström precision, but increasingly in recent years structure "determinations" are being based only on a combination of scanning tunnelling microscopy images and density functional theory calculations. The dangers and limitations of this approach are described using a few specific examples that illustrate the complementarity, rather than competitive use, of these two different approaches.

Solution V, Nb K-edge XANES (X-ray absorption near edge structure) analysis of molecular catalysis, high oxidation state vanadium(V), niobium(V) complexes containing both imido ligands (possessing metal–nitrogen double bond, NR) and mono anionic ancillary donor ligands (L) of type, M(NR)(L)X₂ (X = Cl, Me), which catalyze ethylene dimerization/polymerization in the presence of Al cocatalysts, has been explored. The analysis method is highly useful to obtain the direct information of the active species (oxidation state, basic framework around the centered metal) in solution (in situ), and should thus become a powerful tool for better understanding the catalysis mechanism, basic coordination and organometallic chemistry.

Given the widespread use of density functional theory (DFT), there is an increasing need for the ability to model large systems (beyond 1000 atoms). We present a brief overview of the large-scale DFT code conquest, which is capable of modelling such large systems, and discuss approaches to the generation of consistent, well-converged pseudo-atomic basis sets which will allow such large-scale calculations. We present tests of these basis sets for a variety of materials, comparing to fully converged plane wave results using the same pseudopotentials and grids.

We review a quantitative evaluation method for the charge transport properties of organic semiconductors with static and dynamic disorder using wavepacket dynamics based on quantum theory. The large dynamic disorder in electronic states due to molecular vibrations induces transient localization of the charge carriers, which is a quantum interference effect and determines the intrinsic transport properties of the organic semiconductors. We show that our simulation can reproduce the experimentally observed mobility of single crystals including the temperature dependence. Furthermore, we estimate the effects of static disorder, such as impurities and defects, on the transport properties. To understand the transport properties of realistic organic devices, it is important to evaluate these properties based on quantum theory and consider the competition between static and dynamic disorder.

An X-ray standing wave (XSW) is created in the overlap region of two coherent X-ray waves, e.g. by diffraction or reflection. The XSW intensity maxima move, when traversing the range of total reflection, causing strong modulation of the photo-excitation of a particular element or atomic species, recorded by electron or X-ray fluorescence spectroscopy. The XSW technique is a Fourier technique, particularly useful for identifying and structurally characterizing diluted, active species. In simple cases, a single XSW measurement allows characterization with pm resolution. Otherwise, employing several XSW measurements, an image can be created by Fourier inversion allowing one to identify individual sites. The principle, strength and limitations of the XSW technique are reviewed briefly and we focus on three examples for identifying active sites: catalytically active Al in scolecite, magnetically active and counter-active sites of Mn in GaMnAs and sites on the SrTiO₃(001) surface active in the splitting of water.

The angular distributions of photoelectrons and Auger electrons from single crystal surfaces show characteristic diffraction patterns, which contain information on the local atomic structures surrounding the emitter atoms. Using computational reconstruction processes on the diffraction patterns enables us to determine the local atomic structures of, for example, dopants, catalytic active sites, and surface/interface structures. This method has become known as "photoelectron holography (PEH)". Several advanced photoelectron analyzers for PEH are now available at beamlines at SPring-8, the world's largest synchrotron radiation facility. Recently, the use of micron-sized photon beams, as well as pump-and-probe time-resolved techniques has become possible with relatively high energy resolution. Here, the experimental apparatus and some representative applications are introduced.

Diffracted X-ray tracking (DXT) is one of the single-molecule techniques for investigating intra-molecule dynamics of functional proteins at the single-molecule level with nanocrystal and synchrotron X-ray. In DXT, a nanocrystal is immobilized on a target protein, used as a motion probe and the trajectory of its diffraction spot is analyzed as the internal motion of the protein. It can detect atomic-scale dynamic motion of the protein with several tens of microseconds time resolution. Therefore, DXT is expected to be a powerful tool to investigate protein inter-molecule dynamics, especially for cooperative motion analysis in multimeric proteins. In this article, we review the characteristic features and recent progress of DXT.

This article reviews diffractive imaging using electron beams, particularly the approach using the selector aperture in a transmission electron microscope (TEM). It proposes experimental setups and reconstruction algorithms suitable for the atomic-resolution mode and the medium-resolution mode. In the medium-resolution mode, the phase distribution of a wave field transmitted through a sample is obtained across a field of view of more than 100 nm with a phase accuracy of 0.1–0.2 rad. Through the phase imaging, a thickness map of the sample and an electrostatic potential map in/around the sample are visualized. In the atomic-resolution mode, its high-resolution ability is confirmed to be better than that of aberration-corrected TEM imaging based on experiments and theory, in which this property is attributed to the lack of direct influence of objective lens chromatic aberration.

Photoelectrochemical electrodes used for solar energy harvesting and hydrogen production by water splitting have two essential functional regions: one for photocarrier generation by light absorption and another for hydrogen generation by electrochemical water reduction at the electrode surface. We show that spontaneous segregation of noble metals (Pt, Ir, Pd, Rh) can be used to grow composite materials consisting of an oxide semiconductor matrix (SrTiO₃) and an array of vertically-aligned metal nanopillars that allow these two functional regions to be independently engineered. We discuss the noble metal segregation mechanisms, clustering at the initial growth stage, and the thermodynamic and kinetic aspects of nanopillar formation for several different noble metals. In particular, we focus on the role of surface diffusion of metal and oxide species and noble metal encapsulation in the formation of vertically-aligned nanopillar composite materials.

Fe-porphyrin is a common heme cofactor in the active sites of proteins, and plays important roles in a variety of biochemical functions. However, the origin of the diverse functions of Fe-porphyrin still remains unclear. Recent studies have suggested the possible biological significance of heme distortion in proteins. This article presents a review of the recent computational studies of the distortion effects of heme, an Fe-porphyrin found in a biological active site. A procedure to quantitatively evaluate the structural distortions of Fe-porphyrin is presented. Statistical analyses of the effect of porphyrin distortion in heme proteins and systematic density functional calculations of the change in the redox potential with heme distortions along the normal modes, to elucidate the structure–function relationship of heme, will then be described.

Electrical activation of dopants in semiconductors with high concentration is a significant requirement in device technology. However, the maximum concentration is actually limited depending on the materials and process conditions, and deactivated dopants are considered to form various cluster structures. Photoelectron holography is demonstrated to be useful for analyzing the three-dimensional (3D) atomic arrangements of such structures. Through experiments of As doped in Si, the usefulness of this method as well as the combination of first-principles calculation and simulation is discussed. As a result, the 3D atomic arrangements of individual substitutional As, which is electrically active, and As_nV (n = 2–4) clusters, which are electrically inactive, are revealed. Furthermore, co-doping of As and B is proposed as a new method to enhance the activation rate of As based on structural analyses and theoretical prediction.

Although the local 3D atomic arrangement around specific active-site atoms in a functional materials is very important to reveal the origin of the functionality, the analysis of the atomic arrangement has not been possible so far because this local structure has no translational symmetry. Recently the analysis of this kind of local 3D atomic arrangement around specific atoms which has no translational symmetry has become possible with several atomic-resolution holographies and related techniques, which have been developed in Japan. Hence a project of "3D Active-Site Science" of JSPS Grant-in-Aid for Scientific Research on Innovative Areas has started. This review describes the characteristic of these new local 3D atomic imaging techniques and the achievements of the project especially two representative results and new notation system of active-site.

X-ray fluorescence holography (XFH) is a technique that can directly image the 3D arrangement of atoms around an element in a sample. The holograms contain both intensity and phase information, allowing atomic reconstruction without needing prior structural information or a tentative structural model. XFH has already been used to reveal the local structures of various inorganic samples, and recently, work has begun on XFH for soft matter. In this paper, we review the progress of XFH on soft materials. First, we review the fundamental principles of XFH. Second, we review inverse mode XFH on soft materials, and the results of the experiments on hemoglobin, myoglobin, and κ-(BEDT-TTF)₂Cu[N(CN)₂]Br crystals. In the last section, we report the progress of the development of normal mode holography for soft materials. The new apparatus and scanning method is described, and results of the initial tests on the protein Photosystem II are discussed.

Spatio-time-resolved cathodoluminescence (STRCL), which uses a femtosecond-laser-driven pulsed photoelectron gun instead of the cw electron gun of spatially resolved cathodoluminescence (CL) combined with scanning electron microscopy (SEM), is introduced for probing local luminescence dynamics in quantum structures and nanostructures of wide-bandgap (WBG) semiconductors. As STRCL is based on SEM, multi-scale characterization of a structure with high spatial definition is possible, and the use of pulsed electron-beams allows the sub-picosecond excitation of any WBG semiconductor. By using our STRCL system, high-resolution near-band-edge CL imaging allowed the visualization of nonradiative recombination channels in a low dislocation density GaN substrate: the local CL decay curves of the sample at 300 K showed a nearly single-exponential lineshape, and the lifetimes were sensitively position-dependent. Free- and bound-exciton recombination dynamics with the energy transfer processes in GaN, AlN, and hexagonal BN, as well as local emission dynamics in Al_0.68Ga_0.32N quantum wells, were successfully investigated in the UV to deep UV wavelengths down to 200 nm.

In photoelectron holography, the intensity of the angular distribution of photoelectrons is measured to obtain a hologram. Thus, a hologram can be defined as a function on a sphere. X-ray fluorescence holography is similar to photoelectron holography. In this study, we describe methods for representing spherical functions that are suitable for atomic resolution holography, and the theory of conversion from the coordinate system of measurement to the various projections. We describe methods for rotational transformations and symmetry operations for atomic resolution hologram and the image composition from measured hologram fragments. In addition, several ways to remove the background from the raw hologram data are discussed.

With the increase in the brilliance of synchrotron radiation sources, diffraction techniques have grown and expanded the scientific field of application. Surface X-ray diffraction (SXRD) is one of the state-of-the-art techniques to determine the constellations of atoms on crystal surfaces including adsorbates, thin films, and relaxed layers. We briefly overview SXRD and review the recent advances over decades from both experimental and theoretical viewpoints, including fast observations and imaging surface atoms.

We performed X-ray fluorescence holography measurements on a Pb(Fe_1/2Nb_1/2)O₃ (PFN) multiferroic material in order to investigate the temperature dependence of three dimensional local structure around Fe atoms. It was found that the atomic image intensity of the nearest neighbor Pb atom abruptly decreases when the temperature becomes lower than the Néel temperature (T_N) of about 150 K, while the intensity of the atomic image at nearest Fe/Nb position remains almost unchanged. These observations show that the magnetic transition at T_N induces static positional shifts of Pb atoms but does not strongly influence the Fe/Nb atoms, which suggests the involvement of Pb ions into the superexchange interaction between Fe ions and its contribution to the spin-lattice coupling in PFN.

We investigate the dependence of the Curie temperature (T_C), electronic structure and magnetic properties on hole doping by Zn vacancy (V_Zn) generations in Zn(Sn, Mn)As₂ and (Zn, Mn)SnAs₂ using the Korringa–Kohn–Rostoker method incorporated with the coherent potential approximation and a local spin density approximation (KKR-CPA-LSDA) within density functional theory. We find that T_C of (Zn, V_Zn)(Sn, Mn)As₂ is strongly reduced by hole doping due to the reduced double-exchange interaction. In contrast to this, (Zn, V_Zn, Mn)SnAs₂ shows ferromagnetism because of the introduction of holes into paramagnetic (Zn, Mn)SnAs₂. In this case, T_C is significantly enhanced by the hole doping because of the increased double-exchange interaction.

Series of two-dimensional Auger electron intensity angular distributions (AIAD) were measured from a polycrystalline iron surface using a focused soft X-ray beam and a display-type analyzer. The Fe(110) surface was polycrystallized by annealing up to the Martensitic transition temperature in an ultrahigh vacuum condition. After cooling the sample to room temperature, the crystal orientations of the 21 × 21 scanned points were determined by Fe LMM AIAD measurements. Domain formation of sub mm size was confirmed. The domains oriented in the [001] direction were found adjacent to the domain oriented in the [110] direction, suggesting that the Martensitic transition progressed according to the Bain relationship. The chemical and magnetic properties of domains with different surface orientations were characterized by combining diffraction measurements with X-ray absorption spectroscopy techniques. We show here how the surface oxidation reaction as well as the magnetization axis depend on the surface orientation.

A new superconducting sample, Ba_1−xCs_xTi₂Sb₂O, was prepared and characterized in a wide pressure range. The maximum value of superconducting transition temperature, T_c, of Ba_1−xCs_xTi₂Sb₂O was 4.4 K for x = 0.25 at ambient pressure. The crystal structure was determined to be tetragonal [space group of P4/mmm (No. 123)]. The charge density wave/spin density wave transition was observed at 44 K for Ba_1−xCs_xTi₂Sb₂O (nominal x = 0.25) at ambient pressure, but the transition was suppressed by applying pressure. The pressure dependent X-ray diffraction showed no structural phase transition up to 23.4 GPa, but very interesting T_c–pressure (p) behavior was observed, i.e. the T_c decreases with an increase in pressure up to 4.0 GPa, but it increased above 4.0 GPa, suggestive of non-BCS type behavior. Thus, the systematic study on new pnictide superconductor, Ba_1−xCs_xTi₂Sb₂O, was achieved, and the fascinating behavior of superconductivity against pressure was discovered.

X-ray fluorescence holography (XFH) can be used to conduct atom-resolved structural characterization of materials around a specific element, and has been applied to various functional materials. Recently, a valence-selective function has been found by this technique by employing incident X-ray energies near an absorption edge of a specified element. In this article, the principle and experimental procedure of a valence-selective XFH and subsequent data analysis procedure using the sparse modeling approach of L₁ regression are introduced. Then, the excellent XFH results with valence-selective studies are reviewed, such as Y oxide thin film, YbInCu₄ valence transition material, and Fe₃O₄ mixed valence material.

The local environment of W and Mo atoms in CaW_1−xMo_xO₄ (x = 0.12) solid solution (mixed crystal) scintillator crystal was analyzed by X-ray diffraction (XD), extended X-ray absorption fine structure (EXAFS), and X-ray fluorescence holography (XFH). The XD analysis revealed that W and Mo atoms occupy the same crystallographic site. The analyzes of XFH and EXAFS exhibited that the local environment of Mo atoms is different from that of W atoms. Atomic images of neighbor atoms around the Mo and W atoms were reconstructed using their positional fluctuations. The positional fluctuation of the W atoms was apparently larger than that of Mo atoms. This feature explained the absence of the peak due to next nearest neighbor O atoms around W atoms in the Fourier transfer magnitudes for the W-L₃ edge EXAFS spectrum. It is, therefore, most likely that the different positional fluctuations of the Mo and W atoms are responsible for different atomic images of neighbor atoms between them.

Local atomic arrangements of dielectric ε-Ga₂O₃ epitaxial thin films grown on indium doped tin oxide (ITO) and α-Al₂O₃ substrates were investigated by combining transmission electron microscopy (TEM) and X-ray fluorescence holography (XFH). TEM showed the orthorhombic lattice structure for the ε-Ga₂O₃ thin film on both the substrates and a significant in-plane Ga ion displacement on α-Al₂O₃. However, XFH revealed a partial disorder of Ga vacancies and a large displacement along the a-axis on ITO. On the other hand, highly ordered Ga vacancies and a displacement of Ga ions toward the Ga vacancy sites were observed for the film on α-Al₂O₃ by XFH. Such a high degree of freedom in atomic sites and displacements is believed to contribute to a high dielectric constant of ε-Ga₂O₃.

This study experimentally investigated the atomic structure of a single-crystalline Mn-doped BiFeO₃ (BFO) thin film using X-ray fluorescence holography with synchrotron radiation. Bi atoms can be reconstructed from both Fe Kβ and Mn Kα fluorescence X-ray holograms, indicating Mn doping at B sites in ABO₃-type perovskite structure. The fluorescence intensity of the 1st to 4th nearest Bi atoms around target Fe atoms was lower than those around Mn atoms, confirming the selective formation of Bi vacancies around Fe atoms. In contrast, the 5th to 8th nearest Bi atoms around Fe atoms showed higher intensities than those around Mn atoms, indicating that the Mn-doped BFO thin film had a double-perovskite-like structure. These results provide important information that helps elucidate the mechanism by which Mn doping modifies the conductivity of BFO.

We have investigated the epitaxial growth of Cr-doped ZnSnAs₂ thin films as a function of Zn and Sn fluxes, and characterized their structural, electrical and magnetic properties for possible application in ZnSnAs₂-based devices. Cr-doped ZnSnAs₂ thin films prepared using growth conditions favoring Cr atom substitution on Sn sites showed hole concentrations on the order of 10¹⁷ cm⁻³, but no detectable ferromagnetic properties. On the other hand, films prepared under growth conditions favoring Cr atom substitution on Zn sites, while exhibiting low (non-detectable) hole carrier concentrations, exhibited ferromagnetism even at room-temperature. Our present experimental results are consistent with those reported by Kizaki et al. where they predicted above-room-temperature ferromagnetism for Cr doping at Zn sites in the Cr-doped ZnSnAs₂ system.