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This issue completes the series of articles describing crytallography in Japan that started in Vol 13 No 2. Our thanks to Yuji Ohashi for assembling the information.

Recent developments

Chemical crystallography

[Figure 1]Fig. 1 Photo-produced triplet diphenylcarbene and nitrogen molecule
In Japan, many chemical crystallographers are doing forefront research in solid-state reaction-mechanisms, supra-molecular chemistry, phase transition, and materials science. Multi-dimensional structural chemistry which depends on time, temperature, and humidity etc. is actively investigated together with the development of equipment with two-dimensional detectors.
[Figure 2]Fig. 2 The MSGC detector set up at SPring-8. The detector and the data acquisition system are installed in a cubic box of ca. 25 cm. Rotating the crystal around a vertical axis by 360 degrees on the goniometer, the intensity data can be observed within 0.2 msec.
At the Tokyo Inst. of Technology, Y. Ohashi, H. Uekusa and their coworkers developed crystalline-state reaction, which means the reaction occurs in a single crystal without degradation of crystallinity. Any stage of the reaction process, therefore, can be observed by X-ray crystal structure analysis and the reaction mechanism can be analyzed using the intermediate structures as eyewitness accounts. They defined the reaction cavity, which explains quantitative reactivity in solid-state reactions. Recently, in collaboration with Rigaku, they have developed a new diffractometer with an imaging-plate detector, R-AXIS RAPID, which enables three-dimensional intensity data collection within 2 or 3 hours. Using this new diffractometer, they analyzed a variety of metastable intermediate structures, such as radical pairs of hexaarylbiimidazolyl derivatives, triplet carbenes (Fig. 1) and triplet nitrenes. Moreover, they analyzed the excited-state structures of a series of Pt complexes and a vanadium complex at the equilibrium state between ground and excited states. In order to analyze more rapid structural changes, they are now developing a new detector, Micro-Strip-Gas-Chamber (MSGC). Using this detector and a rotating anode, preliminary intensity data were collected within 2 seconds and the structure was successfully analyzed. Combining the detector and Synchrotron radiation at SPring-8 (Fig. 2), they found that the cell change of the Pt complex due to the formation of the excited state continued for more than 20 seconds and then the equilibrium state appeared.
[Figure 3]Fig. 3 A cutaway view of the [V12O32]4- anion that traps an otherwise unstable NO- anion.
T. Ozeki (Tokyo Inst. of Technology) is working on the structural chemistry of polyoxometalates. His research interests include the crystal structure determinations of novel polyoxometalates, hydrogen bonds involving the polyoxometalates, extended structures using polyoxometalates as building blocks, and inclusion compounds using the polyoxomelatate as the host (Fig. 3). He is also in charge of two diffractometers in the synchrotron radiation facilities: an imaging plate Weissenberg camera at the BL04B2 beamline of SPring-8 and a CCD diffractometer at the NW2 beamline of the Advanced Ring (AR), Photon Factory (PF) of the High Energy Accelerator Research Organization (KEK). Using these facilities, he is exploiting the advantage of the high energy (typically λ=0.33Å) and high flux X-rays to do atomic-resolution single crystal structure analyses of polyoxometalates and other chemically synthesized molecules (sometimes the size of which is stepping out of the realm of smallness and thus the common name “small molecules” is not used here).
[Figure 4]Fig. 4. Low-temperature vacuum X-ray camera at SPring-8 BL02B1 beamline.
K. Toriumi and Y. Ozawa (Univ. of Hyogo) and their coworkers have developed a new low-temperature vacuum X-ray camera (LTV X-ray camera) and installed it at the SPring-8 BL02B1 beamline (Fig. 4) for photo-excited crystallography, phase transition studies at low temperature, and micro-crystal structure analyses. By eliminating X-ray scattering from air and windows, high quality diffraction data with high S/N ratio can be automatically obtained down to 20 K. Direct observation of geometrical changes accompanied by photo-excitation of molecules provides essential information for transient species such as metastable states of chemical reactions. They have developed the multiple-exposure IP method for accurate measurement of intensity changes due to photo-illumination. A photo-excited molecular structure has been observed for the luminescent diplatinum(II) complex [Pt2(pop)4]4-.The observed electron density map shows positive and negative peaks with heights of 1–2 e/Å3 near the Pt atoms (Fig. 5). This indicates that small portions of the metal atoms move toward the positive peaks in the light-on crystal.
[Figure 5]Fig. 5 Difference Fourier map (superimposed with a molecular diagram) of |Fon|–|Foff| in a plane containing Pt(1)—Pt(2) vector and coordinated four P atoms of the ligands. Continuous lines and dashed lines indicate positive and negative density, drawn at every 0.2e/Å3, respectively.
The main subjects of H. Kobayashi (Inst. of Molecular Science) and A. Kobayashi (The Univ. of Tokyo) are: (1) development and physical properties of molecular metals and superconductors and (2) molecular design, development and physical properties of single-component molecular metals. Until the early 1990s they engaged in the development of various molecular superconductors including a k-type BEDT-TTF superconductor (k-(BEDT-TTF)2I3) and a p-acceptor (M(dmit)2, M=Ni, Pd) superconductor without TTF-like donors. Recently they have reported an organic conductors exhibiting colossal magnetoresistance and field-induced superconductivity, l-(BETS)2FeCl4 and the first antiferromagnetic organic superconductor, k-(BETS)2FeBr4 (BETS = Bis(ethylenedithio)tetraselenafulvalene). They have also developed a single-component molecular metal with extended-TTF (tetrathiafulvalene) ligands, [Ni(tmdt)2] (tmdt = trimethylenetetrathia fulvalenedithiolate). The planar molecules are closely packed and three-dimensional S…S interactions were observed in the crystal (Fig. 6). The room temperature conductivity was 400 S cm–1 and metallic behaviour was observed down to 0.6 K. Experimental evidence for the existence of Fermi surfaces was obtained by detecting the quantum oscillations in magnetization (the de Haas-van Alphen (dHvA) effect). Metallic [Au(tmdt)2] is iostructural with [Ni(tmdt)2] and has an unusually high temperature SDW antiferromagnetic transition at around 85 K.
[Figure 6]Fig.6 The molecular and crystal structure of [Ni(tmdt)2].
K. Tanaka (Nagoya Inst. of Technology) has reported 4f-electron transfer to B6 with a decrease in temperature in the study of the electron density distribution (EDD) analysis of the Kondo crystal CeB6 by X-ray atomic orbital methods. This analysis opened the door to many interesting heavy-atoms materials and they have tried to explain precise electron densities for high Tc super conductors, skutteldites and rare-earth garnets. Diffraction measurements under vacuum by the VCIP method is also being developed to get super accurate structure factors for retrieving molecular orbitals from X-ray diffraction.
[Figure 7]Fig. 7 Torsional motion and a conformational change through Pedal motion of (E)-stilbene.
The research activity of J. Mizuguchi and co-workers (Yokohama National Univ.) is focused on molecular structure, crystal structure and intermolecular interactions with potential electronic applications. Organic pigments are basically organic semiconductors which can be used in electronic materials such as photoconductors, electrophotographic photoreceptors, solar cells, optical recording materials, organic transistors etc.
[Figure 8]Fig. 8 Laplacian map of the five coordinated B compound.
Y. Sugawara (Kitasato Univ.), investigated humidity and temperature dependent phase transitions of nucleosides and nucleotide hydrates. Change in the numbers of water molecules or in their ordering at low temperature accompanies reconstruction of hydrogen-bonding networks. Structural transformations and dynamics of phase transitions are being examined using X-ray and neutron diffraction methods, Raman spectroscopy, and computer simulation calculations. These phenomena are interesting from the view points of crystal engineering, pseudopolymorphism of pharmaceuticals, and water structure in biological systems.
[Figure 9]Fig. 9 Mechanism of phase transition of 1-ethyl-3-(4-methylpentanoyl)urea.
K. Ogawa and J. Harada (The Univ. of Tokyo) have discovered a pedal motion in crystals (Fig. 7), an essential molecular motion of stilbene-type molecules. They have also been successful in providing new insight into the chromism of organic crystals.
[Figure 10]Fig. 10 Enantiomeric resolution of a racemic mixed crystal using preferential enrichment.
The main research interests of M. Yasui, F. Iwasaki (Univ. of Electro-Communications) and D. Hashizume (Riken) are: (1) weak intra and intermolecular interactions by a topological analysis of experimental charge density distributions, and (2) the mechanism of phase transitions of organic crystals using detailed temperature-resolved diffraction methods. Topological analyses for tetraazathiapentalenes, pentacoordinated hypervalent boron and carbon compounds show small positive Laplacian values at bond critical points which indicate the electrostatic character of these hypervalent bonds (Fig. 8). Analyses of intermolecular Br...Br contacts shorter than the normal van der Waals contacts revealed an electro-static interaction corresponding to the dispersion force. The magnitude of Br...Br interactions can be estimated to be about half of those of NH...O hydrogen bonds. They also studied intermolecular CH...O interactions in TEMPO radical derivatives. Topological properties prove that at least one H atom has a significant interaction with the p* orbital of the radical O atom which can explain intermolecular magnetic interaction. They have developed a ‘detailed temperature resolved diffraction method’ during the phase transition of organic crystals. This method can make the mechanism of the transition clear by looking at a set of stop-motion photographs. The mechanisms of phase transition of acylurea derivatives and thiocatechole crystals were clarified, and energy barriers of these transitions were estimated (Fig. 9).

R. Tamura (Kyoto Univ.) reported the first instance where enantiomeric resolution by simple recrystallization of a racemic crystal was observed. This unusual enantiomeric resolution phenomenon was referred to as preferential enrichment. Mechanistically, it has been proven that preferential enrichment is a secondary, dynamic enantiomeric resolution phenomenon caused by a solvent-assisted solid-to-solid transformation of a metastable polymorphic form into a thermodynamically stable polymorphic form. It occurs during crystallization of certain kinds of racemic mixed crystals composed of two enantiomers in a supersaturated solution. This phenomenon has been detected in (i) the crystal structures of the stable and metastable polymorphic forms (ii) by a direct-space approach employing the Monte Carlo method followed by Rietveld refinement, (iii) in the in situ ATR-FTIR (ReactIR) spectral data during crystallization, and (iv) in the DSC analytical and solid-state ReactIR spectral data of the deposited crystals (Fig. 10).

R. Kuroda’s research group (Univ. of Tokyo) explores and exploits solid-state chiral chemistry. In crystals, interactions between molecules are expected to be orders of magnitude stronger than in solution. Thus, it is safe to assume that chiral discrimination, recognition, generation and transfer occur most strongly in the solid state. They have studied chirality recognition in solvent-free, solid-solid reactions. Upon co-grinding and heating (without melting) of the crystals of a template compound and a substrate compound, the chirality of the substrate compound was inverted to fit with the chirality of the template compound. They have developed two novel instruments, UCS-1 (Universal Chiroptical Spectrophotometer) and UCS-2, for measuring the chirality of solid materials.

Today, many scientists in Japan, whose main research involves organic or coordination chemistry, have their own diffractometers. Apart from the above examples, splendid work is going on related to chemical crystallography, such as, multicolor phototropism of single crystals by M. Irie (Kyushu Univ.), solid-solid synthesis using host-guest interactions by F. Toda (Okayama Univ. of Science) and K. Tanaka (Kansai Univ.), inclusion phenomena of choric acids by M. Miyata (Osaka Univ.), and synthesis of organic semiconductors with metallic luster by K. Ogura (Chiba Univ.).

F. Iwasaki, Univ. Electro-communication

Materials science

[Figure 11]Fig. 11. A double shell of platonic solids formed by pentagonal-podecahedral La2 charge density in [80-Ih] fullerene: La2@C80
Structural science of materials in Japan is studied not only by crystallographers but also by materials scientists, physicists, chemists and many other researchers in science and technology. This report cannot be expected to cover all the aspects of structural science of materials in Japan but a few aspects of the field give some flavor of our country.
[Figure 12]Fig. 12 Residual factors of Eu3S4 against the mole ratio of Eu2+ ions occupied in the 4a sites in the I-42d structure.
In 1991, S. Iijima and coworkers (NEC Co. LTD.) reported a structure of a nanotube. There are many varieties, such as multi-wall, double-wall, and single-wall carbon nanotubes. These structures are mainly determined by TEM. Structural studies of nanotubes by X-ray are also active in Japan. One of the interesting properties of nanotubes is an inner hollow cavity of nanometer size. Kataura and coworkers reported that a one-dimensional crystal of fullerene molecules were found inside the nanotubes. Takenouchi and coworkers suggested that the nanotube absorbed not only fullerene molecules but also exotic molecules like TCNQ and TMTSF.
[Figure 13]Fig. 13 A new furnace for high-resolution synchrotron powder diffraction study up to 1900K (BL-3A@PF). Isosurface of electron density distribution of the cubic calcium titanate perovskite (1674K). J. Appl. Cryst. 37, 786 (2004).
Another nano-structured carbon material, for which structures are mainly determined in Japan, is metallo-fullerene. M. Sakata, M. Takata and coworkers confirmed the endohedral nature of metallo-fullerene by X-ray powder diffraction at SPring-8. Since then, the structures of endohedral metallofullerenes have shown very unique structures including the disordered states of two La atoms in a C80 carbon cage (Fig. 11).
[Figure 14]Fig. 14 Nuclear density distribution, disorder and the diffusion path of oxide ions in superionic conductors. Chem. Phys. Lett., 378, 395, 380, 391 (2003).
J. Akimitsu and coworkers (Aoyama Gakuin Univ.) discovered that MgB2 has one of the highest transition temperature (Tc = 39 K) of the known metallic superconductors. The superconductivity relating the BCS (Bardeen-Cooper-Schrieffer) mechanism has a superconducting energy gap associated with formation of the superconducting pairs. T. Takahashi (Tokyo Univ.) and S. Sasaki (Tokyo Inst. Tech.) suggested the existence of two kinds of superconducting gaps in MgB2 on the basis of an ARPES (angle-resolved photoemission spectroscopy) study, where the σ and surface bands have large gaps of 6-7 meV and the σ band is dominant in the superconductivity with a stronger coupling to phonons. The electron-phonon coupling in MgB2 causes the high Tc in a particular phonon mode with the E2g symmetry at Γ. The electron-phonon coupling is only possible for phonons with momenta appropriate to move electrons within the neighborhood of a Fermi surface. The softening and broadening of the E2g mode were observed inside the σ surfaces, by using a highly efficient X-ray spectrometer with a 4 meV resolution at SPring-8. K. Ohshima and coworkers reported a Kohn anomaly in TaS2 from the phonon dispersion curves.

Charge ordering and charge fluctuation of mixed-valence compounds are commonly investigated in Japanese universities and governmental insitutes. The valence-difference contrast method with X-ray anomalous scattering and electron-microscopic techniques are used for materials such as RM2O5 (R: Y or a rare earth; M = Mn, Fe) by Y. Yamada, and K. Kohn (Waseda Univ.), La1-xSrxMnO3 by H. Sawa (Photon Factory), Fe3O4 by S. Sasaki (Tokyo Inst. of Technology), CuIr2S4 by H. Ishibashi (Osaka Prefecture Univ.), Pr1-xCaxMnO3 and Nd1-xSrxMnO4 by Y. Matsui (National Inst. for Materials Science(NIMS)), CaFeO3 by S. Morimoto (Osaka Univ.), NaV2O5 by Y. Fujii (Univ. of Tokyo), and La1-x(Ba,Sr)xCuO4 by Y. Noda (Tohoku Univ.). An example of the research by Noda is Eu3S4, where Eu2+ and Eu3+, in a tetragonal cell below Tc = 188.5 K, occupy 4a and 8d sites, having the cation distribution of [Eu3+]4a[Eu2+Eu3+] shown in Fig. 12.

X-ray resonant magnetic scattering was found for Ni single crystals by K. Namikawa (Tokyo Gakugei Univ.) in 1985. Resonant magnetic scattering factors were then obtained from experimental data from Fe3O4 by H. Kawata (Photon Factory) and coworkers. Systematic work on nonresonant magnetic scattering has been devoted to metallic and simple oxides by M. Ito (Gunma Univ.). The resonant X-ray scattering technique has been proved to be a powerful probe of orbital states, and is now being applied to a wide range of systems with improved accuracy. One example is the case of La0.45Sr0.55MnO3/La0.6Sr0.4MnO3 multilayers reported by M. Izumi (NIMS).

The horizontal-type high-speed four-circle diffractometer at beam line 14A at the Photon Factory has been used in a number of electron density studies. Recently a high-speed detector called a stacked avalanche photodiode detector (APD) was employed with the collaboration of S. Kishimoto (Photon factory) and N. Ishizawa (Nagoya Inst. Tech). Studies of La(Sr)2CuO4 and MnS2 revealed an enhanced accuracy of the experimentally determined electron densities.

Micro-beams obtained by using synchrotron radiation are powerful tools. Interplanetary dust particles and meteorites are usually examined by optical microscopy, chemical analysis, micro Raman spectroscopy, and so on. The lower limit of the area for these examinations is about a micrometer. Diffraction data from the same samples is indispensable especially in cases of polymorphs and polytypes. Interplanetary dust particles of iron sulfides and micrometer-sized areas of the same kind in a thin section of meteorite are identified, and the structure is refined based on intensities of the Laue spots obtained by using polychromatic synchrotron radiation at the Photon Factory by K. Ohsumi.

High-resolution synchrotron powder diffractometers are available at beam line 4B2 of the Photon Factory (δd/d=0.04%) and at the BL15XU of SPring-8 (δd/d=0.03%). Two angle-dispersive-type neutron powder diffractometers (HRPD) and HERMES are installed at the JRR-3M research reactor in JAERI. There are two time-of-flight (TOF) neutron powder diffractometers (Sirius and VEGA) at KENS of KEK in Tsukuba. The KENS facility will be shut down soon, but a new powerful neutron facility (JSNS at J-PARC) has been built. At the JSNS, a new high-resolution TOF neutron powder diffractometer will be installed. At the Ceramics Research Laboratory, Nagoya Inst. Tech., the profile functions of powder diffraction data are characterized by T. Ida. F. Izumi (NISM) developed computer programs for Rietveld analysis, maximum-entropy methods and visualization of crystal structure and electron/nuclear density distribution. The superspace group approach to structure analysis of composite crystals has been a successful collaboration between NIMS and Tohoku Univ. T. Ikeda (Tohoku Univ.) analyzed the crystal structures and properties of synthesized zeolites through ab-initio computational methods.

M. Yashima (Tokyo Inst. Tech.) and coworkers have been studying high-temperature neutron and synchrotron powder diffraction techniques for precise structure analysis up to 1900 K. By using the furnace diffusion path, the disorder in some ceramic superionic conductors were visualized (Fig. 13).

Coordinated by Kazumasa Ohsumi
( and
Matt Sakata ( 

High-pressure activity

[Figure 15]Fig. 15 High pressure-temperature phase diagram of GaN determined by in situ X-ray observation. Congruent melting of GaN occurs at high pressures above 6 GPa [1]. Inserted figure is a SEM image of the GaN single crystals obtained by slow cooling from congruent melting at high pressure.
For high pressure studies, a large volume press and diamond anvil cell (DAC) are used. There are two types of large volume presses; one is a DIA type cubic anvil system and the other is a Kawai type double stage anvil system.
[Figure 16]Fig. 16 Atomic arrangements of perovskite type (low pressure phase; left) and post-perovskite type (high pressure phase; right) structures[2].
The DIA type apparatus, MAX80 at the Photon Factory and SMAP-180 at SPring-8, can generate a pressure and temperature around 10 GPa and 2000K, and it is mainly used for materials science. Recent work with SMAP-180 involved the observation of congruent melting of GaN under high pressure and temperature [1]. Fig. 15 shows the phase boundaries of GaN obtained at high pressure and temperature. This observation enables one to obtain bulk single crystals of GaN by slow cooling from a high pressure congruent melt. GaN, a famous green fluorescent material, had so far been made only in thin films. Another exciting result is finding the pressure induced first order transition in liquid states. Phosphorus was found to show a clear first order transition at around 1 GPa and 1000K (Y. Katayama, SPring-8/JAERI). This was confirmed by measurements of XAFS, density, X-ray diffraction and X-ray transmission imaging at the transition. Density was measured by X-ray absorbance by filling the sample in a sapphire or diamond ring. A sharp liquid-liquid transition in liquid germanate accompanied by a fourfold to six fold coordination change was also found around 3 GPa at 1273 K(3) (O. Ohtaka, Osaka Univ.)

The first Kawai type press for SR study named SPEED1500 can generate pressure and temperature around 30 GPa and 2000K with tungsten carbide anvils, and will be used to study the interior of the earth across the lower mantle region. The first result using SPEED 1500 is the determination of the phase boundary of Mg2SiO4 (T. Irifune, Ehime Univ.). Assuming a geotherm of 1650K, dissociation pressure is estimated to be 21GPa, which is apparently lower than the previous result. This was a sensational result to understand the upper to lower mantle structures.

In order to extend the pressure range, a new system named SPEED Mk-II using sintered diamond anvils was developed at SPring-8. At room temperature, pressure generation higher than 60GPa can be routinely achieved. SPEED Mk-II has an oscillation mechanism to avoid the effect of preferred orientation and grain growth. With this oscillation mechanism, the diffraction profiles of NaCl were clearly observed with reasonable integrated intensities very close to the melting temperature, and the phase relations among the B1, B2 and liquid phases are precisely determined (N. Nishiyama, Ehime Univ.).

A unique technique with SR is viscosity measurements using a falling ball method. An image is recorded each 1/125 second and the linear part of the falling distance against time is fit to give an accurate viscosity. Sulfur content dependence in the Fe-FeS system is clearly seen, as well as temperature dependence.

We recently succeeded in measuring ultrasonic velocity at high pressure and temperature. A transducer is set outside the anvil to prevent damage by pressure and temperature. The length of the sample is measured directly by a transmission image of the sample using a CCD camera, and volume and pressure are measured by X-ray diffraction. With this technique, concentration dependence of bulk and shear moduli for ringwoodite are beautifully observed, which agrees very well with finite strain fitting simulations (Y. Higo, Ehime Univ.).

At dedicated DAC stations (BL10XU at SPring-8) one can perform high and low temperature diffraction experiments. Strongly correlated materials, nano-materials, etc. are extensively studied by using the quasi hydrostatic pressure medium of He. Structural behaviors of simple materials such as Sc, BeO, Hg, Cs, H2, O2, and LiH are investigated in the ultra high pressure region above 200GPa.

High temperature experiments with DAC are performed by use of a laser heated DAC. The characteristics of the system at SPring-8 are dual lasers (YAG and YLF) and dual detectors (IP for precise measurement and CCD for rapid measurement). The most exciting result with laser heated DAC is the structural phase transition of MgSiO3 at 125GPa and 2400K[2]. The structure of the lower pressure phase is a well known perovskite type structure with apical sharing. The structure of the high pressure phase, which is explained by a Cmcm structure type, is unique in that it is a layered type two dimensional one (Fig. 16). This pressure and temperature condition corresponds to the mantle to core boundary of the Earth, and this result is believed to help clarify the structure of earth’s core.

Other experiments using DAC such as nuclear X-ray scattering, inelastic scattering, infrared spectroscopy, etc. are performed at each general beamline.

The high pressure neutron group, headed by H. Kagi (Tokyo Univ.) submitted a proposal for the construction of a high pressure system consisting of a DIA type high pressure cell to J-PARC. The proposal is on the waiting list.

Osamu Shimomura,


[1] W. Utsumi, H. Saitoh, H. Kaneko, T. Watanuki, K. Aoki and O. Shimomura. Nature Mater. 2, 735 (2003).
[2] M. Murakami, K. Hirose, K. Kawamura, N. Sata and Y. Ohishi, Science 305, 855 (2004).

Electron diffraction

The electron microscope is unique in that it enables us to simultaneously conduct experiments in diffractometry, microscopy and spectroscopy on a nanometer scale.

Tsuda et al.[1] developed a method to refine crystal structural parameters and charge density using convergent-beam electron diffraction (CBED). The method is based on a least-squares fit between full dynamical calculations and energy-filtered intensities from two-dimensional higher-order Laue zone (HOLZ) and zeroth-order Laue zone (ZOLZ) CBED patterns. Application of this method to the rhombohedral phase of LaCrO3 revealed clear anisotropy of thermal vibration of the oxygen atoms and charge transfer from the metal atoms to the oxygen atoms. With the aid of parallel computations, the structure (30 positional parameters and Debye-Waller factors) of the intermediate phase of hexagonal BaTiO3 was refined. In the orbital ordering phase of LaMnO3, the anisotropic charge distribution caused by orbital ordering of the 3d-electrons of the Mn atoms was found.

Fujiyoshi et al.[2] developed a high-resolution electron cryo-microscope equipped with a top-entry specimen stage. Using the microscope, they determined the atomic structures of several membrane proteins with the use of two-dimensional (2D) and tubular crystals. Image shifts due to beam-induced specimen charging were found to be the most severe problem in imaging of biological macromolecular 2D crystals, especially at highly specimen tilt conditions. To reduce beam-induced movement, Gyobu et al. developed a new sample preparation method, the carbon sandwich method, in which the crystals are put between two carbon films. This method has improved the success ratio of obtaining high-resolution images from tilted specimens, namely from 30 to 90% at a tilt angle of 45 degrees. The method enabled them to collect a full data set (87.0% complete) of aquaporin-4 (AQP4), a water channel protein, and to conduct the structural analysis at 3.2 Å resolution with a Friedel factor and merging R-factor of 11.4 % and 22.3 %, respectively.

Nagayama et al.[3] developed a series of transmission electron microscopes (TEM) capable of retrieving object-retarding phases in electron waves. The Zernike phase contrast (ZPC) method uses a classical π/2 phase plate in the form originally developed by Zernike. The Hilbert differential contrast (HDC) method uses a half-plane π phase plate to generate images similar to the differential-interference-contrast conveniently used in light microscopy. The Foucault differential contrast (FDC) method uses dynamical control for a Foucault knife-edge to perform an accurate differential operation for phases involved in the wave function of electrons. The remarkable high contrast achieved with these phase contrast TEMs without sample staining is now opening a novel field of in vivo electron microscopy in biology.

Matsui et al.[4] carried out intensive structural studies of various new superconductors by means of high-resolution transmission electron microscopy (HRTEM). They found incommensurate superstructures in Bi-2212 and Bi-2223 superconducting phases, and proposed modulated structure models with strongly distorted lattice planes. They developed a new high-voltage (1300kV) HRTEM with an 0.1nm point-resolution and used it to identify new oxycarbonate superconductors which contain CO3 groups forming various types of order/disorder structures. Since new phenomena of colossal magnetoresistivity (CMR) were reported, Matsui et al. also studied the magnetic nanostructures of various magnetic materials by cryo-Lorentz electron microscopy.[5] They examined the formation of ferromagnetic domains in a “double-perovskite” Ba2MoFeO6, and proved that the crystallographic anti-phase boundaries tend to pin the ferromagnetic domains.

Saitoh et al.[6] applied HAADF-STEM and ALCHEMI to quasicrystals and their approximants for the first time. Using the HAADF-STEM method, they first observed an asymmetric atom-cluster and a high degree of quasiperiodic arrangement of clusters in decagonal Al72Ni20Co8, which led to the quasi-unit-cell model. Using the two-dimensional angular-scanning ALCHEMI, Saitoh et al. also found that, in decagonal Al-Ni-Co and Al-Ni-Fe, two kinds of transition metal elements occupy the same sublattice site (chemical disorder), which is compatible with the fact that the quasicrystals are stabilized by the Hume-Rothery mechanism.

Abe et al.[7] demonstrated the real-space imaging of a local thermal vibration anomaly in a solid through atomic-resolution annular dark-field scanning transmission electron microscope (ADF-STEM) observations of an Al72Ni20Co8 quasicrystal. They found significant changes of the ADF intensity at some Al atomic sites, which depend on the observation temperature and the scattering angle range. This anomalous ADF intensity, which is due to an anomaly of the thermal diffuse scattering (TDS) intensity, is explained fairly well by an anomalously large value of the temperature (Debye-Waller) factor of Al at the sites or by a larger mean-square thermal vibration amplitude of the atoms. By introducing angle-resolved and/or in-situ heating/cooling techniques, they have extended the ADF-STEM method as a tool to determine local Debye-Waller factors that crucially affect the physical properties of materials.

Suenaga et al.[8] demonstrated chemical analysis by means of electron energy-loss spectroscopy (EELS) with a sensitivity of a single atom limit and the high-resolution imaging of individual metallofullerene molecules encapsulated in a single-wall carbon nanotube. They directly observed nanotubes composed of single-graphene layers and their structural defects using phase contrast transmission electron microscopy.

Takayanagi et al.[9] developed an ultra-high vacuum electron microscope combined with a scanning tunneling microscope to study structure and electronic conductance quantization of gold atomic chains and nanowires. They observed that a gold atomic chain, which was fabricated between the gold STM tip and the gold substrate, has the conductance quantum of 2e2/h, where e is electron charge and h is the Planck constant. They found gold nanowires having single-wall and multi-wall tubular structures (helical multi-shell magic number seven structure).

Using electron holography, Hirayama et al.[10] observed two-dimensional electric potential distributions in a cross section of a Metal-Oxide-Semiconductor Field-Effect-Transistor (MOSFET) fabricated from a silicon wafer with a boron concentration of 1015cm-3. This implies that electron holography allows the two-dimensional mapping of dopant distributions as low as 1015cm-3. This technique is useful for developing new devices for failure analysis in the semiconductor industry.

Kimoto et al.[11] applied electron energy-loss spectroscopy (EELS) to the analysis of an ultra-thin film of amorphous-Al2O3 on Si. EEL spectra were successfully acquired with a small interval of 0.28 nm in depth using their spatially-resolved technique. From the spectra, they found different Al coordinations of an AlO4 tetrahedron and an AlO6 octahedron with the aid of first-principle calculations. They revealed the detailed depth dependence of Al coordination in the film with sub-nanometer resolution.

Terauchi et al.[12] constructed a high energy-resolution EELS microscope equipped with a Wien-filter monochromator and a Wien-filter analyzer. The EELS microscope was used to measure the bandgap energies and the density of states (DOS) of the conduction bands of BN nano-cones and metal-doped boron micro-crystals with energy resolutions of 0.2-0.26eV. Terauchi et al. have developed a high resolution soft-X-ray spectrometer for X-ray emission spectroscopy (XES) for a transmission electron microscope (TEM). This instrument enables us to obtain the DOS of the valence band with an energy resolution better than 1ev from a small specimen area identified by observing an electron microscope image. They demonstrated using h-BN that the total DOS of the valence and conduction bands can be obtained in the electron microscope from XES and EELS spectra.

Michiyoshi Tanaka


[1] K. Tsuda and M. Tanaka, Acta Cryst., A55 (1999) 939-954.
[2] Y. Fujiyoshi, Adv. Biophys. 35 (1998) 25-80.
[3] R. Danev and K. Nagayama, Ultramicroscopy 88 (2001) 243-252.
[4] Y. Matsui et al., Jpn. J. Appl. Phys. 27, L372 (1988).
[5] Y. Anan et al., J. Electron Microsc. 50, 457 (2001).
[6] K. Saitoh, K. Tsuda, M. Tanaka, K. Kaneko, A. P. Tsai, Jpn. J. Appl. Phys. 36 (1997) L1400.
[7] E. Abe, S. J. Pennycook and A. P. Tsai, Nature 421 (2003) 347-350.
[8] K. Suenaga et al., Science, 290 (2000) 2280-2282.
[9] H.Ohnishi et al., Nature 395 (1998) 780-782.
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XAFS activities

[Figure 17]Fig. 17 Fourier transformed spectra of Pd K-edge EXAFS oscillations of the Pd-perovskite catalyst at oxidized, reduced and re-oxidized states together with that of a Pd foil.
XAFS activities in Japan started in 1982. The EXAFS beamline BL-10B, one of the first beamlines constructed at the Photon Factory (PF), is equipped with a Si(311) channel-cut type monochromator without any focusing optics. A number of papers for structural analysis of materials have been published using data from this beamline. New XAFS beamlines constructed include a sagittal focusing double crystal monochromator (BL-7B), and a Si(111) double crystal monochromator with curved cylindrical mirrors both up- and down-stream of the monochromator. Several upgrades of the PF ring lowered the emittance to 27 nm rad.
[Figure 18]Fig. 18 The Fourier transformed spectra of Rh K-edge EXAFS oscillations of Rh/Al2O3 during the carbonylation process at 298 K measured every 100 ms.
SPring-8, a third generation hard X-ray 8 GeV ring has two beamlines dedicated to XAFS experiments; BL-1B at the bending magnet port and BL-10XU in an undulator port. The former has been used for XAFS experiments in the higher energy region extending to 100 keV, and the latter for focused (0.1-1 mm2), high photon flux XAFS with more than 1013 photons/s. The later beamline is especially useful for XAFS under high pressures. Micro XAFS experiments are conducted at BL37XU using Kirpatrick and Baez (K-B) mirror optics. The beam size was 2 (H) × 4 (V) μm2, with a flux of more than 1010 photons/s at 10 keV.
[Figure 19]Fig. 19 An illustrative mechanism for the disintegration of an Rh cluster on γ-Al2O3 by CO adsorption.
Another 6 GeV storage ring in KEK, which had been used as a booster ring for the TRISTAN main ring (25 GeV), has been renewed as a high current ring with a single bunch mode dedicated for synchrotron radiation use. This is especially useful for time resolved XAFS. In the AR facility, the dispersive XAFS technique was installed, which enables one to measure EXAFS in less than 1 ms. Quick XAFS is also under construction and will be dedicated to structure analysis of catalysts.

One unique feature of XAFS activities is that the laboratory XAFS instruments are prevailing in Japan. TECHNOS I.T Co. Ltd and RIGAKU Co. have independently developed compact XAFS instruments equipped with an X-ray tube. By using a Johansson-type curved crystal, EXAFS measurements can be taken in a reasonable time; typically, 20 min for Cu K-EXAFS of a Cu foil.

There are more than 150 users of XAFS experiments in Japan. The society of XAFS was organized in 2000. Its annual meetings attract more than 100 participants. More than 50% of its members specialize in catalysis and 15% are from industry.

Although XAFS studies are diverse in various fields, two recent highlights:

(1) Self-regeneration of a Pd-perovskite catalyst for automotive emission control. Catalytic conversion of exhaust gases is an essential part of automobiles. Recently, the Japanese motor company, Daihatsu Co. developed an intelligent conversion catalyst, LaFe0.75Co0.38Pd0.05O3, perovskite-based catalysts which has a much longer lifetime than the conventional catalyst, Pd/Al2O3. The structural change of the perovskite catalyst was studied in SPring-8 by using Pd and Co K-edge XAFS as well as X-ray diffraction (Y. Nihshihata et al. Nature 418, 164 (2002)) Fig. 17 shows the Fourier transformed spectra of Pd K-edge EXAFS oscillations of the sample at oxidized, reduced and re-oxidized states together with that of a Pd foil. In the oxidized state, Pd is surrounded by oxygen, while in the reduced state, Pd is surrounded by Co and Pd. Combined with the XRD data, it revealed that Pd is in the B-site (octahedral site) of the perovskite lattice in the oxidized stateand in the reduced state, Pd is segregated with Co to form a PdCo solid solution. This process is reversible and explains the retention of high catalytic activity during long-term use and aging.

(2) Little has been known about the dynamical structural change of active metal sites in supported metal cluster/nanoparticles catalysts. The in-situ time resolved XAFS study of a CO-induced disintegration process of Rh clusters on an Al2O3 surface was performed at PF (Suzuki et. al, Ang. Chem. Int. Ed. 42 (2003) 4795). Rh K-edge EXAFS of an Rh/Al2O3 catalyst was taken under 26.7 kPa of CO at 298 K every 100 ms with the energy dispersive mode. Fig. 18 shows a series of Fourier transforms calculated during the carbonylation process. The peak at 0.2 nm (Rh-Rh) suddenly reduces and the peak at 0.1 nm (Rh-C) increases rapidly. Analysis of the coordination number and bond distances (Rh-Rh, Rh-C) as a function of CO exposure reveals that there are three elementary steps for the surface dynamic structural rearrangement of Rh clusters involving two intermediate states as depicted in Fig. 19. Before CO exposure, each Rh cluster consists of seven atoms in the first layer and three atoms in the second layer on Al2O3. CO exposure causes Rh-CO bond formation for the second layer in 600 ms, and further CO exposure induces Rh-CO bond formation with cluster disintegration and finally each Rh atom adsorbs in the threefold hollow site, forming Rh(CO)2. These results demonstrate that dispersive XAFS is useful to elucidate the mechanism for dynamic surface processes.

Toshiaki Ohta (