Pseudo-Mackay clusters in the Al-Pd-Co System

A great number of complicated intermetallic compounds were reported in binary and ternary alloy systems of Al with transition metals. Al–Co–Pd is one of the most interesting alloys, since a variety of crystalline phases associated with quasicrystals has been reported [1]. Among these crystalline phases, the structures of ε-phases are closely associated with Al3Pd, which is an important crystalline approximant for the decagonal phase with a period of 1.6 nm. W-phase is another approximant for the decagonal phase and its structural information is useful for understanding the columnar unit in the decagonal phase with a periodicity of 0.8 nm [2]. On the other hand, some crystalline phases associated with the icosahedral phase were also found in this Al-Pd-Co system. C2–phase, R-phase (R3: a = 2.91 nm, c = 1.32 nm) and F-phase (Pa3: a = 2.44 nm) are classified into this category. In particular, the structures of R-phase and F-phase consist of a variety of pseudo-Mackay clusters similar to those found in 1/1-AlCuRu and the trigonal χ-AlPdRe. As an example, the structure of R-phase shows two types of pMCs. These pMCs can be ranked by their atomic arrangements of the first shells, nevertheless every outer shell is a harmony of an Al-icosidodecahedron and a Co/Pd-icosahedron. These pMCs interpenetrate each other by sharing edges of Co/Pd-icosahedra and the interstitial space is subsequently filled by the smaller Al-icosahedra around Pd/Al sites [3]. The characteristic structural motifs for R-phase and F-phase readily suggest the importance of pMC as a fundamental structural unit for icosahedral quasicrystals.

The crystal structure of the active domain of AAPP, a powerful anti-coagulant, in complex with an antibody

Blood clotting is a vitally important process that must be carefully regulated to prevent blood loss on one hand and thrombosis on the other. Severe injury and hemophilia may be treated with pro-coagulants, whereas risk of obstructive clotting or embolism may be reduced with anti-coagulants. Anti-coagulants are an extremely important class of drug, one of the most widely used types of medication, but there remains a pressing need for novel treatments however as present drugs such as warfarin have significant drawbacks. Nature provides a number of examples of anti-coagulant proteins produced by blood-sucking animals, which may provide templates for the development of new small molecules with similar physiological effects. We have therefore studied an Anopheles anti-platelet protein (AAPP) from a malaria vector mosquito, and report its crystal structure in complex with an antibody. Overall the protein is extremely sensitive to proteolysis, but the crystal structure reveals a stable domain built from two helices and a turn, which corresponds to the functional region. The antibody raised against AAPP prevents it from binding collagen. Our work therefore opens new avenues to the development of both novel small molecule anti-clotting agents and anti-malarials.

Structure analysis for Fe-based and Ni-based metal-metalloid amorphous alloys

Transition metal-metalloid amorphous systems such as Fe-B and Ni-B are usually applied for the soft magnetic metallic glassy alloys and are counted as one of prominent categories in the field of amorphous alloy technology. Since glass forming ability of these systems correlates closely with the atomic level structure depending on chemical species of metal and metalloid, the local structure analysis for these glassy alloys is strongly required. In order to obtain the reliable structural model for these metal (Fe, Ni)-metalloid (B) amorphous samples, we determined the partial structural functions by combinational use of neutron diffraction (ND) and anomalous X-ray scattering (AXS). The amorphous ribbon samples were produced by the single-roller melt-spinning technique. The AXS measurements at Fe and Ni absorption edges were carried out at BL-7C of Photon Factory, KEK. The ND experiment was performed by using the time-of-flight technique and high intensity total diffractometer, NOVA at MLF, J-PARC. The figure shows the g(r)s for Fe₈₀B₂₀, Ni₈₁B₁₉, and Ni₆₀B₄₀ calculated by the interference functions obtained by ND measurements. The dashed lines in the figure indicate the interatomic distances estimated from Goldschmidt atomic radii (Fe: 1.28 Å, Ni: 1.25 Å, B: 0.97 Å). At the nearest neighbor region up to about 3 Å, the first peak could be accounted for a harmony of metal (M)-B and B-B pair correlations and the second peak is mainly contributed by the M-M pair correlation. As for the three dimensional structural modeling of the amorphous samples, reverse Monte Carlo simulation has been performed starting from an initial model of 2,000 atoms with the b.c.c. structure. The present simulation results are found to reproduce the experimental interference functions obtained by the ND, ordinary X-ray diffraction, and AXS measurements. We will present the obtained structural model and local structural units around B including their arrangement.

Structure refinements of kottogite and symplesite solid-solution

Kottogite and symplesite are zinc and ferrous arsenate minerals, respectively. These minerals make the Zn3-x,Fex(AsO4)2·8H2O solid-solution and belongs to the vivianite group of minerals with the chemical formula M3(TO4)2·8H2O. The structure of vivianite and symplesite were determined firstly by Mori and Ito, (1950). The structure of kottigite was refined by Hill, (1979). The strucrure of Zn1.63Fe1.37(AsO4)2·8H2O solid-solution crystallize in space group C2/m with a= 10.342(1), b= 13.484(2), c= 4.7756(5), β=105. 306(4), and Z=2. We performed the structure refinements of (Zn,Fe)3(AsO4)2·8H2O solid-solutions, Ojuela mine, Mapimi Durango, Mexico and Kiura mine, Ohita, Japan by RIGAKU single-crystal structure analysis system RAPID. The R and S values are around 0.03 and 1.08. We determined detail atomic coordinate and hydrogen atom positions. The hydrogen bonds were revealed based on hydrogen positions and bond valence caluculations. The octahedral edge-shareing M2O6(H2O)4 dimers and insular MO2(H2O)4 octahedra are linked by AsO4 terahedra. Two H2O group bonds to (Zn,Fe). Four hydrogen atoms are in the normal hydrogen bonds. Hydrogen atom positions have a tunnel structure and there is a path of proton-conduction and we conjecture that proton conductivity has large anisotropy of one direction. The related minerals, such as paradamite, legrandite and warikahnite have tunnel structure similar to vivianite group.

Structure and H position of tetragonal hydrogarnet derived from CaGeO₃ garnet

Hydrogarnets, represented by hydrogrossular, are produced by the replacement of (ZO4)4- in garnets by (H4O4)4- (Z: tetrahedral cation) and the vacancies of tetrahedral cations are created by this replacement. Most of reported hydrogarnets crystallizes with cubic symmetry (space group Ia-3d). To our knowledge, Ca3Mn2[SiO4]2.07[H4O4]0.93 with space group I41/acd (tetragonal) [1] has been only reported as a low-symmetry hydrogarnet. In the cubic hydrogarnets, all O atoms are crystallographically equivalent, whereas in low-symmetric one, they can be located at non-equivalent sites. Therefore, the investigation of low-symmetry hydrogarnes is important to gain knowledge of the site preference of H atoms. Recently, we have successfully synthesized the single crystal of a new low-symmetry hydrogarnet CaGe0.924O3H0.304 (= Ca3(CaGe)[GeO4]2.696[H4O4]0.304) with tetragonal space group I41/a, at 3 GPa and 1273 K under the presence of H2O component. This tetragonal hydrogarnet is produced by the partial replacement of (GeO4)4- in high-pressure CaGeO3 garnet, Ca3(CaGe)[GeO4]3, by (H4O4)4-. In the present study, we report the single crystal X-ray diffraction study of this hydrogarnet at 98 and 298 K. In the structure refinement at 298 K, the occupancy parameters resulted in 0.393(2) for tetrahedral Z2(Ge) site, coordinated only by O6 atoms, and showed no significant deviation from 1.0 for the remaining cation sites. The bond valence sums of each atom except O6 atom agree with the valences of occupied atoms, whereas that of O6 atom are 1.50, deviating largely from oxygen valence. Thus, the substitution of OH groups for O atoms in the present sample occurs only at O6 site, which indicates that O6 is the most preferential site for the OH substitution. The position of H atom will be examined from the residual electron density distributions at a low temperature of 98 K, and the hydrogen bonding in the crystal structure will be discussed.