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Makoto Sakata

Publications and source records attributed to Makoto Sakata.

16 recordsLinked to original sources
PubMed2006

Accurate structure factors and experimental charge densities from synchrotron X-ray powder diffraction data at SPring-8.

Accurate structure factors of silicon and diamond have been experimentally determined from powder diffraction data measured at the third-generation synchrotron-radiation source SPring-8, BL02B2. The accuracy of the obtained structure factors has been evaluated by comparing with structure factors in the literature measured by the Pendellösung method and with some from theoretical calculations. The results indicate that the structure factors from powder data are accurate enough to discuss the experimental charge-density distributions of these materials. The number of structure factors of silicon determined in the present study is 104, which is three times more than that of previous Pendellösung data. The experimental charge densities have been obtained by the maximum-entropy method from the present structure factors. The charge densities at bond mid-points for silicon and diamond show good agreement with different kinds of theoretical calculations. The present study proved that the powder diffraction at SPring-8 is a promising method for determination of experimental charge density for a wider range of materials.

Data Interpretation, Statistical↗
PubMed2006

High-resolution analysis of (Sc3C2)@ C80 metallofullerene by third generation synchrotron radiation X-ray powder diffraction.

The X-ray structure of Sc(3)C(82) is redetermined by the MEM/Rietveld method by using synchrotron radiation powder data at SPring-8, where the C(2) encapsulated structure available to discuss the Sc-Sc interatomic distances has been determined. The encapsulated three scandium atoms form a triangle shape. A spherical charge distribution originating from the C(2) molecule is located at the center of the triangle. Interatomic distances between Sc and Sc are 3.61(3) A in the triangle. The distance between Sc and the center of the C(2) molecule is 2.07(1) A.

Journal Article↗
PubMed2006

High-spin- and low-spin-state structures of [Fe(chloroethyltetrazole)6](ClO4)2 from synchrotron powder diffraction data.

The spin-crossover complex [Fe(teec)(6)](ClO(4))(2) (teec = chloroethyltetrazole) exhibits a 50 % incomplete spin crossover in the temperature range 300-30 K. Time-resolved synchrotron powder diffraction experiments have been carried out to elucidate its structural behavior. We report crystal structure models of this material at 300 K (high spin) and 90 K (low spin), as solved from synchrotron powder diffraction data by using Genetic Algorithm and Parallel Tempering techniques and refined with Rietveld refinement. During short synchrotron powder diffraction experiments (five minutes duration) two distinguishable lattices were observed the quantities of which vary with temperature. The implication of this phenomenon, that is interpreted as a structural phase transition associated with the high-to-low spin crossover, and the structural characteristics of the high-spin and low-spin models are discussed in relation to other compounds showing a similar type of spin-crossover behavior.

Journal Article↗
PubMed2006

Magnetic transitions of single-component molecular metal [Au(tmdt)2] and its alloy systems.

A single-component molecular conductor [Au(tmdt)2] (tmdt = trimethylenetetrathiafulvalenedithiolate) undergoes an antiferromagnetic phase transition at unprecedentedly high temperature (TN = 110 K). Black microcrystals of alloys, [Ni1-xAux(tmdt)2] (0.0 < x < 1.0) were prepared. The Au-rich system exhibited an antiferromagnetic transition. Metallic single crystal was obtained for x = 0.25.

Journal Article↗
PubMed2006

Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens.

The prolyl aminopeptidase complexes of Ala-TBODA [2-alanyl-5-tert-butyl-(1, 3, 4)-oxadiazole] and Sar-TBODA [2-sarcosyl-5-tert-butyl-(1, 3, 4)-oxadiazole] were analyzed by X-ray crystallography at 2.4 angstroms resolution. Frames of alanine and sarcosine residues were well superimposed on each other in the pyrrolidine ring of proline residue, suggesting that Ala and Sar are recognized as parts of this ring of proline residue by the presence of a hydrophobic proline pocket at the active site. Interestingly, there was an unusual extra space at the bottom of the hydrophobic pocket where proline residue is fixed in the prolyl aminopeptidase. Moreover, 4-acetyloxyproline-betaNA (4-acetyloxyproline beta-naphthylamide) was a better substrate than Pro-betaNA. Computer docking simulation well supports the idea that the 4-acetyloxyl group of the substrate fitted into that space. Alanine scanning mutagenesis of Phe139, Tyr149, Tyr150, Phe236, and Cys271, consisting of the hydrophobic pocket, revealed that all of these five residues are involved significantly in the formation of the hydrophobic proline pocket for the substrate. Tyr149 and Cys271 may be important for the extra space and may orient the acetyl derivative of hydroxyproline to a preferable position for hydrolysis. These findings imply that the efficient degradation of collagen fragment may be achieved through an acetylation process by the bacteria.

Acetylation↗
PubMed2004

Structures of Fe(II) spin-crossover complexes from synchrotron powder-diffraction data.

Crystal structure determination and analysis have been carried out for the two spin-crossover compounds [Fe(teeX)(6)](BF(4))(2) (teeX is haloethyltetrazole; X = I: teei; X = Br: teeb), in both their high-spin (near 300 K) and their low-spin states (T = 90 K), using high-resolution powder-diffraction data collected at the ESRF (Grenoble, France) and SPring8 (Japan) synchrotron radiation facilities. The structures of teei have been solved using various direct-space structure determination techniques (grid search, genetic algorithm and parallel tempering) and refined with the Rietveld method using geometrical restraints. In the case of teeb, a structural model was found but a full refinement was not successful because of the presence of a significant amount of an amorphous component. Analysis of the structures (space group P2(1)/c, Z = 2) and diffraction data, and the absence of phase transitions, show the overall structural similarity of these compounds and lead to the conclusion that the gradual spin-crossovers are likely to be accompanied by small structural changes only.

Journal Article↗
PubMed2004

Quantum chemical study on the configurations of encapsulated metal ions and the molecular vibration modes in endohedral dimetallofullerene La2@C80.

The configuration of La ions of La(2)@C(80) in the [80]fullerene cage was investigated by use of quantum chemical calculations. We found that the D(3)(d)() configuration is the global minimum in total energy, being more stable by 1.9 kcal/mol than the D(2)(h)() configuration, which has been considered to be the most stable. The potential energy surface calculation clarified that La ions travel between 10 equivalent D(3)(d)() positions through D(2)(h)() positions and consequently form pentagonal dodecahedral trajectory, which is in good agreement with the previous synchrotron radiation structural study. The experimental and theoretical investigation of the Raman spectrum revealed that the symmetry of molecular vibration is dramatically reduced simply by encapsulation of two La ions, and resulting vibrational modes were successfully assigned. The Raman peak at 163 cm(-)(1) was interpreted as the in-phase synchronously coupled mode of the [80]fullerene cage elongation and the La-La stretching, rather than a conventional and naive assignment as a metal-to-cage vibration mode.

Journal Article↗
PubMed2004

Stability of magnesite and its high-pressure form in the lowermost mantle.

Carbonates are important constituents of marine sediments and play a fundamental role in the recycling of carbon into the Earth's deep interior via subduction of oceanic crust and sediments. Study of the stability of carbonates under high pressure and temperature is thus important for modelling the carbon budget in the entire Earth system. Such studies, however, have rarely been performed under appropriate lower-mantle conditions and no experimental data exist at pressures greater than 80 GPa (refs 3-6). Here we report an in situ X-ray diffraction study of the stability of magnesite (MgCO(3)), which is the major component of subducted carbonates, at pressure and temperature conditions approaching those of the core-mantle boundary. We found that magnesite transforms to an unknown form at pressures above approximately 115 GPa and temperatures of 2,100-2,200 K (depths of approximately 2,600 km) without any dissociation, suggesting that magnesite and its high-pressure form may be the major hosts for carbon throughout most parts of the Earth's lower mantle.

Journal Article↗
PubMed2003

Highly conducting crystals based on single-component gold complexes with extended-TTF dithiolate ligands.

Highly conducting crystals based on single-component gold complexes with extended-TTF dithiolate ligands [Au(dmdt)(2)](0+) (1) and [Au(tmdt)(2)](0+) (2) were prepared (dmdt = dimethyltetrathiafulvalenedithiolate and tmdt = trimethylenetetrathiafulvalenedithiolate). On the basis of the synchrotron radiation powder diffraction data, the MEM electron density of 2 was successfully obtained. The conductivities of compacted powder samples of 1 and 2 at room temperature were 12 and 15 S cm(-1), respectively. Pauli-like susceptibility of 1 suggested the system to be essentially metallic at least above 50 K, while 2 showed a magnetic transition around 100 K without loss of its high conductivity.

Journal Article↗
PubMed2002

Formation of a one-dimensional array of oxygen in a microporous metal-organic solid.

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).

Journal Article↗