Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen

The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.     

Dosimetry of fast neutrons in 1W nuclear reactor with plastic nuclear-track detectors

A nuclear reactor at Kinki University is operated at the maximum of 1W. It produces fission neutrons as much as gamma-rays. To facilitate its use for neutron radiobiology, fast neutrons inside the reactor were measured with nuclear-track detectors TS 16 N and a pair of ion chambers. The angular dependence of TS 16 N response, an anisotropy of fast neutron fluxes in the reactor and misuse of the kerma factor assumed for radiation protection business are the major causes of discrepancy is measured doses by the two methods. Correction factors for the three causes are proposed. After correction, neutron doses estimated with TS 16 N and chambers agree within 5%. The dose-rate at the reactor's center is about 20 tissue-cGy/h. This is the first in situ dosimetry of fast neutrons in a reactor with track detectors attached to biologic samples. Our routine usage has demonstrated that, if used with caution, TS 16 N elements are handy, reliable monitors for fast neutron dosimetry as they are insensitive to contaminated gamma-rays and small enough to be attached to biologic samples.     

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Enantioselective synthesis of chelidonine, a B/C-cis-11-hydroxyhexahydrobenzo[c]phenanthridine alkaloid

Both enantiomers of chelidonine, a B/C-cis-11-hydroxyhexahydrobenzo[c]phenanthridine alkaloid, were synthesized by manipulation of the B/C-dehydro ring juncture of benzo[c]phenanthridine skeleton using Sharpless asymmetric dihydroxylation and stereospecific catalytic hydrogenation after introduction of oxygen functions on the C ring as key reaction steps for the construction of stereogenic centers.     

Acid-catalyzed reaction of pyrazolo[1,5-a]pyridines with aldehydes: Formation of bis(pyrazolo[1,5-a]pyrid-3-yl)methane

Reaction of pyrazolo[1,5-a]pyridines with aldehydes in the presence of trifluoroacetic acid gave bis[pyrazolo[1,5-a]pyrid-3-yl)methanes in high yields.     

Fe K‐Edge X‐ray Absorption Fine Structure Determination of γ‐Al2O3‐Supported Iron‐Oxide Species

The structure of FeO_x species supported on γ‐Al₂O₃ was investigated by using Fe K‐edge X‐ray absorption fine structure (XAFS) and X‐ray diffraction (XRD) measurements. The samples were prepared through the impregnation of iron nitrate on Al₂O₃ and co‐gelation of aluminum and iron sulfates. The dependence of the XRD patterns on Fe loading revealed the formation of α‐Fe₂O₃ particles at an Fe loading of above 10 wt %, whereas the formation of iron‐oxide crystals was not observed at Fe loadings of less than 9.0 wt %. The Fe K‐edge XAFS was characterized by a clear pre‐edge peak, which indicated that the Fe?O coordination structure deviates from central symmetry and that the degree of Fe?O?Fe bond formation is significantly lower than that in bulk samples at low Fe loading (<9.0 wt %). Fe K‐edge extended XAFS oscillations of the samples with low Fe loadings were explained by assuming an isolated iron‐oxide monomer on the γ‐Al₂O₃ surface.     

Novel Method for the Fabrication of a Charge‐Transfer Complex Crystal by Photoirradiation

A novel method for the fabrication of a charge‐transfer complex crystal was developed. Photoirradiation of a solution of TPP[Co(tbp)(CN)₂] and TPP[Co(Pc)(CN)₂] (tbp=tetrabenzoporphyrin, Pc=phthalocyanine, TPP=tetraphenylphosphonium) gave a molecular conducting crystal of a charge‐transfer complex TPP[Co(tbp)(CN)₂]₂, which was produced by the process in which the photoexcited electron in tbp was transferred from the LUMO of tbp to that of Pc.     

Structure of tecophilin,a tri-caffeoylanthocyanin from the blue petals of Tecophilaea cyanocrocus, and the mechanism of blue color development

The pigment, tecophilin, in blue flowers of Tecophilaea cyanocrocus was isolated and the structure was determined to be 3-O-(6-O-α-l-rhamnopyranosyl-β-d-glucopyranosyl)-7-O-(6-O-(4-O-(2-O-(4-O-β-d-glucopyranosyl-(E)-caffeoyl)-6-O-(4-O-β-d-glucopyranosyl-(E)-caffeoyl)-β-d-glucopyranosyl)-(E)-caffeoyl)-β-d-glucopyranosyl)delphinidin. The reproduction experiment of the same color as petals according to the results of chemical analysis and measurement of vacuolar pH of blue cells clarified that the blue color solely develops by tecophilin without interaction of metal ions nor co-pigments. ¹H NMR analysis and CD spectrum indicate the co-existence of clockwise intermolecular self-association of the delphinidin nuclei and intramolecular π–π stacking between the chromophore and caffeoyl residues to derive bathochromic shift of the absorption spectrum and stabilize the color by preventing hydration reaction.     

Mechanistic study of electrocatalytic oxidation of formic acid at platinum in acidic solution by time-resolved surface-enhanced infrared absorption spectroscopy

Surface-enhanced infrared absorption spectroscopy (SEIRAS) combined with cyclic voltammetry or chronoamperometry has been utilized to examine kinetic and mechanistic aspects of the electrocatalytic oxidation of formic acid on a polycrystalline Pt surface at the molecular scale. Formate is adsorbed on the electrode in a bridge configuration in parallel to the adsorption of linear and bridge CO produced by dehydration of formic acid. A solution-exchange experiment using isotope-labeled formic acids (H(12)COOH and H(13)COOH) reveals that formic acid is oxidized to CO(2) via adsorbed formate and the decomposition (oxidation) of formate to CO(2) is the rate-determining step of the reaction. The adsorption/oxidation of CO and the oxidation/reduction of the electrode surface strongly affect the formic acid oxidation by blocking active sites for formate adsorption and also by retarding the decomposition of adsorbed formate. The interplay of the involved processes also affects the kinetics and complicates the cyclic voltammograms of formic acid oxidation. The complex voltammetric behavior is comprehensively explained at the molecular scale by taking all these effects into account.     

Ruthenium-catalyzed [1,n]-metallotropic shift (n = 3, 5) of alkynyl carbene complex intermediates

The ruthenium-catalyzed isomerization of diynes and triynes involving propargyl carboxylate moieties affords dienynes and dienediynes, respectively. The [1,n]-metallotropic shift (n = 3, 5) (carbene walk) of in situ generated alkynyl carbene complexes has been proposed for the catalytic isomerization reaction.