X-ray absorption spectroscopy of a structural analogue of the oxidized active sites in the sulfite oxidase enzyme family and related molybdenum(V) complexes

X-ray absorption spectroscopy (XAS) (edge and extended X-ray absorption fine structure (EXAFS)) has been applied to the characterization of three molybdenum(V,VI) monodithiolene complexes with unidentate coligands, [MoO(SC(6)H(2)-2,4,6-Pr(i)()(3))(2)(bdt)](-) (1), [MoOCl(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](-) (2), and [MoO(2)(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](-) (3) (bdt = benzene-1,2-dithiolate). These complexes are related to the active site in the xanthine oxidase and sulfite oxidase families and, as in the enzyme sites, bind monodentate thiolate. By comparison to the data of crystalline oxidized chicken sulfite oxidase, it is shown that complex 3, whose thiolate simulates binding by the highly conserved cysteine, is an accurate structural analogue of the oxidized site of this enzyme. Normalized edge spectra, EXAFS data, Fourier transforms, and GNXAS-based fit results are presented. As in earlier studies, this provides characterization of new analogue complexes by XAS to facilitate identification of related sites in proteins.     

AFM characterization of nanoscale ribbons grown from a series of oligo(p-phenyleneethynylene) derivatives

The key to optimizing the properties of molecular scale wires lies in understanding and controlling the solid-state morphologies. This paper examines the influence of oligomer chain length, solvent, and concentration on the formation of nanoscale ribbons on mica substrates from solutions of oligo(p-phenyleneethynylene)s (OPEs) with hexyloxy side chains and thioacetyl end groups. The OPEs are of different molecular chain lengths, in which the numbers ofp-dihexyloxyphenyleneethynylene repeat units, n, are 1, 3, 5, and 7, respectively, with their two ends capped with 4-thioacetylphenyl alligator groups. The atomic force microscope (AFM) is employed to investigate the thin film morphology and study the self-assembled organizations. Solvent and concentration are found to exert a strong influence on thin film morphology. Under suitable conditions, OPEs with 7 p-dihexyloxyphenyleneethynylene repeat units are driven to form micrometer-long nanoribbons, oriented preferably along the 3-fold symmetry axes of the mica substrate. The cross section of the nanoribbons is composed of 7 molecules as evaluated by AFM characterization. On the other hand, oligomers with shorter chain lengths (n = 1, 3, and 5) produce thin films featuring globular nanoaggregates, chains consisting of elongated grains, and rods, respectively. Plausible reasons for the variation in thin film morphology are discussed, based on the results obtained from investigation of oligomer chain length, solvent, and concentration effects. A subtle balance among molecular size and physicochemical properties of solute molecules, solvent molecules, and substrate is crucial for the formation of desired structures. Among them, oligomer chain length plays a key role in thin film morphology, and the critical number of repeat units in OPE/poly(p-phenyleneethynylene) molecules for the formation of nanoribbon structures with a molecular cross section is supposed to be 8 or 9.     

Monodithiolene molybdenum(V, VI) complexes: a structural analogue of the oxidized active site of the sulfite oxidase enzyme family

The active sites of the xanthine oxidase and sulfite oxidase enzyme families contain one pterin-dithiolene cofactor ligand bound to a molybdenum atom. Consequently, monodithiolene molybdenum complexes have been sought by exploratory synthesis for structural and reactivity studies. Reaction of [MoO(S(2)C(2)Me(2))(2)](1-) or [MoO(bdt)(2)](1-) with PhSeCl results in removal of one dithiolate ligand and formation of [MoOCl(2)(S(2)C(2)Me(2))](1-) (1) or [MoOCl(2)(bdt)](1-) (2), which undergoes ligand substitution reactions to form other monodithiolene complexes [MoO(2-AdS)(2)(S(2)C(2)Me(2))](1-) (3), [MoO(SR)(2)(bdt)](1-) (R = 2-Ad (4), 2,4,6-Pr(i)(3)C(6)H(2) (5)), and [MoOCl(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (6) (Ad = 2-adamantyl, bdt = benzene-1,2-dithiolate). These complexes have square pyramidal structures with apical oxo ligands, exhibit rhombic EPR spectra, and 3-5 are electrochemically reducible to Mo(IV)O species. Complexes 1-6 constitute the first examples of five-coordinate monodithiolene Mo(V)O complexes; 6 approaches the proposed structure of the high-pH form of sulfite oxidase. Treatment of [MoO(2)(OSiPh(3))(2)] with Li(2)(bdt) in THF affords [MoO(2)(OSiPh(3))(bdt)](1-) (8). Reaction of 8 with 2,4,6-Pr(i)(3)C(6)H(2)SH in acetonitrile gives [MoO(2)(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (9, 55%). Complexes 8 and 9 are square pyramidal with apical and basal oxo ligands. With one dithiolene and one thiolate ligand of a square pyramidal Mo(VI)O(2)S(3) coordination unit, 9 closely resembles the oxidized sites in sulfite oxidase and assimilatory nitrate reductase as deduced from crystallography (sulfite oxidase) and Mo EXAFS. The complex is the first structural analogue of the active sites in fully oxidized members of the sulfite oxidase family. This work provides a starting point for the development of both structural and reactivity analogues of members of this family.     

Structure determination of a sildenafil analogue contained in commercial herb drinks

It was found from HPLC analysis that a commercial herb drink contains a putative sildenafil analog. In order to identify the sildenafil-like compound, separation and purification were carried out. The structure determination was performed based on routine 1D and 2D NMR experiments. Unlike sildenafil, the compound contains an ethylpiperazine instead of a methylpiperazine group. In addition, the piperazine and phenyl groups are connected through an acetyl group instead of the sulfonyl group of sildenafil.     

Fabrication of microfluidic mixers and artificial vasculatures using a high-brightness diode-pumped Nd:YAG laser direct write method

This paper describes a direct write laser technology, which is fast and flexible, for fabricating multiple-level microfluidic channels. A high brightness diode-pumped Nd-YAG laser with slab geometry was used for its excellent beam quality. Channels with flat walls and staggered herringbone ridges on the floor have been successfully fabricated and their ability to perform passive mixing of liquid is discussed. Also, a multi-width multi-depth microchannel has been fabricated to generate biomimetic vasculatures whose channel diameters change according to Murray's law, which states that the cube of the radius of a parent vessel equals the sum of the cubes of the radii of the daughters. The multi-depth architecture allows for flow patterns to resemble physiological vascular systems with lower overall resistance and more uniform flow velocities throughout the network compared to planar patterning techniques which generate uniformly thin channels. The ability to directly fabricate multiple level structures using relatively straightforward laser technology enhances our ability to rapidly prototype complex lab-on-a-chip systems and to develop physiological microfluidic structures for tissue engineering and investigations in biomedical fluidics problems.     

Optimization of medium by orthogonal matrix method for submerged mycelial culture and exopolysaccharide production in Collybia maculata

Optimization of submerged culture conditions for the production of mycelial growth and exopolysaccharides (EPSs) by Collybia maculata was investigated. The optimum temperature and the initial pH for EPS production in a shake-flask culture of C. maculata were found to be 20°C and 5.5, respectively. Among the various medium’s constituents examined, glucose, Martone A-1, K₂HPO₄, and CaCl₂ were the most suitable carbon, nitrogen, and mineral sources for EPS production, respectively. The optimum concentration of the medium’s ingredients determined using the orthogonal matrix method was as follows: 30 g/L of glucose, 20 g/L of Martone A-1, 1g/L of K₂HPO₄, and 1g/L of CaCl₂. Under the optimized culture conditions, the maximum concentration of EPSs in a 5-L stirred-tank reactor was 2.4 g/L, which was approximately five times higher than that in the basal medium. A comparative fermentation result showed that the EPS productivity in an airlift reactor was higher than that in the stirred-tank reactor despite the lower mycelial growth rate. The specific productivities and the yield coefficients in the airlift reactor were higher than those in the stirred-tank reactor even though the volumetric productivities were higher in the stirred-tank reactor than in the airlift reactor.     

Characterization of DNA immobilization and subsequent hybridization using in situ quartz crystal microbalance, fluorescence spectroscopy, and surface plasmon resonance

We have characterized the immobilization of thiol-modified oligomers on Au surfaces and subsequent hybridization with a perfectly matched or single-base mismatched target using a quartz crystal microbalance (QCM) and fluorescence spectroscopy. The surface density of immobilized probe molecules and the hybridization efficiency depending on the type of buffer and salt concentration were investigated. We observed some ambiguities in surface coverage deduced from QCM measurement and adopted a complementary fluorescence displacement method. Direct comparison of surface coverage deduced from frequency change in QCM measurement and determined by the fluorescence exchange reaction revealed that QCM results are highly overestimated and the amount of overestimation strongly depends on the type of buffer and the structure of the film. Discrimination capability of the surface attached 15-mer probe was also examined using a single-base mismatched target at various hybridization temperatures. Hybridization efficiency depending on the type of single base mismatch was investigated using surface plasmon resonance (SPR).     

Electrical conduction through linear porphyrin arrays

Electrical conduction measurements were made on two extreme types of directly linked porphyrin arrays by using nanoelectrodes. One type is the directly linked Zn(II)porphyrin arrays, consisting of 48 Zn(II)porphyrin moieties (Z48), and the other type is the completely flat, tape-shaped Zn(II)porphyrin arrays, consisting of eight Zn(II)porphyrin units (T8). The I-V curve for Z48 exhibits the diode-like behavior and the hysteresis depending on the voltage sweep direction presumably due to the conformational heterogeneity arising from the dihedral angle distribution in Z48. On the other hand, the I-V curve for T8 is nearly symmetric without any hysteresis, leading to the higher conductivity and the smaller band gap. These results illustrate that the stronger pi-electron conjugation in T8, as compared with that of Z48, results in better electrical conduction.     

Intramolecular ionic Diels-Alder reactions of alpha-acetylenic acetals

The intramolecular ionic Diels-Alder reaction of alpha-acetylenic acetals as a precursor of the propargyl cation has been investigated in the presence of Lewis acids and in protic acids. The reaction of diene-tethered alpha-acetylenic acetals (1-2) with formic acid yielded the regioselective intramolecular ionic Diels-Alder reaction products, bicyclodienal (9) and bicyclodienone (11) derivatives, in good yields.