Adsorption and reactions of NO on clean and CO-precovered Ir(111)

Adsorption and reactions of NO on clean and CO-precovered Ir(111) were investigated by means of X-ray photoelectron spectroscopy (XPS), high-resolution electron energy loss spectroscopy (HR-EELS), infrared reflection absorption spectroscopy (IRAS), and temperature-programmed desorption (TPD). Two NO adsorption states, indicative of fcc-hollow sites and atop sites, were present on the Ir(111) surface at saturation coverage. NO adsorbed on hollow sites dissociated to Na and Oa at temperatures above 283 K. The dissociated Na desorbed to form N2 by recombination of Na at 574 K and by a disproportionation reaction between atop-NO and Na at 471 K. Preadsorbed CO inhibited the adsorption of NO on atop sites, whereas adsorption on hollow sites was not affected by the coexistence of CO. The adsorbed CO reacted with dissociated Oa and desorbed as CO2 at 574 K.     

An iterative type I polyketide synthase PKSN catalyzes synthesis of the decaketide alternapyrone with regio-specific octa-methylation

A biosynthetic gene cluster containing five genes, alt1-5, was cloned from Alternaria solani, a causal fungus of early blight disease to tomato and potato. Homology searching indicated that the alt1, 2, and 3 genes code for cytochrome P450s and the alt4 gene for a FAD-dependent oxygenase/oxidase. The alt5 gene encodes a polyketide synthase (PKS), named PKSN, that was found to be an iterative type I complex reduced-type PKS with a C-methyltransferase domain. To identify the PKSN function, the alt5 gene was introduced into the fungal host Aspergillus oryzae under an alpha-amylase promoter. The transformant produced a polyketide compound, named alternapyrone, whose structure is shown to be 3,5-dimethyl-4-hydroxy-6-(1,3,5,7,11,13-hexamethyl-3,5,11-pentadecatrienyl)-pyran-2-one. Labeling experiments confirmed that alternapyrone is a decaketide with octa-methylation from methionine on every C(2) unit except the third unit.     

Studies of NO adsorption on Pt(110)-(1 x 2) and (1 x 1) surfaces using density functional theory

Adsorption of NO on Pt(110)-(1 x 2) and (1 x 1) surfaces has been investigated by density functional theory (DFT) method (periodic DMol(3)) with full geometry optimization and without symmetry restriction. Adsorption energies, structures, and N-O stretching vibrational frequencies of NO are studied by considering multiple possible adsorption sites and comparing with the experimental data. Adsorption is strongly dependent on both coverage and surface phase. The assignment of adsorption sites has been carried out with precise calculation of vibrational frequencies for NO on various sites. We clearly show the NO site switching on both of the surfaces as found in the experiments: at low coverages, bridge species is formed on the surface, and at high coverages, NO switches to atop sites.     

BDH-TTP as a Structural Isomer of BEDT-TTF,and Its Two-Dimensional Hexafluorophosphate Salt

Metallic behavior down to low temperature is shown by charge transfer salts of BDH-TTP ( 1 ), a structural isomer of bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF). In the case of (BDH-TTP)₂PF₆ this behavior is attributed to the structure, which is made up of κ-type sheets of BDH-TTP donor molecules and sheets of PF₆⁻ anions.     

Template-directed DNA photoligation via alpha-5-cyanovinyldeoxyuridine

[reaction: see text] We describe an efficient template-directed photoligation of oligodeoxynucleotides (ODNs) using alpha-5-cyanovinyldeoxyuridine (alpha(C)U). An efficient photoligation was produced by photoirradiation of an ODN containing alpha(C)U at the 3' end with an ODN containing thymine at the 5' end in the presence of a template ODN. This photoligation method is a new and efficient way to synthesize branched ODNs.     

Effects of type and physical properties of oil phase on oil-in-water emulsion droplet formation in straight-through microchannel emulsification, experimental and CFD studies

Straight-through microchannel (MC) emulsification is a novel technique for formulating monodisperse emulsions using an array of micrometer-sized channels vertical to the surface of a silicon plate (a straight-through MC). We studied the effects of the type and physical properties of the dispersed oil phase and of the surfactant concentration on droplet formation from a straight-through MC by experiments and computational fluid dynamics (CFD) simulations. Monodisperse oil-in-water emulsions with coefficients of variation below 4% were formulated from an oblong straight-through MC using silicone oils, tetradecane, medium-chain triglyceride, soybean oil, and liquid paraffin as the oil phase. At oil viscosities (eta(d)) lower than a threshold value of 100 mPa s, the values of the resultant droplet diameter (d(ex)) gradually decreased with increasing eta(d), whereas they were not affected by the surfactant concentration. Conversely, at eta(d) higher than the threshold value, the d(ex) values significantly increased with increasing eta(d), and they were affected by the surfactant concentration. An analysis on the basis of droplet formation time and interfacial tension clarified that the trends in d(ex) at eta(d) above the threshold value would be caused by the significant decrease in the dynamic interfacial tension during droplet formation. We thus discovered that the dynamic interfacial tension is also a parameter affecting the d(ex) along with eta(d) in straight-through MC emulsification. CFD simulations using a three-dimensional (3D) model including a straight-through MC confirmed successful formation of micrometer-sized droplets for the above-mentioned oils. The experimental and CFD results for the resultant droplet size were compared using the dimensionless droplet diameter (d, droplet diameter/channel equivalent diameter). The d(CFD) values agreed well with the d(ex) values at eta(d) below the threshold value of 100 mPa s for all the experiment systems and at eta(d) above the threshold value for the experiment systems that did not contain a surfactant.     

Infrared Spectroscopy and X-Ray Diffraction Studies of C?H…O Hydrogen Bonding and Thermal Behavior of Biodegradable Poly(hydroxyalkanoate)

Infrared (IR) spectra and wide-angle X-ray diffraction (WAXD) patterns of poly(3-hydroxybutyrate) (PHB) and its copolyester, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate), P(HB-co-HHx) (HHx = 12 mol%) were measured over a temperature range of 20 °C to higher temperatures (PHB, 185 °C, HHx = 12 mol%, 140 °C) to explore their structure change and thermal behavior and molecular interaction. The WAXD measurements revealed that the a lattice parameter increases significantly with temperature, while the b lattice parameter varies a little in the crystalline PHB and P(HB-co-HHx). It seems that the intermolecular interaction between the CO group of one helical structure and the CH₃ group of the other helical structure decreases along the a axis of crystalline PHB and P(HB-co-HHx) with temperature. The temperature-dependent IR spectral variations were analyzed for the CH stretching, CO stretching, CH₃ deformation, and C O C stretching variation regions, and bands characteristic of crystalline and amorphous parts were identified in each region. It was found from the anomalous frequencies of the CH₃ asymmetric stretching and CO stretching bands of PHB and P(HB-co-HHx) and the X-ray crystallographic structure of PHB that there is an intermolecular interaction (C H…OC hydrogen bond) between the CO group and the CH₃ group combining two helical structures in PHB and P(HB-co-HHx). In this review paper we discuss the role of the C H…OC hydrogen bonding and the crystal and lamella structure of PHB and P(HB-co-HHx) (HHx = 12 mol %) in comparison with the structure of Nylon.     

A free energy calculation study of the effect of H-->F substitution on binding affinity in ligand-antibody interactions

Changes in binding affinity to catalytic antibody 6D9 of chloramphenicol phosphonate derivatives (CPDs) containing H or F were investigated by performing free energy calculations based on molecular dynamics simulations. We calculated the binding free energy, enthalpy, and entropy changes (DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS) attributable to H-->F substitution by comparing results for CPDs containing a trifluoroacetylamino group (CPD-F) or an acetylamino group (CPD-H). The calculated DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS values were -2.9, -6.3, and 3.5 kcal mol(-1) and close to experimental values observed for a series of similar ligands, chloramphenicol phosphonates with F and H (-1.4, -3.5, and 2.1 kcal mol(-1)). Therefore, CPD-F binds more strongly to 6D9 than does CPD-H. To clarify the origin of the large difference in DeltaDeltaG, we apportioned the calculated values of DeltaDeltaG and DeltaG for the associated and dissociated states into contributions from various atomic interactions. We found that the H-->F substitution increased the binding affinity mainly by decreasing the hydration free energy and not by increasing favorable interactions with the antibody. The decreased hydration free energy of the ligand was mainly due to unfavorable coulombic interactions between the trifluoroacetylamino group and solvent waters, which increased the free energy of the dissociated state (by about 3.7 kcal mol(-1)). Also, the trifluoroacetylamino group slightly increased the free energy level of the associated state (about 0.8 kcal mol(-1)) because favorable van der Waals interactions compensated for unfavorable coulombic interactions with antibody atoms. In addition, the enthalpy and entropy changes, DeltaDeltaH and -TDeltaDeltaS (computationally -6.3 and 3.5 kcal mol(-1)), originated mainly from a decrease in hydration free energy in the dissociated state. The CPD-F and CPD-H ligands had substantially different structures in the dissociated and complexed states.     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.