Selective growth of ag nanowires on Si(111) surfaces by electroless deposition

Electroless deposition of Ag on atomically flat H-terminated Si(111) surfaces in aqueous alkaline solutions containing Ag ions produced two different sizes of Ag nanowires along atomic step edges: (1) a narrow nanowire of 10 nm in width and 0.5 nm in height and (2) a wide nanowire of 35 nm in width and 11 nm in height. The narrow and wide nanowires were formed by immersion in the solutions containing less than 1 ppb and 8 ppm dissolved-oxygen concentrations, respectively. This result indicates that the dissolved oxygen initiates the formation of Ag nucleation sites and that the fabrication method has a possibility of controlling the size of Ag nanowires.     

19F NMR characterization of the thermodynamics and dynamics of the acid-alkaline transition in a reconstituted sperm whale metmyoglobin

A 19F NMR study on the acid-alkaline transition in sperm whale myoglobin reconstituted with a perfluoromethyl heme, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporphyrinatoiron(III), demonstrated that the thermodynamics of the transition is predominantly controlled by the stability of acidic form.     

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

Alkane Oxidation with Molecular Oxygen Using a New Efficient Catalytic System: N-Hydroxyphthalimide (NHPI) Combined with Co(acac)(n)() (n = 2 or 3)

A novel class of catalysts for alkane oxidation with molecular oxygen was examined. N-Hydroxyphthalimide (NHPI) combined with Co(acac)(n)() (n = 2 or 3) was found to be an efficient catalytic system for the aerobic oxidation of cycloalkanes and alkylbenzenes under mild conditions. Cycloalkanes were successfully oxidized with molecular oxygen in the presence of a catalytic amount of NHPI and Co(acac)(2) in acetic acid at 100 degrees C to give the corresponding cycloalkanones and dicarboxylic acids. Alkylbenzenes were also oxidized with dioxygen using this catalytic system. For example, toluene was converted into benzoic acid in excellent yield under these conditions. Ethyl- and butylbenzenes were selectively oxidized at their alpha-positions to form the corresponding ketones, acetophenone, and 1-phenyl-1-butanone, respectively, in good yields. A key intermediate in this oxidation is believed to be the phthalimide N-oxyl radical generated from NHPI and molecular oxygen using a Co(II) species. The isotope effect (k(H)/k(D)) in the oxidation of ethylbenzene and ethylbenzene-d(10) with dioxygen using NHPI/Co(acac)(2) was 3.8.     

Determination of chemical form of antimony in contaminated soil around a smelter using X-ray absorption fine structure.

Only limited information is available about the behavior of antimony (Sb) in contaminated soils. However, understanding the behavior of Sb in contaminated soils is important, because the toxicity or solubility of this element depends on its chemical state. In this study, we investigated the levels of Sb and the chemical forms of Sb in the soil around a smelter using X-ray absorption fine structure (XAFS) spectra. The highest Sb concentration in the contaminated soil was 2900 mg/kg dry soil. According to Sb-K edge X-ray absorption near edge (XANE) spectra, the Sb in the soil was in the form of Sb(V) compounds. The similarity of extended XAFS (EXAFS) spectra suggests that Sb speciation was independent of the sampling site, which indicates that Sb or Sb2O3 emitted from the smelter was converted into Sb(V) compounds in the soil.     

Selective generation of organic aggregates included within metal-organic micropores through vapor adsorption

The ethanol vapor adsorption behavior and the inclusion crystal structure of a 1D-transformable coordination polymer host were characterized. The adsorption jump was observed during phase transition or two-phase equilibrium with abnormal adsorption enthalpy caused by the nature of "mass induced phase transition." The included ethanol guests selectively form O-H...O hydrogen bonded pairs inside channels, suggesting selective construction of a specific cluster/aggregate in pores under control of thermodynamic factors and cooperative intermolecular interactions among the guest and channel surface.     

Cloning and characterization of an active fragment of luciferase from a luminescent marine alga, Pyrocystis lunula

Two marine dinoflagellates, Lingulodinium polyedrum and Pyrocystis lunula, emit light in a reaction involving the enzymatic oxidation of its tetrapyrrole luciferin by molecular oxygen. The characteristic properties of P. lunula luciferase have not been clarified, whereas L. polyedrum luciferase, which has three active domains, has been characterized. A cloned partial cDNA of the P. lunula luciferase encodes an active fragment corresponding to part of domain 2 and all of domain 3 of L. polyedrum luciferase. The homology of the amino acid sequence between the two luciferases in domain 3 is about 84.3%. A recombinant His-tagged luciferase fragment containing domain 3 (Mr = 46 kDa) catalyzed the light-emitting oxidation of luciferin (lambdamax = 474 nm). This protein was purified by a single affinity-chromatography procedure. The pH-activity profile and the bioluminescence spectrum of the recombinant enzyme having a third domain are almost identical to those of an extract from P. lunula cultured in vitro. The recombinant enzyme is active at pH 8.0, although the recombinant enzyme derived from the second domain of L. polyedrum luciferase is inactive at pH 8.0. Substitution of Glu-201 by histidine in the third domain of P. lunula luciferase showed a decrease of activity above pH 7.0, suggesting that histidine residues could be responsible for pH-sensitivity in dinoflagellate luciferase.     

Study of salt permeation process into Vigna angularis using Ag/AgCl electrodes

In this work we report a novel method that can monitor in vivo the salt permeation process into a plant Vigna angularis using two Ag/AgCl electrodes. The method is based on the electromotive force (emf) measurement using two Ag/AgCl electrodes, one inserted into the V. angularis pith cavity and the other placed into saline ([NaCl]=1 M) surrounding the roots. Temporary change of emf ranging from 0 to ca. 0.115 V was measured in vivo using the system, and the possible physiological phenomenon during the period was discussed.     

Synthesis of a novel bridged nucleoside bearing a fused-azetidine ring, 3′-amino-3′,4′-BNA monomer

A novel bridged nucleic acid monomer, 3′-amino-3′-deoxy-5-methyl-3′-N,4′-C-methyleneuridine, was successfully synthesized via a useful and convenient azetidine ring formation under Staudinger's conditions. A ¹H NMR experiment and a PM3 calculation revealed that the sugar moiety of the novel bridged nucleic acid monomer, 3′-amino-3′,4′-BNA, was restricted to S-type conformation.     

NAD(P)+-NAD(P)H model. 38. Reduction of aldehyde by 1,4-dihydroquinolin derivative

Benzaldehyde are reduced to benzyl alcohol by a model compound of NAD(P)H almost quantitatively. Reductions of some other aldehydes are also mentioned.