Emission and sputtering characteristics of Ne-Ar mixed gas glow discharge plasmas.

The emission characteristics of several Cu lines emitted from a Ne-Ar mixed gas glow discharge plasma were investigated. The addition of small amounts of Ar to a Ne plasma increases the sputtering rate of a Cu sample because Ar ions, which work as the impinging ions for cathode sputtering, are predominantly produced through Penning ionization collisions between Ne metastables and Ar atoms. Ar addition also elevates the number density of electrons in the plasma. These changes occurring in the Ne-Ar mixed gas plasma result in enhanced emission intensities of the Cu lines. The Cu II 270.10-nm and the Cu II 224.70-nm lines yield different intensity dependence on the Ar partial pressure added. This phenomenon is because these Cu II lines are excited principally through different charge transfer processes: collisions with Ne ions for the Cu II 270.10-nm line and collisions with Ar ions for the Cu II 224.70-nm line. The shape of sputtered craters in the Ne-Ar glow discharge plasma was measured. The depth resolution was improved when Ar was added to a Ne plasma because the crater bottoms were flatter with larger Ar partial pressures.     

Deprotection of dithioacetals with 30% hydrogen peroxide catalyzed by tantalum(V) chloride–sodium iodide or niobium(V) chloride–sodium iodide

The reaction of dithioacetals with 30% hydrogen peroxide in the presence of catalytic amounts of tantalum(V) and iodide ion effectively produced carbonyl compounds in high yields. Dithioacetals also can be deprotected using the niobium(V) catalyzed oxidation of iodide ion by hydrogen peroxide under mild conditions.     

Potentiometric and spectrophotometric flow-injection determinations of metal ions with use of metal ion buffers

Potentiometric and spectrophotometric flow-injection determinations of metal ions, based on metal ion buffers, are described. A copper(II) ion-selective electrode and copper(II) ion buffers containing nitrilotriacetic acid (NTA) or ethylenebis(oxyethylenedinitrilo)tetraacetic acid (EGTA) are used for determination of ca. 10^?3 M transition metal ions or of calcium in the presence of magnesium. Spectrophotometric determination of transition metal ions is achieved by using a zinc ion buffer solution containing NTA and xylenol orange as indicator. Zinc concentrations up to 2 M can be determined by using large dispersion in the manifold. The factors influencing the sensitivity of the proposed methods are discussed.     

Cover Picture

The cover picture shows how protein matrices can regulate the spatial arrangement and orientation of a heme-based donor (Zn-heme: ZnPP)-sensitizer (Ru²⁺(bpy)₃)-acceptor (cyclic viologen: BXV⁴⁺) triad. A U-shape conformation of the triad without protein matrix changes into a triangle arrangement by incorporation into apocytochrome b₅₆₂ (Cyt-b₅₆₂), or into a further extended conformation by apomyoglobin (Mb) matrix. The electron transfer pathways and the lifetimes of the photoinduced charge-separated states were remarkably affected by the protein wrapping effect.     

Semisynthetic Hemoproteins Using Cofactor Engineering: Toward Supramolecular Protein-based Photosynthetic System

Abstract

Methylammonium cations and sugar-related alcohols are bound to the tetrasulphonate derivatives 1a-1c of the resorcinol cyclic tetramer in water. With respect to the change in substituent X on C-2 of the benzene rings of the host, both 1b (X = CH₃, highly hydrophobic and moderately electron-donating) and 1c (X = OH, highly hydrophilic and highly electron-donating) exhibit higher binding abilities than the parent host 1a (X = H). These results suggest that the CH-π interaction, involving polarized C-H bonds of the guest and electron-rich benzene rings of the host, makes a substantial contribution to the guest-binding process. Host 1c even binds more hydrophilic dioxygen-functionalized sugar models (cis-1,2-cyclohexanediol, 2-oxacyclohexyl-1-carbinol and 2-oxacyclopentyl-1-carbinol) more strongly than the corresponding more hydrophobic mono-ols (cyclohexanol, cyclohexylcarbinol and cyclopentylcarbinol).     

Computing bounded-degree phylogenetic roots of disconnected graphs

The Phylogenetic kth Root Problem (PRk) is the problem of finding a (phylogenetic) tree T from a given graph G=(V,E) such that (1) T has no degree-2 internal nodes, (2) the external nodes (i.e., leaves) of T are exactly the elements of V, and (3) (u,v)E if and only if the distance between u and v in tree T is at most k, where k is some fixed threshold k. Such a tree T, if exists, is called a phylogenetic kth root of graph G. The computational complexity of PRk is open, except for k4. Recently, Chen et al. investigated PRk under a natural restriction that the maximum degree of the phylogenetic root is bounded from above by a constant. They presented a linear-time algorithm that determines if a given connected G has such a phylogenetic kth root, and if so, demonstrates one. In this paper, we supplement their work by presenting a linear-time algorithm for disconnected graphs.     

Deprotection of dithioacetals using the tantalum(V) chloride catalyzed oxidation of iodide ion by hydrogen peroxide

Dithioacetals can be deprotected to afford carbonyl groups using the tantalum(V) chloride catalyzed oxidation of iodide ion by hydrogen peroxide under mild conditions.     

Emission characteristics of Grimm-style glow discharge plasmas with helium matrix plasma gas containing small amounts of nitrogen

Glow discharge plasmas with helium–(0–16%) nitrogen mixed gas were investigated as an excitation source in optical emission spectrometry. The addition increases the sputtering rate as well as the discharge current, because nitrogen molecular ions, which act as primary ions for the cathode sputtering, are produced through Penning-type ionization collisions between helium metastables and nitrogen molecules. The intensity of a silver atomic line, Ag I 338.29 nm, is monotonically elevated along with the nitrogen partial pressure added. However, the intensities of silver ionic lines, such as Ag II 243.78 nm and Ag II 224.36 nm, gave different dependence from the intensity of the atomic line: Their intensities had maximum values at a nitrogen pressure of 30 Pa when the helium pressure and the discharge voltage were kept at 2000 Pa and 1300 V. This effect is principally because the excitations of these ionic lines are caused by collisions of the second kind with helium excited species such as helium metastables and helium ion, which are quenched through collisions with nitrogen molecules added to the helium plasma. The sputtering rate could be controlled by adding small amounts of nitrogen to the helium plasma, whereas the cathode sputtering hardly occurs in the pure helium plasma.     

Reduction of an aldehyde by a NADH/Zn2+ -dependent redox active ribozyme

We report here the ability of an alcohol dehydrogenase (ADH) ribozyme to reduce a benzaldehyde. While the ribozyme was initially evolved in vitro based on the activity for the NAD+-dependent oxidation of the benzyl alcohol, we found that this ADH ribozyme is also capable of reducing the aldehyde in the presence of NADH and Zn2+. The rate acceleration gained by ribozyme catalysis was more than 6 orders of magnitude larger than the spontaneous reaction. Although the reversibility of phosphordiester and acyl transfer reactions catalyzed by ribozymes was known, that of other chemical reactions has not been well established. This study has demonstrated the reversibility of a hydride transfer chemistry catalyzed by the ADH ribozyme. Most interestingly, the ribozyme shares many features with the protein ADHs, e.g., reversibility and NADH/Zn2+ dependence.     

Native FKBP12 engineering by ligand-directed tosyl chemistry: labeling properties and application to photo-cross-linking of protein complexes in vitro and in living cells

The ability to modify target "native" (endogenous) proteins selectively in living cells with synthetic molecules should provide powerful tools for chemical biology. To this end, we recently developed a novel protein labeling technique termed ligand-directed tosyl (LDT) chemistry. This method uses labeling reagents in which a protein ligand and a synthetic probe are connected by a tosylate ester group. We previously demonstrated its applicability to the selective chemical labeling of several native proteins in living cells and mice. However, many fundamental features of this chemistry remain to be studied. In this work, we investigated the relationship between the LDT reagent structure and labeling properties by using native FK506-binding protein 12 (FKBP12) as a target protein. In vitro experiments revealed that the length and rigidity of the spacer structure linking the protein ligand and the tosylate group have significant effects on the overall labeling yield and labeling site. In addition to histidine, which we reported previously, tyrosine and glutamate residues were identified as amino acids that are modified by LDT-mediated labeling. Through the screening of various spacer structures, piperazine was found to be optimal for FKBP12 labeling in terms of labeling efficiency and site specificity. Using a piperazine-based LDT reagent containing a photoreactive probe, we successfully demonstrated the labeling and UV-induced covalent cross-linking of FKBP12 and its interacting proteins in vitro and in living cells. This study not only furthers our understanding of the basic reaction properties of LDT chemistry but also extends the applicability of this method to the investigation of biological processes in mammalian cells.