bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Jahn–Teller Effect in Chemistry
Authors: Ceulemans Arnout , Lijnen Erwin 
Published: July 2007

Abstract
A uniform view of electronic degeneracies, resulting from finite point group symmetries, is developed. It relates any n-fold degeneracy to the geometrical structure formed by the set of equidistant points in a space with exactly n dimensions. Jahn–Teller interactions within the degenerate manifold can simply be represented as bond stretchings of this structure. This approach thus can be qualified as the “chemical perspective” to the study of vibronic instabilities. The procedure is described for two-fold, three-fold, four-fold, and five-fold degeneracies. As a result a simple general proof of the Jahn–Teller theorem can be obtained. The electronic degeneracy is connected to the reaction graph of the stable minima on the surrounding Jahn–Teller surface. The findings are illustrated with some structural and dynamic molecular examples.
Role of Modified Nucleosides in the Translation Function of tRNAs from Extreme Thermophilic Bacteria and Animal Mitochondria
Authors: Watanabe Kimitsuna 
Published: July 2007

Abstract
This report characterizes the structure and function of four modified nucleosides first identified by myself or members of my research group in thermophilic bacteria and animal mitochondria over the past 30 years. I identified 2-thioribothymidine (s2T) (or 5-methyl-2-thiouridine (m5s2U)) in 1974 at position 54 in the T loop of tRNAs from an extreme thermophile, Thermus thermophilus, as well as related thermophiles, and a good deal of evidence has shown that it is required for thermostabilization of tRNAs, functioning at high temperatures. The functional roles and the biosynthetic pathway of s2T are outlined here. My research group has identified three novel modified nucleosides, 5-formylcytidine (f5C), N-(uridine-5-ylmethyl)taurine (τm5U), and N-(2-thiouridine-5-ylmethyl)taurine (τm5s2U), at the first anticodon position of mitochondrial (mt) tRNAs from higher animals (f5C is present in tRNAMet, τm5U in tRNALeu(UUR) and tRNATrp, and τm5s2U in tRNAGln, tRNALys, and tRNAGlu). Their chemical structures were determined and their functional roles in translation were examined. Additionally, f5C at the first anticodon position of mt tRNAMet plays a crucial role in decoding the AUA codon (decoded as isoleucine in the universal genetic code system) as methionine, which will form the second topic of this article. Defective modification of τm5U and τm5s2U at the first anticodon position in human mt tRNALeu(UUR) and tRNALys, respectively, is the result of point mutations in these tRNAs in mitochondria. It is strongly suggested that these defects are the direct cause of two mitochondrial diseases, MELAS (mitochondrial encephalomyopathies, encephalopathy, lactic acidosis, and stroke-like episodes) and MERRF (myoclonus epilepsy associated with ragged-red fibers). Their molecular mechanisms are also discussed here. These studies would serve to highlight again the importance of modified tRNA nucleosides in the structure and function of tRNAs.
Development and Industrialization of the Vapor-Phase Beckmann Rearrangement Process
Authors: Izumi Yoshitaka , Ichihashi Hiroshi , Shimazu Yasumoto , Kitamura Masaru , Sato Hiroshi 
Published: July 2007

Abstract
The development of a new catalyst effective for the vapor-phase Beckmann rearrangement of cyclohexanone oxime has made it possible to establish a commercial process for the production of ε-caprolactam without producing any ammonium sulfate. Through fundamental studies of the catalyst, it was discovered that an MFI-type zeolite composed exclusively of silica had a high selectivity and activity for the vapor-phase Beckmann rearrangement. Based on acidity measurements and on the reactivity of oximes with different sizes as well as the calculation results of the deprotonation energies of some silanols, we have suggested that the active sites are nest silanols located close to their mouth of the micro pores. By addition of methanol into the reaction system, the selectivity for ε-caprolactam was markedly improved to the levels required for industrialization. A fluidized bed reactor was used for the reaction system in order to maintain a continuous production. By combining the ammoximation process for production of cyclohexanone oxime using the TS-1 catalyst and the vapor-phase Beckmann rearrangement, a commercial plant has been operating on a 60000 tons per year scale since April 2003, without any troubles.
Monodispersed Dimerization of Isoleucine Zipper–Coiled Coil Trimer
Authors: Kashiwada Ayumi , Sakakibara Atsuko , Nakamura Yohei , Matsuda Kiyomi 
Published: July 2007

Abstract
We describe the synthesis and characterization of novel isoleucine zipper polypeptide dimers, connected with a maleimide-containing linker molecule, that can assemble into structurally defined heterotrimeric α-helical coiled coil dimers on the basis of architectural features of the polypeptide sequences. Linear- and crosslinked-isoleucine zipper polypeptide dimers were designed in this study. Circular dichroism spectroscopy, gel filtration, and HPLC analyses indicate that each polypeptide dimer can noncovalently assemble with four isoleucine zipper polypeptides and lead to heterotrimeric α-helical coiled coil dimer formation. Thus, we concluded that monodispersed dimerization of triple-stranded coiled coil was achieved for the first time. Moreover, the noncovalently assembled supramolecule may be useful as a the building-block for constructing artificial polypeptide fibrillogenesis systems.
Crystal Structures of Solid Solutions of a Symmetrical Ketone/n-Alkane Binary System
Authors: Nakasone Keiko , Nemoto Norio 
Published: July 2007

Abstract
An X-ray diffraction study on the crystal structures of binary mixtures of very pure long-chain symmetrical ketone (K39) and n-alkane (C39) with an odd carbon number of 39 is presented. When the samples were prepared with the solution-crystallization method, which form two different types of solid solutions for the molar fraction (fm) of K39 above and below fm,c=0.204. From composition and temperature dependencies of a long period (L) and two subcell lengths (as and bs) determined from (00l), (200), and (110) reflections, respectively, we show that nearly the same crystal structure as that of pure C39 is maintained for the solid solutions in regime S1 where fm&lt;fm,c, while K39 dominantly affects the crystal structures at room temperature in regime S2 where fm&gt;fm,c. When temperature was raised above the solidus line of the phase diagram in the S2 regime, recrystallization occurred to form a solid solution very rich in the K39 component in the liquid–solid solution coexisting phase before final melting of K39. The solid–solid phase transition behaviors and resulting chain packing in the S1 regime are discussed in relation to anomalous anisotropy of linear thermal expansion coefficients along two lattice directions.
Effects of Ionic Surfactants and Cyclodextrins on Hydride-Transfer Reaction of 1-Benzyl-1,4-dihydronicotinamide with Methylene Blue
Authors: Matsumoto Takeshi , Liu Yingjin , Sueishi Yoshimi , Yamamoto Shunzo 
Published: July 2007

Abstract
The kinetics of the hydride-transfer reaction between methylene blue (MB+) and 1-benzyl-1,4-dihydronictinamide (BNAH) were studied in media containing cyclodextrins (β- and γ-CD) and surfactants (sodium dodecyl sulfate (SDS), dodecyltrimethylammonium bromide, tetradecyltrimethylammonium bromide, and hexadecyltrimethylammonium bromide). Cationic surfactants decreased the apparent first-order rate constant (kobsd) above the cmc, while SDS increased kobsd just above the cmc and then decreased kobsd with increasing surfactant concentration. This behavior for cationic surfactants was typical of micellar effects due to a separation of the reactants by the micelles. BNAH associated with micelles, whereas MB+ ions were repelled from the cationic interface of the micelles. Binding of BNAH and MB+ to the same SDS micelle enhanced the reaction, but dilution of reagents within the micellar interface with the increase in [SDS] caused a decrease in kobsd. In β-CD–cationic surfactant mixtures, the results were interpreted in terms of the model which takes into account the formation of CD–BNAH, CD–MB+, and CD–surfactant complexes and the association of BNAH with micelles. The decrease in kobsd with increasing surfactant concentration observed in γ-CD–cationic surfactant mixtures can be explained by the decrease in the concentration of free γ-CD by the formation of 1:1 and 2:1 complexes of surfactant monomer with γ-CD.
The Alkylation of Biphenyl over Fourteen-Membered Ring Zeolites. The Influence of Zeolite Structure and Alkylating Agent on the Selectivity for 4,4′-Dialkylbiphenyl
Authors: Sugi Yoshihiro , Maekawa Hiroyoshi , Mulla Shafeek Abdul Rashid , Ito Akira , Naitoh Chikayo , Nakagawa Kazunori , Komura Kenichi , Kubota Yoshihiro , Kim Jong-Ho , Seo Gon 
Published: July 2007

Abstract
Alkylation, i.e. isopropylation, s-butylation, and t-butylation, of biphenyl (BP) was examined over fourteen-membered ring (14-MR) zeolites, CIT-5, UTD-1, and SSZ-53, in order to elucidate the relationships between structure of zeolites and bulkiness of alkylating agents on the shape-selective catalysis. CIT-5 zeolite (CFI) yielded 4,4′-diisopropylbiphenyl (4,4′-DIPB) in the level of 50–60% in the isopropylation in the range of 150–300 °C. 2,2′-, 2,3′-, and 2,4′-DIPB (2,x′-DIPB) isomers were obtained as the predominant DIPB isomers at lower temperatures, and the formation of 3,4′- and 3,3′-DIPB isomers increased with an increase in the temperature. However, the selectivities were in the level of 10–15% for UTD-1 (DON) and SSZ-53 (SFH) zeolites in the range of 150–350 °C. The s-butylation with 1-butene gave results similar to the isopropylation, although the selectivities for 4,4′-di-s-butylbiphenyl (4,4′-DSBB) were higher than those for 4,4′-DIPB at 250 °C: 80–85% for CFI, 40–50% for DON, and 30–40% for SFH. High selectivity for 4,4′-di-t-butylbiphenyl (4,4′-DTBB) was observed in the t-butylation at 250 °C: 95% for CFI, 90% for DON, and 80% for SFH. These differences are due to the spatial difference in their channels, and also due to bulkiness of alkylating agents, propene, 1-butene, and 2-methylpropene. The selectivity for 4,4′-dialkylbiphenyl (4,4′-DABP) was governed by the exclusion of the bulky DABP isomers at the transition state by steric restriction in the zeolite channels.
Spatial and temporal changes in non-structural carbohydrate reserves in eelgrass (Zostera marina L.) in Danish coastal waters
Authors: Vichkovitten Tritep , Holmer Marianne , Frederiksen Morten S. 
Published: July 2007

Abstract
The spatial and seasonal changes of total non-structural carbohydrate (TNC) reserves in above- and belowground tissues in eelgrass (Zostera marina) were assessed at four different sampling sites in Danish waters. The study consisted of annual field sampling, where sites differed in water depth and nutrient content in sediments. The TNC concentrations varied considerably in all tissues, and rhizomes generally represented the major storage organ. Sucrose was the main sugar contributing to TNC whilst starch represented the minor (<15%) reserves. Trehalose, which is reported in Z. marina here for the first time, due to the use of a recently developed HPLC method, was found in low concentrations (up to ∼2%) and showed a reverse seasonal variation compared to other sugars, with maximum concentrations in winter. Plants growing near depth limits (5.5 m) had significantly higher reserves, whereas no significant effect of sediment nutrient contents on the TNC concentrations was observed, reflecting the ability of Z. marina to tolerate a range of different growth conditions.
New records of benthic marine algae from the Canary Islands (eastern Atlantic Ocean): morphology, taxonomy and distribution
Authors: Afonso-Carrillo Julio , Sansón Marta , Sangil Carlos , Díaz-Villa Tania 
Published: July 2007

Abstract
Four species of marine algae are reported from the Canary Islands for the first time. Our report of the western Atlantic Gelidiella setacea (Gelidiales, Rhodophyta) is the first from the eastern Atlantic Ocean. Pseudotetraspora marina (Tetrasporales, Chlorophyta) previously known on the eastern side of the Atlantic Ocean from temperate saltmarshes only, is now reported growing in the shallow sublittoral zone, the habitat in which tropical western Atlantic populations also occur. The presence of Lomentaria chylocladiella (Rhodymeniales, Rhodophyta) represents the first report in the Atlantic Ocean of a species previously thought to be endemic to the Mediterranean Sea. The record of the widely distributed Acrochaetium hallandicum (Acrochaetiales, Rhodophyta) was not unexpected. Specimens of A. hallandicum have vegetative cells with a single lobate parietal chloroplast with a single pyrenoid, a feature that among acrochaetioid algae occurs exclusively in the genus Colaconema (Colaconematales), and consequently the species is transferred to this genus. Fertile sporophytes are described for Gelidiella setacea, a species previously known only in its vegetative condition. Cruciately to irregularly divided sporangia are regularly arranged in transverse rows in stichidia laterally formed on the axes. The species is transferred to the genus Parviphycus on the basis of the morphology of the stichidia and the distichous pattern of apical division exhibited by the axes, both exclusive features of this genus.
Determination of serum glucose by horseradish peroxidase‐catalysed imidazole chemiluminescence coupled to a micro‐flow‐injection system
Authors: Nozaki Osamu , Munesue Motonori , Kawamoto Hiroko 
Published: July 2007

AbstractThe reactivity of flow‐injection (FI)‐horseradish peroxidase (HRP)‐catalysed imidazole chemiluminescence (CL) was studied for continuous determination of hydrogen peroxide (H2O2) and serum glucose with immobilized glucose oxidase. Light emission by the HRP‐catalysed imidazole CL was obtained when immobilized HRP, alkaline imidazole (in Tricine solution, pH 9.3) and H2O2 were reacted at room temperature. The optimal pH for the CL reaction was 9.3 and the optimal concentration of imidazole was 100 µmol/L. When no imidazole was added, the light intensity of the same H2O2 specimen decreased to a level that could not be quantitatively determined. The spectrum of the light emitted by imidazole CL was in the range 400–600 nm with a peak at 500 nm. The calibration equation for determination of H2O2 was y = 9860x2 + 3830x + 11 700, where y = light intensity (RLU) and x = concentration of H2O2 (µmol/L). The detection limit of H2O2 was 5 pmol, and the reproducibility of the H2O2 assay was 2.3% of the coefficient of variation (H2O2 48 µmol/L, n = 13). The CL method was successfully applied to assay glucose after on‐line generation of H2O2 with the immobilized glucose oxidase column, resulting in good reproducibility (CV = 3.3% and 1.0% for the standard glucose and the control serum, respectively). Copyright © 2007 John Wiley & Sons, Ltd.
Influence of charged surfaces on the morphology of DNA condensed with multivalent ions
Authors: Besteman K. , van Eijk K. , Vilfan I. D. , Ziese U. , Lemay S. G. 
Published: July 2007

AbstractDNA in solution can be condensed into dense aggregates by multivalent counterions. Here we investigate the effect of a nearby surface on the morphology of DNA condensates. We show that, contrary to what has often been assumed, interactions between DNA condensates and the surface can strongly influence the observed morphology. This limits the usefulness of surface probes such as atomic force microscopy for studying the morphology of condensates in bulk solution. Surprisingly, we find that the most negatively charged surface disturbs the condensate morphology most, suggesting that the microscopic mechanism resulting in DNA condensation is also responsible for the attractive force between DNA and the surface. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 141–148, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Tryptathionine bridges in peptide synthesis
Authors: May Jonathan P. , Perrin David M. 
Published: July 2007

AbstractThe tryptathionine linkage is a crosslink formed between tryptophan and cysteine. This feature is characteristic of the bicyclic peptides: the phallotoxins and the amatoxins. These peptides both bind to protein folds of their respective targets (F‐actin and RNA pol II, respectively) with extremely high affinities. Studies on these peptides have shown that the tryptathionine crosslink is essential for this binding affinity. Tryptathionines have been investigated for many years and several syntheses exist for their formation. In this review, we report on the various methodologies employed in tryptathionine synthesis, and discuss some of the advantages and disadvantages associated with each of them. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 88: 714–724, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Population balance modeling of the conidial aggregation of Aspergillus niger
Authors: Lin P.‐J. , Grimm L.H. , Wulkow M. , Hempel D.C. , Krull R. 
Published: July 2007

AbstractNumerous biotechnological production processes are based on the submerse cultivation of filamentous fungi. Process design, however, is often hampered by the complex growth pattern of these organisms. In the morphologic development of coagulating filamentous fungi, like Aspergillus niger, conidial aggregation is the first step of filamentous morphogenesis. For a proper description of this phenomenon it is necessary to characterize conidial populations. Kinetic studies performed with an in‐line particle size analyzer suggested that two distinct aggregation steps have to be considered. The first step of conidial aggregation starts immediately after inoculation. Both the rate constants of formation and disintegration of aggregates have been determined by measuring the concentration of conidia at the beginning of the cultivation and the concentration of particles at steady state during the first hours of cultivation. In contrast to the first aggregation step, where the collision of conidia is presumed to be responsible for the process, the second aggregation step is thought to be initiated by germination of conidia. Growing hyphae provide additional surface for the attachment of non‐ germinated conidia, which leads to a strong decrease in particle concentration. The specific hyphal length growth rate and the ratio of particle concentration to the growing adhesion hyphal surface are decisive matters of the second aggregation step. Both aggregation steps can be described by population dynamics and simulated using the program package PARSIVAL (PARticle SIze eVALution) for the treatment of general particle population balances. Biotechnol. Bioeng. 2008;99: 341–350. © 2007 Wiley Periodicals, Inc.
Effect of drying on the biological activities of a red microalgal polysaccharide
Authors: Ginzberg Ariel , Korin Eli , (Malis) Arad Shoshana 
Published: July 2007

AbstractThe red microalga Porphyridium sp. produces a polysaccharide exhibiting a variety of biological activities with potential for medical and cosmetic uses. For this reason, it is important that the drying process, which is the end point of production, should not destroy the natural characteristics of the material. The objective of this study was to evaluate the effect of drying at temperatures ranging from 40 to 140°C on the bioactivities of the polysaccharide. Drying the polysaccharide at temperatures above 90°C caused a significant decline in its biological activities (antiviral and anti‐cell proliferation) and reduced elasticity, viscosity, and intrinsic viscosity relative to lyophilized polysaccharide and to the starting product. The relationship between molecular weight and intrinsic viscosity indicated that the polysaccharide takes a rigid coil conformation, which stiffens as a result of drying. FTIR analysis revealed that drying caused both significant conformational alterations in the polymer chains and changes in the interaction between the polysaccharide and the glycoprotein to which it is noncovalently associated. Differential scanning calorimetry analysis of the water adsorbed on the charged groups of the polysaccharide showed that drying at higher temperatures increased the bound water content due to dissociation of the polymer chains. Thus, it is recommended that the polysaccharide be dried in a two‐step process in which free water is removed by convection and bound freezing water is removed by lyphophilization. Biotechnol. Bioeng. 2008;99: 411–420. © 2007 Wiley Periodicals, Inc.
FnTm2, a novel brain‐specific transcript, is dynamically expressed in the song learning circuit of the zebra finch
Authors: Agate Robert J. , Hertel Moritz , Nottebohm Fernando 
Published: July 2007

AbstractZebra finch males learn their song by imitation, a process influenced by social variables. The neural pathways for acquisition and production of learned song are known, but the cellular and molecular underpinnings are not. Here we describe a novel gene named “FnTm2” (“Phantom 2”) that is predicted to encode a small protein (220 aa) with a single fibronectin type III domain and a single transmembrane domain. This gene shows great variability in its expression in song system neurons of the anterior forebrain pathway (AFP), a circuit that influences song discrimination and is necessary for normal song acquisition. AFP nuclei that express FnTm2 include the nucleus HVC (its Area X‐projecting neurons), Area X, and LMAN (core and shell). FnTm2 expression does not correlate with singing behavior like the immediate early gene ZENK. It is expressed variably during sleeping hours and is not dependent on an intact song circuit. FnTm2′s expression is sensitive to hearing, because in deafened birds its expression is substantially reduced in the core of LMAN. Furthermore, a comparison of FnTm2 expression between mice and zebra finches revealed a conserved pattern of expression in the “limbic system.” We suggest that FnTm2 may be sensitive to affective and/or attentional states and thus may provide insights on how social variables influence the production and discrimination of learned vocalizations. J. Comp. Neurol. 504:127–148, 2007. © 2007 Wiley‐Liss, Inc.
Factorization problem on the Hilbert‐Schmidt group and the Camassa‐Holm equation
Authors: Li Luen‐Chau 
Published: July 2007

AbstractIn this paper we solve the Camassa‐Holm equation for a relatively large class of initial data by using a factorization problem on the Hilbert‐Schmidt group. © 2007 Wiley Periodicals, Inc.
Experimental Investigation of Jet Stabilization in Near‐Axis Region of Plasma Reactor
Authors: Volchkov E. P. , Baldinov G. R. , Terekhov V. I. , Tkach Yu. N. 
Published: July 2007

AbstractThe paper presents the results of experimental investigations of aerodynamics and heat transfer in a vortex plasma reactor with gas jet injection along its axis. The process of mixing under quasi‐isothermal conditions (injection of slightly heated jet) and inhomogeneous conditions (injection of helium and argon) as well as with the injection along the axis of plasma jet is studied consistently. A detailed comparison of temperature fields and concentrations is presented for these conditions.The process of jet expansion is shown to be defined mainly by three factors — centrifugal mass forces, buoyancy forces and initial velocity shift in a jet at the chamber inlet. The end flows contribute considerably to the process of jet mass transfer with peripheral flow.