bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid
MS
Authors: Bateman R. H. , Langridge J. I.
Published: January 2005

Tandem mass spectrometry, or MS/MS, is the preferred technology for many applications in which mass spectrometry plays a part. Tandem mass spectrometry allows selection and isolation of specific components in the presence of complex matrices and their subsequent identification and/or quantification. Hybrid MS instruments consist of two mass analyzers in series and a means for fragmenting ions. That means is most commonly that of promoting collision‐induced decomposition (CID) by subjecting ions to energetic collisions with gas molecules. In most hybrid MS instrumentation, the processes of mass selection, fragmentation, and product ion mass analysis take place sequentially in space. In some instances, fragmentation can take place in one of the mass analyzers wherein one or other of the processes take place sequentially in time. Different combinations of mass analyzers have different characteristics that make them more or less suited for certain applications. It is possible to combine most types of mass analyzer in almost any sequence, and numerous combinations have been constructed. A brief description is provided of those hybrid instruments that are most commonly used for studies in the life sciences; namely, the triple quadrupole, the quadrupole–ion trap (Q‐Trap), the ion trap–time‐of‐flight (Trap‐TOF), the time‐of‐flight–time‐of‐flight (TOF‐TOF), the quadrupole–orthogonal time‐of‐flight (Q‐TOF), the ion trap–orthogonal time‐of‐flight (Trap‐TOF), the quadrupole‐FTMS and, the ion trap–FTMS. For each instrument type, the principle applications are discussed.
Making nanocolumns and tips
Authors: Delahunty Claire , Yates John R.
Published: January 2005

This tutorial describes the construction of fritless nanocolumns and tips from 100‐µm microcapillary tubing. Protocols are given for pulling the tips using a commercial laser puller as well as for packing a single‐phase or multidimensional column. The nanocolumns described are for use in in‐line µLC separations and are typically coupled to an ESI source.
Structural biology of protein complexes
Authors: Waksman Gabriel
Published: January 2005

Structural biology has unraveled the structure of a number of protein–protein complexes and has thus contributed to our understanding of the functions that proteins play in the context of the web of interactions to which they contribute within the cell. This brief review summarizes some of the properties of protein–protein interactions that have been characterized by structural biology work and defines the challenges ahead.
Probing protein function in cells usingCALI
Authors: Diefenbach Thomas J. , Jay Daniel G.
Published: January 2005

Chromophore‐assisted laser inactivation (CALI) is a method utilizing dye‐labeled antibodies combined with light of specific wavelengths for acute knockdown of protein function at the cellular and tissue level with high spatial and temporal resolution. In recent years, the techniques of CALI have evolved, although the goal of direct knockdown of the protein function remains the same. This article will examine the utility, applications, and derivations of CALI as a tool to probe in vitro and in vivo protein function.
Immunofluorescent labeling and fluorescent dyes
Authors: Watson Peter , Palmer Krysten J. , Stephens David J.
Published: January 2005

This article sets out to cover some of the key points to consider when processing living cells and tissues for immunofluorescence. We discuss approaches to fix and image cells following immunolabeling, including using high‐throughput screening technologies. We review the production and relative merits of different antibodies and compare different fluorophores, including recently developed reagents such as quantum dots. We also consider the use of recombinant antibody technology and the correlation of images obtained first by immunofluorescence microscopy at low resolution (e.g., confocal), and higher resolution ultrastructural analyses by electron microscopy.
Glycosylphosphatidylinositol anchors – a structural perspective
Authors: Mehlert Angela
Published: January 2005

GPI anchors are found attached to many proteins in eukaryotes. The structural characterization of a GPI is challenging owing to the complex nature of the molecule. Certain techniques that take advantage of the unique nature of certain moieties within the GPIs have been used to analyze their structures. Techniques for labeling GPIs with either a radioactive or fluorescent tracer are described, along with a recent “proteomics” style of detecting GPI‐anchored proteins from Western blots.
Classification of proteins into families
Authors: Mulder Nicola J. , Apweiler Rolf
Published: January 2005

Functional annotation of proteins is vital for a thorough understanding of genomic systems, diseases, and pathogenesis. With the genome era in full swing, thousands of new sequences from genome sequencing projects are available, but they cannot be manually annotated. Reliable methods for automatic functional classification of proteins are being developed. The most useful tools use various methods for identifying motifs or domains found in previously characterized protein families. Protein families can be classified using two main approaches: sequence clustering and protein signatures. Once members of a protein family are discovered, inference of functional annotation to all members is possible. This chapter reviews the existing methods using these approaches and the major databases in the public domain that implement the methods.
Equivalog protein families in the
TIGRFAMs
database
Authors: Selengut Jeremy D. , Haft Daniel H.
Published: January 2005

An equivalog is a family of proteins conserved in function since their last common ancestor. This term differs from the term ortholog, which is not limited to groups with conserved function but is strictly limited to speciation events (and excludes horizontal gene transfers). Hidden Markov Models (HMMs) are mathematical constructs representing multiple sequence alignments. The TIGRFAMs database includes a large number of HMMs that represent equivalog families. The great utility of these models is that a sequence scoring higher than a threshold value versus an equivalog has a very high likelihood of being a member of the family and sharing the same function. Equivalog HMMs are useful in automatic genome annotation. The information that is manually attached to a gene by an annotator is instead attached to the equivalog HMM. This is then used to transfer the information automatically to the appropriate genes. Furthermore, groups of equivalog HMMs can be linked together to create computable objects representing proteins that act together in a biological process (such as a metabolic pathway). Such compound objects can be used in metabolic reconstruction and applied to genomic sequence data even prior to annotation.
Fundamentals of protein structure and function
Authors: Bradford James R. , Siepen Jennifer A. , Westhead David R.
Published: January 2005

This chapter describes the steps involved in the formation of three‐dimensional structure from amino acid sequence. Proteins have adapted their three‐dimensional structures to carry out metabolic and regulatory processes such as enzyme catalysis, molecular transport, signaling, the immune response, and gene expression. To understand the relationship between a protein's structure and function fully, knowledge of that protein's evolutionary history and its interactions is essential. Therefore, we describe the mechanisms by which proteins have evolved. We also describe how molecular recognition drives protein interactions and the types of interaction that take place.
X
‐ray crystallography
Authors: Firbank Susan
Published: January 2005

Since the late 1950s, X‐ray crystallography has been used to determine the structure of proteins with known functions. With the dawn of proteomics, protein‐structure determination is now being carried out in order to shed light upon proteins of unknown function, with the hope that knowledge of the structure itself will allow, or at least assist in, the identification of possible protein action. This article describes the stages of protein‐structure determination by X‐ray crystallography, the basic requirements and considerations at each step, and how crystallography can be applied and is being adapted to benefit the structural‐genomics community.
Spliced alignment
Authors: Huang Xiaoqiu
Published: January 2005

We first describe a dynamic programming algorithm for computing an optimal spliced alignment of a genomic sequence and a cDNA sequence. Then, we present a fast method for dealing with a large set of genomic sequences and a set of cDNA sequences. We also describe methods used in existing spliced alignment programs. We conclude with a discussion of future developments in this area.
Protein repeats
Authors: Perez‐Iratxeta Carolina , Andrade Miguel A.
Published: January 2005

More than 10% of all protein sequences contain a protein domain composed of units of similar structure, often of similar sequence, therefore arising by a process of duplication from an ancestral gene fragment. Structural and evolutionary constraints limit the length and structure of these repeats to a small number of categories. These domains composed of repeats are used mainly for protein binding and are more frequent in metazoan organisms than elsewhere. Low constraints in sequence allow high rates of sequence divergence between repeats, making their detection by sequence similarity difficult.
Sequence complexity of proteins and its significance in annotation
Authors: Eisenhaber Birgit , Eisenhaber Frank
Published: January 2005

If protein sequences are viewed as a string of letters representing amino acid types, the complexity of the text message can be evaluated by analyzing residue composition and repetitive occurrence of short motifs and also by applying entropy‐ or information‐like measures. Low complexity segments represent more than a quarter of the total length of proteins in databases and their relative amount tends to increase with the sequencing of eukaryote genomes. In contrast, only about 0.5% of the residues in structures of known globular domains are located in usually short stretches with strong compositional bias. Low complexity segments with bias toward hydrophobic residues or with a repetitive hydrophobic pattern are typically involved in fibrillar or membrane‐embedded protein structures. In contrast, the structure forming potential and the molecular function of low complexity regions with primarily polar residues remains insufficiently understood, although, for some of them, their mutational variation has already been implicated in pathological processes.
The
P
rotein
D
ata
B
ank (
PDB
) and the
W
orldwide
PDB
http://www.wwpdb.org
Authors: Berman Helen , Nakamura Haruki , Henrick Kim
Published: January 2005

The Protein Data Bank is the primary source of information on the 3D structure of biological macromolecules. The PDB is a rich source of structural information that holds significant promise for the pharmaceutical and biotechnology industries in the search for new drugs, and the efforts to understand the mechanism of disease. The PDB is managed by the wwPDB (
http://www.wwpdb.org
), and the wwPDB members enable science worldwide by providing resources to improve our understanding of structure‐function relationships in biological systems.
TAMBIS
: transparent access to multiple bioinformatics services
Authors: Stevens Robert , Paton Norman W. , Bechhofer Sean , Ng Gary , Peim Martin , Baker Patricia , Goble Carole , Brass Andy
Published: January 2005

Transparent Access to Multiple Bioinformatics Information Sources (TAMBIS) addresses the perennial problem of heterogeneity and distribution of bioinformatics resources in performing bioinformatics analyses. Asking questions of these resources usually requires multiple resources to be used and data transferred between those resources. A biologist using these resources needs much knowledge of which resources to use, where they are to be found, in which order they should be used, and how to overcome the heterogeneity between those resources. TAMBIS seeks to make this knowledge burden transparent by cap turing knowledge about molecular biology and bioinformatics tasks in an ontology. The TAMBIS ontology acts as a global schema over diverse resources and drives a query formulation interface offering a common language over those resources. High‐level, conceptual, source‐independent queries are rewritten to concrete query plans. As a result of its transparency, TAMBIS frees a biologist from needing informatics knowledge to concentrate upon the biological question.
Automatic concept identification in biomedical literature
Authors: Majoros William H.
Published: January 2005

While the potential benefits of automatically extracting useful knowledge from biomedical literature are seemingly many and great, nearly all of the techniques that have been considered for doing this rely on a central, nontrivial problem: that of unambiguously identifying the named entities that occur in a particular text. This problem has two parts: (1) identifying the precise boundaries of phrases in a text which refer to biomedical entities and (2) resolving those entity names to known concepts in a knowledge base such as an ontology. These two tasks represent the
syntactic
and
semantic
aspects of the problem of concept identification, and both are described in this article along with the currently known methods and their limitations.
Detecting protein homology usingNCBItools
Authors: Matten Wayne T. , McGinnis Scott D.
Published: January 2005

The National Center for Biotechnology Information (NCBI) processes more than 100 000 sequence similarity searches a day using the computer program, BLAST®– Basic Local Alignment Search Tool. A common use of BLAST is to locate sequences in the NCBI databases that are related to the query sequence. Various “flavors” of BLAST can also detect known conserved domains in the query sequence, find related sequences that contain a supplied pattern, and perform sensitive searches using automated construction of position‐specific scoring matrices. The results of precomputed BLAST searches are available for nearly all protein sequences housed at the NCBI. Similarly, solved protein structures are compared to identify structurally related proteins using the Vector Alignment Search Tool (VAST).
HiddenMarkov models and neural networks
Authors: Kremer Stefan C. , Baldi Pierre
Published: January 2005

In this contribution, we discuss the application of machine learning methods, particularly hidden Markov models and artificial neural networks, to bioinformatics tasks. We begin with a brief summary of the two paradigms as computational and learning systems and describe the nature of the problems to which these two approaches can be applied. Then, we give some examples of their application to bioinformatics, briefly discuss the strengths and weaknesses of these two approaches, and provide some avenues for further reading.
The
MATLAB
bioinformatics toolbox
Authors: Henson Robert , Cetto Lucio
Published: January 2005

MATLAB
®
(The MathWorks, Inc.) is a general‐purpose technical computing language and development environment that is widely used in scientific and engineering applications. The Bioinformatics Toolbox for MATLAB is a library of functions that adds bioinformatics capabilities to the MATLAB environment. This article describes the functions in the Bioinformatics Toolbox and gives an example of how these can be used for phylogenetic analysis of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV) sequence data.
Inside Front Cover: An Ultraviolet Organic Thin‐Film Solid‐State Laser for Biomarker Applications (Adv. Mater. 1/2005)
Authors: Schneider D. , Rabe T. , Riedl T. , Dobbertin T. , Kröger M. , Becker E. , Johannes H.‐H. , Kowalsky W. , Weimann T. , Wang J. , Hinze P. , Gerhard A. , Stössel P. , Vestweber H.
Published: January 2005

Thin‐film organic solid‐state lasers operating in the ultraviolet wavelength region are fabricated using a novel spiro‐linked material as active organic layer in an optically pumped distributed feedback (DFB) structure in work reported by Riedl and co‐workers on p. 31. The laser wavelength is tunable between 377.7 nm and 395 nm, the shortest laser wavelength reported so far for thin‐film organic solid‐state lasers. The lasers' suitability for spectroscopic applications was tested by use as an excitation source for solutions containing the common fluorescent dyes Coumarin 6, Coumarin 152, and Rhodamine 6G.
Transition to pulsing flow in trickle‐bed reactors studied using MRI
Authors: Sederman A. J. , Gladden L. F.
Published: January 2005

Ultrafast magnetic resonance imaging (MRI) is used to provide two‐dimensional (2‐D) images of gas‐liquid distribution within trickle‐bed reactors with data acquisition times of 20 and 40 ms. Gas‐water, cocurrent downflow through a fixed bed of cylindrical porous pellets of length and dia. 3 mm, packed within a 43 mm internal dia. column, was studied in both the trickle‐ and pulsing‐flow regimes. Superficial gas velocities in the range 50–345 mm s−1 (0.06–0.42 kg m−2 s−1), and superficial liquid velocities in the range 0.4–13.3 mm s−1 (0.4–13.3 kg m−2 s−1) were used. MRI is used to investigate the stability of the gas‐liquid distribution in the trickle‐ and pulsing‐flow regimes. At the onset of the transition to pulsing flow, local pulsing, at the length‐scale of the size of the packing elements is observed within the bed. Increasing liquid velocity causes an increase in the number of these local pulses until a velocity is reached at which the system transforms to the rapidly‐changing gas‐liquid distribution typical of pulsing flow. © 2005 American Institute of Chemical Engineers AIChE J, 51: 615–621, 2005
Reflux–recycle–reactor for high yield and selectivity in TAME and TAEE production
Authors: Boz Nezahat , Dogu Timur
Published: January 2005

The batch reflux–recycle–reactor (RRR) proposed here was shown to give high product yields and selectivities in the production of tert‐ethers. Because the vapor pressures of product ethers are lower than those of the reactants, vapor‐phase reactor inlet stream is always rich in reactants in this batch RRR. A first‐order reversible reaction rate model was shown to give good prediction of experimental results. The apparent activation energy of the rate constant was evaluated as 24.8 kJ mol−1. This low value of activation energy for vapor‐phase synthesis of tert‐amyl methyl ether (TAME) was concluded to be primarily attributed to the significance of transport resistances in the macropores of Amberlyst‐15 and also through the thin liquid film covering catalyst particles. In the case of TAME production fractional conversion values reaching 0.91 were obtained at 82°C with almost 100% selectivity. Comparison of the results obtained for TAME and tert‐amyl ethyl ether (TAEE) synthesis showed that reactivity of methanol was much higher than that of ethanol in the etherification reaction of isoamylene, over Amberlyst‐15. © 2005 American Institute of Chemical Engineers AIChE J, 51:631–640, 2005
Microporous membrane blood oxygenators
Authors: Wickramasinghe S. R. , Han B. , Garcia J. D. , Specht R.
Published: January 2005

Extracorporeal blood oxygenators are used to oxygenate blood during open‐heart surgery. Hydrophobic microporous flat‐sheet or hollow‐fiber membranes are used to separate blood and gas phases. Oxygen diffuses from the gas phase through the gas‐filled membrane pores into the blood. Mass‐transfer and friction‐factor correlations have been developed for flat‐sheet and hollow‐fiber blood oxygenators. Generalized Graetz, Reynolds, and Schmidt numbers are used in these correlations to account for the shear‐thinning behavior of blood. Because oxygen not only dissolves in plasma but also binds to hemoglobin, a mass‐transfer enhancement factor based on film theory has been developed to account for oxygen binding to hemoglobin. Experimental results for oxygen transfer to bovine blood and both non‐Newtonian and Newtonian blood analogue fluids indicate that the correlations developed may be used to predict the performance of a blood oxygenator based on results for an experimentally simple system such as the oxygenation of deionized water. © 2005 American Institute of Chemical Engineers AIChE J, 51: 656–670, 2005
Electrochemical self‐assembly of porous alumina templates
Authors: Sadasivan V. , Richter C. P. , Menon L. , Williams P. F.
Published: January 2005

Porous alumina templates are fabricated by anodization of Al in an acid. The characteristics of the template, such as the pore diameter, interpore separation, and the periodicity of the porous structure depend on the conditions of anodization and the acid that is used as electrolyte. The variation of pore diameter and interpore separation as a function of anodization parameters are described. The use of porous alumina templates as masks to assemble nanoarrays is an important application and the deposition of Au nanodots on a surface of silicon is discussed. © 2005 American Institute of Chemical Engineers AIChE J, 51: 649–655, 2005
Interrogation of a precipitation reaction by electrical resistance tomography (ERT)
Authors: Stanley S. J. , Mann R. , Primrose K.
Published: January 2005

Electrical resistance tomography (ERT) provides a noninvasive and nonintrusive technique for the full 3‐D interrogation of a typical stirred vessel reactor up to a spatial discrimination of approximately 2,500 derived data points. Some recent ERT results are presented for a newly refurbished 8 ring 16‐sensor 2.3 m3 pilot scale vessel, detecting the conductivity changes throughout the whole volume of the vessel during the semi‐batch precipitation of barium sulfate. Fast timewise acquisition at video frame rates provides an augmented‐reality visualization of the precipitation process. Time evolving images created by solid‐body iso‐surfaces, which use color to denote conductivity, are presented during the proceeding reaction. These images provide a 5‐D representation of the conductivity fields within the stirred vessel reactor. The conductivity (or pixel) distributions during the precipitation process provide a real‐time measurement of the homogeneity within the vessel. The timewise conductivity profiles, over the whole of the vessel during the precipitation, indicate three very distinctive regions reflecting the complex reaction kinetics. The ERT system also highlights the very different conductivity profiles during precipitation when the stirred vessel is operated without agitation. This application is believed to be the first example of ERT applied to a precipitation process. ERT offers new possibilities for control action linked to spatio‐temporal distributions of phases and components for industrial applications. © 2005 American Institute of Chemical Engineers AIChE J, 51: 607–614, 2005
Reaction kinetics of polybutylene terephthalate polycondensation reaction
Authors: Darda P. J. , Hogendoorn J. A. , Versteeg G. F. , Souren F.
Published: January 2005

The kinetics of the forward polycondensation reaction of polybutylene terephthalate (PBT) has been investigated using thermogravimetric analysis (TGA). PBT ‐ prepolymer with an initial degree of polymerization of 5.5 was used as starting material. The PBT prepolymer was prepared from dimethyl terephthalate (DMT), and 1,4 ‐ butanediol with 470 ppm wt (with respect to DMT) of tetrabutoxytitanate as catalyst. The process conditions in the TGA were such that the weight loss curves obtained from the TGA could be correlated uniquely and directly to the forward polycondensation reaction kinetics due to the absence of (1) mass transfer limitations in the removal of 1,4 butanediol from the melt, and (2) degradation reactions. It is shown that in the temperature range of 230–270°C, the forward polycondensation reaction can be expressed using second‐order kinetics in terms of the hydroxyl end group concentration of the PBT polymer. © 2005 American Institute of Chemical Engineers AIChE J, 51: 622–630, 2005
Human brain derived neurotrophic factor (BDNF) genes, splicing patterns, and assessments of associations with substance abuse and Parkinson's Disease
Authors: Liu Qing‐Rong , Walther Donna , Drgon Tomas , Polesskaya Oxana , Lesnick Timothy G. , Strain Kari J. , de Andrade Mariza , Bower James H. , Maraganore Demetrius M. , Uhl George R.
Published: January 2005

Potential roles for variants in the human BDNF gene in human brain disorders are supported by findings that include: (a) influences that this trophic factor can exert on important neurons, brain regions, and neurotransmitter systems, (b) changes in BDNF expression that follow altered neuronal activity and drug treatments, and (c) linkages or associations between genetic markers in or near BDNF and human traits and disorders that include depression, schizophrenia, addictions, and Parkinson's disease. We now report assembly of more than 70 kb of BDNF genomic sequence, delineation of 7 noncoding and 1 coding human BDNF exons, elucidation of BDNF transcripts that are initiated at several alternative promoters, identification of BDNF mRNA splicing patterns, elucidation of novel sequences that could contribute to activity‐dependent BDNF mRNA transcription, targeting and/or translation, elucidation of tissue‐specific and brain‐region‐specific use of the alternative human BDNF promoters and splicing patterns, identification of single nucleotide polymorphism (SNP), and simple sequence length polymorphism (SSLP) BDNF genomic variants and identification of patterns of restricted haplotype diversity at the BDNF locus. We also identified type 2 BDNF‐locus transcripts that are coded by a novel gene that is overlapped with type 1 BDNF gene and transcribed in reverse orientation with several alternative splicing isoforms. Association studies of BDNF variants reveal no associations with Parkinson's disease. Comparisons between substance abusers and controls reveal modest associations. These findings increase interest in this diverse human gene. Published 2005 Wiley‐Liss, Inc.
Dithiolproteine als Hüter des intrazellulären Redoxmilieus bei Parasiten: alte und neue Wirkstoff‐Targets bei Trypanosomiasis und Malaria
Authors: Krauth‐Siegel R. Luise , Bauer Holger , Schirmer R. Heiner
Published: January 2005

Parasitäre Erkrankungen wie Schlafkrankheit, Chagas‐Krankheit oder Malaria gehören zu den Hauptursachen weltweiter Armut. Dringend benötigt werden antiparasitäre Medikamente, die nicht nur wirksam, sondern für die Betroffenen auch erschwinglich und verfügbar sind. Ein Ansatz bei der Suche nach neuen Wirkstoffen (und der Wiederentdeckung alter) basiert auf dem Einsatz von Enzyminhibitoren, die die antioxidativen Systeme in den Pathogenen blockieren. Für Parasiten sind die antioxidativen Netzwerke essentiell, da sie vom menschlichen Wirt durch starke Oxidantien wie Peroxynitrit, Hypochlorit und Wasserstoffperoxid bekämpft werden. Das pathogeneigene Schutzsystem besteht aus etwa zwanzig Thiol‐ und Dithiolproteinen, die das intrazelluläre Redoxmilieu bei einem Potential von etwa −250 mV puffern. Im Zentrum dieses Redoxgefüges steht bei Trypanosomen und Leishmanien das parasitenspezifische Dithiol Trypanothion (N1,N8‐Bis(glutathionyl)spermidin). Malariaparasiten hingegen besitzen ein konservativeres System, das auf Glutathion und Thioredoxin basiert. Inhibitoren von antioxidativen Enzymen wie der Trypanothionreduktase sind per se parasitizid, darüber hinaus können sie aber auch die Entwicklung von Resistenz gegen andere antiparasitäre Wirkstoffe verzögern.
Titelbild: Bifunktionale Organokatalysatoren auf Harnstoff‐Basis für die effiziente dynamische kinetische Racemattrennung von Azlactonen (Angew. Chem. 5/2005)
Authors: Berkessel Albrecht , Cleemann Felix , Mukherjee Santanu , Müller Thomas N. , Lex Johann
Published: January 2005

Es war ein langer Weg von Wöhlers Harnstoff‐Synthese aus Ammoniumcyanat 1828 zu den heute in der asymmetrischen Organokatalyse eingesetzten chiralen Harnstoffderivaten. A. Berkessel et al. berichten in der Zuschrift auf S. 817 ff. über einen bifunktionalen Organokatalysator auf Harnstoffbasis für die hoch enantioselektive dynamische kinetische Racemattrennung von Azlactonen. Das Titelbild zeigt das wasserstoffverbrückte supramolekulare Aggregat aus dem Katalysator und dem Azlacton‐Substrat (Graphik: K. Etzenbach‐Effers).
Cover Picture: Highly Efficient Dynamic Kinetic Resolution of Azlactones by Urea‐Based Bifunctional Organocatalysts (Angew. Chem. Int. Ed. 5/2005)
Authors: Berkessel Albrecht , Cleemann Felix , Mukherjee Santanu , Müller Thomas N. , Lex Johann
Published: January 2005

Ureas have come a long way from Wöhler's preparation of urea from ammonium cyanate in 1828 to the chiral ureas that play an important role in asymmetric organocatalysis today. In their Communication on page 807 ff. Berkessel et al. report the use of bifunctional urea‐based organocatalysts for the highly enantioselective dynamic kinetic resolution of azlactones. The cover picture shows the hydrogen‐bonded supramolecular aggregate formed from the urea catalyst and an azlactone substrate (graphic: K. Etzenbach‐Effers).
Crystal structure of cyclic (APGVGV)2, an analog of elastin, and a suggested mechanism for elongation/contraction of the molecule
Authors: Karle Isabella L. , Urry Dan W.
Published: January 2005

Tropoelastin is a complex polymeric protein composed primarily of repeating segments of Val‐Pro‐Gly‐Gly, Val‐Pro‐Gly‐Val‐Gly, and Ala‐Pro‐Gly‐Val‐Gly‐Val that occurs in connective tissue and arteries. It has rubber‐like extensible properties. A synthetic cyclic dodecapeptide, with a double repeat of the hexapeptide sequence, has been shown to undergo a reversible inverse temperature transition; that is, crystals grow at 60°C and dissolve in the mother liquor upon cooling. An x‐ray crystal structure analysis established that the cyclic backbone formed an elongated loop with a Pro‐Gly, type II beta turn at both ends. Six internal cross strand NH···OC hydrogen bonds form between six NH donors and four OC acceptors where two of the carbonyl O atoms are bifurcated acceptors. As a result, the molecule is pulled up into a corrugated profile. The corrugated loops form extended β‐sheets by additional intermolecular hydrogen bonds. An analysis of the dome region in a corrugated sheet suggests a reversible mechanism for extending and contracting the length of the whole molecule, akin to the motion of opening and closing an umbrella, caused by the motion of a water molecule with its associated hydrogen bonds acting as spokes. Crystal parameters: C44H72N12O12˙3H2O, sp. gr. P212121, a = 9.212 Å, b = 19.055 Å, c = 32.247 Å, d = 1.157 g/cm3. © 2005 Wiley Periodicals, Inc. Biopolymers, 2005
Receptor fragment approach to the binding between CCK8 peptide and cholecystokinin receptors: A fluorescence study on type B receptor fragment CCKB‐R (352–379)
Authors: De Luca Stefania , Sanseverino Marina , Zocchi Ivana , Pedone Carlo , Morelli Giancarlo , Ragone Raffaele
Published: January 2005

Fluorescence titrations in a membrane mimetic solvent system allowed us to estimate that the dissociation constant of the bimolecular complex between CCK8 peptide and cholecystokinin type B receptor fragment CCKB‐R (352–379) is in the micromolar range. When considered in the context of the full receptor/ligand model, these experiments demonstrate that the receptor fragment chosen on the basis of previous structural studies represents a reliable model system to monitor the ability of CCK8 or CCK8 analogs to bind the cholecystokinin receptor. Together with previous studies, this confirms that the receptor fragment approach adopted to define the binding mode of the CCK8 fragment of cholecystokinin with its two receptors, CCKA and CCKB, can be used to characterize the binding from the equilibrium standpoint. In this context, fluorescence spectroscopy proves to be the favored technique to measure dissociation constants in the nanomolar to micromolar range. © 2005 Wiley Periodicals, Inc. Biopolymers, 2005
Helix–helix interconversion rates of short 13C‐labeled helical peptides as measured by dynamic NMR spectroscopy
Authors: Kubasik Matthew , Kotz James , Szabo Christopher , Furlong Theresa , Stace Justin
Published: January 2005

The rates at which a peptide hexamer and a peptide octamer interconvert between left‐ and right‐handed helical forms in CD2Cl2 solution have been characterized by 13C dynamic NMR (DNMR) spectroscopy. The peptide esters studied are Fmoc–(Aib)n–OtBu (n = 6 and 8), where Fmoc is 9‐fluorenylmethyoxycarbonyl and Aib is the strongly helix‐forming residue α‐aminoisobutyric acid. Because the Aib residue is itself achiral, homooligomers of this residue form a 50/50 mixture of enantiomeric 310‐helices in solution. It has been demonstrated (R.‐P. Hummel, C. Toniolo, and G. Jung, Angewandte Chemie International Edition, 1987, Vol. 26, pp. 1150–1152) that oligomers of Aib interconvert on the millisecond timescale. We have performed lineshape analysis of 13C‐NMR spectra collected for our peptides enriched with 13C at a single residue. Rate constants for the octamer range from 6 s−1 at 196 K to about 56,500 s−1 at 320 K. At all temperatures, the hexamer interconverts about three times faster than the octamer. Eyring plots of the data reveal experimentally indistinguishable ΔH‡ values for the hexamer and octamer of 37.8 ± 0.6 and 37.6 ± 0.4 kJ mol−1 respectively. The difference in the rates of interconversion is dictated by entropic factors. The hexamer and octamer exhibit negative ΔS‡ values of −29.0−1 ± 2.5 and −37.3 ± 1.7 J K−1 mol−1, respectively. A mechanism for the helix–helix interconversion is proposed. and calculated ΔG‡ values are compared to the estimate for a decamer undergoing a helix–helix interconversion. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 87–95, 2005
Differential susceptibility of C2C12 myoblasts and myotubes to group II phospholipase A2 myotoxins from crotalid snake venoms
Authors: Angulo Yamileth , Lomonte Bruno
Published: January 2005

Group II phospholipase A2 (PLA2) myotoxins isolated from Viperidae/Crotalidae snake venoms induce a rapid cytolytic effect upon diverse cell types in vitro. Previous studies suggested that this effect could be more pronounced on skeletal muscle myotubes than on other cell types, including undifferentiated myoblasts. This study utilized the murine skeletal muscle C2C12 cell line to investigate whether differentiated myotubes are more susceptible than myoblasts, and if this characteristic is specific for the group II myotoxic PLA2s. The release of lactic dehydrogenase was quantified as a measure of cytolysis, 3 h after cell exposure to different group II PLA2s purified from Bothrops asper, Atropoides nummifer, Cerrophidion godmani, and Bothriechis schlegelii venoms. In addition, susceptibility to lysis induced by synthetic melittin and group III PLA2 from bee (Apis mellifera) venom, as well as by anionic, cationic, and neutral detergents, was comparatively evaluated on the two cultures. Myotubes were significantly more susceptible to group II PLA2 myotoxins, but not to the other agents tested, under the same conditions. Moreover, the increased susceptibility of myotubes over myoblasts was also demonstrated with two cytolytic synthetic peptides, derived from the C‐terminal region of Lys49 PLA2 myotoxins, that reproduce the action of their parent proteins. These results indicate that fusion and differentiation of myoblasts into myotubes induce changes that render these cells more susceptible to the toxic mechanism of group II PLA2 myotoxins, but not to general perturbations of membrane homeostasis. Such changes are likely to involve myotoxin acceptor site(s), which remain(s) to be identified. Copyright © 2005 John Wiley & Sons, Ltd.
Analysis of video images from a gas–liquid transfer experiment: a comparison of PCA and PARAFAC for multivariate image analysis
Authors: Gurden Stephen P. , Lage Euler M. , de Faria Cristiano G. , Joekes Inés , Ferreira Márcia M. C.
Published: January 2005

The use of chemical imaging is a developing area which has potential benefits for chemical systems where spatial distribution is important. Examples include processes in which homogeneity is critical, such as polymerizations, pharmaceutical powder blending and surface catalysis, and dynamic processes such as the study of diffusion rates or the transport of environmental pollutants. Whilst single images can be used to determine chemical distribution patterns at a given point in time, dynamic processes can be studied using a sequence of images measured at regular time intervals, i.e. a movie. Multivariate modeling of image data can help to provide insight into the important chemical factors present. However, many issues of how best to apply these models remain unclear, especially when the data arrays involved have four or five different dimensions (height, width, wavelength, time, experiment number, etc.). In this paper we describe the analysis of video images recorded during an experiment to investigate the uptake of CO2 across a free air–water interface. The use of PCA and PARAFAC for the analysis of both single images and movies is described and some differences and similarities are highlighted. Some other image transformation techniques, such as chemical mapping and histograms, are found to be useful both for pretreatment of the raw data and for dimensionality reduction of the data arrays prior to further modeling. Copyright © 2003 John Wiley & Sons, Ltd.
From Discrete Particles to Spherical Aggregates: A Simple Approach to the Self‐Assembly of Au Colloids
Authors: Zhong Ziyi , Subramanian Alamelu Suriya , Highfield James , Carpenter Keith , Gedanken Aharon
Published: January 2005

Here we demonstrate a simple, template‐free approach to the formation of spherical gold aggregates through the reduction of HAuCl4 by NaBH4, in the presence of cysteine (Cys) as a capping agent. The resulting aggregates are quite stable in solution. The pH of the solution and the molar ratio of Au:Cys are two key empirical factors in the formation of such highly ordered aggregates. At slightly alkaline pH (7–10) and with Au:Cys ratios ranging from 1:0.5 to 1:2, spherical Au aggregates of 30–80 nm are formed. At lower Cys ratios (Au:Cys≥1:0.5) very loosely linked aggregates are formed; however, at very high Cys ratios (Au:Cys≤1:3), highly dispersed Au particles of 2–4 nm are obtained, which are virtually indistinguishable from the original colloidal form. Aggregate size is influenced markedly by component concentration; a 3‐fold increase in standard levels resulted in Au spherical aggregates of a larger size, 200–500 nm. In addition, we used a combination of Cys and lysine (Lys) as a capping agent/cross‐linker and found that the morphology of the Au colloid aggregates can be easily manipulated from a linear to a spherical form by adjusting the proportions of Cys and Lys in the capping agent/cross‐linker mixture. The introduction of mercapto (SH)‐containing organic acids reduced the cross‐linking ability of Cys, especially in the case of long‐chain acids. Complete disruption of the spherical aggregates highlights the importance of Cys per se. An explanation of this ordered self‐assembly process is proposed, in the context of the known surface chemistry of Au colloids.
The Rich Stereochemistry of Eight‐Vertex Polyhedra: A Continuous Shape Measures Study
Authors: Casanova David , Llunell Miquel , Alemany Pere , Alvarez Santiago
Published: January 2005

A stereochemical study of polyhedral eight‐vertex structures is presented, based on continuous shape measures (CShM). Reference polyhedra, shape maps, and minimal‐distortion interconversion paths are presented for eight‐vertex polyhedral and polygonal structures within the CShM framework. The application of these stereochemical tools is analyzed for several families of experimental structures: 1) coordination polyhedra of molecular transition‐metal coordination compounds, classified by electron configuration and ligands; 2) edge‐bonded polyhedra, including cubane structures, realgar, and metal clusters; 3) octanuclear transition‐metal supramolecular architectures; and 4) coordination polyhedra in extended structures in inorganic solids. Structural classification is shown to be greatly facilitated by these tools, and the detection of less common structures, such as the gyrobifastigium, is straightforward.
7Li, 31P, and 1H Pulsed Gradient Spin‐Echo (PGSE) Diffusion NMR Spectroscopy and Ion Pairing: On the Temperature Dependence of the Ion Pairing in Li(CPh3), Fluorenyllithium, and Li[N(SiMe3)2] amongst Other Salts
Authors: Fernández Ignacio , Martínez‐Viviente Eloísa , Breher Frank , Pregosin Paul S.
Published: January 2005

7Li, 31P, and 1H variable‐temperature pulsed gradient spin‐echo (PGSE) diffusion methods have been used to study ion pairing and aggregation states for a range of lithium salts such as lithium halides, lithium carbanions, and a lithium amide in THF solutions. For trityllithium (2) and fluorenyllithium (9), it is shown that ion pairing is favored at 299 K but the ions are well separated at 155 K. For 2‐lithio‐1,3‐dithiane (13) and lithium hexamethyldisilazane (LiHMDS 16), low‐temperature data show that the ions remain together. For the dithio anion 13, a mononuclear species has been established, whereas for the lithium amide 16, the PGSE results allow two different aggregation states to be readily recognized. For the lithium halides LiX (X = Br, Cl, I) in THF, the 7Li PGSE data show that all three salts can be described as well‐separated ions at ambient temperature. The solid state structure of trityllithium (2) is described and reveals a solvent‐separated ion pair formed by a [Li(thf)4]+ ion and a bare triphenylmethide anion.
Crystal Structure and Magnetism of the Uranium—Nickel Intermetallic Compounds: U3Ni6Si2 and U3Ni6Ge2.
Authors: Perricone A. , Noel H.
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
New Ternary Barium Ruthenates: 10H‐Type BaRuO3 and Ba2Ru7O18.
Authors: Ogawa Toshiyuki , Sato Hirohiko
Published: January 2005

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Crystal Structures of Ca4Ir8P7 and Ca4Ir8As7 and the Relationship to the ThCr2Si2 Type Structure.
Authors: Loehken Anke , Mewis Albrecht
Published: January 2005

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New Ternary Iodides of Lanthanum and Cerium, AIIMI4 (A: Sr, Ba, Nd, Sm, Eu; M: La, Ce).
Authors: Gerlitzki Niels , Hammerich Stefanie , Meyer Gerd
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
High‐Pressure Synthesis and Crystal Structure of the Structurally New Orthorhombic Rare‐Earth meta‐Oxoborates γ‐Ln(BO2)3 (Ln: La—Nd).
Authors: Emme Holger , Despotopoulou Christina , Huppertz Hubert
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
The Subchloride Bi16PdCl22: Pd@Bi104+ Polycations Inside a Framework of Chloro‐Bismuthate(III) Anions.
Authors: Dubenskyy Vitaly , Ruck Michael
Published: January 2005

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New Arsenides with As‐‐Chains and ‐Rings: BaAs2 and AIBa2As5 (AI: K, Rb).
Authors: Emmerling Franziska , Petri Denis , Roehr Caroline
Published: January 2005

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Fluoromanganate(III) Anions with New Tetrameric and Chain Structures in (pipzH2)3 [Mn4F18(H2O)]×(H2O) and (pipzH2)4[Mn2F9]2 [MnF4(H2O)2] [MnF4(HF)2].
Authors: Stief Ronald , Massa Werner
Published: January 2005

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The Cube‐Shaped Main Group Element Clusters (Bi4S4)4+ and (Bi4Se4)4+ — Synthesis from Chloroaluminate Melts, Crystal Structures and Vibrational Spectra.
Authors: Beck Johannes , Schlueter Stefan , Zotov Nicolay
Published: January 2005

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Ion‐Conducting Sodium Nickel Borate, Na2Ni2B12O21, with an Open Channel Structure.
Authors: Pompetzki M. , Albert B.
Published: January 2005

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[Me4N]5 [WOS3(CuCl)3Cl]Cl2 — A Cluster Compound with Alternating Anion Packing.
Authors: Dilshad R. , Boller H. , Klepp K. O.
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
Carboamination: Additions of Imine C=N Bonds Across Alkynes Catalyzed by Imidozirconium Complexes.
Authors: Ruck Rebecca T. , Zuckerman Rebecca L. , Krska Shane W. , Bergman Robert G.
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
Highly Efficient Double‐Activation Catalysts for the Synthesis of Ketone Cyanohydrins.
Authors: Chen Fu‐Xue , Liu Xiaohua , Qin Bo , Zhou Hui , Feng Xiaoming , Zhang Guolin
Published: January 2005

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Indolizines, Triazolo[4,3‐a]pyridines, Benzimidazo[1,2‐d]oxadiazoles, and Pyrazolo[1,5‐c]triazoles via Nitrogen and Sulfur Ylides.
Authors: Dawood Kamal M.
Published: January 2005

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Cyclization of 4‐Hydroxy‐3‐hydroxyalkylcarbostyrils under Mitsunobu Conditions.
Authors: Coppola Gary M.
Published: January 2005

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A Novel Atom‐Transfer Cyclization Catalyzed by Indium Metal in Halogenated Solvents.
Authors: Bhatti Nadia H. , Salter Matthew M.
Published: January 2005

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2‐Arylhydrazono‐3‐oxopropanals in Heterocyclic Synthesis: Synthesis of Arylazopyrazole, Arylazoisoxazole and Dialkylpyridazine‐5,6‐dicarboxylate Derivatives. New One‐Step Synthesis of Arylazopyrimidines.
Authors: Al‐Shiekh Mariam A. , El‐Din Abdellatif M. Salah , Hafez Ebtisam A. , Elnagdi Mohamed H.
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.
Preparation of New N‐Heterocyclic Carbene Metal—Alkyne Complexes and Application to a Stereocontrolled Pauson—Khand Reaction.
Authors: Poulton Andrew M. , Christie Steven D. R. , Fryatt Ross , Dale Sophie H. , Elsegood Mark R. J. , Andrews David M.
Published: January 2005

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RuCl3 Catalyzed Facile Conversion of Arylalkyl Ketoximes to Amides.
Authors: De Surya Kanta
Published: January 2005

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ReBr(CO)5‐Catalyzed Knoevenagel Condensation.
Authors: Zuo Wei‐Xiong , Hua Ruimao , Qiu Xianqing
Published: January 2005

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Selective Tolyl Carbon Alkylation Mediated by Imidazoline‐Directed Lithiation.
Authors: Calderwood Emily F. , Forsyth Nancy E. , Gould Alexandra E.
Published: January 2005

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Lithiation Reactions Catalyzed by Linear and Cross‐Linked Arene‐Based Polymers. Generation of Functionalized Organolithium Compounds.
Authors: Candela P. , Gomez C. , Yus M.
Published: January 2005

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4‐(Nitro)‐diphenylammonium Triflate(NDPAT) Catalyzed Esterification of Carboxylic Acids with Alcohols.
Authors: Liu Xuan‐Gan , Hu Wei‐Xiao
Published: January 2005

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Synthesis of Esters in the Presence of Chlorosilanes.
Authors: Kozhukhova V. V. , Kalyuzhnaya S. A. , Yatluk Yu. G. , Suvorov A. L.
Published: January 2005

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Room Temperature Preparation of Trifluoroethenylzinc Reagent by Metalation of the Readily Available Halocarbon HFC‐134a and an Efficient, Economically Viable Synthesis of 1,2,2‐Trifluorostyrenes.
Authors: Raghavanpillai Anilkumar , Burton Donald J.
Published: January 2005

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Reactivity of the R‐Phenol—Potassium Carbonate System in the Aromatic Nucleophilic Substitution of the Nitro Group.
Authors: Plakhtinskii V. V. , Abramov I. G. , Abramova M. B. , Yasinskii O. A.
Published: January 2005

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Synthesis of Ketones Containing a Diphenyl Ether Fragment
Authors: Popov Yu. V. , Korchagina T. K. , Ushchenko V. P. , Gross A. I.
Published: January 2005

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Suzuki Reactions Catalyzed by Palladium Complexes Bearing the Bulky (2,6‐Dimesitylphenyl)dimethylphosphine.
Authors: Smith Rhett C. , Woloszynek Robert A. , Chen Weizhong , Ren Tong , Protasiewicz John D.
Published: January 2005

For Abstract see ChemInform Abstract in Full Text.