bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly active copolymerization of ethylene with 10‐undecen‐1‐ol using phenoxy‐based zirconium/methylaluminoxane catalysts
Authors: Zhang Xiaofan , Chen Shangtao , Li Huayi , Zhang Zhicheng , Lu Yingying , Wu Chunhong , Hu Youliang 
Published: October 2005

AbstractActivated with methylaluminoxane (MAO), phenoxy‐based zirconium complexes bis[(3‐tBu‐C6H3‐2‐O)‐CHNC6H5]ZrCl2, bis[(3,5‐di‐tBu‐C6H2‐2‐O)‐PhCNC6H5] ZrCl2, and bis[(3,5‐di‐tBu‐C6H2‐2‐O)‐PhCN(2‐F‐C6H4)]ZrCl2 for the first time have been used for the copolymerization of ethylene with 10‐undecen‐1‐ol. In comparison with the conventional metallocene, the phenoxy‐based zirconium complexes exhibit much higher catalytic activities [>107 g of polymer (mol of catalyst)−1 h−1]. The incorporation of 10‐undecen‐1‐ol into the copolymers and the properties of the copolymers are strongly affected by the catalyst structure. Among the three catalysts, complex c is the most favorable for preparing higher molecular weight functionalized polyethylene containing a higher content of hydroxyl groups. Studies on the polymerization conditions indicate that the incorporated commoner content in the copolymers mainly depends on the comonomer concentration in the feed. The catalytic activity is slightly affected by the Al(MAO)/Zr molar ratio but decreases greatly with an increase in the polymerization temperature. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5944–5952, 2005
Synthesis and characterization of carbon nanotube/polypyrrole core–shell nanocomposites via in situ inverse microemulsion
Authors: Yu Yijun , Ouyang Chu , Gao Yun , Si Zhihuai , Chen Wei , Wang Zhaoqun , Xue Gi 
Published: October 2005

AbstractWe demonstrate here a feasible approach to the preparation of multiwalled carbon nanotube (MWNT)/polypyrrole (PPy) core–shell nanowires by in situ inverse microemulsion. Transmission electron microscopy and scanning electron microscopy showed that the carbon nanotubes were uniformly coated with a PPy layer with a thickness of several to several tens of nanometers, depending on the MWNT content. Fourier transform infrared spectra suggested that there was strong interaction between the π‐bonded surface of the carbon nanotubes and the conjugated structure of the PPy shell layer. The thermal stability and electrical conductivity of the MWNT/PPy composites were examined with thermogravimetric analysis and a conventional four‐probe method. In comparison with pure PPy, the decomposition temperature of the MWNT/PPy (1 wt % MWNT) composites increased from 305 to 335 °C, and the electrical conductivity of the MWNT/PPy (1 wt % MWNT) composites increased by 1 order of magnitude. The current–voltage curves of the MWNT/PPy nanocomposites followed Ohm's law, reflecting the metallic character of the MWNT/PPy nanocomposites. The cyclic voltammetry measurements revealed that PPy/MWNT composites showed an enhancement in the specific charge capacity with respect to that of pure PPy. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6105–6115, 2005
External cross‐validation for unbiased evaluation of protein family detectors: Application to allergens
Authors: Soeria‐Atmadja Daniel , Wallman Mikael , Björklund Åsa K. , Isaksson Anders , Hammerling Ulf , Gustafsson Mats G. 
Published: October 2005

AbstractKey issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10‐fold cross‐validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held‐out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Very fast empirical prediction and rationalization of protein pKa values
Authors: Li Hui , Robertson Andrew D. , Jensen Jan H. 
Published: October 2005

AbstractA very fast empirical method is presented for structure‐based protein pKa prediction and rationalization. The desolvation effects and intra‐protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root‐mean‐square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Comparative molecular dynamics—Similar folds and similar motions?
Authors: Pang Andrew , Arinaminpathy Yalini , Sansom Mark S. P. , Biggin Philip C. 
Published: October 2005

AbstractProteins possessing the same fold may undergo similar motions, particularly if these motions involve large conformational transitions. The increasing amounts of structural data provide a useful starting point with which to test this hypothesis. We have performed a total of 0.29 μs of molecular dynamics across a series of proteins within the same fold family (periplasmic binding proteinlike) in order to address to what extent similarity of motion exists. Analysis of the local conformational space on these timescales (10–20 ns) revealed that the behavior of the proteins could be readily distinguished between an apo‐state and a ligand‐bound state. Moreover, analysis of the root‐mean‐square fluctuations reveals that the presence of the ligand exerts a stabilizing effect on the protein, with similar motions occurring, but with reduced magnitude. Furthermore, the conformational space in the presence of the ligand appears to be dictated by sequence but not by the type of ligand present. In contrast, apo‐simulations showed considerable overlap of conformational space across the fold as a result of their ability to undergo larger fluctuations. Indeed, we observed several transitions from different simulations between states corresponding to the closed‐cleft and open‐cleft forms of the fold, with the predominant motions being conserved across the different proteins. Thus, large‐scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Folding behavior of chaperonin‐mediated substrate protein
Authors: Xu Wei‐Xin , Wang Jun , Wang Wei 
Published: October 2005

AbstractChaperonin‐mediated protein folding is complex. There have been diverse results on folding behavior, and the chaperonin molecules have been investigated as enhancing or retarding the folding rate. To understand the diversity of chaperonin‐mediated protein folding, we report a study based on simulations using a simplified Gō‐type model. By considering effects of affinity between the substrate protein and the chaperonin wall and spatial confinement of the chaperonin cavity, we study the thermodynamics and kinetics of folding of an unfrustrated substrate protein encapsulated in a chaperonin cavity. The affinity makes the hydrophobic residues of the protein bind to the chaperonin wall, and a strong (or weak) affinity results in a large (or small) effect of binding. Compared with the folding in bulk, the folding in chaperonin cavity with different strengths of affinity shows two kinds of behaviors: one with less dependence on the affinity but more reliance on the spatial confinement effect and the other relying strongly on the affinity. It is found that the enhancement or retardation of the folding rate depends on the competition between the spatial confinement and the affinity due to the chaperonin cavity, and a strong affinity produces a slow folding while a weak affinity induces a fast folding. The crossover between two kinds of folding behaviors happens in the case that the favorable effect of confinement is balanced by the unfavorable effect of the affinity, and a critical affinity strength is roughly defined. By analyzing the contacts formed between the residues of the protein and the chaperonin wall and between the residues of the protein themselves, the role of the affinity in the folding processes is studied. The binding of the residues with the chaperonin wall reduces the formation of both native contacts and nonnative contact or mis‐contacts, providing a loose structure for further folding after allosteric change of the chaperonin cavity. In addition, 15 single‐site‐mutated mutants are simulated in order to test the validity of our model and to investigate the importance of affinity. Inspiringly, our results of the folding rates have a good correlation with those obtained from experiments. The folding rates are inversely correlated with the strength of the binding interactions, i.e., the weaker the binding, the faster the folding. We also find that the inner hydrophobic residues have larger effects on the folding kinetics than those of the exterior hydrophobic residues. We suggest that, besides the confinement effect, the affinity acts as another important factor to affect the folding of the substrate proteins in chaperonin systems, providing an understanding of the folding mechanism of the molecular chaperonin systems. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm
Authors: Tuffery Pierre , Derreumaux Philippe 
Published: October 2005

AbstractDiscretization of protein conformational space and fragment assembly methods simplify the search of native structures. These methods, mostly of Monte Carlo and genetic‐type, do not exploit, however, the fact that short fragments describing consecutive parts of proteins are conformation‐dependent. Yet, this information should be useful in improving ab initio and comparative protein structure modeling. In a preliminary study, we have assessed the possibility of using greedy algorithms for protein structure reconstruction based on the assembly of fragments of four‐residue length. Greedy algorithms differ from Monte Carlo and genetic approaches in that they grow a polypeptide chain one fragment after another. Here, we move one step further in complexity, and provide strong evidence that the dependence between consecutive local conformations during assembly makes possible the reconstruction of protein structures from their secondary structures using a Go potential. Overall our procedure can reproduce 20 protein structures of 50–164 amino acids within 2.7 to 6.5 Å RMSd and is able to identify native topologies for all proteins, although some targets are stabilized by very long‐range interactions. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Weighing in on a timeless controversy
Authors: Perry Jason 
Published: October 2005

AbstractTimeless (Tim) and Period (Per) are coordinately synthesized interacting proteins that in response to positional/environmental cues comigrate to the nucleus as obligate heterodimers where they act to suppress their own gene expression as part of the circadian rhythm network in Drosophila. There has been considerable controversy about the structural nature of Tim because of somewhat conflicting results generated by the automated threading algorithm 3D‐PSSM. With use of a computer‐assisted but largely manual approach, it is shown here that Tim is composed of repetitive structural elements and that those elements comprise two ARM repeat domains, validating the essence of the original 3D‐PSSM prediction. Eleven individual ARM structural units are assigned, and a phylogenetic analysis showing their relatedness to one another is performed. In addition, there appears to be a small domain of prenyltransferase‐like repeats C‐terminal to the second ARM domain, which went undetected in previous analyses. Although we cannot know the precise conformation it adopts until a structure is solved, Tim emerges here as clearly a member of the helical repeat protein superfamily. Given its role in periodic nuclear translocation, Tim may, therefore, have a functional analogy with the photoperiod‐responsive protein Phor1 and other karyopherin‐like molecules. Proteins 2005. © 2005 Wiley‐Liss, Inc.
X‐ray topography of GdCa4O(BO3)3 single crystals grown by the Czochralski method
Authors: Wierzbicka E. , Kłos A. , Lefeld‐Sosnowska M. , Pajączkowska A. 
Published: October 2005

AbstractGdCa4O(BO3)3 single crystals grown by the Czochralski technique were investigated by conventional transmission and back‐reflection X‐ray topography. The results were correlated with the growth conditions and stoichiometry of the crystals. Extended defects, especially dislocations, with different density, in samples cut perpendicular and parallel to the b‐axis were investigated. Long, straight dislocations lying perpendicular to [100] and [010] directions were observed. Periodical, small fluctuations of the diameter induced some defects. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large dielectric constant arising from space‐charge polarization in a SrTiO3 thin film grown on an YBa2Cu3O7–δ layer
Authors: Prijamboedi B. , Takashima H. , Wang R. , Shoji A. , Itoh M. 
Published: October 2005

AbstractThe frequency and temperature dependence of the dielectric constant of SrTiO3 (STO) thin‐film capacitors in multilayer structures of YBa2Cu3O7–δ/SrTiO3/YBa2Cu3O7–δ films were measured over the frequency range 100 to 106 Hz at 2–300 K. In a 750‐nm‐thick STO film, a low‐frequency dielectric dispersion gradually occurs in the temperature region below 50 K; at 5 K, the dielectric constant εr increases to 1.1 × 105 at frequencies below 103 Hz. A space‐charge polarization mechanism is responsible for the large observed dielectric constant of the STO thin films at low temperatures. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology of LiBr/LiF system studied by C‐AFM
Authors: Mazur P. , Gołek F. 
Published: October 2005

AbstractIn this work we investigate the growth of LiBr on LiF(100) by means of atomic force microscopy using its contact mode. To avoid electron or photon stimulated decomposition of the sample the substrate and the adlayer orientations were determined without use of any ionizing radiation. It is shown that LiBr deposited on the LiF(100) single crystal surface forms flat and well oriented layers. Furthermore, the LiBr layers being heated form rectangular and deep pits that open uncovered substrate areas. The edges of the pits are found to be par‐ allel to the substrate step edges ([100] and [010] directions). More effective heating enlarges the pits and rectangular patterns of nanobelts are formed. The average height of such belts is significantly larger than the initial thickness of the film indicating massive rearrangement of the deposited LiBr. The results give evidence of epitaxial growth of LiBr on the LiF(100) surface and clearly show that the LiBr adlayer orientation is intact with the substrate (i.e. the [100] LiBr axis is parallel to the substrate LiF [100] axis). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The characterization of InN growth under high‐pressure CVD conditions
Authors: Dietz N. , Alevli M. , Woods V. , Strassburg M. , Kang H. , Ferguson I. T. 
Published: October 2005

AbstractGaining insight into the gas phase and surface chemistry processes that govern the growth of InN and indium‐rich group III‐nitrides alloys is of crucial importance for understanding and controlling their materials properties. High‐pressure chemical vapor deposition (HPCVD) has been shown to be a valuable method for achieving this goal. First results show that InN layers can be grown under HPCVD conditions at 850–900 °C in the laminar flow regime of the HPCVD reactor at pressures around 15 bar and ammonia to TMI precursor flow ratio below 200. This is a major step towards the growth of indium rich group III‐nitride heterostructures due to the close processing windows. The ex situ InN layers analysis shows that the absorption edge in the InN depends strongly on the precursor flow ratio, indicating that the debated InN properties are strongly influenced by the indium‐to‐nitrogen stoichiometry. By controlling the InN point defect chemistry we showed that the absorption edge shifts from 1.8 eV down to 0.7 eV. The results show a close relation between absorption edge shift in InN and In–N stoichiometry. In order to study the growth under high‐pressure CVD conditions, real‐time optical characterization techniques have been developed and applied to analyze gas phase constituents as well as the film nucleation and steady state growth at elevated pressures. Principal angle reflection and laser light scattering are employed to study surface chemistry processes at a sub‐monolayer level, showing their superiority in optimizing and controlling the growth process. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum dynamics simulations of photodissociation reactions
Authors: Lasorne B. , Bacchus‐Montabonel M. C. , Vaeck N. , Desouter‐Lecomte M. 
Published: October 2005

AbstractWave packet simulations using ab initio potential energy surfaces (PES) have been developed within the framework of the constrained Hamiltonian methodology. The approach is presented with the example of bromoacetyl chloride photodissociation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Reactions of methyllithium with CO and CNMe: Theoretical study
Authors: Tacke Matthias , Leyden Rosaria , Cuffe Laurence P. 
Published: October 2005

AbstractHexameric methyllithium was allowed to react with carbon monoxide (or isonitrile) to form a main group metal carbonyl in the first reaction step. The species rearranges to a lithium acetyl via formal insertion of CO into the lithium carbon bond. In a further step, it is seen that a substituted ethane is formed, probably through the formation of an oxycarbene intermediate. The results of density functional theory (DFT) calculations at the B3LYP/6‐31G** level are compared with spectroscopic results, which show the existence of lithium carbonyl and acetyl species (as well as their isonitrile counterparts) at low temperature. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Reaction of trimethylsilylketene with HCl: Mechanistic study
Authors: Gaudel‐Siri Anouk , Pons Jean‐Marc , Piétri Nathalie , Tamburelli‐Couturier Isabelle , Aycard Jean‐Pierre 
Published: October 2005

AbstractKetenes are involved in various important reactions, such as [2+2] cycloadditions or nucleophilic additions. Among them, silylketenes are particularly stable, and their reactivity reveals interesting features. Indeed, they can behave as nucleophiles or electrophiles. Recent experimental results in our laboratory showed that trimethylsilylketene 1 can react with hydrogen chloride at room temperature, leading to the cleavage of the SiC bond of the ketene moiety and the formation of trimethylsilylchloride 4 and acetylchloride 5. To propose a reaction profile for this unexpected result, a theoretical study was carried out at the density functional theory (DFT) level. This mechanistic study was supported by a spectroscopic analysis in a cryogenic argon matrix in order to monitor the reaction. Intermediate 2 was then identified, and we accounted for it in the postulated reaction pathways. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Extraction of shape‐consistent spin‐orbit pseudo‐potential from an effective spin‐orbit parameter and application to the tellurium atom
Authors: Fromager Emmanuel , Teichteil Christian , Maron Laurent 
Published: October 2005

AbstractA hybrid procedure to extract spin‐orbit pseudo‐potentials is proposed, taking information from both the orbital shape in the valence region and the atomic spin‐orbit splitting. An effective atomic spin‐orbit parameter is derived from a Dirac–Coulomb–Fock reference atomic calculation and is then used to extract the spin‐orbit pseudo‐potential. This method is tested for the ground‐state configuration (5s25p4) of the tellurium atom. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Nanometer‐Scale Modification and Welding of Silicon and Metallic Nanowires with a High‐Intensity Electron Beam
Authors: Xu Shengyong , Tian Mingliang , Wang Jinguo , Xu Jian , Redwing Joan M. , Chan Moses H. W. 
Published: October 2005

AbstractWe demonstrate that a high‐intensity electron beam can be applied to create holes, gaps, and other patterns of atomic and nanometer dimensions on a single nanowire, to weld individual nanowires to form metal–metal or metal–semiconductor junctions, and to remove the oxide shell from a crystalline nanowire. In single‐crystalline Si nanowires, the beam induces instant local vaporization and local amorphization. In metallic Au, Ag, Cu, and Sn nanowires, the beam induces rapid local surface melting and enhanced surface diffusion, in addition to local vaporization. These studies open up a novel approach for patterning and connecting nanomaterials in devices and circuits at the nanometer scale.
Spherical harmonics expansion of the Vlasov‐Poisson initial boundary value problem
Authors: Dogbe C. 
Published: October 2005

AbstractWe derive and analyze the 'SHE' (Spherical Harmonics Expansion) type system of equations coupled in energy. We also show that diffusive behavior occurs on long time and distance scales and we determine the diffusion tensor. The analysis is based on the governing kinetic equations arising in electron transport in semiconductors.