bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation of a Siloxane Acrylic Functional Siloxane Colloid for UV‐Curable Organic‐Inorganic Hybrid Films
Authors: He Jianyun , Nebioglu Ahmet , Zong Zhengang , Soucek Mark D. , Wollyung Kathleen M. , Wesdemiotis Chrys
Published: April 2005

Summary: A new siloxane colloid was developed, for the use in UV‐curable inorganic‐organic hybrid films. The UV‐crosslinkable silica‐colloids were prepared from vinyltrimethoxysilane (VTMS) via a sol‐gel method. The structure of silica‐colloids was characterized using 1H NMR, 29Si NMR, FT‐IR, and matrix‐assisted laser desorption/ionization (MALDI‐TOF) mass spectrometry (MS). The particle size of the siloxane colloid was evaluated using atomic force microscopy (AFM) and small angle light scattering (SALS). Organic phase was based on an acrylated polyester which was synthesized using 1,4‐cyclohexane dimethanol (1,4‐CHDM), neopentyl glycol (NPG), 1,6‐hexanediol (1,6‐HD), maleic anhydride (MA), adipic acid (ADA), and acrylic acid (AA). The acrylated polyester was characterized by gel‐permeation chromatography (GPC) and acid titration. A photo‐initiator was added to the formulation and the UV‐crosslinking reaction of hybrid film was monitored via photo‐differential scanning calorimetry (Photo‐DSC) and real‐time infrared spectroscopy (RT‐IR). The effect of the concentration of VTMS colloids, UV‐light intensity, and exposure time on the polymerization rate was investigated and compared with an inorganic‐organic hybrid film based on TEOS oligomers. Photo‐DSC and RT‐IR results indicated that VTMS colloids can greatly increase free radical polymerization rate and the VTMS colloids functioned effectively as cross‐linker and reactive diluent. AFM and small angle light scattering (SALS) data showed that the silica‐colloids were well dispersed in the organic phase.

magnified image
Synthesis of Poly(urethane acrylate‐co‐styrene) Films Containing Silver Nanoparticles by a Simultaneous Copolymerization/in situ Electron Transfer Reaction
Authors: Kim Ju‐Young , Shin Dong‐Hyun , Ihn Kyo‐Jin
Published: April 2005

Summary: A novel process for the synthesis of nanocomposite films containing silver nanoparticles is presented. Unlike conventional synthetic processes, silver nanoparticles and the polymer film constituting the nanocomposite film were synthesized simultaneously through an in situ electron transfer reaction and the copolymerization of styrene and amphiphilic urethane acrylate nonionomer (UAN), which contains hydrophobic poly(propylene oxide) segments and hydrophilic poly(ethylene oxide) segments along the same backbone. Silver nitrate crystals were first dissolved in a UAN/styrene solution through the formation of a complex between silver salts and the poly(ethylene oxide) chains of UAN, and then the transparent solutions obtained were directly converted to transparent free‐standing films containing silver nanoparticles by copolymerization and an electron transfer reaction by radicals. The amount of radical initiator strongly influenced the size and number of silver nanoparticles formed within the polymer films. The formation of silver nanoparticles was confirmed by transmission electron microscopy (TEM) and characteristic UV absorbance spectra. Hydrophobic/hydrophilic microphase separation in the UAN/styrene solution was also confirmed by TEM and mechanical property measurements.

TEM image of poly(urethane‐co‐styrene) film containing silver nanoparticles.

magnified image

TEM image of poly(urethane‐co‐styrene) film containing silver nanoparticles.
Enthalpy Relaxation in Poly(4‐hydroxystyrene)/Poly(methyl methacrylate) Blends
Authors: Cowie Iain M. G. , Arrighi Valeria , McGonigle Elizabeth‐Anne
Published: April 2005

Summary: The influence of blend composition on enthalpy relaxation behaviour was assessed for miscible blends of poly(4‐hydroxystyrene)/poly(methyl methacrylate) (PHS/PMMA). Values of enthalpy lost (ΔH(Ta, ta)) were calculated from experimental data plotted against log10(ta) and modelled using the Cowie‐Ferguson (CF) semi‐empirical model. This gives a set of values for three adjustable parameters, ΔH∞(Ta), log10(tc) and β. The blends relaxed more slowly than PMMA, but more quickly and less co‐operatively than PHS. Moreover, the blends released more enthalpy than PMMA, but less than PHS. The enthalpy lost by the fully relaxed glass (ΔH∞(Ta)) was less than the theoretical amount possible on reaching the state defined by the liquid enthalpy line extrapolated into the glassy region (ΔHmax(Ta)). Infrared spectroscopy was used for assessing the hydrogen bonding interactions in the blends. The ageing results are discussed with reference to the hydrogen bonding interactions.

Dependence of ΔT (□) and ΔCp (▴) on PHS/PMMA blend composition.

magnified image

Dependence of ΔT (□) and ΔCp (▴) on PHS/PMMA blend composition.
Telechelic and Star‐Shaped Poly(ε‐caprolactone) Functionalized with Triethoxysilyl Groups – New Biodegradable Coatings and Adhesives
Authors: Kricheldorf Hans R. , Hachmann‐Thießen Heiko
Published: April 2005

Summary: Monofunctional poly(εCL) having one CH2OH and one CO2CH3 endgroup was prepared by SnOct2 + MeOH‐initiated polymerizations of εCL at 80 °C. The CH2OH endgroups were reacted with IPTES. In this way, poly(εCL) having one CO2CH3 and one TES endgroup was obtained. Poly(εCL) having two CH2OH endgroups were prepared by means of SnOct2 and Tetra EG or 1,4‐butanediol as coinitiators. The molecular weight distribution significantly broadened when the polymerization temperature increased from 80 to 120 °C. The OH endgroups were quantitatively functionalized by addition of IPTES. Star‐shaped poly(εCL)s having three or four OH endgroups were prepared with 1,1,1‐tris(hydroxymethyl)propane or pentaerythritol as coinitiators. All endgroups were modified with IPTES. The lengths of the poly(εCL) segments were varied via the monomer/coinitiator ratio. All functionalized oligomers were characterized by 1H NMR spectroscopy and MALDI‐TOF mass spectrometry. Preliminary studies of film formation and adhesive properties were performed.

MALDI‐TOF mass spectrum of a poly(εCL) initiated with Sn(Oct)2 and 1,4‐butanediol and functionalized with IPTES.

magnified image

MALDI‐TOF mass spectrum of a poly(εCL) initiated with Sn(Oct)2 and 1,4‐butanediol and functionalized with IPTES.
Morphological Studies of Epoxy/Polyaniline Blends
Authors: Tsotra Panayota , Gryshchuk Oleg , Friedrich Klaus
Published: April 2005

Summary: Polyaniline‐dodecybenzenesulfonic acid (PANI‐DBSA)/epoxy resin (EP) blends were prepared by a solution‐in‐toluene process and direct mixing of PANI‐DBSA with EP. The dispersion quality of PANI‐DBSA proved to be strongly related to the final electrical properties of the cured blends. The solution processed blends showed enhanced electrical properties with small PANI‐DBSA contents (percolation threshold determined was around 2.3 wt.‐% PANI‐DBSA). The morphologies of these blends were investigated by atomic force (AFM), scanning electron (SEM) and transmission electron (TEM) microscopy. The existence of a translucent PANI‐DBSA network exists within the EP matrix. The microscopy investigations were in agreement with the results from differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA).

SEM image of the PANI‐DBSA‐rich regions (indicated by arrows) surrounded by the conductive EP/PANI‐DBSA matrix (5 wt.‐% PANI‐DBSA).

magnified image

SEM image of the PANI‐DBSA‐rich regions (indicated by arrows) surrounded by the conductive EP/PANI‐DBSA matrix (5 wt.‐% PANI‐DBSA).
Vacuum Ultraviolet Photolysis of Hydrocarbon Polymers
Authors: Truica‐Marasescu Florina‐Elena , Wertheimer Michael R.
Published: April 2005

Summary: The wavelength‐dependent vacuum ultraviolet (VUV) photolysis of several polymers, low density polyethylene (LDPE), biaxially oriented poly(propylene) (BOPP), atactic polystyrene (PS), and poly(methyl methacrylate) (PMMA), was studied by irradiation in vacuum with the well‐characterized emissions from four different resonant or excimer VUV sources. These lamps comprise radiofrequency (r.f.) discharges in different noble gases, such as krypton, xenon (at low pressures, producing near‐monochromatic resonant line radiations), xenon excimer (at “high” pressure), and a deuterium/argon mixture (producing a broad‐band emission). VUV‐induced mass loss (ablation or etching) was monitored in situ by quartz crystal microbalance measurements. Following irradiation, samples were analysed by ATR‐FTIR and XPS, to evaluate near‐surface structural changes (e.g., creation of unsaturation, cross‐linking) resulting from the VUV‐initiated bond scissions and radical‐creation reactions. PMMA was the most readily ablatable polymer, whereas the mass loss of BOPP was higher than that of LDPE, regardless of the irradiation wavelength, λ. All polymers were found to form double bonds, with the exception of PS, which is rather stable, probably due to energy dissipation by fluorescence.

Formation of double bonds in a) vinyl‐, b) vinylidene‐, and c) vinylene‐like unsaturated groups, as a function of the radiation dose, D, for KrL (▪), XeL (▴), and D2Ar‐irradiated (•) PMMA.

magnified image

Formation of double bonds in a) vinyl‐, b) vinylidene‐, and c) vinylene‐like unsaturated groups, as a function of the radiation dose, D, for KrL (▪), XeL (▴), and D2Ar‐irradiated (•) PMMA.
2H NMR Study of Aromatic Guest Dynamics in Clathrate Phases of Syndiotactic Polystyrene
Authors: Albunia Alexandra R. , Graf Robert , Guerra Gaetano , Spiess Hans Wolfgang
Published: April 2005

Summary: 2H NMR solid‐state spectra of aromatic molecules (benzene, toluene, chlorobenzene, naphthalene) included in clathrate phases of syndiotactic polystyrene (s‐PS) or absorbed in the amorphous phase of s‐PS, have been recorded and analyzed for a broad range of temperature (230–360 K). The dynamic processes accessible to aromatic molecules absorbed in s‐PS clathrate phases are essentially temperature independent for the whole temperature range under investigation. Moreover, the molecular re‐orientations reflected in the NMR line‐shapes are similar to those accessible to the same molecules when absorbed in polystyrene amorphous phase at temperatures substantially lower than the polymer glass transition temperature. A simulation procedure for 2H NMR line‐shape analysis has been used to establish models for the dynamic processes of the different aromatic guest molecules.

Solid‐state 2H NMR spectrum of naphtalene‐d8 in the amorphous phase of a semi‐crystalline s‐PS film (A), in the s‐PS clathrate phase (B) and the simulated spectrum for a static CD bond (C).

magnified image

Solid‐state 2H NMR spectrum of naphtalene‐d8 in the amorphous phase of a semi‐crystalline s‐PS film (A), in the s‐PS clathrate phase (B) and the simulated spectrum for a static CD bond (C).
FTIR‐Spectroscopy on Segmental Reorientation of a Nematic Elastomer under External Mechanical Fields
Authors: Tammer Michael , Li Jianjun , Komp Ansgar , Finkelmann Heino , Kremer Friedrich
Published: April 2005

Summary:Fourier transform infrared (FTIR) spectroscopy with polarized light is employed to study the segmental orientation and the order of a nematic liquid crystalline elastomers (NLCEs) with a monodomain structure in response to an external mechanical field. The reorientation and the order parameter of the different molecular moieties are analyzed in detail, revealing information about angular excursion in the rearrangement of the mesogens, the spacer molecules, and the main‐chain. In case of an elongation of the NLCE films perpendicular to the initial mesogen orientation, no reorientation or change of order is observed for an elongation ratio less than 1.3. At higher strain, a molecular reorientation process is induced on all molecular segments and the order of alignment is decreased. When the NLCE‐films are stretched parallel to the mesogens, no molecular reorientation takes place and the order parameters show no significant change.

Angular reorientation of different molecular moieties at mechanical strain perpendicular to the initial mesogen orientation.

magnified image

Angular reorientation of different molecular moieties at mechanical strain perpendicular to the initial mesogen orientation.
Cover Picture: Macromol. Chem. Phys. 7/2005
Authors: Horiuchi Shin , Yin Dehui , Ougizawa Toshiaki
Published: April 2005

Cover: The interface of PMMA/SAN was investigated by energy‐filtering TEM. The graphics at the top show the spectral analysis across the interface with a spatial resolution of 10 nm performed by means of Image‐EELS. The upper region, in the left image, is PMMA and the lower region is SAN. After background subtraction, changes in the nitrogen and the oxygen concentrations across the interface can be seen. The graphics at the bottom show the element maps of N and O, and the interfacial layer, visualized by combining the two maps by simple RGB technique. Further details can be found in the Full Paper by S. Horiuchi,* D. Yin, and T. Ougizawa on page 725.
A Semi‐Batch Process for Nitroxide Mediated Radical Polymerization
Authors: Wang Yanxiang , Hutchinson Robin A. , Cunningham Michael F.
Published: April 2005

Summary: A semi‐batch process using nitroxide mediated polymerization, was explored for the design of low molecular weight solvent‐borne coatings, typical of those used in the automotive industry. While living radical polymerization (LRP) offers many advantages in the control of polymer chain microstructure that may confer important physical and chemical property benefits to coatings, adapting LRP to a semi‐batch process poses significant challenges in the design and operation of the process. Using styrene monomer, various two‐component initiating systems (free radical initiator, 4‐hydroxy‐TEMPO) were studied to understand the effects of different initiators on the course of polymerization. In addition, an alkoxyamine was synthesized and used as the initiating source. The initiators Luperox 7M75 and Luperox 231 give higher polymerization rates and reasonable control over polymerization, while benzoyl peroxide (BPO), Vazo 67, and the alkoxyamine are less effective. The number of polymer chains in the final product is always less than the theoretical value, reflecting poor initiation efficiency, probably resulting from undesirable termination reactions that become important due to the nature of the semi‐batch process. Adding camphorsulfonic acid (CSA) or charging initiator concurrently with monomer during semi‐batch feed, can increase the polymerization rate while maintaining the living character of the polymerization. The copolymerization of styrene and butyl acrylate is also shown to exhibit living character.

Schematic representation of the exchange reaction to produce N‐TEMPO capped polymer chains.

magnified image

Schematic representation of the exchange reaction to produce N‐TEMPO capped polymer chains.
A New Heterogenization Technique for Single‐Site Polymerization Catalysts
Authors: Bartke Michael , Oksman Marita , Mustonen Marja , Denifl Peter
Published: April 2005

Summary: Silica‐supported single‐site catalysts show limitations with respect to catalyst homogeneity and maximum metal content. A novel emulsion‐based catalyst heterogenization concept is described, which allows these limitations to be overcome. The method produces catalyst particles with an inherently perfect spherical shape and unique intra‐ and inter‐particle homogeneity. The catalyst particles are very compact and have a low surface area. Video microscopic studies confirm that the improved catalyst homogeneity leads to a more uniform polymerization behavior on a single particle level. The catalysts contain significantly more complex, compared to silica‐supported catalyst systems, which leads to correspondingly higher catalyst activities. No differences, in terms of the mass‐transfer kinetics of these low‐porosity catalysts, compared to porous catalyst systems have been observed.

Electron microscopy image of self‐supported single‐site catalyst prepared by the emulsion‐based method.

magnified image

Electron microscopy image of self‐supported single‐site catalyst prepared by the emulsion‐based method.
Production of Polymeric Materials with Controlled Pore Structure: the “Reactive Gelation” Process
Authors: Marti Nadia , Quattrini Francesca , Butté Alessandro , Morbidelli Massimo
Published: April 2005

Summary: A new approach for the production of macroporous polymer materials is presented. Cross‐linked polystyrene particles are first produced by emulsion polymerization. This latex is then swollen by a further addition of monomer and it is successively destabilized, by addition of salt, in such a way that a controlled aggregation is achieved. The system is left aggregating until a gel is obtained. Although polymer gels have their own consistency, latex particles are kept together by weak interactions only, e.g. Van der Waals' forces. In order to impart enough mechanical resistance to the material, the residual monomer is polymerized, thus bridging the polymer particles with cross‐linked polymer. Accordingly, the process has been named “reactive gelation”. In this work, it is shown how it is possible to obtain an accurate control upon the pore structure of the material by properly tuning each step of the process. An application of the obtained material as stationary phase in a separation carried out by high performance liquid chromatography is presented.

SEM picture of the macroporous material obtained by reactive gelation.

magnified image

SEM picture of the macroporous material obtained by reactive gelation.
Down‐regulation of a morphogen (sonic hedgehog) gradient in the gastric epithelium of Helicobacter pylori‐infected Mongolian gerbils
Authors: Suzuki Hidekazu , Minegishi Yuriko , Nomoto Yohei , Ota Takayuki , Masaoka Tatsuhiro , van den Brink Gijs R , Hibi Toshifumi
Published: April 2005

Sonic hedgehog (Shh) is a morphogen involved in many aspects of patterning of the gut during embryogenesis and in gastric fundic gland homeostasis in the adult. Intestinal metaplastic change of the gastric epithelium is associated with the loss of Shh expression, and mice that lack Shh expression show intestinal transformation of the gastric mucosa. The present study was designed to investigate the alteration of Shh expression in the stomach of an experimental model of Helicobacter pylori (H. pylori) colonization. Male Mongolian gerbils were inoculated with H. pylori and examined 4 and 51 weeks later. The level of Shh mRNA expression was determined by quantitative RT‐PCR and in situ hybridization. Shh protein expression was determined by immunoblotting and immunohistochemistry. Shh was expressed in the parietal cells, zymogenic cells, and mucous neck cells of the gastric fundic glands of gerbils. Prolonged colonization by H. pylori led to extension of the inflammation from the antrum to the corpus of the stomach, with loss of Shh expression. Loss of Shh expression correlated with loss of parietal cells, disturbed maturation of the mucous neck cell–zymogenic cell lineage, and increased cellular proliferation. Shh expression is significantly reduced in H. pylori‐associated gastritis. These data show for the first time that H. pylori infection leads to down‐regulation of the expression of a morphogen with an established role (Shh) in gastric epithelial differentiation. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Homozygosity for a CHEK2*1100delC mutation identified in familial colorectal cancer does not lead to a severe clinical phenotype
Authors: van Puijenbroek Marjo , van Asperen Christi J , van Mil Anneke , Devilee Peter , van Wezel Tom , Morreau Hans
Published: April 2005

It has recently been suggested that the frequency of the germline CHEK2*1100delC mutation is higher among breast cancer families with colorectal cancer, although the mutation does not seem to be significantly associated with familial colorectal cancer. Five hundred and sixty‐four familial colorectal tumours were studied for expression of CHEK2 using tissue microarrays and an antibody against the NH2‐terminal SQ regulatory domain of the CHEK2 protein. Normal colonic tissue from patients whose tumours showed loss of CHEK2 expression was investigated further using fragment and sequence analysis for the presence of a CHEK2*1100delC mutation and five other (R117G, R137Q, R145W, I157T, and R180H) known germline variants in CHEK2. Twenty‐nine tumours demonstrated loss of expression for CHEK2. Analysis of matched normal colonic tissue from these patients revealed germline CHEK2*1100delC mutation in three cases. In two of these, the mutation was heterozygous but, interestingly, the third patient proved to be homozygous for the deletion, using six different primer pair combinations. None of the other tested germline variants were identified. No CHEK2*1100delC mutations were found in patients whose tumours stained positive. Homozygosity for the CHEK2*1100delC mutation appears not to be lethal in humans. No severe clinical phenotype was apparent, although the patient died from colonic carcinoma at age 52 years. This observation is in line with recent knockout mouse models, although in the latter, cellular defects in apoptosis and increased resistance to irradiation seem to exist. It is also concluded that CHEK2 protein abrogation is not caused by the CHEK2 germline variants R117G, R137Q, R145W, I157T, and R180H in familial colorectal cancer. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Ultrafast single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization of acrylates initiated with iodoform in water at room temperature and catalyzed by sodium dithionite
Authors: Percec Virgil , Ramirez‐Castillo Ernesto , Popov Anatoliy V. , Hinojosa‐Falcon Luis A. , Guliashvili Tamaz
Published: April 2005

Sodium dithionite in the presence of NaHCO3 in water acts as a single‐electron‐transfer agent and facilitates the single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization (SET–DTLRP) of acrylates initiated with iodoform at room temperature. The resulting α,ω‐di(iodo)polyacrylates can be used as macroinitiators for the SET–DTLRP of other acrylates. Ultrahigh‐molar‐mass poly(tert‐butyl acrylate) can be synthesized via the SET–DTLRP of tert‐butyl acrylate and has a very low weight‐average molecular weight/number‐average molecular weight ratio of 1.15. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2178–2184, 2005
Synthesis and characterization of alt‐copoly(carbosiloxane)s containing oligodiphenylsiloxane segments
Authors: Gädda Thomas M. , Weber William P.
Published: April 2005

Novel α,ω‐divinyloligodiphenylsiloxanes (1,9‐divinyldecaphenylpentasiloxane, 1,7‐divinyloctaphenyltetrasiloxane, 1,5‐divinylhexaphenyltrisiloxane, and 1,3‐divinyltetraphenyldisiloxane) were prepared and copolymerized by Pt‐catalyzed hydrosilylation with α,ω‐dihydridopentasiloxanes. The molecular weights of the copolymers were measured with gel permeation chromatography, and their thermal properties were characterized with differential scanning calorimetry and thermogravimetric analysis. The polymers had high thermal stability in air and nitrogen. The oligomer and polymer structures were determined with 1H, 13C, 19F, and 29Si NMR and IR spectrometry. The molecular weights of the oligomers were measured with high‐resolution mass spectrometry. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2155–2163, 2005
Ethylene polymerization over supported catalysts [2,6‐bis(imino)pyridyl iron dichloride/magnesium dichloride] with AlR3 as an activator
Authors: Mikenas Tatiana B. , Zakharov Vladimir A. , Echevskaya Lyudmila G. , Matsko Michail A.
Published: April 2005

Data on ethylene polymerization over supported LFeCl2/MgCl2 catalysts {L = 2,6‐bis[1‐(2,6‐dimethylphenylimino)ethyl]pyridyl} containing AlR3 (R = Me, Et, i‐Bu, or n‐Oct) as an activator are presented. These catalysts are highly active (100–300 kg of polyethylene/g of Fe h bar of C2H4) and stable in ethylene polymerization at 70–80 °C. Data on the effects of the iron content, AlR3 type, Al(i‐Bu)3 concentration, and hydrogen presence on the catalyst activity are presented. The molecular structure of polyethylene produced with these catalysts (including the molecular masses, molecular mass distribution, branching, and number of CC bonds) has been studied; data on the effects of AlR3 and hydrogen on the molecular structure are presented. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2128–2133, 2005
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
Authors: Snyder David A. , Montelione Gaetano T.
Published: April 2005

An important open question in the field of NMR‐based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple “RMSD‐stable domains”—locally well‐defined regions that are not aligned in global superimpositions—complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into “RMSD‐stable domains” and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR‐derived structural ensembles, superimposing each RMSD‐stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis‐based criterion, the ϵ‐value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology. Proteins 2005. © 2005 Wiley‐Liss, Inc.
How does nitrous oxide reductase interact with its electron donors?—A docking study
Authors: Mattila Kimmo , Haltia Tuomas
Published: April 2005

Electron transfer reactions are crucial for respiration and denitrification. In this article, we analyze the interaction of nitrous oxide reductase with its electron donors cytochrome c550 and pseudoazurin. Our docking protocol comprises generation of candidate complexes followed by a selection step based on the distance of the donor and acceptor groups in each partner protein. Finally, the structures of the candidate complexes were optimized using a force field calculation, together with a second distance filtering step. The prediction power of this protocol was studied using the crystal structure of the cytochrome c2/photosynthetic reaction center of Rhodobacter sphaeroides as a reference. The results suggest that both cytochrome c550 and pseudoazurin bind at the same hydrophobic surface patch residing near the CuA center of nitrous oxide reductase. The central, well‐conserved interaction surface of the donors is hydrophobic, but it is surrounded by numerous lysine side‐chains, which interact electrostatically with analogously positioned side‐chain carboxylates of the acceptor. The prediction output is an ensemble of energetically similar structures that are rotationally related to each other. While such an ensemble may reflect incomplete prediction power of the docking protocol, it may also manifest a biological situation where there are multiple ways of forming a productive electron transfer complex. Analyses of the predicted structures and the conservation pattern of the amino acid residues suggest the existence of specific electron transfer pathways to and from the CuA center of nitrous oxide reductase. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Quantifying allosteric effects in proteins
Authors: Ming Dengming , Wall Michael E.
Published: April 2005

In allosteric regulation, protein activity is altered when ligand binding causes changes in the protein conformational distribution. Little is known about which aspects of protein design lead to effective allosteric regulation, however. To increase understanding of the relation between protein structure and allosteric effects, we have developed theoretical tools to quantify the influence of protein–ligand interactions on probability distributions of reaction rates and protein conformations. We define the rate divergence, $\bar{D}$k, and the allosteric potential, $\bar{D}$x, as the Kullback–Leibler divergence between either the reaction‐rate distributions or protein conformational distributions with and without the ligand bound. We then define Dx as the change in the conformational distribution of the combined protein/ligand system, derive Dx in the harmonic approximation, and identify contributions from 3 separate terms: the first term, D, results from changes in the eigenvalue spectrum; the second term, D, results from changes in the mean conformation; and the third term, D, corresponds to changes in the eigenvectors. Using normal modes analysis, we have calculated these terms for a natural interaction between lysozyme and the ligand tri‐N‐acetyl‐D‐glucosamine, and compared them with calculations for a large number of simulated random interactions. The comparison shows that interactions in the known binding‐site are associated with large values of D. The results motivate using allosteric potential calculations to predict functional binding sites on proteins, and suggest the possibility that, in Nature, effective ligand interactions occur at intrinsic control points at which binding induces a relatively large change in the protein conformational distribution. Proteins 2005. Published 2005 Wiley‐Liss, Inc.
Computational analysis of molecular basis of 1:1 interactions of NRG‐1β wild‐type and variants with ErbB3 and ErbB4
Authors: Luo Cheng , Xu Lingfei , Zheng Suxin , Luo Xiaomin , Shen Jianhua , Jiang Hualiang , Liu Xifu , Zhou Mingdong
Published: April 2005

The neuregulin/ErbB system is a growth factor/receptor cascade that has been proven to be essential in the development of the heart and the sympathetic nervous system. However, the basis of the specificity of ligand–receptor recognition remains to be elucidated. In this study, the structures of NRG‐1β/ErbB3 and NRG‐1β/ErbB4 complexes were modeled based on the available structures of the homologous proteins. The binding free energies of NRG‐1β to ErbB3 and ErbB4 were calculated using the molecular mechanics Poisson–Boltzmann surface area (MM‐PBSA) computational method. In addition, computational alanine‐scanning mutagenesis was performed in the binding site of NRG‐1β and the difference in the binding free energies between NRG‐1β mutants and the receptors was calculated. The results specify the contribution of each residue at the interaction interfaces to the binding affinity of NRG‐1β with ErbB3 and ErbB4, identifying several important interaction residue pairs that are in agreement with previously acquired experimental data. This indicates that the presented structural models of NRG‐1β/ErbB3 and NRG‐1β/ErbB4 complexes are reliable and could be used to guide future studies, such as performing desirable mutations on NRG‐1β to increase the binding affinity and selectivity to the receptor and discovering new therapeutic agents for the treatment of heart failure. Proteins 2005. © 2005 Wiley‐Liss, Inc.
O‐raffinose crosslinked hemoglobin lacks site‐specific chemistry in the central cavity: Structural and functional consequences of β93Cys modification
Authors: Boykins Robert A. , Buehler Paul W. , Jia Yiping , Venable Richard , Alayash Abdu I.
Published: April 2005

Reacting human deoxyHbA0with oxidized raffinose (O‐raffinose), a trisaccharide, results in a low oxygen affinity “blood substitute,” stabilized in a noncooperative T‐conformation and possesses readily oxidizable rhombic heme. In this study, we fractionated theO‐raffinose–modified HbA0heterogeneous polymer (O‐R‐PolyHbA0) into six distinct fractions with a molecular weight distribution ranging from 64 to ∼600 kDa using size‐exclusion chromatography (SEC). Oxygen equilibrium and kinetics binding parameters of all fractions were nearly identical, reflecting a lack of heterogeneity in ligand binding properties amongO‐R‐PolyHbA0species (Hill coefficientnequal to 1.0). Several mass spectrometry techniques were used to evaluate undigested and digested HbA0,O‐R‐PolyHbA0, andO‐R‐PolyHbA0fractions. Proposed sites of intramolecular crosslinking (i.e., β1Lys82, β2Lys82, and β1Val1) were not found to be the predominant site of crosslinking within the central cavity. Intermolecular crosslinking withO‐raffinose results in no discernible site of amino acids modifications with the exception of β93Cys and α104Cys. Based on accessible surface area (ASA) calculations in intact deoxyHbA0, slight conformational changes are required to allow for the S on α104Cys to be modified during the reaction withO‐raffinose or its partially oxidized product(s). The stabilization of HbA0in the T‐conformation may not be a direct correlate ofO‐raffinose induced changes, but an indirect consequence of changing hydration in the water‐filled central cavity and/or the distal heme pocket leading in the latter case to accelerated iron oxidation. Structural data presented here when taken together with the oxidative instability ofO‐R‐PolyHbA0may provide some basis for the reported toxicity of this oxygen carrier. Proteins 2005. Published 2005 Wiley‐Liss, Inc.
Amphipathic α‐helices in proteins: Results from analysis of protein structures
Authors: Sharadadevi Ambure , Sivakamasundari Chandrasekaran , Nagaraj Ramakrishnan
Published: April 2005

Amphipathic α‐helices play a crucial role in mediating the interaction of peptides and proteins with membranes. We have analyzed protein structures for the occurrence of 18‐residue amphipathic helices. We find several of these α‐helices having average hydrophobic moments and average hydrophobicities that would favor their interaction with membranes. We have analyzed the distribution of net charge, helix length, normalized frequency of occurrence, and propensities of the 20 amino acids in the delineated 18‐residue helices. We have observed distinct differences in the frequencies of occurrence of polar and hydrophobic amino acids at positions 1–18 in amphipathic and nonamphipathic helices. There are also differences in propensities of the 20 amino acids to occur at positions 1–18 of amphipathic and nonamphipathic helices. Synthetic peptides corresponding to some of these surface‐seeking helices do possess antibacterial and/or hemolytic activities. Knowledge of the distribution of charges in 18‐residue surface‐seeking amphipathic α‐helices, as well as propensity of occurrence of amino acids at various positions, would be useful inputs in the de novo design of amphipathic peptides. Proteins 2005. © 2005 Wiley‐Liss, Inc.
High accuracy prediction of β‐turns and their types using propensities and multiple alignments
Authors: Fuchs Patrick F.J. , Alix Alain J.P.
Published: April 2005

We have developed a method that predicts both the presence and the type of β‐turns, using a straightforward approach based on propensities and multiple alignments. The propensities were calculated classically, but the way to use them for prediction was completely new: starting from a tetrapeptide sequence on which one wants to evaluate the presence of a β‐turn, the propensity for a given residue is modified by taking into account all the residues present in the multiple alignment at this position. The evaluation of a score is then done by weighting these propensities by the use of Position‐specific score matrices generated by PSI‐BLAST. The introduction of secondary structure information predicted by PSIPRED or SSPRO2 as well as taking into account the flanking residues around the tetrapeptide improved the accuracy greatly. This latter evaluated on a database of 426 reference proteins (previously used on other studies) by a sevenfold crossvalidation gave very good results with a Matthews Correlation Coefficient (MCC) of 0.42 and an overall prediction accuracy of 74.8%; this places our method among the best ones. A jackknife test was also done, which gave results within the same range. This shows that it is possible to reach neural networks accuracy with considerably less computional cost and complexity. Furthermore, propensities remain excellent descriptors of amino acid tendencies to belong to β‐turns, which can be useful for peptide or protein engineering and design. For β‐turn type prediction, we reached the best accuracy ever published in terms of MCC (except for the irregular type IV) in the range of 0.25–0.30 for types I, II, and I′ and 0.13–0.15 for types VIII, II′, and IV. To our knowledge, our method is the only one available on the Web that predicts types I′ and II′. The accuracy evaluated on two larger databases of 547 and 823 proteins was not improved significantly. All of this was implemented into a Web server called COUDES (French acronym for: Chercher Où Une Déviation Existe Sûrement), which is available at the following URL: http://bioserv.rpbs.jussieu.fr/Coudes/index.html within the new bioinformatics platform RPBS. Proteins 2005;59. © 2005 Wiley‐Liss, Inc.
An explosion caused by mixing incompatible liquids
Authors: Lacoursiere PE J. P.
Published: April 2005

Two workers of a waste handling contractor lost their lives as a result of the explosion of a vacuum truck where they had inadvertently mixed sulfuric acid and hydrogen peroxide. The consequences of the explosion were simulated and documented. Root causes and contributing factors were identified and, in particular, failure of the management systems are underlined: (1) inadequate procedures, (2) poor training, and (3) poor management controls. Improved procedures, training, and management controls will prevent accidents of this type. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Investigation of a naphtha storage tank fire
Authors: Rodante Thomas V.
Published: April 2005

In October 1988, one of the world's largest combined loss storage tank fires occurred at a refinery located on the island of Pulau Merlimau, Singapore. At the height of the incident, the blaze involved three floating roof naphtha storage tanks, each approximately 134 feet in diameter and containing a total of 294,500 barrels of product. The resultant property loss was estimated at over USD 6.6 million in 1988 dollars.

At several stages, the fire threatened to involve tankage in adjacent dikes containing kerosene, reformate, motor gasoline, and diesel product. Because the refinery was located on an island, equipment and manpower were ferried to the site. Despite the size of the fire and adverse logistics, fire‐fighting efforts were successful in containing the incident to the primary dike tankage.

This paper investigates the incidents leading up to the fire, operational and design engineering considerations, and analyzes the basic fire‐fighting strategy, prefire and emergency response plans, fire water management, and fixed/semifixed foam systems. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Lessons learned from fires and explosions involving air pollution control systems
Authors: Ogle Russell A. , Carpenter Andrew R. , Morrison Delmar “Trey”
Published: April 2005

Six case studies of fires or explosions involving air pollution control (APC) systems are reviewed in this paper. These case studies have been generalized from actual accident investigations performed by the authors.

The case studies cover the APC technologies of thermal oxidation, catalytic oxidation, gas scrubbers, adsorption, and condensation. Each of the technologies was used to control emissions of volatile organic compounds (VOCs). The accidents encompass a broad range of industries, ignition sources, and circumstances. The causal factors for these accidents are compared with applicable safety guidelines and standards to show how safeguards could have prevented or mitigated these accidents.

The common theme that emerges from these accident investigations is that APC systems should not be specified and installed strictly by intuition or experience, but rather through careful engineering design. The key findings of this study are:

Characterize the waste stream to be treated.

Conduct a process hazard analysis for each APC system, with particular emphasis on fire and explosion hazards.

Design the APC system using good engineering practices.

Operate the APC system within its design specifications.

Periodically verify that the APC system performance satisfies its technical and regulatory objectives.

Perform maintenance activities in accordance with manufacturer's recommendations.

Each of the accidents was the direct result of the omission of one or more of these basic tenets. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Large quasi‐linear electro‐optical response of BaZr0.75Hf0.25O3 thin films by pulsed laser deposition
Authors: Tian H. Y. , Wang D. Y. , Zhou X. Y. , Wang Y. , Chan H. L. W. , Choy C. L.
Published: April 2005

Epitaxial BaZr0.75Hf0.25O3 (BZH) thin films were grown successfully on MgO (100) substrates by pulsed laser deposition. The FWHM of the rocking curve of the BZH thin film deposited at 650 °C is about 0.6°, and the pole‐figure shows that the BZH thin film has fourfold symmetry with 0.5–1.1° FWHM in the ϕ‐scanning. A large quasi‐linear electro‐optic effect was observed under an external electric field in a transverse geometry at 633 nm. The electric‐optic coefficient Rc and birefringence shift are found to be 9.145 × 10–11 m/V and 4 × 10–3 at 10 kV/mm, respectively. The microstructure of the films and its relation to the observed electric‐optic properties is discussed. It is expected that BZH thin films will have various electric‐optic and microwave applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of annealing and lithium substitution on conductivity in nickel–cobalt oxide spinel films
Authors: Owings Robert R. , Holloway Paul H. , Exarhos Gregory J. , Windisch Charles F.
Published: April 2005

Mixed transition‐metal oxide spinels exhibit high electrical conductivity and enhanced infrared transmissivity resulting from the presence of small polarons in the NiCo2O4 lattice. Polarons are formed as a result of judicious choice of component metal cations and attendant resident cation charge states. Substitution of lithium for cobalt (Ni1+xCo2−x−zLizO4) while maintaining the spinel stoichiometry and controlled post‐deposition annealing was found to influence measured conductivity in both solution‐ and sputter‐deposited thin films. For lithium concentrations < 10% an improvement in conductivity was observed, depending upon whether the oxide film was deposited from solution (large increase) or sputter deposited (small increase). However, higher lithium concentrations degraded conductivity. Both XPS and SIMS analyses of films with high lithium concentrations (z > 0.3) revealed that lithium was concentrated near the film surface and the formation of carbonate was detected by XPS and Fourier transform infrared data. Results indicate that additions of lithium to transition‐metal spinel oxides can lead to increased conductivity by increased polaron formation. However, in high concentration, lithium is an interstitial that diffuses to the surface to form compounds that degrade electrical conductivity. Copyright © 2005 John Wiley & Sons, Ltd.
A population genetic model for lateral dimorphism frequency in fishes
Authors: Nakajima Mifuyu , Matsuda Hiroyuki , Hori Michio
Published: April 2005

Two morphological types, righty and lefty, are found in several fish species. Righty predators mainly prey on lefty prey and vice versa (called “cross predation”). This dimorphism is heritable in a Mendelian one‐locus–two‐allele fashion. The frequency of righty individuals in a population oscillates periodically. To determine the effect of cross predation on this oscillation, we constructed mathematical models that describe a genetic basis of lateral dimorphism assuming genetic drift in a one‐predator–two‐prey system and three trophic levels with omnivory. Both models have an equilibrium of both righty and lefty types at a frequency of 0.5. Mathematical analyses and computer simulations showed that the dimorphism is maintained and that its frequency oscillated with or without genetic drift. Large degrees of drift and high intrinsic growth rates and predation efficiencies of prey species caused the frequency oscillations to be amplified and their period to be long. When cross predation decreased as a proportion of all predation, the righty frequency of a prey species fluctuated non‐periodically. These differences in fluctuation patterns were observed in natural systems. Our model suggests that both cross predation and genetic drift dictate the maintenance of dimorphism and the patterns of its fluctuations.
Blowing up solutions for an elliptic Neumann problem with sub- or supercritical nonlinearity. Part II: \( N\geq4 \)
Authors: Rey Olivier , Wei Juncheng
Published: April 2005

We consider the sub- or supercritical Neumann elliptic problem

−\mathrm{\Delta }u + \mu u = u^{\frac{N + 2}{N−2} + ɛ}

,

u > 0

in

Ω

;

\frac{\partial u}{\partial n} = 0

on

∂Ω

,

Ω

being a smooth bounded domain in

\mathbb{R}^{N}

,

N⩾4

,

\mu > 0

and

ɛ \neq 0

a small number. We show that for

ɛ > 0

, there always exists a solution to the slightly supercritical problem, which blows up at the most curved part of the boundary as

ɛ

goes to zero. On the other hand, for

ɛ < 0

, assuming that the domain is not convex, there also exists a solution to the slightly subcritical problem, which blows up at the least curved part of the domain.

Ω

étant un domaine borné régulier de

\mathbb{R}^{N}

,

N⩾4

, on considère le problème elliptique de Neumann

−\mathrm{\Delta }u + \mu u = u^{\frac{N + 2}{N−2} + ɛ}

,

u > 0

dans

Ω

;

\frac{\partial u}{\partial n} = 0

sur

∂Ω

, où

\mu > 0

est un paramètre fixé. On montre que pour

ɛ > 0

assez petit, le problème admet une solution non-constante, qui se concentre quand

ɛ

tend vers zéro en un point de la frontière où la courbure moyenne est maximum. En supposant que le domaine n'est pas convexe, on montre aussi, pour

ɛ < 0

assez proche de zéro, l'existence d'une solution non-constante, qui se concentre quand

ɛ

tend vers zéro en un point de la frontière où la courbure moyenne est minimum.