bluuebunny/crossref_metadata_2025 huggingface dataset:
Abilities of 2‐arylmethyloxy‐6‐cyanonaphthalene derivatives to initiate radical and cationic photopolymerizations
Authors: Tanaka Kenta , Akimoto Ryoichi , Igarashi Tetsutaro , Sakurai Tadamitsu
Published: November 2005

An investigation was undertaken to shed much light on the bond‐cleavage mode (heterolysis vs homolysis) of bichromophoric photoinitiators in styrene (St) and 1,2‐epoxycyclohexane (EpC) and then to develop a highly efficient hybrid‐type photoinitiator. Excited‐state 2‐(9‐anthrylmethyloxy)‐6‐cyanonaphthalene in toluene and 1,2‐dimethoxyethane, which were used instead of St and EpC, respectively, underwent both homolytic ArOCH2 bond cleavage and heterolytic ArOCH2 bond cleavage to give the corresponding radical‐pair and ion‐pair intermediates. The charge‐separated state characteristic of the naphthol chromophore in the singlet excited state was found to play a pivotal role in this heterolytic bond‐cleavage mode. An inspection of the radical (St) and cationic (EpC) photopolymerization behavior observed in the presence of some 2‐arylmethyloxy‐6‐cyanonaphthalenes led us to conclude that the aforementioned 9‐anthrylmethyloxy‐substituted naphthalene derivative is a candidate for a functional hybrid‐type photoinitiator containing no halogen and/or metal. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 25–31, 2006
Ring‐Opening and polymerization of 1‐[2′‐(heptaphenylcyclotetrasiloxanyl)ethyl]‐1,3,3,5,5‐pentamethylcyclotrisiloxane
Authors: Gädda Thomas M. , Weber William P.
Published: November 2005

1‐[2′‐(Heptaphenylcyclotetrasiloxanyl)ethyl]‐1,3,3,5,5‐pentamethylcyclotetrasiloxane (II) was prepared from 1‐[2′‐(methyldichlorosilyl)ethyl]‐1,3,3,5,5,7,7‐heptaphenylcyclotetrasiloxane (I) and tetramethyldisiloxane‐1,3‐diol. Acid‐catalyzed ring‐opening of II in the presence of tetramethyldisiloxane gave 1,9‐dihydrido‐5‐[2′‐(heptaphenylcyclotetrasiloxanyl)ethyl]nonamethylpentasiloxane (III) and 1,9‐dihydrido‐3‐[2′‐(heptaphenylcyclotetrasiloxanyl)ethyl]nonamethylpentasiloxane (IV). Both acid‐ and base‐catalyzed ring‐opening polymerization of II gives highly viscous, transparent polymers. The structures of I–IV and polymers were determined by UV, IR, 1H, 13C, and 29Si NMR spectroscopy. In addition, molecular weights obtained by GPC and NMR end group analysis were confirmed with mass spectrometry. On the basis of 29Si NMR spectroscopy, the polymers appear to result exclusively from ring‐opening of the cyclotrisiloxane ring. No evidence for ring‐opening of the cyclotetrasiloxane ring was observed. Polymer properties were determined by DSC and TGA. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 137–146, 2006
Stimuli‐responsive polymers. VIII. Polyesters and poly(ester amides) containing azobenzene and chiral binaphthylene segments: Highly adaptive materials endowed with light‐, heat‐, and solvent‐regulated optical rotatory power
Authors: Jaycox Gary D.
Published: November 2005

Azobenzene‐modified polyesters and poly(ester amide)s fitted with chiral, atropisomeric binaphthylene segments were prepared by a series of low‐temperature polycondensation reactions carried out in polar solvent media. When compared with their polyaramide counterparts studied earlier, these materials had significantly improved solubility behaviors and were readily dissolved by a wide range of organic solvents. In solution, each of these constructs underwent photoinduced oscillations in optical rotatory power when subjected to multiple UV‐light/visible‐light illumination cycles that drove trans↔cis isomerization reactions along their polymer chains. Light‐regulated chiroptical perturbations were dependent on polymer backbone structures and were further modulated by well‐coordinated temperature fluctuations and by the nature of the solvent medium employed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 207–218, 2006
Copolymerization of N‐vinylcaprolactam and glycidyl methacrylate: Reactivity ratio and composition control
Authors: Qiu Xingping , Sukhishvili Svetlana A.
Published: November 2005

Free‐radical copolymerizations of N‐vinylcaprolactam (VCL) and glycidyl methacrylate (GMA) were investigated to synthesize temperature‐responsive reactive copolymers with minimized compositional heterogeneity. The average copolymer composition was determined by Fourier transform infrared and nuclear magnetic resonance techniques. The reactivity ratios for VCL and GMA were found to be 0.0365 ± 0.0009 and 6.44 ± 0.36 by the Fineman–Ross method and 0.039 ± 0.006 and 6.75 ± 0.29 by the Kelen–Tudos method, respectively. When prepared by batch polymerization, VCL–GMA copolymers had a highly heterogeneous composition and fractions of different solubilities in water. The use of a gradual feeding technique, which included the sequential addition of more reactive GMA monomer into the reaction, yielded copolymers with much more homogeneous composition. The produced copolymers with 0.9 and 0.11 fractional GMA contents preserved their temperature‐responsive properties and precipitated from aqueous solutions when the temperature exceeded 31 °C. The GMA units in the VCL–GMA copolymers were capable of reacting with amino end‐functionalized poly(ethylene oxide) at room temperature to produce poly(N‐vinylcaprolactam)–poly(ethylene oxide) graft copolymers. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 183–191, 2006
Development of organotellurium‐mediated and organostibine‐mediated living radical polymerization reactions
Authors: Yamago Shigeru
Published: November 2005

Organotellurium‐mediated living radical polymerizations (TERPs) and organostibine‐mediated living radical polymerizations (SBRPs) provide well‐defined polymers with a variety of polar functional groups via degenerative chain‐transfer polymerization. The high controllability of these polymerizations can be attributed to the rapid degenerative‐transfer process between the polymer‐end radicals and corresponding dormant species. The versatility of the methods allows the synthesis of AB diblock, ABA triblock, and ABC triblock copolymers by the successive addition of different monomers. This review summarizes the current status of TERP and SBRP. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1–12, 2006
New method of synthesis of electroactive polyamide with amine‐capped aniline pentamer in the main chain
Authors: Chao Danming , Lu Xiaofeng , Chen Jingyu , Zhao Xiaogang , Wang Lifeng , Zhang Wanjin , Wei Yen
Published: November 2005

A novel way to prepare an electroactive polyamide (alternating copolymer) is presented. Well‐defined molecular structure polyamide with amine‐capped aniline pentamer in the main chain was obtained. The copolymer has been characterized by Fourier‐transform infrared (FTIR) spectra, 1H NMR, elemental analysis (EA), and gel permeation chromatography (GPC). Its chemical oxidation process was studied by UV–vis spectra and the electrochemical analysis was checked by cyclic voltammetry (CV). It was found that the obtained electroactive polyamide shows three redox peaks in the cyclic voltammetry, which is different from the polyaniline. Moreover, the thermal properties of the copolymer were evaluated by thermogravimetric analysis (TGA). The electrical conductivity is about 2.5 × 10−6 S cm−1 at room temperature. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 477–482, 2006
Preparation of ABC miktoarm star terpolymer containing poly(ethylene glycol), polystyrene, and poly(tert‐butylacrylate) arms by combining diels–alder reaction, atom transfer radical, and stable free radical polymerization routes
Authors: Durmaz Hakan , Karatas Figen , Tunca Umit , Hizal Gurkan
Published: November 2005

The ABC type miktoarm star terpolymer was prepared utilizing “core‐in” and “core‐out” methods via combination of Diels–Alder reaction (DA), stable free radical polymerization (SFRP), and atom transfer radical polymerization (ATRP). First, in DA reaction, poly(ethylene glycol)‐maleimide (PEG‐maleimide) precursor was reacted with succinic acid anthracen‐9‐ylmethyl ester 3‐(2‐bromo‐2‐methyl‐propionyloxy)‐2‐methyl‐2‐[2‐phenyl‐2‐(2,2,6,6‐tetramethyl‐piperidin‐1‐yloxy)‐ethoxy‐carbonyl]‐propyl ester, 8, to give DA adduct, 9, which has appropriate functional groups for SFRP and ATRP. Second, a previously obtained 9 was used as a macroinitiator for SFRP of styrene at 125 °C. As a third step, this PEG‐polystyrene (PEG‐PSt) precursor with a bromine functionality in the core was employed as a macroinitiator for ATRP of tert‐butylacrylate (tBA) in the presence of Cu(I)Br and pentamethyldiethylenetriamine at 80 °C to give ABC type miktoarm star terpolymer (PEG‐PSt‐PtBA) with controlled molecular weight and low polydispersity (Mw/Mn < 1.27). The obtained polymers were characterized by gel permeation chromatography and 1H NMR. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 499–509, 2006
Synthesis and characterization of amphiphilic copolymer of linear poly(ethylene oxide) linked with [poly(styrene‐co‐2‐hydroxyethyl methacrylate)‐graft‐poly(ε‐caprolactone)] using sequential controlled polymerization
Authors: Xu Xuewei , Huang Junlian
Published: November 2005

A well‐defined amphiphilic copolymer of ‐poly(ethylene oxide) (PEO) linked with comb‐shaped [poly(styrene‐co‐2‐hydeoxyethyl methacrylate)‐graft‐poly(ε‐caprolactone)] (PEO‐b‐P(St‐co‐HEMA)‐g‐PCL) was successfully synthesized by combination of reversible addition‐fragmentation chain transfer polymerization (RAFT) with ring‐opening anionic polymerization and coordination–insertion ring‐opening polymerization (ROP). The α‐methoxy poly(ethylene oxide) (mPEO) with ω,3‐benzylsulfanylthiocarbonylsufanylpropionic acid (BSPA) end group (mPEO‐BSPA) was prepared by the reaction of mPEO with 3‐benzylsulfanylthiocarbonylsufanyl propionic acid chloride (BSPAC), and the reaction efficiency was close to 100%; then the mPEO‐BSPA was used as a macro‐RAFT agent for the copolymerization of styrene (St) and 2‐hydroxyethyl methacrylate (HEMA) using 2,2‐azobisisobutyronitrile as initiator. The molecular weight of copolymer PEO‐b‐P(St‐co‐HEMA) increased with the monomer conversion, but the molecular weight distribution was a little wide. The influence of molecular weight of macro‐RAFT agent on the polymerization procedure was discussed. The ROP of ε‐caprolactone was then completed by initiation of hydroxyl groups of the PEO‐b‐P(St‐co‐HEMA) precursors in the presence of stannous octoate (Sn(Oct)2). Thus, the amphiphilic copolymer of linear PEO linked with comb‐like P(St‐co‐HEMA)‐g‐PCL was obtained. The final and intermediate products were characterized in detail by NMR, GPC, and UV. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 467–476, 2006
Synthesis of well‐defined naphthalene and photo‐labile group‐labeled polystyrene via ATRP
Authors: Zhang Wei , Zhou Nianchen , Zhu Jian , Sun Bin , Zhu Xiulin
Published: November 2005

The atom transfer radical polymerizations of styrene were successfully carried out in bulk and solution, respectively, at 115 °C, with a novel photoiniferter reagent, (1‐naphthyl)methyl N,N‐diethyldithiocarbamate (NMDC), as an initiator in the presence of copper (I) bromide and N,N,N′,N″,N″‐pentamethyldiethylenetriamine. The results showed that NMDC was an effective initiator with high initiation efficiency for ATRP of St. The polymerization rate was first‐order with respect to the monomer concentration and the molecular weights of the obtained polystyrene (PS) increased linearly with the monomer conversion, with very narrow molecular weight distributions (Mw/Mn = 1.07–1.29). The functionalized naphthalene‐labeled PS bearing N,N‐(diethylamino)dithiocarbamoyl group which was confirmed by 1H NMR analysis, and chain extension of the PS exhibited fluorescence and ultraviolet absorption in chloroform (CHCl3). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 510–518, 2006
Dibenzyl trithiocarbonate mediated reversible addition–fragmentation chain transfer polymerization of acrylonitrile
Authors: Liu Xiao‐Hui , Zhang Gui‐Bao , Lu Xian‐Feng , Liu Jing‐Yu , Pan Ding , Li Yue‐Sheng
Published: November 2005

Reversible addition–fragmentation chain transfer polymerization has been successfully applied to polymerize acrylonitrile with dibenzyl trithiocarbonate as the chain‐transfer agent. The key to success is ascribed to the improvement of the interchange frequency between dormant and active species through the reduction of the activation energy for the fragmentation of the intermediate. The influence of several experimental parameters, such as the molar ratio of the chain‐transfer agent to the initiator [azobis(isobutyronitrile)], the molar ratio of the monomer to the chain‐transfer agent, and the monomer concentration, on the polymerization kinetics and the molecular weight as well as the polydispersity has been investigated in detail. Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and 1H NMR analyses have confirmed the chain‐end functionality of the resultant polymer. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 490–498, 2006
Neodymium oxide‐assisted melt free‐radical grafting of maleic anhydride on isotactic‐polypropylene by reactive extrusion
Authors: Zhu Lianchao , Tang Gongben , Shi Qiang , Cai Chuanlun , Yin Jinghua
Published: November 2005

Rare earth oxide, neodymium oxide (Nd2O3), ‐assisted melt free‐radical grafting of maleic anhydride (MAH) on isotactic‐polypropylene (i‐PP) was carried out by reactive extrusion. The experimental results reveal that the addition of Nd2O3 into reactive system leads to an enhancement of the grafting degree of MAH, along with an elevated degradation of i‐PP matrix. When Nd2O3 content is 4.5 mmol %, the increment of the grafting degree of MAH (maximally) is up to about 30% compared with that of the related system without adding Nd2O3, while the severest degradation of i‐PP matrix simultaneously occurs. On the basis of the reaction mechanism of PP‐g‐MAH proposed before, the sequence of β‐scission and grafting reaction is discussed in detail. It is found that, for the reactive system studied, most tertiary macroradicals first undergo β‐scission, and then, grafting reaction with MAH takes place at the new radical chain ends. The imported Nd2O3 has no effect on the aforementioned reaction mechanism, whereas it enhances the initiating efficiency of the initiator, dicumyl peroxide (DCP). We tentatively explain the experimental results by means of synergistic effect between DCP and Nd2O3. It is calculated that the synergistic effect is maximal when the molar ratio of DCP to Nd2O3 is approximately 1:6. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 134–142, 2006
Enhancing the electroluminescent efficiency of poly{5‐methoxy‐2‐[(2′‐ethyl‐hexyl)‐oxy]‐p‐phenylenevinylene}/poly(2,3‐diphenyl‐5‐octyl‐p‐phenylenevinylene) polyblends by the introduction of chemical bonding through a thermal treatment
Authors: Chow Hsuan‐Liang , Lin King‐Fu , Wang Ding‐Chang
Published: November 2005

A significant improvement in the electroluminescence (EL) properties was observed for a poly{5‐methoxy‐2‐[(2′‐ethyl‐hexyl)‐oxy]‐p‐phenylenevinylene} (MEH–PPV)/poly(2,3‐diphenyl‐5‐octyl‐p‐phenylenevinylene) (DPO–PPV) blend after a thermal treatment at 200 °C for 2 h in vacuo to furnish the chemical bonding between polymer chains. 1H NMR spectroscopy and two‐photon excitation microscopy revealed that the chemical bonding turned the immiscible polyblend into a system more like a block copolymer with a vertically segregated morphology. Because both the lowest unoccupied molecular orbital and highest occupied molecular orbital levels of MEH–PPV in the wetting layer were higher than those of DPO–PPV in the upper layer, the heterojunction between the two layers of the polymers fit the category of so‐called type II heterojunctions. As a result, the turn‐on voltage of the polymer light‐emitting diode prepared with the thermally treated polyblend decreased to ∼0.6 V, and the EL emission intensities and quantum efficiencies increased to about 4 times those of the untreated polyblend. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 62–69, 2006
Damage effects of 120‐keV electron radiation on AG‐80 resin
Authors: Yu Gao , Shangli Dong , Dezhuang Yang , Shiyu He , Zhijun Li
Published: November 2005

AG‐80 epoxy resin, namely tetraglycidyl diaminodiphenyl methane (TGDDM), was irradiated with electrons of 120 keV. The results show that the irradiation leads to four major damage effects on the surface layer of the AG‐80 resin, including the discharging, mass loss, degradation, and carbon enrichment. With increasing fluence to 1.05 × 1016 cm−2, the mass loss ratio increases gradually, and then tends to level off. The mass loss behavior can be attributed to a combined effect of the formation of gaseous radiolytic products and a degraded layer, the surface ablation due to discharging, and the skin carbon enrichment. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 177–184, 2006
Novel temperature‐responsive water‐soluble copolymers based on 2‐hydroxyethylacrylate and vinyl butyl ether and their interactions with poly(carboxylic acids)
Authors: Mun Grigoriy A. , Nurkeeva Zauresh S. , Akhmetkalieva Gulnara T. , Shmakov Sergey N. , Khutoryanskiy Vitaliy V. , Cheon Lee Sang , Park Kinam
Published: November 2005

Novel water‐soluble amphiphilic copolymers have been synthesized by free radical copolymerization of 2‐hydroxyethylacrylate with vinyl butyl ether. In water these copolymers exhibit lower critical solution temperature, which depends on the content of hydrophobic vinyl butyl ether units. The interaction between these copolymers and poly(acrylic acid) or poly(methacrylic acid) in aqueous solutions results in formation of interpolymer complexes stabilized by hydrogen bonds and hydrophobic interactions. An increase in hydrophobicity of the copolymers leads to the enhancement of their complex formation ability with respect to poly(acrylic acid) and poly(methacrylic acid). Poly(methacrylic acid) forms stronger complexes with the copolymers when compared with poly(acrylic acid). The complexes exhibit dual sensitivity to pH‐ and temperature and this property may be easily adjusted regulating the strength of interaction. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 195–204, 2006
Chemical Vapor Deposition of Organosilicon Thin Films from Methylmethoxysilanes
Authors: Casserly Thomas B. , Gleason Karen K.
Published: November 2005

Summary: Plasma enhanced chemical vapor deposition was used to deposit organosilicate glass (OSG) thin films from trimethylmethoxysilane, dimethyldimethoxysilane, and methyltrimethoxysilane. Depositions were performed from the pure OSG precursor, as well as from mixtures where either oxygen or hydrogen was added to the gas feed. These films were analyzed via Fourier transform infrared spectroscopy (FTIR), variable angle spectroscopic ellipsometry (VASE), and electrical measurements. Reactions involved in the deposition of OSG thin films from methylmethoxysilanes with oxygen are not selective and lead to the undesirable loss of methyl functionality. Reducing chemistry achieved with hydrogen addition is selective, with hydrogen atoms reacting preferentially with the methoxy groups creating silanol or siloxyl radicals. This selectively forms bonds networking through condensation reactions without sacrificing the “built‐in” alkyl content of the precursor. Low‐k OSG thin films from methylmethoxysilanes and hydrogen were deposited via a low power, W/FM from 10.0 to 10.5 J/g dependent upon OSG precursor, PECVD process resulting in material dielectric constants ranging from 2.84 to 3.18.

Dielectric constant as a function of increasing methyl substitution in the silicon precursor (n) shown for discharges the pure precursor, and for the cases of gas mixtures with H2 and O2 (OMe≡methoxy, Me≡methyl).

magnified image

Dielectric constant as a function of increasing methyl substitution in the silicon precursor (n) shown for discharges the pure precursor, and for the cases of gas mixtures with H2 and O2 (OMe≡methoxy, Me≡methyl).
Prediction of transporter family from protein sequence by support vector machine approach
Authors: Lin H. H. , Han L. Y. , Cai C. Z. , Ji Z. L. , Chen Y. Z.
Published: November 2005

Transporters play key roles in cellular transport and metabolic processes, and in facilitating drug delivery and excretion. These proteins are classified into families based on the transporter classification (TC) system. Determination of the TC family of transporters facilitates the study of their cellular and pharmacological functions. Methods for predicting TC family without sequence alignments or clustering are particularly useful for studying novel transporters whose function cannot be determined by sequence similarity. This work explores the use of a machine learning method, support vector machines (SVMs), for predicting the family of transporters from their sequence without the use of sequence similarity. A total of 10,636 transporters in 13 TC subclasses, 1914 transporters in eight TC families, and 168,341 nontransporter proteins are used to train and test the SVM prediction system. Testing results by using a separate set of 4351 transporters and 83,151 nontransporter proteins show that the overall accuracy for predicting members of these TC subclasses and families is 83.4% and 88.0%, respectively, and that of nonmembers is 99.3% and 96.6%, respectively. The accuracies for predicting members and nonmembers of individual TC subclasses are in the range of 70.7–96.1% and 97.6–99.9%, respectively, and those of individual TC families are in the range of 60.6–97.1% and 91.5–99.4%, respectively. A further test by using 26,139 transmembrane proteins outside each of the 13 TC subclasses shows that 90.4–99.6% of these are correctly predicted. Our study suggests that the SVM is potentially useful for facilitating functional study of transporters irrespective of sequence similarity. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Unique GMP‐binding site in Mycobacterium tuberculosis guanosine monophosphate kinase
Authors: Hible Guillaume , Christova Petya , Renault Louis , Seclaman Edward , Thompson Andrew , Girard Eric , Munier‐Lehmann Hélène , Cherfils Jacqueline
Published: November 2005

Bacterial nucleoside monophosphate (NMP) kinases, which convert NMPs to nucleoside diphosphates (NDP), are investigated as potential antibacterial targets against pathogenic bacteria. Herein, we report the biochemical and structural characterization of GMP kinase from Mycobacterium tuberculosis (GMPKMt). GMPKMt is a monomer with an unusual specificity for ATP as a phosphate donor, a lower catalytic efficiency compared with eukaryotic GMPKs, and it carries two redox‐sensitive cysteines in the central CORE domain. These properties were analyzed in the light of the high‐resolution crystal structures of unbound, GMP‐bound, and GDP‐bound GMPKMt. The latter structure was obtained in both an oxidized form, in which the cysteines form a disulfide bridge, and a reduced form which is expected to correspond to the physiological enzyme. GMPKMt has a modular domain structure as most NMP kinases. However, it departs from eukaryotic GMPKs by the unusual conformation of its CORE domain, and by its partially open LID and GMP‐binding domains which are the same in the apo‐, GMP‐bound, and GDP‐bound forms. GMPKMt also features a unique GMP binding site which is less close‐packed than that of mammalian GMPKs, and in which the replacement of a critical tyrosine by a serine removes a catalytic interaction. In contrast, the specificity of GMPKMt for ATP may be a general feature of GMPKs because of an invariant structural motif that recognizes the adenine base. Altogether, differences in domain dynamics and GMP binding between GMPKMt and mammalian GMPKs should reveal clues for the design of GMPKMt‐specific inhibitors. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Target selection and deselection at the Berkeley Structural Genomics Center
Authors: Chandonia John‐Marc , Kim Sung‐Hou , Brenner Steven E.
Published: November 2005

At the Berkeley Structural Genomics Center (BSGC), our goal is to obtain a near‐complete structural complement of proteins in the minimal organisms Mycoplasma genitalium and M. pneumoniae, two closely related pathogens. Current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. We report on the process used to select these proteins, as well as our target deselection procedure. Target deselection reduces experimental effort by eliminating targets similar to those recently solved by the structural biology community or other centers. We measure the impact of the 69 structures solved at the BSGC as of July 2004 on structure prediction coverage of the M. pneumoniae and M. genitalium proteomes. The number of Mycoplasma proteins for which the fold could first be reliably assigned based on structures solved at the BSGC (24 M. pneumoniae and 21 M. genitalium) is approximately 25% of the total resulting from work at all structural genomics centers and the worldwide structural biology community (94 M. pneumoniae and 86 M. genitalium) during the same period. As the number of structures contributed by the BSGC during that period is less than 1% of the total worldwide output, the benefits of a focused target selection strategy are apparent. If the structures of all current targets were solved, the percentage of M. pneumoniae proteins for which folds could be reliably assigned would increase from approximately 57% (391 of 687) at present to around 80% (550 of 687), and the percentage of the proteome that could be accurately modeled would increase from around 37% (254 of 687) to about 64% (438 of 687). In M. genitalium, the percentage of the proteome that could be structurally annotated based on structures of our remaining targets would rise from 72% (348 of 486) to around 76% (371 of 486), with the percentage of accurately modeled proteins would rise from 50% (243 of 486) to 58% (283 of 486). Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Misfolding of the amyloid β‐protein: A molecular dynamics study
Authors: Flöck Dagmar , Colacino Stefano , Colombo Giorgio , Di Nola Alfredo
Published: November 2005

Amyloid β‐proteins spontaneously aggregate and build plaques in the brains of Alzheimer's disease patients. The polypeptide has been the subject of extensive in vitro and computational research. Still, the pathway to aggregational forms and their exact conformations remain largely unclear. Here we present an extensive molecular dynamics approach simulating the protein in various temperatures, pH conditions, and with different charge states of the N‐ and C‐termini, thus exploring the conformational space of the protein at large. Our results show that the protein is able to sample different conformations, many of which are rich in β structure content, and all characterized by a rapid loss of helix 1 that converts into a π‐helix, while helix 2 samples random and β‐rich structures. Moreover, a hydrophobic cluster is observed involving Val18, Phe19, Ala21, and Gly25. The results are carefully compared with recent NMR and spectroscopic data, and are in global agreement with the experimental findings. Proteins 2006. © 2005 Wiley‐Liss, Inc.
B. subtilis ykuD protein at 2.0 Å resolution: Insights into the structure and function of a novel, ubiquitous family of bacterial enzymes
Authors: Bielnicki Jakub , Devedjiev Yancho , Derewenda Urszula , Dauter Zbigniew , Joachimiak Andrzej , Derewenda Zygmunt S.
Published: November 2005

The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 Å resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram‐positive and Gram‐negative bacteria. The deduced amino acid sequence reveals the presence of an N‐terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys‐containing motif of hitherto unknown structure. As the wild‐type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112‐residue‐long C‐terminal domain has a novel tertiary fold consisting of a β‐sandwich with two mixed sheets, one containing five strands and the other, six strands. The two β‐sheets form a cradle capped by an α‐helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Dynamics of the trimeric AcrB transporter protein inferred from a B‐factor analysis of the crystal structure
Authors: Lu W.C. , Wang C.Z. , Yu E.W. , Ho K.M.
Published: November 2005

The Escherichia coli AcrB multidrug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown. Herein, we describe normal mode analyses to study important regions for drug recognition and extrusion in this transporter. Based on the X‐ray structure of AcrB, an elastic network model has been able to correct errors arising from crystal imperfection in the experimental B‐factors. The results allow us to understand the functional dynamics of this membrane protein. It is expected that this technique can be applied to other membrane proteins with known structures. Proteins 2006. © 2005 Wiley‐Liss, Inc.
SimFold energy function for de novo protein structure prediction: Consensus with Rosetta
Authors: Fujitsuka Yoshimi , Chikenji George , Takada Shoji
Published: November 2005

Predicting protein tertiary structures by in silico folding is still very difficult for proteins that have new folds. Here, we developed a coarse‐grained energy function, SimFold, for de novo structure prediction, performed a benchmark test of prediction with fragment assembly simulations for 38 test proteins, and proposed consensus prediction with Rosetta. The SimFold energy consists of many terms that take into account solvent‐induced effects on the basis of physicochemical consideration. In the benchmark test, SimFold succeeded in predicting native structures within 6.5 Å for 12 of 38 proteins; this success rate was the same as that by the publicly available version of Rosetta (ab initio version 1.2) run with default parameters. We investigated which energy terms in SimFold contribute to structure prediction performance, finding that the hydrophobic interaction is the most crucial for the prediction, whereas other sequence‐specific terms have weak but positive roles. In the benchmark, well‐predicted proteins by SimFold and by Rosetta were not the same for 5 of 12 proteins, which led us to introduce consensus prediction. With combined decoys, we succeeded in prediction for 16 proteins, four more than SimFold or Rosetta separately. For each of 38 proteins, structural ensembles generated by SimFold and by Rosetta were qualitatively compared by mapping sampled structural space onto two dimensions. For proteins of which one of the two methods succeeded and the other failed in prediction, the former had a less scattered ensemble located around the native. For proteins of which both methods succeeded in prediction, often two ensembles were mixed up. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Pressure effect on the stability and the conformational dynamics of the D‐Galactose/D‐Glucose‐binding protein from Escherichia coli
Authors: Marabotti Anna , Herman Petr , Staiano Maria , Varriale Antonio , de Champdoré Marcella , Rossi Mosè , Gryczynski Zygmunt , D'Auria Sabato
Published: November 2005

The effect of the pressure on the structure and stability of the D‐Galactose/D‐Glucose binding protein (GGBP) from Escherichia coli was studied by steady‐state and time‐resolved fluorescence spectroscopy, and the ability of glucose ligand to stabilize the GGBP structure was also investigated. Steady‐state fluorescence experiments showed a marked quenching of fluorescence emission of GGBP in the absence of glucose. Instead, the presence of glucose seems to stabilize the structure of GGBP at low and moderate pressure values. Time‐resolved fluorescence measurements showed that the GGBP τmean in the absence of glucose varies significantly up to 600 bar, while in the presence of the ligand it is almost unaffected by pressure increase up to 600 bar. The effect of the pressure on GGBP was also studied by molecular dynamics simulations. The simulation data support the spectroscopic results and confirm that the presence of glucose is able to contrast the negative effects of pressure on the protein structure. Taken together, the spectroscopic and computer simulation studies suggest that at pressure values up to 2000 bar the structure of GGBP in the absence of glucose remains folded, but a significant perturbation of the protein secondary structures can be detected. The binding of glucose reduces the negative effect of pressure on protein structure and confers protection from perturbation especially at moderate pressure values. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: Implications for drug design
Authors: Gabelli Sandra B. , McLellan Jason S. , Montalvetti Andrea , Oldfield Eric , Docampo Roberto , Amzel L. Mario
Published: November 2005

Typanosoma cruzi, the causative agent of Chagas disease, has recently been shown to be sensitive to the action of the bisphosphonates currently used in bone resorption therapy. These compounds target the mevalonate pathway by inhibiting farnesyl diphosphate synthase (farnesyl pyrophosphate synthase, FPPS), the enzyme that condenses the diphosphates of C5 alcohols (isopentenyl and dimethylallyl) to form C10 and C15 diphosphates (geranyl and farnesyl). The structures of the T. cruzi FPPS (TcFPPS) alone and in two complexes with substrates and inhibitors reveal that following binding of the two substrates and three Mg2+ ions, the enzyme undergoes a conformational change consisting of a hinge‐like closure of the binding site. In this conformation, it would be possible for the enzyme to bind a bisphosphonate inhibitor that spans the sites usually occupied by dimethylallyl diphosphate (DMAPP) and the homoallyl moiety of isopentenyl diphosphate. This observation may lead to the design of new, more potent anti‐trypanosomal bisphosphonates, because existing FPPS inhibitors occupy only the DMAPP site. In addition, the structures provide an important mechanistic insight: after its formation, geranyl diphosphate can swing without leaving the enzyme, from the product site to the substrate site to participate in the synthesis of farnesyl diphosphate. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Limited validity of group additivity for the folding energetics of the peptide group
Authors: Avbelj Franc , Baldwin Robert L.
Published: November 2005

The principle of group additivity is a standard feature of analyses of the energetics of protein folding, but it is known that it may not always be valid for the polar peptide group. The neighboring residue effect shows that group additivity is not strictly valid for a heteropeptide. We show here that group additivity fails seriously for peptide groups close to either peptide end, even for a homopeptide that has blocked end groups with no formal charges involved. The failure of group additivity is caused by the electrostatic character of the solvation of peptide polar groups and is illustrated with values of the electrostatic solvation free energy (ESF) calculated by DelPhi. Solvation free energies and enthalpies are known experimentally for monoamides and are often used to model the solvation of peptide groups, but ESF results show that monoamide values are very different from those of peptide groups. A main cause of the difference is that peptide solvation depends on the dipole–dipole interactions made between adjacent peptide groups, which vary with peptide conformation. Ligands that interact with the peptide backbone by an electrostatic mechanism could show a similar peptide end effect, and hydrogen exchange results from the literature confirm that exchange rates are position‐dependent close to peptide ends. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Natively unfolded regions of the vertebrate fibrinogen molecule
Authors: Doolittle Russell F. , Kollman Justin M.
Published: November 2005

Although it has long been realized that a large portion of the fibrinogen α chain has little if any defined structure, the physiological significance of this flexible appendage remains mysterious. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family
Authors: Adekoya Olayiwola A. , Helland Ronny , Willassen Nils‐Peder , Sylte Ingebrigt
Published: November 2005

Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence‐structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold‐adapted enzymes have a more flexible three‐dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation–π electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The CDR1 of the human λVI light chains adopts a new canonical structure
Authors: del Pozo Yauner L. , Ortiz E. , Becerril B.
Published: November 2005

We performed a comparative analysis of the conformation of the CDR1 of the human λVI variable domains JTO and WIL and the equivalent loop of the λI light chains RHE and KOL, which are representative of the type I canonical structure for λ light chains. On the basis of the differences found in the main chain conformation, as well as the identity of the residues at key positions, we showed that the L1 of some λVI light chains adopts a conformation that represents a new type of canonical structure. The conformation of the L1 of those λVI light chains, is primarily determined by the presence of an Arg residue at position 25. The analysis of the λVI light chain sequences so far reported, showed that near 25% of those proteins have Gly at position 25 instead of Arg, which represents an allotypic variant of the λVI variable locus. The presence of Gly at position 25 in the L1 of λVI light chains would imply a different conformation for this loop. Additionally, the position 68 in λVI light chains, which is at the top of the FR3 loop, showed such spatial orientation and variability that suggested its participation in the conformation of the antigen recognition surface in this subgroup of λ chains. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Explosion of a hot‐oil circuit as a consequence of process, plant engineering, and management shortcomings
Authors: Piccinini N. , Demichela M.
Published: November 2005

On June 3, 1993, an explosion occurred at the Mediterranea refinery, in Milazzo, Sicily. Seven people died and eighteen people were injured with burns. An explosion in the accumulation tank 27V‐16 involved hot‐oil circuits subserving the refining units Topping 3, Topping 4, and HDT‐RC. The explosion was caused by a sudden overpressure in the 27V‐16 tank, probably as a result of the sudden vaporization of a small quantity of water. Shortcomings in the process design and in the management were at the origin of the accident, in particular:

Some process choices undertaken a couple of years before the accident, such as the use of gas oil from a Topping column in place of diathermic oil and the use of a combustible gas in place of nitrogen.

Some operational mistakes in the 13F‐2 oven conduction and the failure (or inadequacy or exclusion) of control systems or automatic and manual safety devices.

A detailed Fault Tree connects the process, design and management shortcomings identified. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2006
Electric properties of single‐crystal PMN‐31% PT/epoxy 1–3 piezoelectric composites
Authors: Wang Haixia , Xu Haiqing , He Tianhou , Zhao Xiangyong , Luo Haosu , Yin Zhiwen
Published: November 2005

PMN‐31% PT/expoxy 1–3 piezoelectric composites with a different volume fraction of PMN‐31% PT single crystals from 0.4 to 0.7 have been studied as regards fabrication and electric properties. The 〈001〉 oriented piezoelectric composites exhibit functional properties of low dielectric constant, high electromechanical coupling coefficient (0.80), and low acoustic impendence compared to the 〈110〉 oriented ones. The vibration characteristics of the piezoelectric composites strongly depend on the rod geometry and the volume fraction. The results obtained indicate that these piezoelectric composites with better global properties are promising candidates for biomedical imaging and underwater transducer applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study of prelocalized graphite/styrene acrylonitrile conducting composites for device applications
Authors: Sachdev V. K. , Panwar Varij , Singh H. , Mehra N. C. , Mehra R. M.
Published: November 2005

Conductive polymer composites were prepared by compression molding of prelocalized graphite on to styrene acrylonitrile (SAN) particles. The electrical conductivity is found to be strongly dependent on the graphite content. Three different series were prepared for different processing and material parameters. A low percolation threshold has been noticed when only 1 wt% of graphite is incorporated. Resistivity as low as ∼14 Ω cm has been achieved in a composite with SAN resin particles of 180–212 µm size and graphite 10–20 µm at 90 °C, 105 MPa and 15 min. An electrically conducting network of graphite channels has been observed using scanning electron microscopy. V–I characteristic reveals that at a lower percentage of graphite the increase in current with increase in electric field is due to the hopping/tunneling of electrons, while for higher percentages of graphite ohmic behavior similar to metals has been observed. The data has been analyzed using percolation model. The value of the exponent t that determines the increase in electrical conductivity above the percolation threshold is found to be close to the values given in the literature. The theoretically calculated values of conductivity are found to be in satisfactory agreement with the experimental ones. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling of spatially inhomogeneous solar cells by a multi‐diode approach
Authors: Grabitz P. O. , Rau U. , Werner J. H.
Published: November 2005

An equivalent circuit model consisting of parallel connected diodes with different electronic quality simulates the electronic properties of solar cells with spatially inhomogeneous material quality. Variations of the local saturation current density result in a degradation of the open circuit voltage, the fill factor and, in consequence, of the overall power conversion efficiency. However, a local series resistance introduced into this network limits this degradation by preventing areas with high saturation current density to dominate the electronic losses of the entire device. Analyzing the integral current/voltage‐curves of the networks shows the diode ideality larger than unity to result from resistive limitations to the spatially inhomogeneous current flow. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Twinning and extended defects in hcp metals with large c/a ratio: modelling and microscopic observations
Authors: Béré A. , Braisaz T. , Ruterana P. , Nouet G.
Published: November 2005

In hexagonal metals of largest c/a ratio, experimental observations hardly agree with the theoretical models of extended defects. For Zn and Cd, we have developed a semi‐empirical tight‐binding method to calculate the energy of extended defects. It was then possible to obtain a good correlation for polytypes or basal stacking faults. For the (10$ \bar 1 $2) twin, two possible interfaces have been shown to be stable in agreement with the available experimental results for Zn. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Deformation mechanisms of silicon during nanoscratching
Authors: Gassilloud R. , Ballif C. , Gasser P. , Buerki G. , Michler J.
Published: November 2005

The deformation mechanisms of silicon {001} surfaces during nanoscratching were found to depend strongly on the loading conditions. Nanoscratches with increasing load were performed at 2 µm/s (low velocity) and 100 µm/s (high velocity). The load‐penetration‐distance curves acquired during the scratching process at low velocity suggests that two deformation regimes can be defined, an elasto‐plastic regime at low loads and a fully plastic regime at high loads. High resolution scanning electron microscopy of the damaged location shows that the residual scratch morphologies are strongly influenced by the scratch velocity and the applied load. Micro‐Raman spectroscopy shows that after pressure release, the deformed volume inside the nanoscratch is mainly composed of amorphous silicon and Si‐XII at low scratch speeds and of amorphous silicon at high speeds. Transmission electron microscopy shows that Si nanocrystals are embedded in an amorphous matrix at low speeds, whereas at high speeds the transformed zone is completely amorphous. Furthermore, the extend of the transformed zone is almost independent of the scratching speed and is delimited by a dislocation rich area that extends about as deep as the contact radius into the surface. To explain the observed phase and defect distribution a contact mechanics based decompression model that takes into account the load, the velocity, the materials properties and the contact radius in scratching is proposed. It shows that the decompression rate is higher at low penetration depth, which is consistent with the observation of amorphous silicon in this case. The stress field under the tip is computed using an elastic contact mechanics model based on Hertz’s theory. The model explains the observed shape of the transformed zone and suggests that during load increase, phase transformation takes place prior to dislocation nucleation. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)