bluuebunny/crossref_metadata_2025 huggingface dataset:
A sensitive magnetic bead method for the detection and identification of tyrosine phosphorylation in proteins by MALDI‐TOF/TOF MS
Authors: Condina Mark R. , Guthridge Mark A. , McColl Shaun R. , Hoffmann Peter
Published: June 2009

Phosphorylation is one of the most important PTMs and is estimated to occur on 30% of the mammalian proteome. Its perturbed regulation has been implicated in many pathologies. The rarity of phosphotyrosine compared with phosphoserine or phosphothreonine is prompting the development of more sensitive approaches because proteomic technologies that are currently used to assess tyrosine phosphorylation in proteins are inadequate, identifying only a fraction of the predicted tyrosine phosphoproteome. Here we describe the development of a reproducible, high‐sensitivity methodology for the detection and mapping of phosphotyrosine residues by MS. The anti‐phosphotyrosine antibody 4G10 was coupled covalently to super para‐magnetic beads or by affinity to super para‐magnetic beads with protein G covalently attached. Using this approach, we successfully enriched phosphotyrosine peptides mixed with non‐phosphorylated peptides at a ratio of up to 1:200, enabling detection at a level representing the highest sensitivity reported for tyrosine phosphorylation. The beads were subsequently used to enrich tyrosine phosphopeptides from a digest of the in vitro‐phosphorylated recombinant β‐intracellular region of the granulocyte‐macrophage colony‐stimulating factor receptor, which was subsequently analysed by MALDI‐TOF/TOF MS. Our results define this methodology as a sensitive approach for tyrosine phosphoproteome analysis.
New changes in the plasma‐membrane‐associated proteome of rice roots under salt stress
Authors: Cheng Yanwei , Qi Yaocheng , Zhu Qian , Chen Xi , Wang Ning , Zhao Xin , Chen Haiyan , Cui Xiangju , Xu Langlai , Zhang Wei
Published: June 2009

To gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (Oryza sativa) root plasma‐membrane‐associated proteins following treatment with 150 mmol/L NaCl. With or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt‐sensitive rice cultivar, Wuyunjing 8, were purified by PEG aqueous two‐phase partitioning, and plasma‐membrane‐associated proteins were separated by IEF/SDS‐PAGE using an optimized rehydration buffer. Comparative analysis of three independent biological replicates revealed that the expressions of 18 proteins changed by more than 1.5‐fold in response to salt stress. Of these proteins, nine were up‐regulated and nine were down‐regulated. MS analysis indicated that most of these membrane‐associated proteins are involved in important physiological processes such as membrane stabilization, ion homeostasis, and signal transduction. In addition, a new leucine‐rich‐repeat type receptor‐like protein kinase, OsRPK1, was identified as a salt‐responding protein. Immuno‐blots indicated that OsRPK1 is also induced by cold, drought, and abscisic acid. Using immuno‐histochemical techniques, we determined that the expression of OsRPK1 was localized in the plasma membrane of cortex cells in roots. The results suggest that different rice cultivars might have different salt stress response mechanisms.
The hemolymph proteome of the honeybee: Gel‐based or gel‐free?
Authors: Bogaerts Annelies , Baggerman Geert , Vierstraete Evy , Schoofs Liliane , Verleyen Peter
Published: June 2009

The honeybee has an invaluable economic impact and is a model for studying immunity, development and social behavior. The recent sequencing and annotation of the honeybee genome facilitates the study of its hemolymph, which reflects the physiological condition and mediates immune responses. We aimed at making a proteomic reference map of honeybee hemolymph and compared gel‐free and gel‐based techniques. One hundered and four 2‐DE spots corresponding to 62 different proteins were identified. Eight identical 2‐DLC experiments resulted in the identification of 32 unique proteins. One repeat was clearly not representative for the potential of the given 2‐DLC setup. Only 27% of the identified hemolymph proteins were found by both techniques. In addition, we found proteins of three different viruses which creates possibilities for biomarker design. Future hemolymph studies will benefit from this work.
Proteomic analysis on the temperature‐dependent complexes in Thermoanaerobacter tengcongensis
Authors: Meng Bo , Qian Zhong , Wei Fan , Wang Weiwei , Zhou Chuanqi , Wang Zhuowei , Wang Quanhui , Tong Wei , Wang Qian , Ma Yanhe , Xu Ningzhi , Liu Siqi
Published: June 2009

It is generally accepted that protein complexes play an active role in avoiding the protein degradation of the thermophiles. Thermoanaerobacter tengcongensis was cultured at three different temperatures (55, 75 and 80°C) and the extracts of protein complexes were prepared. Through blue native PAGE, the changes of the relative band volumes in response to different temperatures were semi‐quantitatively compared and six temperature‐dependent bands were obtained. These bands were excised, digested with trypsin and then analyzed with MS for the identification of protein components. With the combination of the proteins identified by LC MS/MS and MALDI TOF/TOF MS, a total of 92 unique proteins were ascertained in these complexes. Besides, some protein components were examined with Western blot, which gave us insights into the survival mechanism of thermophiles. These included (i) the composition of complex at 80°C was significantly different from that at the other two temperatures; (ii) HSPs presented in all temperature‐dependent complexes; (iii) several proteins associated with the functional pathways existed in the same complexes, indicating that the complex structure provided facility for the functional efficiency.
Identification and comparative analysis of the structural proteomes of ϕKZ and EL, two giant Pseudomonas aeruginosa bacteriophages
Authors: Lecoutere Elke , Ceyssens Pieter‐Jan , Miroshnikov Konstantin A. , Mesyanzhinov Vadim V. , Krylov Victor N. , Noben Jean‐Paul , Robben Johan , Hertveldt Kirsten , Volckaert Guido , Lavigne Rob
Published: June 2009

Giant bacteriophages ϕKZ and EL of Pseudomonas aeruginosa contain 62 and 64 structural proteins, respectively, identified by ESI‐MS/MS on total virion particle proteins. These identifications verify gene predictions and delineate the genomic regions dedicated to phage assembly and capsid formation (30 proteins were identified from a tailless ϕKZ mutant). These data form the basis for future structural studies and provide insights into the relatedness of these large phages. The ϕKZ structural proteome strongly correlates to that of Pseudomonas chlororaphis bacteriophage 201ϕ2‐1. Phage EL is more distantly related, shown by its 26 non‐conserved structural proteins and the presence of genomic inversions.
Multiplexed LC‐MS/MS analysis of horse plasma proteins to study doping in sport
Authors: Barton Chris , Beck Paul , Kay Richard , Teale Phil , Roberts Jane
Published: June 2009

The development of protein biomarkers for the indirect detection of doping in horse is a potential solution to doping threats such as gene and protein doping. A method for biomarker candidate discovery in horse plasma is presented using targeted analysis of proteotypic peptides from horse proteins. These peptides were first identified in a novel list of the abundant proteins in horse plasma. To monitor these peptides, an LC‐MS/MS method using multiple reaction monitoring was developed to study the quantity of 49 proteins in horse plasma in a single run. The method was optimised and validated, and then applied to a population of race‐horses to study protein variance within a population. The method was finally applied to longitudinal time courses of horse plasma collected after administration of an anabolic steroid to demonstrate utility for hypothesis‐driven discovery of doping biomarker candidates.
Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis
Authors: Dumas Emilie , Desvaux Mickaël , Chambon Christophe , Hébraud Michel
Published: June 2009

WhileListeria monocytogenesis responsible for listeriosis, it is also a saprophytic species with exceptional survival aptitudes. Secreted proteins are one of the main tools used by bacteria to interact with their environment. In order to take into account the biodiversity ofL. monocytogenesspecies, exoproteomic analysis was carried out on 12 representative strains. Following 2‐DE and MALDI‐TOF MS, a total of 151 spots were identified and corresponded to 60 non‐orthologous proteins. To categorize and analyze these proteomic data, a rational bioinformatic approach predicting final subcellular localization was carried out. Fifty‐two out of the 60 proteins identified (86.7%) were indeed predicted as localized in the extracellular milieu (gene ontology (GO): 0005576). Most of them (65.4%) were actually predicted as secretedviathe Sec translocon. Comparative analysis allowed for proteins found in all or only in a subset ofL. monocytogenesstrains to be defined. While the core exoproteome included most proteins related to bacterial virulence, cell wall biogenesis, as well as proteins secreted by unknown pathways, a slight variation in the protein members of these categories were observed and constituted the variant exoproteome. This investigation resulted in the first definition of the core and variant exoproteomes ofL. monocytogeneswhere corollaries on bacterial physiology are further discussed.
A novel fractionation method of the rough ER integral membrane proteins; Resident proteins versus exported proteins?
Authors: Sakai Kumiko , Hamanaka Ryoji , Yuki Hideo , Watanabe Makoto
Published: June 2009

We treated the high salt‐washed canine pancreatic rough ER (KRM) with 0.18% Triton X‐100, separated the extract from the residual membrane (0.18%Tx KRM), and processed the extract with SM‐2 beads to recover membrane proteins in proteoliposomes. To focus on integral membrane proteins, KRM, 0.18%Tx KRM and proteoliposomes were subjected to sodium carbonate treatment, and analyzed by 2‐D gel electrophoresis. Consequently we found that a distinct group of integral membrane protein of KRM preferentially extracted from the membrane and recovered in proteoliposomes did exist, while majority of KRM integral membrane proteins were fractionated in 0.18%Tx KRM, which retained the basic structure and functions of KRM. Protein identification showed that the former group was enriched with proteins exported from the ER and the latter group comprised mostly of ER resident proteins. This result will potentially affect the prevailing view of the ER membrane structure as well as protein sorting from the ER.
Application of quantitative immunoprecipitation combined with knockdown and cross‐linking to Chlamydomonas reveals the presence of vesicle‐inducing protein in plastids 1 in a common complex with chloroplast HSP90C
Authors: Heide Heinrich , Nordhues André , Drepper Friedel , Nick Sabine , Schulz‐Raffelt Miriam , Haehnel Wolfgang , Schroda Michael
Published: June 2009

Knowledge of the interaction partners of a protein of interest may provide important information on its function. Common to currently available tools for the identification of protein–protein interactions, however, is their high rates of false positives. Only recently an assay was reported that allowed for the unequivocal identification of protein–protein interactions in mammalian cells in a single experiment. This assay, termed quantitative immunoprecipitation combined with knockdown (QUICK), combines RNAi, stable isotope labeling with amino acids in cell culture, immunoprecipitation, and quantitative MS. We are using the unicellular green alga Chlamydomonas reinhardtii to understand the roles of chaperones in chloroplast biogenesis. The goal of this work was to apply QUICK to Chlamydomonas for the identification of novel interaction partners of vesicle‐inducing protein in plastids 1 (VIPP1), a protein required for the biosynthesis/maintenance of thylakoid membranes and known substrate of chloroplast HSP70B. We report here a robust QUICK protocol for Chlamydomonas that has been improved (i) by introducing a cross‐linking step (‐X) to improve protein complex stability and (ii) by including a control for the correction of unequal immunoprecipitation and/or labeling efficiencies. Using QUICK and cross‐linking we could verify that HSP70B and CGE1 form a complex with VIPP1 and could also demonstrate that chloroplast HSP90C is part of this complex. Moreover, we could show that the chaperones interact with VIPP1 also in membrane fractions.
A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: A case study using Glycine max
Authors: Krishnan Hari B. , Oehrle Nathan W. , Natarajan Savithiry S.
Published: June 2009

2‐D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non‐abundant proteins within seeds is difficult when 60–80% is storage proteins. Resolution can be improved through sample fractionation using separation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca2+ to precipitate soybean (Glycine max) seed storage globulins, glycinin and β‐conglycinin. This method removes 87±4% of the highly abundant seed proteins from the extract, allowing for 541 previously inconspicuous proteins present in soybean seed to be more detectable (volume increase of ≥50%) using fluorescent detection. Of those 541 enhanced spots, 197 increased more than 2.5‐fold when visualized with Coomassie. The majority of those spots were isolated and identified using peptide mass fingerprinting. Fractionation also provided detection of 63 new phosphorylated protein spots and enhanced the visibility of 15 phosphorylated protein spots, using 2‐D electrophoretic separation and an in‐gel phosphoprotein stain. Application of this methodology toward other legumes, such as peanut, bean, pea, alfalfa and others, also containing high amounts of storage proteins, was examined, and is reported here.
Integrated platform for manual and high‐throughput statistical validation of tandem mass spectra
Authors: Yu Kebing , Sabelli Anthony , DeKeukelaere Lisa , Park Richard , Sindi Suzanne , Gatsonis Constantine A. , Salomon Arthur
Published: June 2009

As proteomic data sets increase in size and complexity, the necessity for database‐centric software systems able to organize, compare, and visualize all the proteomic experiments in a lab grows. We recently developed an integrated platform called high‐throughput autonomous proteomic pipeline (HTAPP) for the automated acquisition and processing of quantitative proteomic data, and integration of proteomic results with existing external protein information resources within a lab‐based relational database called PeptideDepot. Here, we introduce the peptide validation software component of this system, which combines relational database‐integrated electronic manual spectral annotation in Java with a new software tool in the R programming language for the generation of logistic regression spectral models from user‐supplied validated data sets and flexible application of these user‐generated models in automated proteomic workflows. This logistic regression spectral model uses both variables computed directly from SEQUEST output in addition to deterministic variables based on expert manual validation criteria of spectral quality. In the case of linear quadrupole ion trap (LTQ) or LTQ‐FTICR LC/MS data, our logistic spectral model outperformed both XCorr (242% more peptides identified on average) and the X!Tandem E‐value (87% more peptides identified on average) at a 1% false discovery rate estimated by decoy database approach.
Oxalic acid‐mediated stress responses in Brassica napus L.
Authors: Liang Yue , Strelkov Stephen E. , Kav Nat N. V.
Published: June 2009

Oxalic acid (OA) occurs extensively in nature and plays diverse roles, especially in pathogenic processes involving various plant pathogens. However, proteome changes and modifications of signaling and oxidative network of plants in response to OA are not well understood. In order to investigate the responses of Brassica napus toward OA, a proteome analysis was conducted employing 2‐DE with MS/MS. A total of 37 proteins were identified as responding to OA stress, of which 13 were up‐regulated and 24 were down‐regulated. These proteins were categorized into several functional groups including protein processing, RNA processing, photosynthesis, signal transduction, stress response, and redox homeostasis. Investigation of the effect of OA on phytohormone signaling and oxidative responses revealed that jasmonic acid‐, ethylene‐, and abscisic acid‐mediated signaling pathways appear to increase at later time points, whereas those pathways mediated by salicylic acid appear to be suppressed. Moreover, the activities of the antioxidant enzymes catalase, peroxidase, superoxide dismutase and oxalic acid oxidase, but not NADPH oxidase, were suppressed by OA stress. Our findings are discussed within the context of the proposed role(s) of OA during infection by Sclerotinia sclerotiorum and subsequent disease progression.
Quantitation of glycogen synthase kinase‐3 sensitive proteins in neuronal membrane rafts
Authors: Thompson Andrew J. , Williamson Ritchie , Schofield Emma , Stephenson John , Hanger Diane , Anderton Brian
Published: June 2009

We report a quantitative proteomic study to investigate the changes induced in membrane rafts by the inhibition of glycogen synthase kinase‐3. Sensitive quantitation of membrane raft proteins using isobaric tagging chemistries was enabled by a novel hybrid proteomic method to isolate low‐microgram (10–30 μg) membrane raft protein preparations as unresolved bands in a low‐density acrylamide gel. Samples were in‐gel digested, differentially tagged and combined for 2‐D LC and quantitative MS. Analysis of hippocampal membrane preparations using this approach resulted in a sixfold increase in sensitivity and a threefold increase in the number of quantifiable proteins compared with parallel processing using a traditional in‐solution method. Quantitative analysis of membrane raft preparations from a human neuronal cell line treated with glycogen synthase kinase‐3 inhibitors SB415286 or lithium chloride, that have been reported to modulate processing of the Alzheimer amyloid precursor protein, identified several protein changes. These included decreases in lamin B1 and lamin B receptor, as well as increases in several endosome regulating rab proteins, rab5, rab7 and rab11 that have been implicated in processing of the amyloid precursor protein in Alzheimer's disease.
Mapping of the chaperone AcrH binding regions of translocators AopB and AopD and characterization of oligomeric and metastable AcrH‐AopB‐AopD complexes in the type III secretion system of Aeromonas hydrophila
Authors: Tan Yih Wan , Yu Hong Bing , Sivaraman J. , Leung Ka Yin , Mok Yu‐Keung
Published: June 2009

In the type III secretion system (T3SS) of Aeromonas hydrophila, AcrH acts as a chaperone for translocators AopB and AopD. AcrH forms a stable 1:1 monomeric complex with AopD, whereas the 1:1 AcrH‐AopB complex exists mainly as a metastable oligomeric form and only in minor amounts as a stable monomeric form. Limited protease digestion shows that these complexes contain highly exposed regions, thus allowing mapping of intact functional chaperone binding regions of AopB and AopD. AopD uses the transmembrane domain (DF1, residues 16–147) and the C‐terminal amphipathic helical domain (DF2, residues 242–296) whereas AopB uses a discrete region containing the transmembrane domain and the putative N‐terminal coiled coil domain (BF1, residues 33–264). Oligomerization of the AcrH‐AopB complex is mainly through the C‐terminal coiled coil domain of AopB, which is dispensable for chaperone binding. The three proteins, AcrH, AopB, and AopD, can be coexpressed to form an oligomeric and metastable complex. These three proteins are also oligomerized mainly through the C‐terminal domain of AopB. Formation of such an oligomeric and metastable complex may be important for the proper formation of translocon of correct topology and stoichiometry on the host membrane.
Kinetically trapped metastable intermediate of a disulfide‐deficient mutant of the starch‐binding domain of glucoamylase
Authors: Sugimoto Hayuki , Nakaura Miho , Nishimura Shigenori , Karita Shuichi , Miyake Hideo , Tanaka Akiyoshi
Published: June 2009

Refolding of a thermally unfolded disulfide‐deficient mutant of the starch‐binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and 1H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half‐lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with β‐cyclodextrin as the native state, suggesting that the intermediate is highly‐ordered and native‐like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far‐UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off‐pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.
Rational design of a fusion partner for membrane protein expression in E. coli
Authors: Luo Jianying , Choulet Julie , Samuelson James C.
Published: June 2009

We have designed a novel protein fusion partner (P8CBD) to utilize the co‐translational SRP pathway in order to target heterologous proteins to the E. coli inner membrane. SRP‐dependence was demonstrated by analyzing the membrane translocation of P8CBD‐PhoA fusion proteins in wt and SRP‐ffh77 mutant cells. We also demonstrate that the P8CBD N‐terminal fusion partner promotes over‐expression of a Thermotoga maritima polytopic membrane protein by replacement of the native signal anchor sequence. Furthermore, the yeast mitochondrial inner membrane protein Oxa1p was expressed as a P8CBD fusion and shown to function within the E. coli inner membrane. In this example, the mitochondrial targeting peptide was replaced by P8CBD. Several practical features were incorporated into the P8CBD expression system to aid in protein detection, purification, and optional in vitro processing by enterokinase. The basis of membrane protein over‐expression toxicity is discussed and solutions to this problem are presented. We anticipate that this optimized expression system will aid in the isolation and study of various recombinant forms of membrane‐associated protein.
An application of spatially autoregressive models to the study of US county mortality rates
Authors: Sparks Patrice Johnelle , Sparks Corey S.
Published: June 2009

County mortality rates in the US tend to be associated with social and economic resources of counties and the unequal distribution of these resources across space. The processes that generate these social and economic inequalities are often tied to geographical location. In this paper, we present an application of spatially autoregressive models of US county mortality rates that control for the social and economic conditions that often influence mortality rates and the effects of spatial structure of counties in the US. We suggest that arguments are missing from the social science and demographic literatures to offer possible explanations for the spatial patterning of county mortality rates and ecological correlates of these rates at the county level. We find that, after controlling for spatial structure in the data, several key social variables become insignificant in the analysis. We suggest that spatial statistical models are valuable tools in the social and behavioural sciences but that the use of these methods needs to be well grounded in considerations about the spatial process inherent to the outcome studied, and the applications of these methods should not be used solely for post hoc statistical correction. Copyright © 2009 John Wiley & Sons, Ltd.
Novel red phosphor of Eu3+, Bi3+ coactivated double tungstates
Authors: Wang Zhengliang , Liang Hongbin , Wang Qin , Chen Minghong , Gong Menglian , Su Qiang
Published: June 2009

Eu3+, Bi3+ coactivated double‐tungstate phosphors were prepared by the solid‐state reaction technique, and their photoluminescent properties were investigated. No concentration quenching of Eu3+ was observed in the series samples of NaLa1–x (WO4)2:x Eu3+. With the introducing of Bi3+ions, the intensities of the excitation and emission of these phosphors were increased. The phosphor NaEu0.70(WO4)2:0.30Bi3+ showed a broadened excitation band around 400 nm and intensely red emissions under ∼400 nm light excitation, with the CIE chromaticity coordinates (x = 0.66, y = 0.34). Hence, the novel phosphor NaEu0.70(WO4)2:0.30Bi3+ may find application in the fabrication of near‐UV InGaN‐based LEDs. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of addition of Al2O3 on physical, structural, acoustical and in‐vitro bioactive properties of phosphate glasses
Authors: Manupriya  , Thind K. S. , Singh K. , Sharma G. , Rajendran V.
Published: June 2009

Four different formulations of phosphate glasses in the system P2O5–CaO–Na2O–Al2O3 were developed. The elastic moduli have been obtained using the known method at room temperature. Their physicochemical and structural evolution was analyzed during in‐vitro degradation in SBF (simulating body fluid) at 37 °C after 30 days. The results showed that the weight loss of the glass is greatly reduced with the incorporation of only 3 mol% of Al2O3 in P2O5–CaO–Na2O glass composition. Fourier transform infrared (FTIR) spectroscopy performed on glasses before and after dipping in SBF showed calcium phosphate glasses in the system P2O5–CaO–Na2O reinforced with Al2O3 offer an interesting option for slowly resorbable materials as compared to other calcium phosphate glasses with high degradation velocity. The chemical formulation of these glasses allows the synthesis of materials with a controlled solubility. However, the substitution of Al2O3 ≥ 5 mol% negatively affects the bioactivity of the P2O5–CaO–Na2O glasses. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron emission from nanometric apertures in CNTs‐based field emission triode structures on silicon substrates
Authors: Koohsorkhi Javad , Mohajerzadeh Shamsoddin
Published: June 2009

In this paper, we report a simple analytical model for carbon nanotube (CNT) based electron emitters and triode field emission devices on silicon substrates. Carbon nano‐tubes have been grown in a direct current plasma enhanced chemical vapour deposition (dc PECVD) reactor from Ni catalyst islands. CNTs are electrically isolated by a TiO2 film and a chromium layer acts as the metal gate. The effects of the surrounding gate as well as the current–voltage behavior are investigated. To verify the experimental results of this structure a theoretical model is developed, using the Fowler–Nordheim tunneling effect combined with the electrodynamics theory. With certain simplifying assumptions, we replace the complex structure of triode devices with a simple structure which arrives at a closed formulation to predict field emission properties. Field enhancement factor is an important factor that depends on the CNT shape, gate opening and the applied voltage. In our fabrication process, the gate opening diameter can be of the order of the CNT diameter. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Studies on organic light‐emitting diodes based on rubrene‐doped zinc quinolate
Authors: Saxena Kanchan , Mehta Dalip Singh , Rai Virender Kumar , Srivastava Ritu , Chauhan Gayatri , Kamalasanan M. N. , Jain V. K.
Published: June 2009

We report on the fabrication and performance of organic light‐emitting diodes (OLEDs) employing rubrene‐doped metal chelate namely, zinc quinolate (Znq2) as emissive layer. Different OLED architectures were carried out to improve the device performance by doping varying concentrations (by wt%) of rubrene dye into Znq2 host. Enhanced electroluminescence (EL) intensity was achieved using oxygen‐plasma‐treated indium tin oxide as anode, N,N′‐di‐1‐naphthyl‐N,N′‐diphenyl‐1,1′‐biphenyl‐4,4′diamine (α‐NPD) as hole‐transport layer, 10 weight percent rubrene‐doped Znq2 as emission layer, Znq2 as electron‐transport layer, LiF as electron‐injection layer and aluminum as cathode. It has been demonstrated that by using Znq2 as electron‐transport layer and host for dopant (rubrene) is the most suitable device structure for achieving low drive voltage and high efficiency. Electroluminescence spectra of rubrene‐doped OLED devices were also studied. The EL spectral peak was found to be shifted to 565 nm and spectral full‐width at half maximum (FWHM) of rubrene‐doped device was found to be 58 nm, while it was 95 nm in the case of a pure Znq2‐based OLED device. No further significant changes in EL spectra, such as, spectral broadening, narrowing or peak shifting were observed on changing the concentration of the rubrene dye. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reliability aspects of SiC Schottky diodes
Authors: Holz Matthias , Hilsenbeck Jochen , Rupp Roland
Published: June 2009

In recent years, silicon carbide (SiC) high‐voltage power devices have gained an ever‐increasing market share. The fast development of new device concepts and technologies, e.g. for SiC Schottky diodes, has led to devices with superior switching behaviour, which renders SiC power devices especially favourable for high‐frequency applications. As of today, SiC devices enter various fields like, e.g. server power supplies, solar inverters, and drives. These applications pose quite different requirements not only on the electrical properties, but also on the long‐term reliability of the devices. In this paper, we describe in detail how Infineon's SiC Schottky diodes excel the reliability requirements. We point out how material properties, device design and packaging technology affect the overall device reliability and how they can be optimized. In addition, we describe measurement results after stress tests that go far beyond standard stress tests according to JEDEC. E.g., we show that SiC devices can safely be operated at high voltage slopes of 120 V/ns. In addition, we show that the use of high performance die attach further improves the device properties and reliability. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lattice dynamics and thermal properties of SrHfO3 by first‐principles calculations
Authors: Murata Hidenobu , Yamamoto Tomoyuki , Moriwake Hiroki , Tanaka Isao
Published: June 2009

First‐principles lattice dynamics calculations are systematically made on four polymorphs of SrHfO3. The hierarchy of the total energy at the ground state is Pm$ \bar 3 $m > I4/mcm > Cmcm > Pnma, which agrees with the sequence of iterative transitions with temperature as reported by experiments. Three structures, Pm$ \bar 3 $m, I4/mcm and Cmcm, are found to be dynamically unstable at the ground state. A soft mode of phonons appears in I4/mcm and Cmcm at the Γ‐point. The atomic displacements for the soft mode are analogous to those of the R25 mode of Pm$ \bar 3 $m, which is related to the rotation of the HfO6 octahedron. Pnma phase shows lowest energy and it is the only dynamically stable structure among the four phases. The volume expansion coefficient, bulk modulus and heat capacity are computed within quasi‐harmonic approximations using the vibrational density of states. They are compared to experimental data. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
NEXAFS studies of copper phthaloyanine on Ge(001)‐2 × 1 and Ge(111)‐c(2 × 8) surfaces
Authors: Holland B. N. , Peltekis N. , Farrelly T. , Wilks R. G. , Gavrila G. , Zahn D. R. T. , McGuinness C. , McGovern I. T.
Published: June 2009

A comparative investigation of the molecular orientation of copper phthalocyanine on the surfaces of Ge(001)‐2 × 1 and Ge(111)‐c(2 × 8) is presented. As a first step, intrinsic NEXAFS spectra are established through a combination of the computational technique of DFT and an experiment of a well ordered monolayer film on the weakly interacting highly oriented pyrolytic graphite substrate. This reveals σ * intensity in the usual π* region, which is excluded in subsequent analysis of the orientation of molecules. At monolayer coverage the molecules lie close to parallel to the substrate, whereas in a thin film they tend towards perpendicular to the substrate. On the more weakly interacting Ge(111) surface the orientation is more extremal for both monolayer and thin film, indicating possible contributions from both disorder and an adsorption‐related extrinsic effect on Ge(001). (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Flexomagnetoelectric effect in bismuth ferrite
Authors: Zvezdin Anatoly K. , Pyatakov Alexander P.
Published: June 2009

There is a profound analogy between the inhomogeneous magnetoelectric effect in multiferroics and the flexoelectric effect in liquid crystals. This similarity gives rise to the flexomagnetoelectric polarization induced by spin modulation. The theoretical estimations of flexomagnetoelectric polarization agree with the value of jumps of magnetoelectric dependences (∼20 μC/m2) observed at spin cycloid suppression in a critical magnetic field of 200 kOe. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Defects in zinc doped silicon studied on base of X‐ray diffuse scattering analysis
Authors: Privezentsev Vladimir
Published: June 2009

In the this work are presented results of investigation of the defects in n‐Si crystal lattices by the X‐ray diffractometry method at triplet‐crystal combination mode. Experimental n‐Si samples were made by a high‐temperature diffusion annealing of Zn with subsequent quenching. After analysis of diffusion scattering it was established, that crystal lattice Si contains plenty defects of micron sizes. There are revealed likewise small‐scale defects with sizes nearby 50 nm. The type of them is admittedly chaotically distributed dislocations, but part of them may be connected with spherical clusters or dislocation loops. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preface: Phys. Status Solidi C 6/7
Authors: Nassiopoulou Androula , Canham Leigh , Sailor Michael , Schmuki Patrik
Published: June 2009

Dear reader of these proceedings,

We hope you find this collection of papers interesting and useful for your research. These are the submit‐ted papers that were accepted for publication at PSST 2008, the 6th International Conference on Porous Semi‐conductor Science & Technology held at Sa Coma, Mallorca, Spain from 10–14 March 2008. A full collection of extended abstracts is also available in hardback (ISBN 978‐84‐608‐0720‐9) and via www.upv.es/psst‐2008.

This biennial scientific forum focuses entirely on porous semiconductors, and as one of its traditions, has been held in varying locations across Spain since being initiated in 1998.

Technical programme

The conference was preceded by a series of short courses, given by the four conference chairs, which covered most of the current and emerging topics of this scientific field:

Semiconductor electrochemistry

Chemical and biological sensing

Medical and nutritional applications

Electronics and micromachining

There were then technical sessions on:

Semiconductor anodization

Pore initiation control and patterning

Semiconductor and metal nanocomposites

Photonics and energy applications

Mesoporous titania and zinc oxide

MEMS and advanced electronics

Luminescence and energy transfer

Nanocrystal suspensions and bioimaging

Chemical and biological sensing

Manipulation of surface chemistry

Biointerfaces: Proteins, cells, bacteria and viruses

Medical therapeutics and treatments

Advanced characterization

Microfluidics and separations

The two evening poster sessions had over 100 contributions and were the focus of many discussions and debate.

Social programme

Both the local organizers and chairs cherish the biennial PSST friendly ambiance maintained over a dec‐ade to date. This year was no exception and the delegates were brought together socially via a mid‐week ex‐cursion to Palma de Mallorca and by a very memorable conference dinner and disco.

Acknowledgements

We would like to thank all delegates for their contributions, and once again apologize for the long time it took us as Guest Editors to complete the refereeing process. Special thanks go to our sponsors and the fantastic team of local organ‐izers led by Eugenia Matveeva. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic spectrum of 2‐pyridone+: Ab initio and time‐dependent density functional calculations
Authors: Hammoutène D. , Hochlaf M. , Ciofini I. , Adamo C.
Published: June 2009

In a comparative study, the doublet and quartet electronic states of the 2‐pyridone+ cation are calculated using the PBE0/6‐311+G(d,p) technique and the CASSCF and MRCI(+Q) methods in connection with the cc‐pVDZ and cc‐pVTZ Dunning's basis sets. Our data show that TD‐DFT describes quite well the vertical excitation energies of these electronic states, whereas, multiconfiguration methods should be used for the investigation of the fragmentation and the dynamics of this molecular species. This is related to the change of the nature of the wavefunction of these electronic states along the corresponding reactive coordinates not accounted for by TD‐DFT methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Obtaining positions and widths of scattering resonances from a complex multiconfigurational self‐consistent field state using the M1 method
Authors: Samanta Kousik , Yeager Danny L.
Published: June 2009

We present a complex multiconfigurational self‐consistent field (CMCSCF)‐based approach to investigate electron‐atom scattering resonances. It is made possible by the use of second quantization algebra adapted for biorthogonal spin orbitals, which has been applied to develop a quadratically convergent CMCSCF method. To control the convergence to the correct CMCSCF stationary point, a modified step‐length control algorithm is introduced. Convergence to a tolerance of 1.0 × 10−10 a.u. for the energy gradient is found to be typically within 10 iterations or less. A method involving the first block of the M matrix defined in the multiconfigurational spin tensor electron propagator method (MCSTEP) based on the CMCSCF reference state has been implemented to investigate 2P Be− shape resonances. The position and width of these resonances have been calculated for different complete active space choices. The wide distribution of the position and width of the resonance reported in the literature is explained by the existence of two distinct resonances which are close in energy. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Cluster nature of the solvent features of single‐wall carbon nanohorns
Authors: Torrens Francisco , Castellano Gloria
Published: June 2009

The existence of single‐wall carbon nanotubes (SWNTs) in organic solvents, in the form of clusters, is discussed. A theory is developed based on a bundlet model for clusters, describing the distribution function of clusters by size. The phenomena have a unified explanation in the bundlet model of clusters, in accordance with which the free energy of an SWNT, involved in a cluster, is combined from two components: a volume one, proportional to the number of molecules n in a cluster, and a surface one proportional to n1/2. The bundlet model for clusters enables describing the distribution function of SWNT clusters by size. The droplet model is formally analogous to the one for fullerene clusters. From purely geometrical differences, the models predict different behaviors. Single‐wall carbon nanocones (SWNCs) of various disclinations are investigated via energetic and structural analyses. Several SWNC's terminations are studied, which are different among each other because of the type of closing structure and the arrangement of them. The SWNC packing efficiencies, and interaction‐energy parameters, are intermediate between the ones of fullerene and SWNT clusters; an in‐between behavior is expected. However, SWNC properties are calculated closer to those of fullerene and more distant from those of SWNT. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Explicit solvation effects on the conventional resonance model for protonated imine, carbonyl, and thiocarbonyl compounds
Authors: Braïda Benoît , Hiberty Philippe C.
Published: June 2009

The conventional resonance model describes carbonyls, imines, and thiocarbonyls, as well as their protonated analogues, by a superposition of two valence bond structures. Ab initio Breathing‐Orbital Valence Bond computations on formaldehyde, formimine, and thioformaldehyde as well as their protonated forms are performed to directly quantify the weights of their valence bond structures. Following a gas phase study that showed that protonation significantly increases the weight of the carbenic form relative to the π polar‐covalent bonded form (Braida, et al., Org Lett, 2008, 10, 1951), the present work estimates the influence of a polar protic solvent, modelized by water. Solvation effects are modeled explicitly by performing VB calculations on supersystems made of the organic substrate surrounded by four water molecules. It is shown that protonation significantly increases the polarity of the CX π bond in all three cases (X = O, NH, S) in solvated phase, in line with the known acceleration of nucleophilic additions on these compounds by acidic catalysis. Moreover, solvation significantly enhances the polarity of the CX π bond in the protonated forms of formaldehyde and thioformaldehyde, but has practically no effect on the CX π bond of protonated formimine. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Computational study of the molecular mechanisms of caffeine action: Caffeine complexes with adenosine receptors
Authors: Poltev V. I. , Rodríguez E. , Grokhlina T. I. , Deriabina A. , Gonzalez E.
Published: June 2009

To understand the molecular basis of the principal biological action of the caffeine (CAF), the molecular mechanics calculations of possible complexes between CAF and the fragments of human A1adenosine receptor were performed. The fragments were selected after considerations of the CAF molecular structure and its possible interactions, as well as after an analysis of the extensive bibliography on the structure, biological role, site‐directed mutagenesis, and the modeling of the adenosine receptors. The minimum energy configurations of these complexes were obtained using two different computer programs with different force fields. The most favorable configurations correspond to the formation of two hydrogen bonds between the CAF molecule and hydrophilic amino acid residues of the fragments of transmembrane domains of the receptor. These configurations are supposed to contribute to CAF blocking of the adenosine receptors. They will be used later for the construction of model CAF complexes with two transmembrane domains simultaneously. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
CASSCF/CASPT2 analysis of the fragmentation of H2 on a Pd4 cluster
Authors: Barone Giampaolo , Duca Dario , Ferrante Francesco , La Manna Gianfranco
Published: June 2009

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
A theoretical study of the rotational structure of the ϵ(0,0) band of NO
Authors: Velasco A. M. , Lavín C. , Martin I. , Vega M. V. , Pitarch‐Ruiz J. , Sánchez‐Marín J.
Published: June 2009

This study has been focused on the ϵ(0,0) band of the nitric oxide molecule, associated with the absorption electronic transition D2Σ+←X 2Π, in the energetic vacuum ultraviolet region. A temperature of 295 K has been considered. The Molecular Quantum Defect Orbital (MQDO) methodology, with which reliable spectroscopic data have been reached in the γ(0,0), δ(0,0), and δ(1,0) bands of the same molecule, has also been used for these calculations. We hope that the present results might be of straightforward use in atmospheric and interstellar chemistry. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Theoretical study of mechanism of cycloaddition reaction between dimethylmethylene carbene and formaldehyde
Authors: Lu Xiu Hui , Wu Wei Rong , Che Xin , Han Jun Feng , Shi Le Yi
Published: June 2009

The cycloaddition mechanism of forming a polycyclic compound between singlet dimethylmethylene carbene(R1) and formaldehyde(R2) has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated with CCSD(T)//MP2/6‐31G* method. From the potential energy profile, it can be predicted that the dominant reaction pathway of the cycloadditional reaction between singlet dimethylmethylene carbene and formaldehyde consists of two steps: (1) the two reactants(R1, R2) firstly form an energy‐enricheded intermediate (INT1a) through a barrier‐free exothermic reaction of ΔE = 11.3 kJ/mol. (2) Intermediate (INT1a) then isomerizes to a three‐membered product (P1) via a transition state (TS1a) with an energy barrier of 20.0 kJ/mol. The dominant reaction has an excellent selectivity and differs considerably from its competitive reactions in reaction rate. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Theoretical study of mechanism of forming a silapolycyclic compound between methylenesilylene and acetone
Authors: Tian Chun Liang , Yu Hai Bin , Lu Xiu Hui
Published: June 2009

The mechanism of the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by CCSD(T)//MP2/6‐31G* method. From the potential energy profile, we predict that the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has two competitive dominant reaction pathways. First dominant reaction pathway consists of four steps: (I) the two reactants (R1, R2) first form an intermediate (INT1) through a barrier‐free exothermic reaction of 46.2 kJ/mol; (II) intermediate (INT1) then isomerizes to a planar four‐membered ring product (P3) via transition state (TS3) with an energy barrier of 47.1 kJ/mol; (III) planar four‐membered ring product (P3) further reacts with acetone (R2) to form an intermediate (INT4), which is also a barrier‐free exothermic reaction of 40.0 kJ/mol; (IV) intermediate (INT4) isomerizes to a silapolycyclic compound (P4) via transition state (TS4) with an energy barrier of 57.0 kJ/mol. Second dominant reaction pathway consists of three steps: (I) the two reactants (R1, R2) first form a four‐membered ring intermediate (INT2) through a barrier‐free exothermic reaction of 0.5 kJ/mol; (II) INT2 further reacts with acetone (R2) to form an intermediate (INT5), which is also a barrier‐free exothermic reaction of 45.4 kJ/mol; (III) intermediate (INT5) isomerizes to a silapolycyclic compound (P5) via transition state (TS5) with an energy barrier of 49.3 kJ/mol. P4 and P5 are isomeric compounds. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010