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Structural Data (structural + data)
Kinds of Structural Data Selected AbstractsK-Ar age determination, whole-rock and oxygen isotope geochemistry of the post-collisional Bizmi,en and Çalt, plutons, SW Erzincan, eastern Central Anatolia, TurkeyGEOLOGICAL JOURNAL, Issue 4 2005Ayten Önal Abstract Post-collisional granitoid plutons intrude obducted Neo-Tethyan ophiolitic rocks in central and eastern Central Anatolia. The Bizmi,en and Çalt, plutons and the ophiolitic rocks that they intrude are overlain by fossiliferous and flyschoidal sedimentary rocks of the early Miocene Kemah Formation. These sedimentary rocks were deposited in basins that developed at the same time as tectonic unroofing of the plutons along E,W and NW,SE trending faults in Oligo-Miocene time. Mineral separates from the Bizmi,en and Çalt, plutons yield K-Ar ages ranging from 42 to 46,Ma, and from 40 to 49,Ma, respectively. Major, trace, and rare-earth element geochemistry as well as mineralogical and textural evidence reveals that the Bizmi,en pluton crystallized first, followed at shallower depth by the Çalt, pluton from a medium-K calcalkaline, I-type hybrid magma which was generated by magma mixing of coeval mafic and felsic magmas. Delta 18O values of both plutons fall in the field of I-type granitoids, although those of the Çalt, pluton are consistently higher than those of the Bizmi,en pluton. This is in agreement with field observations, petrographic and whole-rock geochemical data, which indicate that the Bizmi,en pluton represents relatively uncontaminated mantle material, whereas the Çalt, pluton has a significant crustal component. Structural data indicating the middle Eocene emplacement age and intrusion into already obducted ophiolitic rocks, suggest a post-collisional extensional origin. However, the pure geochemical discrimination diagrams indicate an arc origin which can be inherited either from the source material or from an upper mantle material modified by an early subduction process during the evolution of the Neo-Tethyan ocean. Copyright © 2005 John Wiley & Sons, Ltd. [source] New Insights on Near-Infrared Emitters Based on Er-quinolinolate Complexes: Synthesis, Characterization, Structural, and Photophysical Properties,ADVANCED FUNCTIONAL MATERIALS, Issue 14 2007F. Artizzu Abstract Erbium quinolinolates, commonly assumed to be mononuclear species with octahedral co-ordination geometry, have been proposed as promising materials for photonic devices but difficulties in obtaining well defined products have so far limited their use. We report here the conditions to obtain in high yields three different kinds of pure neutral erbium quinolinolates by mixing an erbium salt with 8-quinolinol (HQ) and 5,7-dihalo-8-quinolinol (H5,7XQ: X,=,Cl and Br): i),the trinuclear complex Er3Q9 (1) which is obtained with HQ deprotonated by NH3 in water or ethanol/water mixtures; ii),the already known dimeric complexes based on the unit [Er(5,7XQ)3(H2O)2] [X,=,Cl (2) and Br (3)]; iii) the mononuclear [Er(5,7XQ)2(H5,7XQ)2Cl] [X,=,Cl (4) and Br (5)] complexes, obtained in organic solvents without base addition, where the ion results coordinated to four ligands, two deprotonated chelating, and two as zwitterionic monodentate oxygen donors. These results represent a further progress with respect to a recent reinvestigation on this reaction, which has shown that obtaining pure and anhydrous octahedral ErQ3, the expected reaction product, is virtually impossible, but failed in the isolation of 1 and of the neutral tetrakis species based on H5,7XQ ligands. Structural data provide a detailed description of the molecules and of their packing which involves short contacts between quinoxaline ligands, due to ,,, interactions. Electronic and vibrational studies allow to select the fingerprints to distinguish the different products and to identify the presence of water. The structure/property relationship furnishes a satisfactory interpretation of the photo-physical properties. Experimental evidence confirms that the most important quenchers for the erbium emission are the coordinated water molecules and shows that the ligand emission is significantly affected by the ,,, interactions. [source] Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus speciesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2001Gerold Bacher Abstract A general approach for the detailed characterization of sodium borohydride-reduced peptidoglycan fragments (syn. muropeptides), produced by muramidase digestion of the purified sacculus isolated from Bacillus subtilis (vegetative cell form of the wild type and a dacA mutant) and Bacillus megaterium (endospore form), is outlined based on UV matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) quadrupole ion trap (QIT) mass spectrometry (MS). After enzymatic digestion and reduction of the resulting muropeptides, the complex glycopeptide mixture was separated and fractionated by reversed-phase high-performance liquid chromatography. Prior to mass spectrometric analysis, the muropeptide samples were subjected to a desalting step and an aliquot was taken for amino acid analysis. Initial molecular mass determination of these peptidoglycan fragments (ranging from monomeric to tetrameric muropeptides) was performed by positive and negative ion MALDI-MS using the thin-layer technique with the matrix ,-cyano-4-hydroxycinnamic acid. The results demonstrated that for the fast molecular mass determination of large sample numbers in the 0.8,10 pmol range and with a mass accuracy of ±0.07%, negative ion MALDI-MS in the linear TOF mode is the method of choice. After this kind of muropeptide screening often a detailed primary structural analysis is required owing to ambiguous data. Structural data could be obtained from peptidoglycan monomers by post-source decay (PSD) fragment ion analysis, but not from dimers or higher oligomers and not with the necessary sensitivity. Multistage collision-induced dissociation (CID) experiments performed on an nESI-QIT instrument were found to be the superior method for structural characterization of not only monomeric but also of dimeric and trimeric muropeptides. Up to MS4 experiments were sometimes necessary to obtain unambiguous structural information. Three examples are presented: (a) CID MSn (n = 2,4) of a peptidoglycan monomer (disaccharide-tripeptide) isolated from B. subtilis (wild type, vegetative cell form), (b) CID MSn (n = 2,4) of a peptidoglycan dimer (bis-disaccharide-tetrapentapeptide) obtained from a B. subtilis mutant (vegetative cell form) and (c) CID MS2 of a peptidoglycan trimer (a linear hexasaccharide with two peptide side chains) isolated from the spore cortex of B. megaterium. All MSn experiments were performed on singly charged precursor ions and the MS2 spectra were dominated by fragments derived from interglycosidic bond cleavages. MS3 and MS4 spectra exhibited mainly peptide moiety fragment ions. In case of the bis-disaccharide-tetrapentapeptide, the peptide branching point could be determined based on MS3 and MS4 spectra. The results demonstrate the utility of nESI-QIT-MS towards the facile determination of the glycan sequence, the peptide linkage and the peptide sequence and branching of purified muropeptides (monomeric up to trimeric forms). The wealth of structural information generated by nESI-QIT-MSn is unsurpassed by any other individual technique. Copyright © 2001 John Wiley & Sons, Ltd. [source] Manganoan rockbridgeite Fe4.32Mn0.62Zn0.06(PO4)3(OH)5: structure analysis and 57Fe Mössbauer spectroscopyACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2006Günther J. Redhammer The structure of the basic iron phosphate rockbridgeite [iron manganese zinc tris(phosphate) pentahydroxide] was reinvestigated with special emphasis on the cation distribution deduced from new X-ray and 57Fe Mössbauer data. Rockbridgeite is orthorhombic, space group Cmcm, and shows three different Fe sites, one with symmetry, another with m symmetry and the third in a general position. One phosphate group has the P atom on a site with m symmetry, while the other has the P atom at a site with mm symmetry. Two Fe sites are fully occupied by ferric iron, while Mn3+ and Fe2+ are situated at a third, principally Fe, site. Structural data, bond-valence sums and polyhedral distortion parameters suggest a new interpretation of the rockbridgeite 57Fe Mössbauer spectrum. [source] A novel heterocyclic sulfonamide: N -benzyl-5-[N -benzyl- N -(tert -butyloxycarbonyl)amino]- N -(tert -butyloxycarbonyl)-1,3,4-thiadiazole-2-sulfonamideACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2000Gerardo Camí The title compound, C26H32N4O6S2, is a heterocyclic sulfonamide which is a 1,3,4-thiadiazole derivative. Structural data for this compound are compared with those of related compounds. [source] A high-resolution structure of ligand-free human glutamate carboxypeptidase IIACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2007Cyril Barinka Human glutamate carboxypeptidase II (GCPII; EC 3.4.17.21) is an established marker for prostate-cancer diagnosis as well as a candidate therapeutic target for the treatment of diverse pathologies that involve glutamatergic transmission. Structural data on GCPII are thus valuable for the design and optimization of GCPII-specific inhibitors and diagnostic probes. The currently available structure of ligand-free GCPII was refined to a resolution of 3.5,Å. This work reports the structure of the protein refined to 1.65,Å resolution, with crystallographic values of R = 0.207 and Rfree = 0.228. The new structure extends the resolution appreciably and the new model based on this data shows significant differences when compared with the previously published model. [source] The nodPQ genes in Azospirillum brasilense Sp7 are involved in sulfation of lipopolysaccharidesENVIRONMENTAL MICROBIOLOGY, Issue 11 2005Els Vanbleu Summary Here we report on the presence of sulfated lipopolysaccharide molecules in Azospirillum brasilense, a plant growth-promoting rhizosphere bacterium. Chemical analysis provided structural data on the O-antigen composition and demonstrated the possible involvement of the nodPQ genes in O-antigen sulfation. [source] Molecular modeling of metal complexation by a fluoroquinolone antibioticENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2008Ludmilla Aristilde Abstract An understanding of the factors controlling the chemodynamics of fluoroquinolone antibiotics in different environmental matrices is a necessary prerequisite to the assessment of their potential impact on nontarget organisms in soils and receiving waters. Of particular interest are the complexes formed between fluoroquinolones and metal cations, which are believed to be important in the mechanism of sequestration of the antibiotic by minerals and natural organic matter. The structures of these complexes have not been fully resolved by conventional spectroscopy; therefore, molecular simulations may provide useful complementary insights. We present results from apparently the first molecular dynamics simulations of a widely used fluoroquinolone antibiotic, ciprofloxacin (Cipro), in aqueous complexes with five metal cations typically found in soils and surface waters: Ca2+, Mg2+, Fe2+, Na+, and K+. The interatomic potential functions employed in the simulations were validated by comparison with available structural data for solid-phase Cipro-hexahydrate and for the metal cations in aqueous solution. Although no comprehensive structural data on the aqueous complexes appear to be available, properties of the metal complexes predicted by our simulations agree with available data for solid-phase metal,Cipro complexes. Our results indicate that the ionic potential of the metal cation controls the stability of the complex formed and that the hydration number of the metal cation in aqueous solution determines its coordination number with O atoms in the metal,Cipro complex. In respect to environmental chemodynamics, our results imply that Cipro will form two configurations of bidendate chelates with metal centers on exposed surfaces of mineral oxides, water-bridged surface complexes with exchangeable cations in clay mineral interlayers, and cation-bridged complexes with functional groups in natural organic matter. [source] Oxidative Addition of B,Br Bonds to Pd0: Synthesis and Structure of trans -Bromo(boryl)palladium ComplexesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 9 2008Holger Braunschweig Abstract The oxidative addition of several bromoboranes to the Pd0 species [Pd(PCy3)2] yielded the novel palladium boryl complexes trans -[(Cy3P)2Pd(Br)(BCat)] (1) (Cat = 1,2-dioxophenylene), trans -[(Cy3P)2Pd(Br)(BCat,)] (2) (Cat, = Cat-4- tBu) and trans -[(Cy3P)2Pd(Br){B(X)X,}] {X = Br, X, = NMe2 (3), Pip (4) (Pip = NC5H10), Mes (5) [Mes = 2,4,6-(CH3)3C6H2]}. Compounds 1,5 were characterized by multinuclear NMR spectroscopy in solution; single crystals for X-ray analyses were acquired from 2 and 3, which thus allowed comparison of the structural data. The few palladium boryl complexes published so far were obtained by ,-bond metathesis; the oxidative addition of the corresponding bromoboranes to Pd0 has not yet been reported.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Phase Relations Between ,-Tricalcium Phosphate and Hydroxyapatite with Manganese(II): Structural and Spectroscopic PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 7 2006Isaac Mayer Abstract The preparation of Mn-containing ,-tricalcium phosphate (,-TCP) samples was achieved in two ways: a) transformation of precipitated Mn-containing calcium hydroxyapatite (HA) to ,-TCP by heating at 1100 °C, and b) preparation by solid-state reaction of a mixture of CaCO3, (NH4)2HPO4, and Mn(NO3)2 at 1100 °C. Powder X-ray diffraction (XRD) analyses of the samples, obtained by both methods, show well-defined patterns with structural data of the rhombohedral R3c, ,-TCP phase. The calculated lattice constants are smaller than those known for ,-Ca3(PO4)2 because of substitution of Ca2+ by Mn2+. EPR spectroscopy indeed reveals that manganese is divalent in the samples. Apparently, the Ca(5) site in the ,-TCP structure is occupied by Mn2+. The distribution of Mn2+ between the ,-TCP and the HA phase in the case of preparation (b) was studied by EPR spectroscopy, and a pronounced preference for the former lattice was found. Micron- and submicron-sized crystals with visible faces were observed by TEM in the case of ,-TCP prepared by solid-state reaction, and large micron-sized, droplike-shaped crystals, sensitive to beam radiation, were found in the case of samples prepared by heating HA at elevated temperatures. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Synthesis and Structural Characterization of Planar Chiral Cr(CO)3 -Complexed Aromatic Nitrones , Valuable Substrates for Asymmetric SmI2 -Induced Coupling ReactionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 5 2010Murielle Chavarot-Kerlidou Abstract The synthesis of Cr(CO)3 -complexed aromatic nitrones 2 is reported. These new planar-chiral complexes were fully characterized in solution by 1H and 13C NMR, IR and cyclic voltammetry. Moreover, structural data were obtained from X-ray structures of nitrones 2b, 2d, 2e and 2f. These analyses converge to give evidence of a favoured anti conformation of ortho -substituted nitrones, with an unusual N,O···Haryl intramolecular interaction forming a six-membered ring. The reactivity of these chiral nitrones in SmI2 -induced pinacol-type reactions was investigated. The reductive cross-coupling of nitrones 2a,d with carbonyl compounds proved to be highly chemo- and diastereoselective and afforded precursors of enantioenriched ,-amino alcohols in excellent yields. [source] 4-Substituted and 4,5-Disubstituted 3,6-Di(2-pyridyl)pyridazines: Ligands for Supramolecular AssembliesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 9 2008Edwin C. Constable Abstract The syntheses by inverse electron demand Diels,Alder reactions and characterization of 28 members of a family of 3,6-di(2-pyridyl)pyridazines, functionalized in the 4- or 4,5-positions are reported. Single crystal structural data are presented for four representative derivatives. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Dewetting of an Organic Semiconductor Thin Film Observed in Real-time,ADVANCED ENGINEERING MATERIALS, Issue 4 2009Stefan Kowarik We study the growth and the post-growth dewetting process of the organic semiconductor diindenoperylene (DIP) using real-time X-ray reflectivity measurements. We show that a DIP monolayer deposited in UHV onto silicon oxide dewets via the formation of bilayer islands. From the time resolved structural data we estimate the rate constant for interlayer diffusion of DIP molecules. Post-growth AFM measurements confirm the conclusions from the X-ray data and show the morphology of the dewetted film. [source] Mutagenic probes of the role of Ser209 on the cavity shaping loop of human monoamine oxidase AFEBS JOURNAL, Issue 16 2009Jin Wang The available literature implicating human monoamine oxidase A (MAO A) in apoptotic processes reports levels of MAO A protein that do not correlate with activity, suggesting that unknown mechanisms may be involved in the regulation of catalytic function. Bioinformatic analysis suggests Ser209 as a possible phosphorylation site that may be relevant to catalytic function because it is adjacent to a six-residue loop termed the ,cavity shaping loop' from structural data. To probe the functional role of this site, MAO A Ser209Ala and Ser209Glu mutants were created and investigated. In its membrane-bound form, the MAO A Ser209Glu phosphorylation mimic exhibits catalytic and inhibitor binding properties similar to those of wild-type MAO A. Solubilization in detergent solution and purification of the Ser209Glu mutant results in considerable decreases in these functional parameters. By contrast, the MAO A Ser209Ala mutant exhibits similar catalytic properties to those of wild-type enzyme when purified. Compared to purified wild-type and Ser209Ala MAO A proteins, the Ser209Glu MAO A mutant shows significant differences in covalent flavin fluorescence yield, CD spectra and thermal stability. These structural differences in the purified MAO A Ser209Glu mutant are not exhibited in quantitative structure,activity relationship patterns using a series of para -substituted benzylamine analogs similar to the wild-type enzyme. These data suggest that Ser209 in MAO A does not appear to be the putative phosphorylation site for regulation of MAO A activity and demonstrate that the membrane environment plays a significant role in stabilizing the structure of MAO A and its mutant forms. [source] Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosusFEBS JOURNAL, Issue 16 2004A member of a novel protein family related to protein disulfide-isomerase Protein disulfide oxidoreductases are ubiquitous redox enzymes that catalyse dithiol,disulfide exchange reactions with a CXXC sequence motif at their active site. A disulfide oxidoreductase, a highly thermostable protein, was isolated from Pyrococcus furiosus (PfPDO), which is characterized by two redox sites (CXXC) and an unusual molecular mass. Its 3D structure at high resolution suggests that it may be related to the multidomain protein disulfide-isomerase (PDI), which is currently known only in eukaryotes. This work focuses on the functional characterization of PfPDO as well as its relation to the eukaryotic PDIs. Assays of oxidative, reductive, and isomerase activities of PfPDO were performed, which revealed that the archaeal protein not only has oxidative and reductive activity, but also isomerase activity. On the basis of structural data, two single mutants (C35S and C146S) and a double mutant (C35S/C146S) of PfPDO were constructed and analyzed to elucidate the specific roles of the two redox sites. The results indicate that the CPYC site in the C-terminal half of the protein is fundamental to reductive/oxidative activity, whereas isomerase activity requires both active sites. In comparison with PDI, the ATPase activity was tested for PfPDO, which was found to be cation-dependent with a basic pH optimum and an optimum temperature of 90 °C. These results and an investigation on genomic sequence databases indicate that PfPDO may be an ancestor of the eukaryotic PDI and belongs to a novel protein disulfide oxidoreductase family. [source] Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressorsFEMS MICROBIOLOGY REVIEWS, Issue 2 2006Antonio J. Molina-Henares Abstract Members of the IclR family of regulators are proteins with around 250 residues. The IclR family is best defined by a profile covering the effector binding domain. This is supported by structural data and by a number of mutants showing that effector specificity lies within a pocket in the C-terminal domain. These regulators have a helix-turn-helix DNA binding motif in the N-terminal domain and bind target promoters as dimers or as a dimer of dimers. This family comprises regulators acting as repressors, activators and proteins with a dual role. Members of the IclR family control genes whose products are involved in the glyoxylate shunt in Enterobacteriaceae, multidrug resistance, degradation of aromatics, inactivation of quorum-sensing signals, determinants of plant pathogenicity and sporulation. No clear consensus exists on the architecture of DNA binding sites for IclR activators: the MhpR binding site is formed by a 15-bp palindrome, but the binding sites of PcaU and PobR are three perfect 10-bp sequence repetitions forming an inverted and a direct repeat. IclR-type positive regulators bind their promoter DNA in the absence of effector. The mechanism of repression differs among IclR-type regulators. In most of them the binding sites of RNA polymerase and the repressor overlap, so that the repressor occludes RNA polymerase binding. In other cases the repressor binding site is distal to the RNA polymerase, so that the repressor destabilizes the open complex. [source] Molecular basis of antibiotic resistance and ,-lactamase inhibition by mechanism-based inactivators: perspectives and future directionsFEMS MICROBIOLOGY REVIEWS, Issue 3 2000Christian Therrien Abstract Antibacterial chemotherapy is particularly striking in the family of penicillins and cephalosporins. Over 40 structurally different ,-lactam molecules are available in 73 formulations and the majority of them are currently prescribed for medical use in hospitals. ,-Lactams are well tolerated by humans with few side effects. They interact very specifically with their bacterial target, the d -alanyl- d -alanine carboxypeptidase-transpeptidase usually referred to as dd -peptidase. The outstanding number of ,-lactamases produced by bacteria represent a serious threat to the clinical utility of ,-lactams. The discovery of ,-lactamase inhibitors was thought to solve, in part, the problem of resistance. Unfortunately, bacteria have evolved new mechanisms of resistance to overcome the inhibitory effects of ,-lactamase inactivators. Here, we summarize the diversified mechanistic features of class A ,-lactamases interactions with mechanism-based inhibitors using available microbiological, kinetic and structural data for the prototype TEM ,-lactamases. A brief historical overview of the strategies developed to counteract ,-lactamases will be presented followed by a short description of the chemical events which lead to the inactivation of TEM ,-lactamase by inhibitors from different classes. Finally, an update on the clinical prevalence of natural and inhibitor-resistant enzyme mutants, the total chemical synthesis to design and synthesize a new structure and produced a broad spectrum ,-lactamase inhibitor that mimics the ,-lactam ring, but does not contain it is discussed. [source] Vegetation structure characteristics and relationships of Kalahari woodlands and savannasGLOBAL CHANGE BIOLOGY, Issue 3 2004J.L. Privette Abstract The Kalahari Transect is one of several International Geosphere,Biosphere Programme (IGBP) transects designed to address global change questions at the regional scale, in particular by exploiting natural parameter gradients (Koch et al., 1995). In March 2000, we collected near-synoptic vegetation structural data at five sites spanning the Kalahari's large precipitation gradient (about 300,1000 mm yr,1) from southern Botswana (,24°S) to Zambia (,15°S). All sites were within the expansive Kalahari sandsheet. Common parameters, including plant area index (PAI), leaf area index (LAI) and canopy cover (CC), were measured or derived using several indirect instruments and at multiple spatial scales. Results show that CC and PAI increase with increasing mean annual precipitation. Canopy clumping, defined by the deviation of the gap size distribution from that of randomly distributed foliage, was fairly constant along the gradient. We provide empirical relationships relating these parameters to each other and to precipitation. These results, combined with those in companion Kalahari Transect studies, provide a unique and coherent test bed for ecological modeling. The data may be used to parameterize process models, as well as test internally predicted parameters and their variability in response to well-characterized climatological differences. [source] Mechanisms Controlling Crystal Habits of Gold and Silver ColloidsADVANCED FUNCTIONAL MATERIALS, Issue 7 2005C. Lofton Abstract Examples of gold and silver anisotropic colloids, such as prisms and rods, have appeared in the literature for many years. In most cases, the morphologies of these thermodynamically unfavorable particles have been explained by the particular reaction environment in which they were synthesized. The mechanisms used to explain the growth generally fall into two categories, one in which chemically adsorbed molecules regulate the growth of specific crystal faces kinetically, and the other where micelle-forming surfactants physically direct the shape of the particle. This paper raises questions about the growth of anisotropic metal colloids that the current mechanisms cannot adequately address, specifically, the formation of multiple shapes in a single homogeneous reaction and the appearance of similar structures in very different synthesis schemes. These observations suggest that any growth mechanism should primarily take into consideration nucleation and kinetics, and not only thermodynamics or physical constrictions. The authors suggest an alternative mechanism where the presence and orientation of twin planes in these face-centered cubic (fcc) metals direct the shape of the growing particles. This explanation follows that used for silver halide crystals, and has the advantage of explaining particle growth in many synthesis methods. In this mechanism, twin planes generate reentrant grooves, favorable sites for the attachment of adatoms. Shape and structural data are presented for gold and silver particles synthesized using several different techniques to support this new model. Triangular prisms are suggested to contain a single twin plane which directs that growth of the initial seed in two dimensions, but limits the final size of the prism. Hexagonal platelets are suggested to contain two parallel twin planes that allow the fast growing edges to regenerate one another, allowing large sizes and aspect ratios to form. Rods and wires were found to have a fivefold symmetry, which may only allow growth in one dimension. It is expected that a superior mechanistic understanding will permit shape-selective synthesis schemes to be developed. [source] The SAAPdb web resource: A large-scale structural analysis of mutant proteins,HUMAN MUTATION, Issue 4 2009Jacob M. Hurst Abstract The Single Amino Acid Polymorphism database (SAAPdb) is a new resource for the analysis and visualization of the structural effects of mutations. Our analytical approach is to map single nucleotide polymorphisms (SNPs) and pathogenic deviations (PDs) to protein structural data held within the Protein Data Bank. By mapping mutations onto protein structures, we can hypothesize whether the mutant residues will have any local structural effect that may "explain" a deleterious phenotype. Our prior work used a similar approach to analyze mutations within a single protein. An analysis of the contents of SAAPdb indicates that there are clear differences in the sequence and structural characteristics of SNPs and PDs, and that PDs are more often explained by our structural analysis. This mapping and analysis is a useful resource for the mutation community and is publicly available at http://www.bioinf.org.uk/saap/db/. Hum Mutat 0, 1,9, 2009. © 2009 Wiley-Liss, Inc. [source] On the relative stability of cobalt- and nickel-based amidinate complexes against ,-migrationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2009Jiaye Li Abstract We present a first-principles study on the relative stability of cobalt- and nickel-based amidinate complexes against ,-migration using density functional theory. Factors that influence the reactivity of these compounds were carefully addressed and the calculated molecular structures are in excellent agreement with the available crystal structural data. Reaction energies as well as activation barriers of ,-migration were evaluated. The predicted relative stability of the selected compounds is consistent with experimental observations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Molecular relaxation and metalloenzyme active site modelingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002James W. Whittaker Abstract Metalloenzymes represent a broad class of important biomolecules containing an essential metal ion cofactor in their catalytic active sites, forming biologic metal complexes that perform a wide range of important functions: activation of small molecules (O2, N2, H2, CO), atom transfer chemistry, and the control of oxidation equivalents. The structures of many metalloenzyme active sites have been defined by X-ray crystallography, revealing transition metal ions in unique low-symmetry environments. These bioinorganic complexes present significant challenges for computational studies aimed at going beyond crystal structures to develop a detailed understanding of the catalytic mechanisms. Considerable progress has been made in the theoretical characterization of these sites in recent years, supported by the availability of efficient computational tools, in particular density functional methods. However, the ultimate success of a theoretical model depends on a number of factors independent of the specific computational method used, including the quality of the initial structural data, the identification of important environmental perturbations and constraints, and experimental validation of theoretical predictions. We explore these issues in detail and illustrate the effects of molecular relaxation in calculations of two metalloenzymes, manganese superoxide dismutase and galactose oxidase. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Large-scale folding in the Asemi-gawa region of the Sanbagawa Belt, southwest JapanISLAND ARC, Issue 2 2010Hiroshi Mori Abstract The Sanbagawa Belt generally shows higher metamorphic grade at higher structural levels. This inversion can be interpreted as reflecting an original inverted thermal structure typical of subduction zone environments. However, repetitions in the distribution of the metamorphic zones seen in central Shikoku, Japan, clearly show the original thermal structure has been affected by deformation after the peak of metamorphism. This repetition has been attributed to both the action of tectonic discontinuities and regional folding. It is important to distinguish between these two interpretations to determine the extent to which the original subduction zone sequence is preserved. Analyses of lithological and structural data reveal the presence of a large-scale post-metamorphic fold in the central part of the highest grade region. This folding has an axis that coincides with the thermal axis implied by the distribution of the metamorphic zonation, suggesting the repetition of metamorphic zones in this area can be accounted for by folding without the need for major discontinuities. [source] Structural position of the Seba eclogite unit in the Sambagawa Belt: Supporting evidence for an eclogite nappeISLAND ARC, Issue 2 2002Article first published online: 4 JUL 200, Mutsuki Aoya Abstract Eclogite-bearing units in the Sambagawa Metamorphic Belt have long been considered tectonic blocks that have disparate tectonic and metamorphic histories that are distinct from each other and from the major non-eclogitic Sambagawa schists. However, recent studies have shown that eclogite facies metamorphism of the Seba eclogite unit is related to the subduction event that caused the metamorphism of the non-eclogitic Sambagawa schist. New structural data further show that the Seba eclogite unit, which appears to be isolated from the other eclogite units, is in fact in structural continuity with them, occupying the highest structural levels in the Sambagawa Belt. This suggests that eclogitic metamorphism of the other eclogite units is also related to the Sambagawa subduction event. It is, therefore, possible that all eclogite units in the Sambagawa Belt constitute a single coherent unit, the eclogite nappe, members of which underwent the same eclogitic metamorphism related to the Sambagawa subduction event. [source] Geology of the Kokchetav UHP-HP metamorphic belt, Northern KazakhstanISLAND ARC, Issue 3 2000Y. Kaneko Abstract Ultrahigh-pressure metamorphic (UHPM) rocks of the Kokchetav Massif of Kazakhstan contain metamorphic microdiamond and coesite inclusions inside rigid capsules such as garnet and zircon. Precambrian protoliths of the UHPM rocks were metamorphosed at around 530 Ma, at pressures of about 7 GPa, which suggests that crustal protoliths were subducted to depths of over 200 km. Primary UHPM minerals are poorly preserved due to partial obliteration by subsequent Barrovian overprint during exhumation and later collision events in Caledonian times. We report the results of detailed mapping of the Kokchetav Massif and use structural data to propose intrusion and exhumation mechanisms for the UHPM rocks. Detailed mapping revealed that many subvertical structures in the ultrahigh-pressure,high-pressure (UHP,HP) units were formed due to later folding. The primary structure appears to be subhorizontal and the total thickness of the UHP rocks is estimated at around 2 km. The first order structure is sandwich-like; that is, the UHP,HP units are separated from underlying low-P metamorphic rocks of the Daulet Series and from feebly metamorphosed to unmetamorphosed sedimentary strata on the top by subhorizontal faults. Kinematic indicators show top-to-the-south sense of shear along the top, and top-to-the-north displacement along the bottom boundaries. These shear senses, together with the observed metamorphic gradients, suggest that the thin UHPM sheet was extruded toward the north. We consider wedge extrusion to have been the most effective mechanism for the exhumation of the UHPM rocks. [source] A cyberenvironment for crystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystallography Open DatabaseJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2008Jacob R. Fennick With the advent and subsequent evolution of the Internet the ways in which computational crystallographic research is conducted have dramatically changed. Consequently, secure, robust and efficient means of accessing remote data and computational resources have become a necessity. At present scientists in computational crystallography access remote data and resources via separate technologies, namely SSH and Web services. Computational Science and Engineering Online (CSE-Online) combines these two methods into a single seamless environment while simultaneously addressing issues such as stability with regard to Internet interruption. Presently CSE-Online contains several applications which are useful to crystallographers; however, continued development of new tools is necessary. Toward this end a Java application capable of running in CSE-Online, namely the Crystallography Open Database User Interface (CODUI), has been developed, which allows users to search for crystal structures stored in the Crystallography Open Database and Predicted Crystallography Open Database, to export structural data for visualization, or to input structural data in other CSE-Online applications. [source] Relationship between the crystalline structure and mechanical behavior in isotropic and oriented polyamide 12JOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2008Nadya Dencheva Abstract This study reports on the relationship between the crystalline structure and mechanical behavior of differently processed and annealed polyamide 12 (PA12) samples. Two sets of samples were obtained: isotropic PA12 films prepared by hot pressing and oriented cables prepared by consecutive extrusion and cold drawing. These samples were isothermally annealed in the range of 80,160°C and then subjected to tensile tests at room temperature. A combination of solid-state 13C-NMR and synchrotron wide- and small-angle X-ray scattering was used to obtain reliable structural data from these samples before and after the tensile tests. These structural data were related to the mechanical properties of the respective PA12 samples. Deformation models explaining all the experimental results were suggested for the different PA12 samples. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] Silicon carbonitride thin-film coatings fabricated by remote hydrogen,nitrogen microwave plasma chemical vapor deposition from a single-source precursor: Growth process, structure, and properties of the coatings,JOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2007A. M. Wrobel Abstract Silicon carbonitride (Si:C:N) films were produced by remote hydrogen,nitrogen microwave plasma chemical vapor deposition (RP-CVD) from a 1,1,3,3-tetramethyldisilazane precursor with a nitrogen content {[N2]/([H2] + [N2])} of 0.88 in the plasma-generating mixture and a substrate temperature in the range of 30,400°C. The effects of the substrate temperature on the rate and yield of the RP-CVD process and chemical structure (examined by Fourier transform infrared spectroscopy) of the resulting films were investigated. The Si:C:N film properties were characterized in terms of the density, hardness, elastic modulus, and friction coefficient. With the IR structural data, reasonable structure,property relationships were determined. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 105: 122,129, 2007 [source] Recombinant Human Parathyroid Hormone (1,34) [Teriparatide] Improves Both Cortical and Cancellous Bone StructureJOURNAL OF BONE AND MINERAL RESEARCH, Issue 11 2003Yebin Jiang MD Abstract Histomorphometry and ,CT of 51 paired iliac crest biopsy specimens from women treated with teriparatide revealed significant increases in cancellous bone volume, cancellous bone connectivity density, cancellous bone plate-like structure, and cortical thickness, and a reduction in marrow star volume. Introduction: We studied the ability of teriparatide (rDNA origin) injection [rhPTH(1,34), TPTD] to improve both cancellous and cortical bone in a subset of women enrolled in the Fracture Prevention Trial of postmenopausal women with osteoporosis after a mean treatment time of 19 months. This is the first report of a biopsy study after treatment with teriparatide having a sufficient number of paired biopsy samples to provide quantitative structural data. Methods: Fifty-one paired iliac crest bone biopsy specimens (placebo [n = 19], 20 ,g teriparatide [n = 18], and 40 ,g teriparatide [n = 14]) were analyzed using both two-dimensional (2D) histomorphometry and three-dimensional (3D) microcomputed tomography (,CT). Data for both teriparatide treatment groups were pooled for analysis. Results and Conclusions: By 2D histomorphometric analyses, teriparatide significantly increased cancellous bone volume (median percent change: teriparatide, 14%; placebo, ,24%; p = 0.001) and reduced marrow star volume (teriparatide, ,16%; placebo, 112%; p = 0.004). Teriparatide administration was not associated with osteomalacia or woven bone, and there were no significant changes in mineral appositional rate or wall thickness. By 3D cancellous and cortical bone structural analyses, teriparatide significantly decreased the cancellous structure model index (teriparatide, ,12%; placebo, 7%; p = 0.025), increased cancellous connectivity density (teriparatide, 19%; placebo, ,14%; p = 0.034), and increased cortical thickness (teriparatide, 22%; placebo, 3%; p = 0.012). These data show that teriparatide treatment of postmenopausal women with osteoporosis significantly increased cancellous bone volume and connectivity, improved trabecular morphology with a shift toward a more plate-like structure, and increased cortical bone thickness. These changes in cancellous and cortical bone morphology should improve biomechanical competence and are consistent with the substantially reduced incidences of vertebral and nonvertebral fractures during administration of teriparatide. [source] A new molecular mechanics force field for the oxidized form of blue copper proteinsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2002Peter Comba Abstract A molecular mechanics force field for blue copper proteins has been developed, based on a rigid potential energy surface scan of the CuII/His/His/Cys/Met chromophore, using DFT (B3LYP) calculations and the AMBER force field for the protein backbone. The strain,energy-minimized structures of the model chromophore alone are in excellent agreement with the DFT-optimized structure, and those of the entire set of cupredoxins (five structures are considered) are, within the experimental error limits, in good agreement with the single crystal structural data. However, the structural variation in the computed structures is much smaller than those in the experimental structures. It is shown that, due to the large error limits in the experimental data, a validation of the force field with experimental structural data is impossible because, within the error limits, all experimental structures considered are virtually identical. A validation on the basis of spectroscopic data and their correlation with experimental and computed structural data is proposed, and, as a first example, the correlation of intensity ratios of the charge transfer transitions with a specific distortion mode is presented. The quality of the correlation, using the computed structures, is higher than that with the X-ray structures, and this indicates that the computed structures are meaningful. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 697,705, 2002 [source] | |||||||||||||||||||||||||||||||||||||||||||