Ferroelectricity in epitaxial pulsed laser deposited bismuth-layered perovskite thin films of different crystallographic orientations

Epitaxial thin films Of various bismuth-layered perovskites SrBi(2)Ta(2)O(9), Bi(4)Ti(3)O(12), BaBi(4)Ti(4)O(15), and Ba(2)Bi(4)Ti(5)O(18) were deposited by pulsed laser deposition onto epitaxial conducting LaNiO(3) or SrRuO(3) electrodes on single crystalline SrTiO(3) substrates with different crystallographic orientations or on top of epitaxial buffer layers on (100) silicon. The conductive perovskite electrodes and the epitaxial ferroelectric films are strongly influenced by the nature of the substrate, and bismuth-layered perovskite ferroelectric films with mixed (100), (110)- and (001)-orientations as well as with uniform (001)-, (116)- and (103)- orientations have been obtained. Structure and morphology investigations performed by X-ray diffraction analysis, scanning probe microscopy, and transmission electron microscopy reveal the different epitaxial relationships between films and substrates. A clear correlation of the crystallographic orientation of the epitaxial films with their ferroelectric properties is illustrated by macroscopic and microscopic measurements of epitaxial bismuth-layered perovskite thin films of different crystallographic orientations.

Statistical evaluation of texture analysis from the biocrystallization method

The consumers are becoming more concerned about food quality, especially regarding how, when and where the foods are produced (Haglund et al., 1999; Kahl et al., 2004; Alföldi, et al., 2006). Therefore, during recent years there has been a growing interest in the methods for food quality assessment, especially in the picture-development methods as a complement to traditional chemical analysis of single compounds (Kahl et al., 2006). The biocrystallization as one of the picture-developing method is based on the crystallographic phenomenon that when crystallizing aqueous solutions of dihydrate CuCl2 with adding of organic solutions, originating, e.g., from crop samples, biocrystallograms are generated with reproducible crystal patterns (Kleber & Steinike-Hartung, 1959). Its output is a crystal pattern on glass plates from which different variables (numbers) can be calculated by using image analysis. However, there is a lack of a standardized evaluation method to quantify the morphological features of the biocrystallogram image. Therefore, the main sakes of this research are (1) to optimize an existing statistical model in order to describe all the effects that contribute to the experiment, (2) to investigate the effect of image parameters on the texture analysis of the biocrystallogram images, i.e., region of interest (ROI), color transformation and histogram matching on samples from the project 020E170/F financed by the Federal Ministry of Food, Agriculture and Consumer Protection(BMELV).The samples are wheat and carrots from controlled field and farm trials, (3) to consider the strongest effect of texture parameter with the visual evaluation criteria that have been developed by a group of researcher (University of Kassel, Germany; Louis Bolk Institute (LBI), Netherlands and Biodynamic Research Association Denmark (BRAD), Denmark) in order to clarify how the relation of the texture parameter and visual characteristics on an image is. The refined statistical model was accomplished by using a lme model with repeated measurements via crossed effects, programmed in R (version 2.1.0). The validity of the F and P values is checked against the SAS program. While getting from the ANOVA the same F values, the P values are bigger in R because of the more conservative approach. The refined model is calculating more significant P values. The optimization of the image analysis is dealing with the following parameters: ROI(Region of Interest which is the area around the geometrical center), color transformation (calculation of the 1 dimensional gray level value out of the three dimensional color information of the scanned picture, which is necessary for the texture analysis), histogram matching (normalization of the histogram of the picture to enhance the contrast and to minimize the errors from lighting conditions). The samples were wheat from DOC trial with 4 field replicates for the years 2003 and 2005, “market samples”(organic and conventional neighbors with the same variety) for 2004 and 2005, carrot where the samples were obtained from the University of Kassel (2 varieties, 2 nitrogen treatments) for the years 2004, 2005, 2006 and “market samples” of carrot for the years 2004 and 2005. The criterion for the optimization was repeatability of the differentiation of the samples over the different harvest(years). For different samples different ROIs were found, which reflect the different pictures. The best color transformation that shows efficiently differentiation is relied on gray scale, i.e., equal color transformation. The second dimension of the color transformation only appeared in some years for the effect of color wavelength(hue) for carrot treated with different nitrate fertilizer levels. The best histogram matching is the Gaussian distribution. The approach was to find a connection between the variables from textural image analysis with the different visual criteria. The relation between the texture parameters and visual evaluation criteria was limited to the carrot samples, especially, as it could be well differentiated by the texture analysis. It was possible to connect groups of variables of the texture analysis with groups of criteria from the visual evaluation. These selected variables were able to differentiate the samples but not able to classify the samples according to the treatment. Contrarily, in case of visual criteria which describe the picture as a whole there is a classification in 80% of the sample cases possible. Herewith, it clearly can find the limits of the single variable approach of the image analysis (texture analysis).

Overproduction, purification and preliminary X-ray diffraction analysis of YncE, an iron-regulated Sec-dependent periplasmic protein from Escherichia coli

The yncE gene of Escherichia coli encodes a predicted periplasmic protein of unknown function. The gene is de-repressed under iron restriction through the action of the global iron regulator Fur. This suggests a role in iron acquisition, which is supported by the presence of the adjacent yncD gene encoding a potential TonB-dependent outer-membrane transporter. Here, the preliminary crystallographic structure of YncE is reported, revealing that it consists of a seven-bladed beta-propeller which resembles the corresponding domain of the `surface-layer protein' of Methanosarcina mazei. A full structure determination is under way in order to provide insight into the function of this protein.

Electronic properties of 4,4 ',5,5 '-tetramethyl-2,2 '-biphosphinine (tmbp) in the redox series fac-[Mn(Br)(CO)(3)(tmbp)], [Mn(CO)(3)(tmbp)](2), and [Mn(CO)(3)(tmbp)](-): crystallographic, spectroelectrochemical, and DFT computational study

Stepwise electrochemical reduction of the complex fac-[Mn(Br)(CO)(3)(tmbp)] (tmbp = 4,4',5,5'-tetramethyl-2,2'-biphosphinine) produces the dimer [Mn(CO)(3)(tmbp)](2) and the five-coordinate anion [Mn(CO)(3)(tmbp)](-). All three members of the redox series have been characterized by single-crystal X-ray diffraction. The crystallographic data provide valuable insight into the localization of the added electrons on the (carbonyl)manganese and tmbp centers. In particular, the formulation of the two-electron-reduced anion as [Mn-0(CO)(3)(tmbp(-))](-) also agrees with the analysis of its IR nu(CO) wavenumbers and with the results of density functional theoretical (DFT) MO calculations on this compound. The strongly delocalized pi-bonding in the anion stabilizes its five-coordinate geometry and results in the appearance of several mixed Mn-to-tmbp charge-transfer/IL(tmbp) transitions in the near-UV-vis spectral region. A thorough voltammetric and UV-vis/IR spectroelectrochemical study of the reduction path provided evidence for a direct formation of [Mn(CO)(3)(tmbp)](-) via a two-electron ECE mechanism involving the [Mn(CO)(3)(tmbp)](.) radical transient. At ambient temperature [Mn(CO)(3)(tmbp)](-) reacts rapidly with nonreduced fac-[Mn(Br)(CO)(3)(tmbp)] to produce [Mn(CO)(3)(tmbp)](2). Comparison with the analogous 2,2'-bipyridine complexes has revealed striking similarity in the bonding properties and reactivity, despite the stronger pi-acceptor character of the tmbp ligand.

Accurate analysis of noble gas concentrations in small water samples and its application to fluid inclusions in stalagmites

The concentrations of dissolved noble gases in water are widely used as a climate proxy to determine noble gas temperatures (NGTs); i.e., the temperature of the water when gas exchange last occurred. In this paper we make a step forward to apply this principle to fluid inclusions in stalagmites in order to reconstruct the cave temperature prevailing at the time when the inclusion was formed. We present an analytical protocol that allows us accurately to determine noble gas concentrations and isotope ratios in stalagmites, and which includes a precise manometrical determination of the mass of water liberated from fluid inclusions. Most important for NGT determination is to reduce the amount of noble gases liberated from air inclusions, as they mask the temperature-dependent noble gas signal from the water inclusions. We demonstrate that offline pre-crushing in air to subsequently extract noble gases and water from the samples by heating is appropriate to separate gases released from air and water inclusions. Although a large fraction of recent samples analysed by this technique yields NGTs close to present-day cave temperatures, the interpretation of measured noble gas concentrations in terms of NGTs is not yet feasible using the available least squares fitting models. This is because the noble gas concentrations in stalagmites are not only composed of the two components air and air saturated water (ASW), which these models are able to account for. The observed enrichments in heavy noble gases are interpreted as being due to adsorption during sample preparation in air, whereas the excess in He and Ne is interpreted as an additional noble gas component that is bound in voids in the crystallographic structure of the calcite crystals. As a consequence of our study's findings, NGTs will have to be determined in the future using the concentrations of Ar, Kr and Xe only. This needs to be achieved by further optimizing the sample preparation to minimize atmospheric contamination and to further reduce the amount of noble gases released from air inclusions.

Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri

In Xanthomonas axonopodis pv. citri (Xac or X citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala(38) and Ser(151), are shown to be part of the ligand-binding pocket. (c) 2007 Elsevier B.V All rights reserved.

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

The Crystal Complex of Phosphofructokinase-2 of Escherichia coli with Fructose-6-phosphate KINETIC AND STRUCTURAL ANALYSIS OF THE ALLOSTERIC ATP INHIBITION

Substrate inhibition by ATP is a regulatory feature of the phosphofructokinases isoenzymes from Escherichia coli (Pfk-1 and Pfk-2). Under gluconeogenic conditions, the loss of this regulation in Pfk-2 causes substrate cycling of fructose-6-phosphate (fructose-6-P) and futile consumption of ATP delaying growth. In the present work, we have broached the mechanism of ATP-induced inhibition of Pfk-2 from both structural and kinetic perspectives. The crystal structure of Pfk-2 in complex with fructose-6-P is reported to a resolution of 2 angstrom. The comparison of this structure with the previously reported inhibited form of the enzyme suggests a negative interplay between fructose-6-P binding and allosteric binding of MgATP. Initial velocity experiments show a linear increase of the apparent K(0.5) for fructose-6-P and a decrease in the apparent k(cat) as a function of MgATP concentration. These effects occur simultaneously with the induction of a sigmoidal kinetic behavior (n(H) of approximately 2). Differences and resemblances in the patterns of fructose-6-P binding and the mechanism of inhibition are discussed for Pfk-1 and Pfk-2, as an example of evolutionary convergence, because these enzymes do not share a common ancestor.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Hydrolysis of bis((trimethylsilyl)methyl)tin dihalides. Crystallographic and spectroscopic study of the hydrolysis pathway

The synthesis and characterization by multinuclear NMR spectroscopy of the diorganotin dihalides (Me₃SiCH₂)₂SnX₂ (1, X = Cl; 2, X = Br), the diorganotin dichloride water adduct (Me₃SiCH₂)₂SnCl₂·H₂O (1a), the dimeric tetraorganodistannoxanes [(Me₃SiCH₂)₂(X)SnOSn(Y)(CH₂SiMe₃)₂]₂ (3, X = Y = Cl; 4, X = Br, Y = OH; 5, X = Br, Y = F; 6, X = Y = OH; 8, X = Cl, Y = OH), and the molecular diorganotin oxide cyclo-[(Me₃SiCH₂)₂SnO]₃ (7) are reported. The structures in the solid state of compounds 1a, 3, 6, and 7 were determined by single-crystal X-ray analysis. In toluene solution, the hydroxy-substituted tetraorganodistannoxane 6 is in equilibrium with the diorganotin oxide 7 and water. The eight-membered diorganotin oxide cyclo-[(Me₃SiCH₂)₂SnO]₄ (7a) is proposed to be involved in this equilibrium. On the basis of the results of this and previous works, a general hydrolysis pathway is developed for diorganotin dichlorides containing reasonably bulky substituents.

Electron backscattering diffraction analysis of an ancient wootz steel blade from central India

The electron backscattering diffraction technique was used to analyse the nature of carbides present in an ancient wootz steel blade. Bulky carbides, pro-eutectoid carbide along the prior austenite grain boundaries and fine spheroidized carbides were detected. Electron backscattering diffraction was employed to understand the texture of these carbides. The orientations of the cementite frequently occur in clusters, which points to a common origin of the members of the cluster. For the bands of coarse cementite, the origin is probably large coarse particles formed during the original cooling of the wootz cake. Pearlite formed earlier in the forging process has led to groups of similarly oriented fine cementite particles. The crystallographic texture of the cementite is sharp whereas that of the ferrite is weak. The sharp cementite textures point to the longevity of the coarse cementite throughout the repeated forging steps and to the influence of existing textured cementite on the nucleation of new cementite during cooling.

Conductivity, NMR and crystallographic study of N,N,N,N-tetramethylammonium dicyanamide plastic crystal phases : an archetypal ambient temperature plastic electrolyte material

N,N,N,N-Tetramethylammonium dicyanamide (Me₄NDCA) has been examined via differential scanning calorimetry (DSC), thermogravimetric analysis, conductivity, single crystal X-ray diffraction and ¹H nuclear magnetic resonance (NMR) analyses, and was found to be highly conductive in the solid state (σ =10−3 S cm⁻² at 420 K) and to also exhibit unusual plastic crystal behaviour. To investigate the correlation between such behaviour and the occurrence of molecular rotations in the crystal, ¹H NMR second moment measurements are compared with calculated values predicted from the crystal structure. While DSC analysis indicates a number of solid–solid transitions at ambient temperatures, subsequent ¹H NMR analysis of the Me₄N⁺ cation shows that a variety of rotational motions become active at low (<240 K) temperatures, and that such transitions in rotational states occur over a range of temperatures rather than in a sharp transition. Conductivity analysis reveals that between 320 K and 420 K the conductivity increases by more than six orders of magnitude in the solid state, in line with the transition of the Me₄N⁺ cation to a diffusive state, and that other phase transitions observed in this temperature range have no marked effect on the conductivity. Conduction in this solid state is therefore envisaged to involve a vacancy-diffusion model, involving Me₄N⁺ cation vacancies.

Crystallographic features during martensitic transformation in Ni-Mn-Ga ferromagnetic shape memory alloys

The martensitic transformation crystallography in two Ni ₅₃Mn₂₅Ga₂₂ (at. %) ferromagnetic shape memory alloys (FSMAs) was investigated by means of misorientation calculation and pole figure analysis based on the orientation of the martensitic lamellae obtained from electron backscattered diffraction (EBSD) measurements. In the alloy that was first annealed at 1073K for 4h, and then cooled to 473K at ~4K/min and held for 30min, followed by cooling to room temperature at ~10K/min, there are only two kinds of differently orientated martensitic lamellae with a misorientation angle of ~82° distributed alternatively in each initial austenite grain. There is a compound twinning orientation relationship between the two lamellae. The prevalent orientation relationship between austenite and martensite is Kurdjumov-Sachs (K-S) relationship with (111)_A//(10I)_M, [1-10]_a//[11-1]_m. In the alloy that was annealed at 1173K for 4h followed by furnace cooling, nanoscale twins inside the martensitic lamellae were observed and the orientation relationships both between the nanotwins within one lamella and between the nanotwins in two neighboring lamellae were determined. The results presented in this paper will enrich the crystallographic data of the FSMAs and offer useful information for the development of novel FSMAs with optimal performances.

Variant selection and intervariant crystallographic planes distribution in martensite in a Ti-6Al-4V alloy

The transformation texture was studied in a Ti-6Al-4V alloy for two microstructures produced through different phase transformation mechanisms (i.e. diffusional vs. displacive). Both microstructures revealed qualitatively similar crystallographic texture characteristics, having two main texture components with Euler angles of (90°, 90°, 0°) and (90°, 30°, 0°). However, the overall α texture strength was considerably weaker in the martensitic structure (i.e. displacive mechanism) compared with the α + β microstructure produced through slow cooling (i.e. diffusional mechanism). The intervariant boundary distribution in martensite mostly revealed five misorientations associated with the Burgers orientation relationship. The five-parameter boundary analysis also showed a very strong interface plane orientation texture, with interfaces terminated mostly on the prismatic planes {hki0}, when misorientation was ignored. The highest intervariant boundary populations belonged to the 63.26°/[10 553 ] and 60°/[112 0] misorientations, with length fractions of 0.38 and 0.3, respectively. The former was terminated on (41 3 0), and the latter was a symmetric tilt boundary, terminated on (1 011). The intervariant plane distribution in martensite was determined more by the constraints of the phase transformation than by the relative interface energies.