Electron diffraction structure analysis: structural research with low-quality diffraction data

Electron Diffraction Structure Analysis (EDSA) with data from standard selected-area electron diffraction (SAED) is still the method of choice for structure determination of nano-sized single crystals. The recently determined heavy atom structure α-Ti2Se (Albe & Weirich, 2003) is used as an example to illustrate the developed procedure for structure determination from two-dimensionally SAED data via direct methods and kinematical least-squares refinement. Despite the investigated crystallite had a relatively large effective thickness of about 230 Å as determined from dynamical calculations, the obtained structural model from SAED data was found in good agreement with the result from an earlier single crystal X-ray study (Weirich, Pöttgen & Simon, 1996). Arguments, which support the validity of the used quasi-kinematical approach, are given in the text. The influences of dynamical and secondary scattering on the quality of the data and the structure solution are discussed. Moreover, the usefulness of first-principles calculations for verifying the results from EDSA is demonstrated by two examples, whereas one of the structures was unattainable by conventional X-ray diffraction.

A kinetic study of the phase transformations in Al2O3 and Na2O · 6Al2O3 by a combined use of 27Al MAS NMR spectroscopy and x-ray diffraction: Importance of nucleation

Phase transformations of Al2O3 and Na2O · 6Al2O3 prepared by the gel route have been investigated for the first time by 27Al MAS NMR spectroscopy in combination with x-ray diffraction. Of particular interest in the study is the kinetics of the γ → α and γ → β transformations, respectively, in these two systems. Analysis of the kinetic data shows the important role of nucleation in both these transformations.

Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

Structured Learning for Non-Smooth Ranking losses

Learning to rank from relevance judgment is an active research area. Itemwise score regression, pairwise preference satisfaction, and listwise structured learning are the major techniques in use. Listwise structured learning has been applied recently to optimize important non-decomposable ranking criteria like AUC (area under ROC curve) and MAP(mean average precision). We propose new, almost-lineartime algorithms to optimize for two other criteria widely used to evaluate search systems: MRR (mean reciprocal rank) and NDCG (normalized discounted cumulative gain)in the max-margin structured learning framework. We also demonstrate that, for different ranking criteria, one may need to use different feature maps. Search applications should not be optimized in favor of a single criterion, because they need to cater to a variety of queries. E.g., MRR is best for navigational queries, while NDCG is best for informational queries. A key contribution of this paper is to fold multiple ranking loss functions into a multi-criteria max-margin optimization.The result is a single, robust ranking model that is close to the best accuracy of learners trained on individual criteria. In fact, experiments over the popular LETOR and TREC data sets show that, contrary to conventional wisdom, a test criterion is often not best served by training with the same individual criterion.

Multicomponent solids of lamotrigine with some selected coformers and their characterization by thermoanalytical, spectroscopic and X-ray diffraction methods

The present study investigates the structural and pharmaceutical properties of different multicomponent crystalline forms of lamotrigine (LTG) with some pharmaceutically acceptable coformers viz. nicotinamide (1), acetamide (2), acetic acid (3), 4-hydroxy-benzoic acid (4) and saccharin (5). The structurally homogeneous phases were characterized in the solid state by DSC/TGA, FT-IR and XRD (powder and single crystal structure analysis) as well as in the solution phase. Forms 1 and 2 were found to be cocrystal hydrate and cocrystal, respectively, while in forms 3, 4 and 5, proton transfer was observed from coformer to drug. The enthalpy of formation of multicomponent crystals from their components was determined from the enthalpy of solution of the cocrystals and the components separately. Higher exothermic values of the enthalpy of formation for molecular complexes 3, 4 and 5 suggest these to be more stable than 1 and 2. The solubility was measured in water as well as in phosphate buffers of varying pH. The salt solvate 3 exhibited the highest solubility of the drug in water as well as in buffers over the pH range 7-3 while the cocrystal hydrate 1 showed the maximum solubility in a buffer of pH 2. A significant lowering of the dosage profile of LTG was observed for 1, 3 and 5 in the animal activity studies on mice.

A comparison of the structure of liquid alloys derived from thermodynamic and diffraction studies

A significant amount of research on the thermodynamic properties of molten alloys is undertaken for obtaining insights into their structure . The partial and integral molar enthalpies, entropies and volumes of mixing provide some general information on the nature and strength of atomic bonds and the distribution of atoms. However, until recently it has been difficult to derive specific quantitative information because the excess entropy of mixing contains configurational , vibrational , electronic , and sometimes magnetic contributions which cannot be easily separated.

Crystallization and preliminary X-ray diffraction studies of sortase A from Streptococcus pneumoniae

Sortases are cell-membrane-anchored cysteine transpeptidases that are essential for the assembly and anchoring of cell-surface adhesins in Gram-positive bacteria. Thus, they play critical roles in virulence, infection and colonization by pathogens. Sortases have been classified into four types based on their primary sequence and the target-protein motifs that they recognize. All Gram-positive bacteria express a class A housekeeping sortase (SrtA). Sortase A from Streptococcus pneumoniae (NP_358691) has been crystallized in two crystal forms. Diamond-shaped crystals of Delta N(59)SrtA diffracted to 4.0 angstrom resolution and belonged to a tetragonal system with unit-cell parameters a = b = 122.8, c = 86.5 angstrom, alpha = beta = gamma = 90 degrees, while rod-shaped crystals of Delta N(81)SrtA diffracted to 2.91 angstrom resolution and belonged to the monoclinic space group P2(1) with unit-cell parameters a = 66.8, b = 103.47, c = 74.79 angstrom, alpha = gamma = 90, beta = 115.65 degrees. The Matthews coefficient (V(M) = 2.77 angstrom(3) Da(-1)) with similar to 56% solvent content suggested the presence of four molecules in the asymmetric unit for Delta N(81)SrtA. Also, a multi-copy search using a monomer as a probe in the molecular-replacement method resulted in the successful location of four sortase molecules in the asymmetric unit, with statistics R = 41.61, R(free) = 46.44, correlation coefficient (CC) = 64.31, CC(free) = 57.67.

Optical diffraction of second-harmonic signals in the LiBO2-Nb2O5 glasses induced by self-organized LiNbO3 crystallites

The nanocrystallites ( ≈ 3 nm) of LiNbO3, evolved in the (100−x)LiBO2-xNb2O5 (5x20, in molar ratio) glass system exhibited intense second-harmonic signals in transmission mode when exposed to infrared (IR) light at λ = 1064 nm. The second-harmonic waves were found to undergo optical diffraction which was attributed to the presence of self-organized submicrometer-sized LiNbO3 crystallites that were grown within the glass matrix along the parallel damage fringes created by the IR laser radiation. Micro-Raman studies carried out on the laser-irradiated samples confirmed the self-organized crystallites to be LiNbO3.

High-pressure synchrotron x-ray diffraction study of RMnO3 (R=Eu, Gd, Tb and Dy) upto 50 GPa

We have carried out synchrotron based high-pressure x-ray diffraction study of orthorhombic EuMnO3, GdMnO3, TbMnO3 and DyMnO3 up to 54.4, 41.6, 47.0 and 50.2 GPa, respectively. The diffraction peaks of all the four manganites shift monotonically to higher diffraction angles and the crystals retain the orthorhombic structure till the highest pressure. We have fitted the observed volume versus pressure data with the Birch-Murnaghan equation of state and determined the bulk modulus to be 185 +/- 6 GPa, 190 +/- 16 GPa, 188 +/- 9 GPa and 192 +/- 8 GPa for EuMnO3, GdMnO3, TbMnO3 and DyMnO3, respectively. The bulk modulus of EuMnO3 is comparable to other manganites, in contrast to theoretical predictions.

Angular amplification by a diffraction grating for chiro-optical measurements

The angles at which a light beam gets diffracted by a grating depend strongly on the direction of incidence for diffraction angles close to a right angle. Accordingly, it is possible to amplify small beam deflections by placing a grating at an optimal orientation to the light path. We use this principle to amplify small beam deviations arising out of a light beam refracting at the interface of an optically active medium, and demonstrate a new technique of enhancing the limit of detection of chiro-optical measurements. (C) 2012 Optical Society of America

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus

The crystal structure of the region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 was determined at a resolution of 2.5 angstrom. Severe diffraction anisotropy, rotational pseudo-symmetry and twinning complicated the refinement of this structure. A systematic explanation confirming the crystal pathologies and describing how the structure was successfully refined is given in this report.

Evaluation of mechanical losses in a linear motor pressure wave generator

A moving magnet linear motor compressor or pressure wave generator (PWG) of 2 cc swept volume with dual opposed piston configuration has been developed to operate miniature pulse tube coolers. Prelimnary experiments yielded only a no-load cold end temperature of 180 K. Auxiliary tests and the interpretation of detailed modeling of a PWG suggest that much of the PV power has been lost in the form of blow-by at piston seals due to large and non-optimum clearance seal gap between piston and cylinder. The results of experimental parameters simulated using Sage provide the optimum seal gap value for maximizing the delivered PV power.

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.