ana Synthesis, crystal structure and Hirshfeld and thermal analysis of bis[benzyl 2-(heptan-4-ylidene)hydrazine-1-carboxylate-κ2N2,O]bis(thiocyanato)nickel(II) By scripts.iucr.org Published On :: 2020-04-07 The title centrosymmetric NiII complex, [Ni(NCS)2(C15H22N2O2)2], crystallizes with one half molecule in the asymmetric unit of the monoclinic unit cell. The complex adopts an octahedral coordination geometry with two mutually trans benzyl-2-(heptan-4-ylidene)hydrazine-1-carboxylate ligands in the equatorial plane with the axial positions occupied by N-bound thiocyanato ligands. The overall conformation of the molecule is also affected by two, inversion-related, intramolecular C—H⋯O hydrogen bonds. The crystal structure features N—H⋯S, C—H⋯S and C—H⋯N hydrogen bonds together with C—H⋯π contacts that stack the complexes along the b-axis direction. The packing was further explored by Hirshfeld surface analysis. The thermal properties of the complex were also investigated by simultaneous TGA–DTA analyses. Full Article text
ana Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 2-(2,3-dihydro-1H-perimidin-2-yl)-6-methoxyphenol By scripts.iucr.org Published On :: 2020-04-03 The title compound, C18H16N2O2, consists of perimidine and methoxyphenol units, where the tricyclic perimidine unit contains a naphthalene ring system and a non-planar C4N2 ring adopting an envelope conformation with the NCN group hinged by 47.44 (7)° with respect to the best plane of the other five atoms. In the crystal, O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl (Phnl = phenol and Prmdn = perimidine) hydrogen bonds link the molecules into infinite chains along the b-axis direction. Weak C—H⋯π interactions may further stabilize the crystal structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.0%), H⋯C/C⋯H (35.8%) and H⋯O/O⋯H (12.0%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, the O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl hydrogen-bond energies are 58.4 and 38.0 kJ mol−1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
ana Crystal structure and Hirshfeld surface analysis of hexyl 1-hexyl-2-oxo-1,2-dihydroquinoline-4-carboxylate By scripts.iucr.org Published On :: 2020-04-09 The asymmetric unit of the title compound, C22H31NO3, comprises of one molecule. The molecule is not planar, with the carboxylate ester group inclined by 33.47 (4)° to the heterocyclic ring. Individual molecules are linked by aromaticC—H⋯Ocarbonyl hydrogen bonds into chains running parallel to [001]. Slipped π–π stacking interactions between quinoline moieties link these chains into layers extending parallel to (100). Hirshfeld surface analysis, two-dimensional fingerprint plots and molecular electrostatic potential surfaces were used to quantify the intermolecular interactions present in the crystal, indicating that the most important contributions for the crystal packing are from H⋯H (72%), O⋯H/H⋯O (14.5%) and C⋯H/H⋯C (5.6%) interactions. Full Article text
ana Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of 3-butyl-2,6-bis(4-fluorophenyl)piperidin-4-one By scripts.iucr.org Published On :: 2020-04-09 The title compound, C21H23F2NO, consists of two fluorophenyl groups and one butyl group equatorially oriented on a piperidine ring, which adopts a chair conformation. The dihedral angle between the mean planes of the phenyl rings is 72.1 (1)°. In the crystal, N—H⋯O and weak C—H⋯F interactions, which form R22[14] motifs, link the molecules into infinite C(6) chains propagating along [001]. A weak C—H⋯π interaction is also observed. A Hirshfeld surface analysis of the crystal structure indicates that the most significant contributions to the crystal packing are from H⋯H (53.3%), H⋯C/C⋯H (19.1%), H⋯F/F⋯H (15.7%) and H⋯O/O⋯H (7.7%) contacts. Density functional theory geometry-optimized calculations were compared to the experimentally determined structure in the solid state and used to determine the HOMO–LUMO energy gap and compare it to the UV–vis experimental spectrum. Full Article text
ana 2-[(2,4,6-Trimethylbenzene)sulfonyl]phthalazin-1(2H)-one: crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-04-21 The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-trimethylbenzene)sulfonyl]-1,2-dihydrophthalazin-1-one}, features a tetrahedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the molecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supramolecular tape along the a-axis direction; tapes assemble without directional interactions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking interactions but, also H⋯H and C—H⋯C contacts. The calculation of the interaction energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking interactions. Full Article text
ana Crystal structure, Hirshfeld surface analysis and DFT studies of 6-bromo-3-(12-bromododecyl)-2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine By scripts.iucr.org Published On :: 2020-04-21 The title compound, C24H30Br2N4O2, consists of a 2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine entity with a 12-bromododecyl substituent attached to the pyridine N atom. The middle eight-carbon portion of the side chain is planar to within 0.09 (1) Å and makes a dihedral angle of 21.9 (8)° with the mean plane of the imidazolopyridine moiety, giving the molecule a V-shape. In the crystal, the imidazolopyridine units are associated through slipped π–π stacking interactions together with weak C—HPyr⋯ONtr and C—HBrmdcyl⋯ONtr (Pyr = pyridine, Ntr = nitro and Brmdcyl = bromododecyl) hydrogen bonds. The 12-bromododecyl chains overlap with each other between the stacks. The terminal –CH2Br group of the side chain shows disorder over two resolved sites in a 0.902 (3):0.098 (3) ratio. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (48.1%), H⋯Br/Br⋯H (15.0%) and H⋯O/O⋯H (12.8%) interactions. The optimized molecular structure, using density functional theory at the B3LYP/ 6–311 G(d,p) level, is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
ana Crystal structure and Hirshfeld surface analysis of 2-phenyl-1H-phenanthro[9,10-d]imidazol-3-ium benzoate By scripts.iucr.org Published On :: 2020-04-24 In the title compound, C21H15N2+·C7H5O2−, 2-phenyl-1H-phenanthro[9,10-d]imidazole and benzoic acid form an ion pair complex. The system is consolidated by hydrogen bonds along with π–π interactions and N—H⋯π interactions between the constituent units. For a better understanding of the crystal structure and intermolecular interactions, a Hirshfeld surface analysis was performed. Full Article text
ana Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)methyl]amino}benzoic acid dimethylformamide monosolvate By scripts.iucr.org Published On :: 2020-04-24 The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a dimethylformamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic molecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Caryl—CH2—NH—Caryl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supramolecular network, resulting from hydrogen-bonding interactions between the carboxylic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carboxylic group and additional C—H⋯π interactions. Hirshfeld surface analysis was performed to quantify the intermolecular interactions. Full Article text
ana Crystal structure and Hirshfeld surface analysis of 6-benzoyl-3,5-diphenylcyclohex-2-en-1-one By scripts.iucr.org Published On :: 2020-04-21 In the title compound, C25H20O2, the central cyclohexenone ring adopts an envelope conformation. The mean plane of the cyclohexenone ring makes dihedral angles of 87.66 (11) and 23.76 (12)°, respectively, with the two attached phenyl rings, while it is inclined by 69.55 (11)° to the phenyl ring of the benzoyl group. In the crystal, the molecules are linked by C—H⋯O and C—H⋯π interactions, forming a three-dimensional network. Full Article text
ana Synthesis, crystal structure and Hirshfeld surface analysis of N-(4-chlorophenyl)-5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxamide By scripts.iucr.org Published On :: 2020-04-30 The title compound, C19H17ClN4O2, was obtained via a two-step synthesis involving the enol-mediated click Dimroth reaction of 4-azidoanisole with methyl 3-cyclopropyl-3-oxopropanoate leading to the 5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxylic acid and subsequent acid amidation with 4-chloroaniline by 1,1'-carbonyldiimidazole (CDI). It crystallizes in space group P21/n, with one molecule in the asymmetric unit. In the extended structure, two molecules arranged in a near coplanar fashion relative to the triazole ring planes are interconnected by N—H⋯N and C—H⋯N hydrogen bonds into a homodimer. The formation of dimers is a consequence of the above interaction and the edge-to-face stacking of aromatic rings, which are turned by 58.0 (3)° relative to each other. The dimers are linked by C—H⋯O interactions into ribbons. DFT calculations demonstrate that the frontier molecular orbitals are well separated in energy and the HOMO is largely localized on the 4-chlorophenyl amide motif while the LUMO is associated with aryltriazole grouping. A Hirshfeld surface analysis was performed to further analyse the intermolecular interactions. Full Article text
ana SVAT4: a computer program for visualization and analysis of crystal structures By scripts.iucr.org Published On :: 2020-05-05 SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures, including chemical bonds and magnetic moments. A wide range of functions, e.g. revealing atomic layers and polyhedral clusters, are available for further structural analysis. Atomic sizes, colors, appearance, view directions and view modes (orthographic or perspective views) are adjustable. Customized work for the visualization and analysis can be saved and then reloaded. SVAT4 provides a template to simplify the process of preparation of a new data file. SVAT4 can generate high-quality images for publication and animations for presentations. The usability of SVAT4 is broadened by a software suite for simulation and analysis of electron diffraction patterns. Full Article text
ana Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination By scripts.iucr.org Published On :: 2019-07-12 Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal–organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool. Full Article text
ana Symmetry-mode analysis for intuitive observation of structure–property relationships in the lead-free antiferroelectric (1−x)AgNbO3–xLiTaO3 By scripts.iucr.org Published On :: 2019-06-21 Functional materials are of critical importance to electronic and smart devices. A deep understanding of the structure–property relationship is essential for designing new materials. In this work, instead of utilizing conventional atomic coordinates, a symmetry-mode approach is successfully used to conduct structure refinement of the neutron powder diffraction data of (1−x)AgNbO3–xLiTaO3 (0 ≤ x ≤ 0.09) ceramics. This provides rich structural information that not only clarifies the controversial symmetry assigned to pure AgNbO3 but also explains well the detailed structural evolution of (1−x)AgNbO3–xLiTaO3 (0 ≤ x ≤ 0.09) ceramics, and builds a comprehensive and straightforward relationship between structural distortion and electrical properties. It is concluded that there are four relatively large-amplitude major modes that dominate the distorted Pmc21 structure of pure AgNbO3, namely a Λ3 antiferroelectric mode, a T4+ a−a−c0 octahedral tilting mode, an H2 a0a0c+/a0a0c− octahedral tilting mode and a Γ4− ferroelectric mode. The H2 and Λ3 modes become progressively inactive with increasing x and their destabilization is the driving force behind the composition-driven phase transition between the Pmc21 and R3c phases. This structural variation is consistent with the trend observed in the measured temperature-dependent dielectric properties and polarization–electric field (P-E) hysteresis loops. The mode crystallography applied in this study provides a strategy for optimizing related properties by tuning the amplitudes of the corresponding modes in these novel AgNbO3-based (anti)ferroelectric materials. Full Article text
ana A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples By scripts.iucr.org Published On :: 2019-07-10 The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology. Full Article text
ana Isomorphism: `molecular similarity to crystal structure similarity' in multicomponent forms of analgesic drugs tolfenamic and mefenamic acid By scripts.iucr.org Published On :: 2020-01-07 The non-steroidal anti-inflammatory drugs mefenamic acid (MFA) and tolfenamic acid (TFA) have a close resemblance in their molecular scaffold, whereby a methyl group in MFA is substituted by a chloro group in TFA. The present study demonstrates the isomorphous nature of these compounds in a series of their multicomponent solids. Furthermore, the unique nature of MFA and TFA has been demonstrated while excavating their alternate solid forms in that, by varying the drug (MFA or TFA) to coformer [4-dimethylaminopyridine (DMAP)] stoichiometric ratio, both drugs have produced three different types of multicomponent crystals, viz. salt (1:1; API to coformer ratio), salt hydrate (1:1:1) and cocrystal salt (2:1). Interestingly, as anticipated from the close similarity of TFA and MFA structures, these multicomponent solids have shown an isomorphous relation. A thorough characterization and structural investigation of the new multicomponent forms of MFA and TFA revealed their similarity in terms of space group and structural packing with isomorphic nature among the pairs. Herein, the experimental results are generalized in a broader perspective for predictably identifying any possible new forms of comparable compounds by mapping their crystal structure landscapes. The utility of such an approach is evident from the identification of polymorph VI of TFA from hetero-seeding with isomorphous MFA form I from acetone–methanol (1:1) solution. That aside, a pseudopolymorph of TFA with dimethylformamide (DMF) was obtained, which also has some structural similarity to that of the solvate MFA:DMF. These new isostructural pairs are discussed in the context of solid form screening using structural landscape similarity. Full Article text
ana Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis By scripts.iucr.org Published On :: 2019-10-01 Full Article text
ana Industrial cryo-EM facility setup and management By scripts.iucr.org Published On :: 2020-04-06 Cryo-electron microscopy (cryo-EM) has rapidly expanded with the introduction of direct electron detectors, improved image-processing software and automated image acquisition. Its recent adoption by industry, particularly in structure-based drug design, creates new requirements in terms of reliability, reproducibility and throughput. In 2016, Thermo Fisher Scientific (then FEI) partnered with the Medical Research Council Laboratory of Molecular Biology, the University of Cambridge Nanoscience Centre and five pharmaceutical companies [Astex Pharmaceuticals, AstraZeneca, GSK, Sosei Heptares and Union Chimique Belge (UCB)] to form the Cambridge Pharmaceutical Cryo-EM Consortium to share the risks of exploring cryo-EM for early-stage drug discovery. The Consortium expanded with a second Themo Scientific Krios Cryo-EM at the University of Cambridge Department of Materials Science and Metallurgy. Several Consortium members have set up in-house facilities, and a full service cryo-EM facility with Krios and Glacios has been created with the Electron Bio-Imaging Centre for Industry (eBIC for Industry) at Diamond Light Source (DLS), UK. This paper will cover the lessons learned during the setting up of these facilities, including two Consortium Krios microscopes and preparation laboratories, several Glacios microscopes at Consortium member sites, and a Krios and Glacios at eBIC for Industry, regarding site evaluation and selection for high-resolution cryo-EM microscopes, the installation process, scheduling, the operation and maintenance of the microscopes and preparation laboratories, and image processing. Full Article text
ana TEXS: in-vacuum tender X-ray emission spectrometer with 11 Johansson crystal analyzers By scripts.iucr.org Published On :: 2020-04-07 The design and first results of a large-solid-angle X-ray emission spectrometer that is optimized for energies between 1.5 keV and 5.5 keV are presented. The spectrometer is based on an array of 11 cylindrically bent Johansson crystal analyzers arranged in a non-dispersive Rowland circle geometry. The smallest achievable energy bandwidth is smaller than the core hole lifetime broadening of the absorption edges in this energy range. Energy scanning is achieved using an innovative design, maintaining the Rowland circle conditions for all crystals with only four motor motions. The entire spectrometer is encased in a high-vacuum chamber that allocates a liquid helium cryostat and provides sufficient space for in situ cells and operando catalysis reactors. Full Article text
ana Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria By scripts.iucr.org Published On :: 2020-04-17 Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored. Full Article text
ana GIDVis: a comprehensive software tool for geometry-independent grazing-incidence X-ray diffraction data analysis and pole-figure calculations By scripts.iucr.org Published On :: 2019-05-31 GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacenequinone crystallites on a single-crystalline Au(111) surface. Full Article text
ana Crystallography at the nanoscale: planar defects in ZnO nanospikes By scripts.iucr.org Published On :: 2019-08-29 The examination of anisotropic nanostructures, such as wires, platelets or spikes, inside a transmission electron microscope is normally performed only in plan view. However, intrinsic defects such as growth twin interfaces could occasionally be concealed from direct observation for geometric reasons, leading to superposition. This article presents the shadow-focused ion-beam technique to prepare multiple electron-beam-transparent cross-section specimens of ZnO nanospikes, via a procedure which could be readily extended to other anisotropic structures. In contrast with plan-view data of the same nanospikes, here the viewing direction allows the examination of defects without superposition. By this method, the coexistence of two twin configurations inside the wurtzite-type structure is observed, namely [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 1) and [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 3), which were not identified during the plan-view observations owing to superposition of the domains. The defect arrangement could be the result of coalescence twinning of crystalline nuclei formed on the partially molten Zn substrate during the flame-transport synthesis. Three-dimensional defect models of the twin interface structures have been derived and are correlated with the plan-view investigations by simulation. Full Article text
ana Mercury 4.0: from visualization to analysis, design and prediction By scripts.iucr.org Published On :: 2020-02-01 The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization. Full Article text
ana Structure analysis of supported disordered molybdenum oxides using pair distribution function analysis and automated cluster modelling By scripts.iucr.org Published On :: 2020-02-01 Molybdenum oxides and sulfides on various low-cost high-surface-area supports are excellent catalysts for several industrially relevant reactions. The surface layer structure of these materials is, however, difficult to characterize due to small and disordered MoOx domains. Here, it is shown how X-ray total scattering can be applied to gain insights into the structure through differential pair distribution function (d-PDF) analysis, where the scattering signal from the support material is subtracted to obtain structural information on the supported structure. MoOx catalysts supported on alumina nanoparticles and on zeolites are investigated, and it is shown that the structure of the hydrated molybdenum oxide layer is closely related to that of disordered and polydisperse polyoxometalates. By analysing the PDFs with a large number of automatically generated cluster structures, which are constructed in an iterative manner from known polyoxometalate clusters, information is derived on the structural motifs in supported MoOx. Full Article text
ana Detailed surface analysis of V-defects in GaN films on patterned silicon(111) substrates by metal–organic chemical vapour deposition. Corrigendum By scripts.iucr.org Published On :: 2020-02-01 An error in the article by Gao, Zhang, Zhu, Wu, Mo, Pan, Liu & Jiang [J. Appl. Cryst. (2019), 52, 637–642] is corrected. Full Article text
ana PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data By scripts.iucr.org Published On :: 2020-03-13 Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs. Full Article text
ana In meso crystallogenesis. Compatibility of the lipid cubic phase with the synthetic digitonin analogue, glyco-diosgenin By scripts.iucr.org Published On :: 2020-03-25 Digitonin has long been used as a mild detergent for extracting proteins from membranes for structure and function studies. As supplied commercially, digitonin is inhomogeneous and requires lengthy pre-treatment for reliable downstream use. Glyco-diosgenin (GDN) is a recently introduced synthetic surfactant with features that mimic digitonin. It is available in homogeneously pure form. GDN is proving to be a useful detergent, particularly in the area of single-particle cryo-electron microscopic studies of membrane integral proteins. With a view to using it as a detergent for crystallization trials by the in meso or lipid cubic phase method, it was important to establish the carrying capacity of the cubic mesophase for GDN. This was quantified in the current study using small-angle X-ray scattering for mesophase identification and phase microstructure characterization as a function of temperature and GDN concentration. The data show that the lipid cubic phase formed by hydrated monoolein tolerates GDN to concentrations orders of magnitude in excess of those used for membrane protein studies. Thus, having GDN in a typical membrane protein preparation should not deter use of the in meso method for crystallogenesis. Full Article text
ana Bragg Edge Analysis for Transmission Imaging Experiments software tool: BEATRIX By journals.iucr.org Published On :: BEATRIX, is a new tool for performing data analysis of energy-resolved neutron-imaging experiments involving intense fitting procedures of multi-channel spectra. The use of BEATRIX is illustrated for a test specimen, providing spatially resolved 2D maps for residual strains and Bragg edge heights. Full Article text
ana Shape-fitting analyses of two-dimensional X-ray diffraction spots for strain-distribution evaluation in a β-FeSi2 nanofilm By journals.iucr.org Published On :: New fitting analyses of two-dimensional diffraction-spot shapes are demonstrated to evaluate strain, strain distribution and domain size in a crystalline ultra-thin film. The evaluations are displayed as residual and population maps as a function of strain or domain size. Full Article text
ana sasPDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data By journals.iucr.org Published On :: The sasPDF method, an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime, is presented. The method is applied to characterize the structure of nanoparticle assemblies with different levels of structural order. Full Article text
ana SVAT4: a computer program for visualization and analysis of crystal structures By journals.iucr.org Published On :: SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures. A wide range of functions are available for structural analysis. Full Article text
ana A novel experimental approach for nanostructure analysis: simultaneous small-angle X-ray and neutron scattering By journals.iucr.org Published On :: A portable small-angle X-ray scattering instrument with geometrical dimensions suitable for installation at the D22 instrument was designed and constructed for simultaneous small-angle X-ray and neutron scattering experiments at ILL. Full Article text
ana Dual-energy crystal-analyzer scheme for spectral tomography By journals.iucr.org Published On :: The principles of using the Laue-analyzer as an X-ray optical element for separating two characteristic lines of an X-ray tube are presented. Full Article text
ana EDDIDAT: a graphical user interface for the analysis of energy-dispersive diffraction data By journals.iucr.org Published On :: EDDIDAT is a program that provides a graphical user interface (GUI) for the evaluation of energy-dispersive X-ray diffraction data with the focus on the depth-resolved residual stress analysis. Full Article text
ana Dark-field electron holography as a recording of crystal diffraction in real space: a comparative study with high-resolution X-ray diffraction for strain analysis of MOSFETs By journals.iucr.org Published On :: A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are being applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized. Full Article text
ana job related post for Forensic Analyst By www.bleepingcomputer.com Published On :: 2019-07-24T02:05:24-05:00 Full Article
ana Fossil teeth of 15-million-year-old browsing horse found in Panama Canal excavations. By insider.si.edu Published On :: Wed, 22 Jul 2009 08:10:19 +0000 The fossil teeth of a 15- to 18-million-year-old three-toed browsing horse, Anchitherium clarencei, were recently discovered by scientists from the Smithsonian Tropical Research Institute and the […] The post Fossil teeth of 15-million-year-old browsing horse found in Panama Canal excavations. appeared first on Smithsonian Insider. Full Article Dinosaurs & Fossils Research News Science & Nature fossils prehistoric Tropical Research Institute
ana A dry spring in Panama means more sulfur butterflies, study reveals By insider.si.edu Published On :: Fri, 02 Oct 2009 13:38:10 +0000 A new census of tropical sulfur butterflies (Aphrissa statira) migrating across the Panama Canal has revealed the central role that weather plays in determining why populations of these lemon-yellow insects vary from year to year. The post A dry spring in Panama means more sulfur butterflies, study reveals appeared first on Smithsonian Insider. Full Article Research News Science & Nature biodiversity conservation conservation biology Tropical Research Institute
ana Shipping industry sends help as project in Panama tackles amphibian crisis By insider.si.edu Published On :: Fri, 23 Apr 2010 13:34:26 +0000 The rescue pods will be part of the project’s Amphibian Rescue Center at Summit Municipal Park, which will also include a lab with a quarantine facility. The post Shipping industry sends help as project in Panama tackles amphibian crisis appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature amphibian biodiversity chytrid fungus conservation conservation biology endangered species extinction Tropical Research Institute
ana Two new frog species discovered in Panama’s fungal war zone By insider.si.edu Published On :: Mon, 24 May 2010 13:19:40 +0000 “We are working as hard as we can to find and identify frogs before the disease reaches them, and to learn more about a disease that has the power to ravage an entire group of organisms,” said Roberto Ibanez, research scientist at STRI and local director of the Panama Amphibian Rescue and Conservation Project. The post Two new frog species discovered in Panama’s fungal war zone appeared first on Smithsonian Insider. Full Article Research News Science & Nature chytrid fungus Colombia extinction frogs new species South America
ana New frog species pose challenge for conservation project in Panama By insider.si.edu Published On :: Thu, 29 Jul 2010 12:06:04 +0000 Discoveries of three new from species in Panama lead to hope that project researchers can save these animals from a deadly fungus killing frogs worldwide and the fear that many species will go extinct before scientists even know they exist. The post New frog species pose challenge for conservation project in Panama appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature amphibian biodiversity chytrid fungus conservation conservation biology endangered species extinction frogs new species Tropical Research Institute
ana Coral bleaching event caused by warming ocean waters is documented in Panama By insider.si.edu Published On :: Wed, 13 Oct 2010 12:56:24 +0000 Scientists and local dive operators first noticed coral bleaching in the waters surrounding Isla Colon, in Panama’s Bocas del Toro province in July. Smithsonian staff scientist Nancy Knowlton and colleagues documented an extensive bleaching event in late September. The post Coral bleaching event caused by warming ocean waters is documented in Panama appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature biodiversity Caribbean climate change conservation conservation biology coral reefs endangered species fungi Tropical Research Institute
ana Facebook friends help scientists quickly identify nearly 5,000 fish specimens collected in Guyana By insider.si.edu Published On :: Thu, 24 Mar 2011 18:49:46 +0000 Faced with insufficient time and inadequate library resources to tackle the problem on their own, they instead posted a catalog of specimen images to Facebook and turned to their network of colleagues for help. The post Facebook friends help scientists quickly identify nearly 5,000 fish specimens collected in Guyana appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature biodiversity Colombia conservation fishes National Museum of Natural History South America
ana Charles Doolittle Walcott (1850-1927) family campsite in the Canadian Rockies By insider.si.edu Published On :: Wed, 25 May 2011 13:25:26 +0000 Collecting trips for Charles Doolittle Walcott (1850-1927), paleontologist and fourth Secretary of the Smithsonian Institution, were often a family affair. This 1910 photograph shows their […] The post Charles Doolittle Walcott (1850-1927) family campsite in the Canadian Rockies appeared first on Smithsonian Insider. Full Article Dinosaurs & Fossils History & Culture Research News Science & Nature Spotlight National Museum of Natural History
ana Green-headed Tanager (Tangara seledon) of east-central South America By insider.si.edu Published On :: Tue, 14 Jun 2011 17:36:07 +0000 A description and photos of the green-headed tanager (Tangara seledon), a bird native to east-central South America, can be found in the Species of the […] The post Green-headed Tanager (Tangara seledon) of east-central South America appeared first on Smithsonian Insider. Full Article Animals Science & Nature Spotlight conservation Migratory Bird Center National Museum of Natural History South America
ana Manakins, birds of tropical forests, form alliances for common good By insider.si.edu Published On :: Wed, 22 Jun 2011 11:37:36 +0000 Some--birds called wire-tailed manakins, residents of tropical forests in the Americas--are cooperators as well as competitors. They cooperate, forming alliances for a common cause. The post Manakins, birds of tropical forests, form alliances for common good appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature birds Ecuador Migratory Bird Center Smithsonian's National Zoo South America spiders
ana Fossil skull of an extinct toothed whale excavated from Panamanian sediments By insider.si.edu Published On :: Fri, 24 Jun 2011 12:47:13 +0000 A scientist from the Smithsonian Tropical Research Institute uses a pick to dislodge the fossil skull of an extinct toothed whale from sediments on the […] The post Fossil skull of an extinct toothed whale excavated from Panamanian sediments appeared first on Smithsonian Insider. Full Article Dinosaurs & Fossils Marine Science Research News Science & Nature Spotlight Caribbean collections fossils geology National Museum of Natural History prehistoric Tropical Research Institute
ana Whole-genome analysis at center of effort to save Tasmanian devil By insider.si.edu Published On :: Tue, 28 Jun 2011 14:57:41 +0000 The whole-genome analysis of two Tasmanian devils—one that died of a new contagious cancer known as Devil Facial Tumor Disease (DFTD) and one healthy animal—is at the center of a new management strategy to help prevent the extinction of this species. The post Whole-genome analysis at center of effort to save Tasmanian devil appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature biodiversity conservation conservation biology endangered species extinction mammals National Museum of Natural History
ana Unlocking the mysteries of Jefferson’s bible with high-tech analysis and microscopic testing By insider.si.edu Published On :: Wed, 24 Aug 2011 16:27:23 +0000 The Life and Morals of Jesus of Nazareth, more commonly known as the Jefferson bible, is a volume created by Thomas Jefferson containing passages he […] The post Unlocking the mysteries of Jefferson’s bible with high-tech analysis and microscopic testing appeared first on Smithsonian Insider. Full Article Science & Nature Spotlight conservation materials science National Museum of American History
ana Halocoryza acapulcana Whitehead By insider.si.edu Published On :: Wed, 19 Oct 2011 18:27:23 +0000 Halocoryza acapulcana Whitehead (Acapulco Saline Catarrh Beetle), described in 1966 by Donald R. Whitehead. This image is from a recent paper by Terry L. Erwin, […] The post Halocoryza acapulcana Whitehead appeared first on Smithsonian Insider. Full Article Marine Science Science & Nature Spotlight biodiversity insects National Museum of Natural History
ana Two closely related bee species discovered far apart in Panama and northern Colombia By insider.si.edu Published On :: Thu, 20 Oct 2011 14:34:20 +0000 Our studies of the genetic relationships between these bees tells us that they originated in the Amazon about 22 million years ago and that they moved north into Central America before 3 million years ago. The post Two closely related bee species discovered far apart in Panama and northern Colombia appeared first on Smithsonian Insider. Full Article Animals Science & Nature bees Colombia South America