PLEASE REDUCE TO 1-2 SENTENCES. The capability of X-ray diffraction for the microstructure investigations of metastable systems is illustrated on the example of thin films of titanium aluminium nitrides with high aluminium content, which are supersaturated and partially decomposed. In addition to the chemical composition, the surface mobility of the deposited species was employed as a factor influencing the microstructure of the thin films. It is shown how the micromechanical properties of the partially decomposed (Ti,Al)N thin films, which were deduced from the synchrotron diffraction experiments, are related to the thin film microstructure and to the decomposition mechanism. The prominent role of the crystallographic anisotropy of the macroscopic and microscopic lattice deformations in the understanding of the micromechanical properties is addressed.

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Solution structure of β-amylase 2 from Arabidopsis thaliana shows the role of the conserved N-terminus in enzyme tetramer formation.

This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.

Six new 1-aroyl-4-(4-meth­oxy­phen­yl)piperazines have been prepared, using coupling reactions between benzoic acids and N-(4-meth­oxy­phen­yl)piperazine. There are no significant hydrogen bonds in the structure of 1-benzoyl-4-(4-meth­oxy­phen­yl)piperazine, C18H20N2O2, (I). The mol­ecules of 1-(2-fluoro­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19FN2O2, (II), are linked by two C—H⋯O hydrogen bonds to form chains of rings, which are linked into sheets by an aromatic π–π stacking inter­action. 1-(2-Chloro­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19ClN2O2, (III), 1-(2-bromo­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19BrN2O2, (IV), and 1-(2-iodo­benzo­yl)-4-(4-meth­oxyphen­yl)piperazine, C18H19IN2O2, (V), are isomorphous, but in (III) the aroyl ring is disordered over two sets of atomic sites having occupancies of 0.942 (2) and 0.058 (2). In each of (III)–(V), a combination of two C—H⋯π(arene) hydrogen bonds links the mol­ecules into sheets. A single O—H⋯O hydrogen bond links the mol­ecules of 1-(2-hy­droxy­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H20N2O3, (VI), into simple chains. Comparisons are made with the structures of some related compounds.

Twelve 4-(4-meth­oxy­phen­yl)piperazin-1-ium salts containing organic anions have been prepared and structurally characterized. The monohydrated benzoate, 4-fluoro­benzoate, 4-chloro­benzoate and 4-bromo­benzoate salts, C11H17N2O+·C7H5O2−·H2O (I), C11H17N2O+·C7H4FO2−·H2O (II), C11H17N2O+·C7H4ClO2−·H2O (III), and C11H17N2O+·C7H4BrO2−·H2O (IV), respectively, are isomorphous and all exhibit disorder in the 4-meth­oxy­phenyl unit: the components are linked by N—H⋯O and O—H⋯O hydrogen bond to form chains of rings. The unsolvated 2-hy­droxy­benzoate, pyridine-3-carboxyl­ate and 2-hy­droxy-3,5-di­nitro­benzoate salts, C11H17N2O+·C7H5O3− (V), C11H17N2O+·C6H4NO2− (VI) and C11H17N2O+·C7H3N2O7− (VII), respectively, are all fully ordered: the components of (V) are linked by multiple N—H⋯O hydrogen bonds to form a chain of rings; those of (VI) are linked into a three-dimensional framework by a combination of N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds and those of (VII), where the anion has a structure reminiscent of the picrate anion, are linked into a three-dimensional array by N—H⋯O and C—H⋯O hydrogen bonds. The hydrogensuccinate and hydrogenfumarate salts, C11H17N2O+·C4H5O4− (VIII) and C11H17N2O+·C4H3O3− (IX), respectively, are isomorphous, and both exhibit disorder in the anionic component: N—H⋯O and O—H⋯O hydrogen bonds link the ions into sheets, which are further linked by C—H⋯π(arene) inter­actions. The anion of the hydrogenmaleate salt, C11H17N2O+·C4H3O3− (X), contains a very short and nearly symmetrical O⋯H⋯O hydrogen bond, and N—H⋯O hydrogen bonds link the anions into chains of rings. The ions in the tri­chloro­acetate salt, C11H17N2O+·C2Cl3O2− (XI), are linked into simple chains by N—H⋯O hydrogen bonds. In the hydrated chloranilate salt, 2C11H17N2O+·C6Cl2O42−·2H2O (XII), which crystallizes as a non-merohedral twin, the anion lies across a centre of inversion in space group P21/n, and a combination of N—H⋯O and O—H⋯O hydrogen bonds generates complex sheets. Comparisons are made with the structures of some related compounds.

Two new chalcones containing both pyrazole and thio­phene substituents have been prepared and structurally characterized. 3-(3-Methyl-5-phen­oxy-1-phenyl-1H-pyrazol-4-yl)-1-(thio­phen-2-yl)prop-2-en-1-one, C23H18N2O2S (I), and 3-[3-methyl-5-(2-methyl­phen­oxy)-1-phenyl-1H-pyrazol-4-yl]-1-(thio­phen-2-yl)prop-2-en-1-one, C24H20N2O2S (II), are isomorphous as well as isostructural, and in each the thio­phene substituent is disordered over two sets of atomic sites having occupancies 0.844 (3) and 0.156 (3) in (I), and 0.883 (2) and 0.117 (2) in (II). In each structure, the mol­ecules are linked into sheets by a combination of C—H⋯N and C—H⋯O hydrogen bonds. Comparisons are made with some related compounds.

The crystal structure of the polymeric title compound, catena-poly[[[di­aqua­lithium]-μ-γ-cyclo­dextrin(1−)-[aqua­lithium]-μ-γ-cyclo­dextrin(1−)] pentadecahydrate], {[Li2(C48H79O40)2(H2O)3]·15H2O}n, consists of deprotonated γ-cyclo­dextrin (CD) mol­ecules assembled by lithium ions into metal–organic ribbons that are cross-linked by multiple O—H⋯O hydrogen bonds into sheets extending parallel to (0overline11). Within a ribbon, one Li+ ion is coordinated by one deprotonated hydroxyl group of the first γ-CD torus and by one hydroxyl group of the second γ-CD torus as well as by two water mol­ecules. The other Li+ ion is coordinated by one deprotonated hydroxyl and by one hydroxyl group of the second γ-CD torus, by one hydroxyl group of the first γ-CD torus as well as by one water mol­ecule. The coordination spheres of both Li+ cations are distorted tetra­hedral. The packing of the structure constitute channels along the a axis. Parts of the hy­droxy­methyl groups in cyclo­dextrin molecules as well as water mol­ecules show two-component disorder. Electron density associated with additional disordered solvent mol­ecules inside the cavities was removed with the SQUEEZE [Spek (2015). Acta Cryst. C71, 9–18] routine in PLATON. These solvent mol­ecules are not considered in the given chemical formula and other crystal data. Five out of the sixteen hy­droxy­methyl groups and one water mol­ecule are disordered over two sets of sites.

Temperature is a ubiquitous environmental variable used to explore materials structure, properties and reactivity. This article reports a new paradigm for variable-temperature measurements that varies the temperature continuously across a sample such that temperature is measured as a function of sample position and not time. The gradient approach offers advantages over conventional variable-temperature studies, in which temperature is scanned during a series measurement, in that it improves the efficiency with which a series of temperatures can be probed and it allows the sample evolution at multiple temperatures to be measured in parallel to resolve kinetic and thermodynamic effects. Applied to treat samples at a continuum of temperatures prior to measurements at ambient temperature, the gradient approach enables parametric studies of recovered systems, eliminating temperature-dependent structural and chemical variations to simplify interpretation of the data. The implementation of spatially resolved variable-temperature measurements presented here is based on a gradient-heater design that uses a 3D-printed ceramic template to guide the variable pitch of the wire in a resistively heated wire-wound heater element. The configuration of the gradient heater was refined on the basis of thermal modelling. Applications of the gradient heater to quantify thermal-expansion behaviour, to map metastable polymorphs recovered to ambient temperature, and to monitor the time- and temperature-dependent phase evolution in a complex solid-state reaction are demonstrated.

Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool.

The stressosome transduces environmental stress signals to SigB to upregulate SigB-dependent transcription, which is required for bacterial viability. The stressosome core is composed of RsbS and at least one of the RsbR paralogs. A previous cryo-electron microscopy (cryo-EM) structure of the RsbRA–RsbS complex determined under a D2 symmetry restraint showed that the stressosome core forms a pseudo-icosahedron consisting of 60 STAS domains of RsbRA and RsbS. However, it is still unclear how RsbS and one of the RsbR paralogs assemble into the stressosome. Here, an assembly model of the stressosome is presented based on the crystal structure of the RsbS icosahedron and cryo-EM structures of the RsbRA–RsbS complex determined under diverse symmetry restraints (nonsymmetric C1, dihedral D2 and icosahedral I envelopes). 60 monomers of the crystal structure of RsbS fitted well into the I-restrained cryo-EM structure determined at 4.1 Å resolution, even though the STAS domains in the I envelope were averaged. This indicates that RsbS and RsbRA share a highly conserved STAS fold. 22 protrusions observed in the C1 envelope, corresponding to dimers of the RsbRA N-domain, allowed the STAS domains of RsbRA and RsbS to be distinguished in the stressosome core. Based on these, the model of the stressosome core was reconstructed. The mutation of RsbRA residues at the binding interface in the model (R189A/Q191A) significantly reduced the interaction between RsbRA and RsbS. These results suggest that nonconserved residues in the conserved STAS folds between RsbS and RsbR paralogs determine stressosome assembly.

The disposition of functional groups can induce variations in the nature and type of interactions and hence affect the molecular recognition and self-assembly mechanism in cocrystals. To better understand the formation of cocrystals on a molecular level, the effects of disposition of functional groups on the formation of cocrystals were systematically and comprehensively investigated using cresol isomers (o-, m-, p-cresol) as model compounds. Consistency and variability in these cocrystals containing positional isomers were found and analyzed. The structures, molecular recognition and self-assembly mechanism of supramolecular synthons in solution and in their corresponding cocrystals were verified by a combined experimental and theoretical calculation approach. It was found that the heterosynthons (heterotrimer or heterodimer) combined with O—H⋯N hydrogen bonding played a significant role. Hirshfeld surface analysis and computed interaction energy values were used to determine the hierarchical ordering of the weak interactions. The quantitative analyses of charge transfers and molecular electrostatic potential were also applied to reveal and verify the reasons for consistency and variability. Finally, the molecular recognition, self-assembly and evolution process of the supramolecular synthons in solution were investigated. The results confirm that the supramolecular synthon structures formed initially in solution would be carried over to the final cocrystals, and the supramolecular synthon structures are the precursors of cocrystals and the information memory of the cocrystallization process, which is evidence for classical nucleation theory.

Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX.

X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450–457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.

Olfactomedins are a family of modular proteins found in multicellular organisms that all contain five-bladed β-propeller olfactomedin (OLF) domains. In support of differential functions for the OLF propeller, the available crystal structures reveal that only some OLF domains harbor an internal calcium-binding site with ligands derived from a triad of residues. For the myocilin OLF domain (myoc-OLF), ablation of the ion-binding site (triad Asp, Asn, Asp) by altering the coordinating residues affects the stability and overall structure, in one case leading to misfolding and glaucoma. Bioinformatics analysis reveals a variety of triads with possible ion-binding characteristics lurking in OLF domains in invertebrate chordates such as Arthropoda (Asp–Glu–Ser), Nematoda (Asp–Asp–His) and Echinodermata (Asp–Glu–Lys). To test ion binding and to extend the observed connection between ion binding and distal structural rearrangements, consensus triads from these phyla were installed in the myoc-OLF. All three protein variants exhibit wild-type-like or better stability, but their calcium-binding properties differ, concomitant with new structural deviations from wild-type myoc-OLF. Taken together, the results indicate that calcium binding is not intrinsically destabilizing to myoc-OLF or required to observe a well ordered side helix, and that ion binding is a differential feature that may underlie the largely elusive biological function of OLF propellers.

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.

Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.

The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

The photovoltaic perovskite, methyl­ammonium lead triiodide [CH3NH3PbI3 (MAPbI3)], is one of the most efficient materials for solar energy conversion. Various kinds of chemical and physical modifications have been applied to MAPbI3 towards better understanding of the relation between composition, structure, electronic properties and energy conversion efficiency of this material. Pressure is a particularly useful tool, as it can substantially reduce the interatomic spacing in this relatively soft material and cause significant modifications to the electronic structure. Application of high pressure induces changes in the crystal symmetry up to a threshold level above which it leads to amorphization. Here, a detailed structural study of MAPbI3 at high hydro­static pressures using Ne and Ar as pressure transmitting media is reported. Single-crystal X-ray diffraction experiments with synchrotron radiation at room temperature in the 0–20 GPa pressure range show that atoms of both gaseous media, Ne and Ar, are gradually incorporated into MAPbI3, thus leading to marked structural changes of the material. Specifically, Ne stabilizes the high-pressure phase of NexMAPbI3 and prevents amorphization up to 20 GPa. After releasing the pressure, the crystal has the composition of Ne0.97MAPbI3, which remains stable under ambient conditions. In contrast, above 2.4 GPa, Ar accelerates an irreversible amorphization. The distinct impacts of Ne and Ar are attributed to differences in their chemical reactivity under pressure inside the restricted space between the PbI6 octahedra.

As one of the most important phenomena in crystallization, the crystal nucleation process has always been the focus of research. In this work, influences of pre-assembly species and the desolvation process on the crystal nucleation process were studied. p-Nitro­benzoic acid (PNBA) was taken as a model compound to investigate the relationship between solution chemistry and nucleation kinetics in seven different solvents. One unsolvated form and four solvates of PNBA were obtained and one of the solvates was newly discovered. The nucleation behaviours and nucleation kinetics of PNBA in the seven solvents were studied and analyzed. Density functional theory (DFT) and solvation energy calculation were adopted to evaluate the strength of solute–solvent interactions. Vibrational spectroscopy combined with molecular simulation was applied to reveal the pre-assembly species in the solution. Based on these results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics was proposed and discussed. It was found that the structural similarity between solution chemistry and crystal structure, the interaction between specific sites and the overall strength of solvation will jointly affect the nucleation process.

A tandem-double-slit optical system was constructed to evaluate the practical beam emittance of undulator radiation. The optical system was a combination of an upstream slit (S1) and downstream slit (S2) aligned on the optical axis with an appropriate separation. The intensity distribution after the double slits, I(x1, x2), was measured by scanning S1 and S2 in the horizontal direction. Coordinates having 1/sqrt e intensity were extracted from I(x1, x2), whose contour provided the standard deviation ellipse in the x1–x2 space. I(x1, x2) was converted to the corresponding distribution in the phase space, I(x1, x1'). The horizontal beam emittance was evaluated to be 3.1 nm rad, which was larger than the value of 2.4 nm rad estimated by using ray-tracing. It was found that the increase was mainly due to an increase in beam divergence rather than size.

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.

A gas- and vapour-pressure control system synchronized with the continuous data acquisition of millisecond high-resolution powder diffraction measurements was developed to study structural change processes in gas storage and reaction materials such as metal organic framework compounds, zeolite and layered double hydroxide. The apparatus, which can be set up on beamline BL02B2 at SPring-8, mainly comprises a pressure control system of gases and vapour, a gas cell for a capillary sample, and six one-dimensional solid-state (MYTHEN) detectors. The pressure control system can be remotely controlled via developed software connected to a diffraction measurement system and can be operated in the closed gas and vapour line system. By using the temperature-control system on the sample, high-resolution powder diffraction data can be obtained under gas and vapour pressures ranging from 1 Pa to 130 kPa in temperatures ranging from 30 to 1473 K. This system enables one to perform automatic and high-throughput in situ X-ray powder diffraction experiments even at extremely low pressures. Furthermore, this developed system is useful for studying crystal structures during the adsorption/desorption processes, as acquired by millisecond and continuous powder diffraction measurements. The acquisition of diffraction data can be synchronized with the control of the pressure with a high frame rate of up to 100 Hz. In situ and time-resolved powder diffraction measurements are demonstrated for nanoporous Cu coordination polymer in various gas and vapour atmospheres.

Double-sided Fresnel zone plates are diffractive lenses used for high-resolution hard X-ray microscopy. The double-sided structures have significantly higher aspect ratios compared with single-sided components and hence enable more efficient imaging. The zone plates discussed in this paper are fabricated on each side of a thin support membrane, and the alignment of the zone plates with respect to each other is critical. Here, a simple and reliable way of quantifying misalignments by recording efficiency maps and measuring the absolute diffraction efficiency of the zone plates as a function of tilting angle in two directions is presented. The measurements are performed in a setup based on a tungsten-anode microfocus X-ray tube, providing an X-ray energy of 8.4 keV through differential measurements with a Cu and an Ni filter. This study investigates the sources of the misalignments and concludes that they can be avoided by decreasing the structure heights on both sides of the membrane and by pre-programming size differences between the front- and back-side zone plates.

The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.

This paper reports an Fe-added Y2O3 crucible which is capable of balancing the solution spontaneously and is employed to effectively enhance the homogeneity of YBa2(Cu1−xFex)3O7−δ single crystals.

Book review

Single-crystalline-like thin films composed of crystallographically aligned grains are a new prototype of 2D materials developed recently for low-cost and high-performance flexible electronics as well as second-generation high-temperature superconductors. In this work, significant texture improvement in single-crystalline-like materials is achieved through growth of a 330 nm-thick silver layer.

An X-ray cross-correlation study of the impact of ligand composition and salt content on the self-assembly of soft-shell nanoparticles is presented, indicating symmetry-selective formation of order.

A new approach to variable-temperature measurements is presented, where the sample temperature changes continuously as a function of position.

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.

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) applied through DiSCaMB software library in the structure refinement against X-ray diffraction data largely improves the X—H bond lengths and make them comparable to the averaged neutron bond lengths.

A new ZnII metallocryptand is presented, with an unprecedented diflexure helix.

Already under siege from overfishing, disease and poor water quality, the oyster population in the Chesapeake Bay today stands at 2 percent of what it was in colonial times. Now, new data show that rising acidity in the Bay will have a negative impact on oyster shells.

The post Rising acidification of estuary waters spells trouble for Chesapeake Bay oysters appeared first on Smithsonian Insider.

The Smithsonian’s National Air and Space Museum has opened a new Public Observatory that contains a 16-inch, 3,000-pound Boller and Chivens telescope, on loan from the Smithsonian Astrophysical Observatory. Through this powerful telescope, museum visitors can now observe the sun (with a special filter), the moon and the brighter stars and planets, such as Venus, Jupiter and Saturn, during daylight hours. Funding for the project was provided by the National Science Foundation.

The post The Smithsonian’s National Air and Space Museum opens new Public Observatory on the Mall in Washington, D.C. appeared first on Smithsonian Insider.

The Smithsonian’s National Air and Space Museum recently obtained two monumental instruments on loan from NASA’s Goddard Space Flight Center.

The post New Acquisition: Corrective instruments from the Hubble Space Telescope appeared first on Smithsonian Insider.

Koenig and his colleagues examined an area of space called W5, which lies about 6,500 light-years away toward the constellation Cassiopeia—about 6 trillion miles. Their research indicates the prospects for hypothetical alien life there are disappointing.

The post Planets form around many star types, but intelligent life is probably rare appeared first on Smithsonian Insider.

Birds do it. Bees do it. And in a laboratory in northern California, scientists using bumblebees recently figured out the best way to measure it--vertical lift!

The post Laboratory tests reveal precise way to measure vertical lift in bumblebees and other small insects and birds appeared first on Smithsonian Insider.

Smithsonian astronomers have just discovered a rare example of a galaxy that appears to have a pair of giant black holes. Now they are trying to determine if those black holes are partners tied together by gravity, or if one of the two has been kicked out in a cosmic breakup.

The post Double Black-Hole Mystery: Dance Partners or Breakup Survivors? appeared first on Smithsonian Insider.