Crystals of the new compound, AgSr4Cu4.5(PO4)6, were grown successfully by the hydro­thermal process. The asymmetric unit of the crystal structure of the title compound contains 40 independent atoms (4 Sr, 4.5 Cu, 1 Ag, 6 P and 24 O), which are all in general positions except for one Cu atom, which is located on an inversion centre. The Cu atoms are arranged in CuOn (n = 4 or 5) polyhedra, linked through common oxygen corners to build a rigid three-dimensional motif. The connection of these copper units is assured by PO4 tetra­hedra. This arrangement allows the construction of layers extending parallel to the (100) plane and hosts suitable cavities in which Ag+ and Sr2+ cations are located. The crystal-structure cohesion is ensured by ionic bonds between the silver and strontium cations and the oxygen anions belonging to two adjacent sheets. Charge-distribution analysis and bond-valence-sum calculations were used to validate the structural model.

The title compound, C8H7NO5, is planar with an r.m.s. deviation for all non-hydrogen atoms of 0.018 Å. An intra­molecular O—H⋯O hydrogen bond involving the adjacent hy­droxy and nitro groups forms an S(6) ring motif. In the crystal, mol­ecules are linked by O—H⋯O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C—H⋯O hydrogen bonds, forming layers parallel to the bc plane. The layers are linked by a further C—H⋯O hydrogen bond, forming slabs, which are linked by C=O⋯π inter­actions, forming a three-dimensional supra­molecular structure. Hirshfeld surface analysis was used to investigate inter­molecular inter­actions in the solid state. The mol­ecule was also characterized spectroscopically and its thermal stability investigated by differential scanning calorimetry and by thermogravimetric analysis.

A copper(II) dimer with the deprotonated anion of 2-bromo­nicotinic acid (2-BrnicH), namely, tetrakis(μ-2-bromonicotinato-κ2O:O')bis[aquacopper(­II)](Cu—Cu), [Cu2(H2O)2(C6H3BrNO2)4] or [Cu2(H2O)2(2-Brnic)4], (1), was prepared by the reaction of copper(II) chloride dihydrate and 2-bromo­nicotinic acid in water. The copper(II) ion in 1 has a distorted square-pyramidal coordination environment, achieved by four carboxyl­ate O atoms in the basal plane and the water mol­ecule in the apical position. The pair of symmetry-related copper(II) ions are connected into a centrosymmetric paddle-wheel dinuclear cluster [Cu⋯Cu = 2.6470 (11) Å] via four O,O'-bridging 2-bromo­nicotinate ligands in the syn-syn coordination mode. In the extended structure of 1, the cluster mol­ecules are assembled into an infinite two-dimensional hydrogen-bonded network lying parallel to the (001) plane via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of various hydrogen-bond ring motifs: dimeric R22(8) and R22(16) loops and a tetra­meric R44(16) loop. The Hirshfeld surface analysis was also performed in order to better illustrate the nature and abundance of the inter­molecular contacts in the structure of 1.

The title pyrazine dicarboxamide ligand, N2,N3-bis­(quinolin-8-yl)pyrazine-2,3-dicarboxamide (H2L1), C24H16N6O2, has a twisted conformation with the outer quinoline groups being inclined to the central pyrazine ring by 9.00 (6) and 78.67 (5)°, and by 79.94 (4)° to each other. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming layers parallel to the (10overline{1}) plane, which are in turn linked by offset π–π inter­actions [inter­centroid distances 3.4779 (9) and 3.6526 (8) Å], forming a supra­molecular three-dimensional structure. Reaction of the ligand H2L1 with Cu(ClO4)2 in aceto­nitrile leads to the formation of the binuclear complex, [μ-(3-{hy­droxy[(quinolin-8-yl)imino]­meth­yl}pyrazin-2-yl)[(quinolin-8-yl)imino]­methano­lato]bis­[diaceto­nitrile­copper(II)] tris­(per­chlor­ate) aceto­nitrile disolvate, [Cu2(C24H15N6O2)(CH3CN)4](ClO4)3·2CH3CN or [Cu2(HL1−)(CH3CN)4](ClO4)3·2CH3CN (I). In the cation of complex I, the ligand coordinates to the copper(II) atoms in a bis-tridentate fashion. A resonance-assisted O—H⋯O hydrogen bond is present in the ligand; the position of this H atom was located in a difference-Fourier map. Both copper(II) atoms are fivefold coordinate, being ligated by three N atoms of the ligand and by the N atoms of two aceto­nitrile mol­ecules. The first copper atom has a perfect square-pyramidal geometry while the second copper atom has a distorted shape. In the crystal, the cation and perchlorate anions are linked by a number of C—H⋯O hydrogen bonds, forming a supra­molecular three-dimensional structure.

In the title compound, [Cu(C16H8Br3N2O)2]·C2H6OS, the CuII atom is tetra­coordinated in a square-planar coordination, being surrounded by two N atoms and two O atoms from two N,O-bidentate (E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naphthalen-2-olate ligands. The two N atoms and two O atoms around the metal center are trans to each other, with an O—Cu—O bond angle of 177.90 (16)° and a N—Cu—N bond angle of 177.8 (2)°. The average distances between the CuII atom and the coordinated O and N atoms are 1.892 (4) and 1.976 (4) Å, respectively. In the crystal, complexes are linked by C—H⋯O hydrogen bonds and by π–π inter­actions involving adjacent naphthalene ring systems [centroid–centroid distance = 3.679 (4) Å]. The disordered DMSO mol­ecules inter­act weakly with the complex mol­ecules, being positioned in the voids left by the packing arrangement of the square-planar complexes. The DMSO solvent mol­ecule is disordered over two positions with occupancies of 0.70 and 0.30.

The title compound, [Mn(C3H7NO)4(H2O)2][Cu5(C7H4NO3)4]·C3H7NO or cis-[Mn(H2O)2(DMF)4]{Cu[12-MCCu(II)N(shi)-4]}·DMF, where MC is metallacrown, shi3− is salicyl­hydroximate, and DMF is N,N-di­methyl­formamide, crystallizes in the monoclinic space group P21/n. Two crystallographically independent metallacrown anions are present in the structure, and both anions exhibit minor main mol­ecule disorder by an approximate (non-crystallographic) 180° rotation with occupancy ratios of 0.9010 (9) to 0.0990 (9) for one anion and 0.9497 (8) to 0.0503 (8) for the other. Each penta­copper(II) metallacrown contains four CuII ions in the MC ring and a CuII ion captured in the central cavity. Each CuII ion is four-coordinate with a square-planar geometry. The anionic {Cu[12-MCCu(II)N(shi)-4]}2− is charged-balanced by the presence of a cis-[Mn(H2O)2(DMF)4]2+ cation located in the lattice. In addition, the octa­hedral MnII counter-cation is hydrogen bonded to both MC anions via the coordinated water mol­ecules of the MnII ion. The water mol­ecules form hydrogen bonds with the phenolate and carbonyl oxygen atoms of the shi3− ligands of the MCs.

This study explores the possibility of measuring the dynamics of proteins in solution using X-ray photon correlation spectroscopy (XPCS) at nearly diffraction-limited storage rings (DLSRs). We calculate the signal-to-noise ratio (SNR) of XPCS experiments from a concentrated lysozyme solution at the length scale of the hydrodynamic radius of the protein molecule. We take into account limitations given by the critical X-ray dose and find expressions for the SNR as a function of beam size, sample-to-detector distance and photon energy. Specifically, we show that the combined increase in coherent flux and coherence lengths at the DLSR PETRA IV yields an increase in SNR of more than one order of magnitude. The resulting SNR values indicate that XPCS experiments of biological macromolecules on nanometre length scales will become feasible with the advent of a new generation of synchrotron sources. Our findings provide valuable input for the design and construction of future XPCS beamlines at DLSRs.

Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.

In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.

Nitric oxide (NO) promotes vasodilation through the activation of guanylate cyclase, resulting in the relaxation of the smooth muscle vasculature and a subsequent decrease in blood pressure. Therefore, its regulation is of interest for the treatment and prevention of heart disease. An example is pulmonary hypertension which is treated by targeting this NO/vasodilation pathway. In bacteria, plants and fungi, nitrite (NO2−) is utilized as a source of NO through enzymes known as nitrite reductases. These enzymes reduce NO2− to NO through a catalytic metal ion, often copper. Recently, several studies have shown nitrite reductase activity of mammalian carbonic anhydrase II (CAII), yet the molecular basis for this activity is unknown. Here we report the crystal structure of copper-bound human CAII (Cu–CAII) in complex with NO2− at 1.2 Å resolution. The structure exhibits Type 1 (T-1) and 2 (T-2) copper centers, analogous to bacterial nitrite reductases, both required for catalysis. The copper-substituted CAII active site is penta-coordinated with a `side-on' bound NO2−, resembling a T-2 center. At the N terminus, several residues that are normally disordered form a porphyrin ring-like configuration surrounding a second copper, acting as a T-1 center. A structural comparison with both apo- (without metal) and zinc-bound CAII (Zn–CAII) provides a mechanistic picture of how, in the presence of copper, CAII, with minimal conformational changes, can function as a nitrite reductase.

Estimates of heat-transfer rates during plunge-cooling and the patterns of ice observed in cryo-EM samples indicate that the grid bars cool much more slowly than do the support foil and sample near the middle of the grid openings. The resulting transient temperature differences generate transient tensile stresses in the support foil. Most of this foil stress develops while the sample is liquid and cooling toward its glass transition Tg, and so does not generate tensile sample stress. As the grid bars continue cooling towards the cryogen temperature and contracting, the tensile stress in the foil is released, placing the sample in compressive stress. Radiation-induced creep in the presence of this compressive stress should generate a doming of the sample in the foil openings, as is observed experimentally. Crude estimates of the magnitude of the doming that may be generated by this mechanism are consistent with observation. Several approaches to reducing beam-induced motion are discussed.

Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.

This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/sil­oxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.

Copper-containing nitrite reductases (CuNiRs) are found in all three kingdoms of life and play a major role in the denitrification branch of the global nitro­gen cycle where nitrate is used in place of di­oxy­gen as an electron acceptor in respiratory energy metabolism. Several C- and N-terminal redox domain tethered CuNiRs have been identified and structurally characterized during the last decade. Our understanding of the role of tethered domains in these new classes of three-domain CuNiRs, where an extra cytochrome or cupredoxin domain is tethered to the catalytic two-domain CuNiRs, has remained limited. This is further compounded by a complete lack of substrate-bound structures for these tethered CuNiRs. There is still no substrate-bound structure for any of the as-isolated wild-type tethered enzymes. Here, structures of nitrite and product-bound states from a nitrite-soaked crystal of the N-terminal cupredoxin-tethered enzyme from the Hyphomicrobium denitrificans strain 1NES1 (Hd1NES1NiR) are provided. These, together with the as-isolated structure of the same species, provide clear evidence for the role of the N-terminal peptide bearing the conserved His27 in water-mediated anchoring of the substrate at the catalytic T2Cu site. Our data indicate a more complex role of tethering than the intuitive advantage for a partner-protein electron-transfer complex by narrowing the conformational search in such a combined system.

Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF–EBS shutdown.

Recent developments have resulted in electron cryo-microscopy (cryo-EM) becoming a useful tool for the structure determination of biological macromolecules. For samples containing inherent flexibility, heterogeneity or preferred orientation, the collection of extensive cryo-EM data using several conditions and microscopes is often required. In such a scenario, merging cryo-EM data sets is advantageous because it allows improved three-dimensional reconstructions to be obtained. Since data sets are not always collected with the same pixel size, merging data can be challenging. Here, two methods to combine cryo-EM data are described. Both involve the calculation of a rescaling factor from independent data sets. The effects of errors in the scaling factor on the results of data merging are also estimated. The methods described here provide a guideline for cryo-EM users who wish to combine data sets from the same type of microscope and detector.

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.

Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

In recent years, there have been numerous efforts worldwide to develop the synchrotron X-ray scanning tunneling microscopy (SX-STM) technique. Here, the inauguration of XTIP, the world's first beamline fully dedicated to SX-STM, is reported. The XTIP beamline is located at Sector 4 of the Advanced Photon Source at Argonne National Laboratory. It features an insertion device that can provide left- or right-circular as well as horizontal- and vertical-linear polarization. XTIP delivers monochromatic soft X-rays of between 400 and 1900 eV focused into an environmental enclosure that houses the endstation instrument. This article discusses the beamline system design and its performance.

A versatile, compact heater designed at National Synchrotron Light Source-II for in situ X-ray nano-imaging in a full-field transmission X-ray microscope is presented. Heater design for nano-imaging is challenging, combining tight spatial constraints with stringent design requirements for the temperature range and stability. Finite-element modeling and analytical calculations were used to determine the heater design parameters. Performance tests demonstrated reliable and stable performance, including maintaining the exterior casing close to room temperature while the heater is operating at above 1100°C, a homogenous heating zone and small temperature fluctuations. Two scientific experiments are presented to demonstrate the heater capabilities: (i) in situ 3D nano-tomography including a study of metal dealloying in a liquid molten salt extreme environment, and (ii) a study of pore formation in icosahedral quasicrystals. The progression of structural changes in both studies were clearly resolved in 3D, showing that the new heater enables powerful capabilities to directly visualize and quantify 3D morphological evolution of materials under real conditions by X-ray nano-imaging at elevated temperature during synthesis, fabrication and operation processes. This heater design concept can be applied to other applications where a precise, compact heater design is required.

Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.

Whole-mount (WM) platelet preparation followed by transmission electron microscopy (TEM) observation is the standard method currently used to assess dense granule (DG) deficiency (DGD). However, due to the electron-density-based contrast mechanism in TEM, other granules such as α-granules might cause false DG detection. Here, scanning transmission X-ray microscopy (STXM) was used to identify DGs and minimize false DG detection of human platelets. STXM image stacks of human platelets were collected at the calcium (Ca) L2,3 absorption edge and then converted to optical density maps. Ca distribution maps, obtained by subtracting the optical density maps at the pre-edge region from those at the post-edge region, were used to identify DGs based on the Ca richness. DGs were successfully detected using this STXM method without false detection, based on Ca maps for four human platelets. Spectral analysis of granules in human platelets confirmed that DGs contain a richer Ca content than other granules. The Ca distribution maps facilitated more effective DG identification than TEM which might falsely detect DGs. Correct identification of DGs would be important to assess the status of platelets and DG-related diseases. Therefore, this STXM method is proposed as a promising approach for better DG identification and diagnosis, as a complementary tool to the current WM TEM approach.

The optical design of a Hettrick–Underwood-style soft X-ray spectrometer with Wolter type 1 mirrors is presented. The spectrometer with a nominal length of 3.1 m can achieve a high resolving power (resolving power higher than 10000) in the soft X-ray regime when a small source beam (<3 µm in the grating dispersion direction) and small pixel detector (5 µm effective pixel size) are used. Adding Wolter mirrors to the spectrometer before its dispersive elements can realize the spatial imaging capability, which finds applications in the spectroscopic studies of spatially dependent electronic structures in tandem catalysts, heterostructures, etc. In the pump–probe experiments where the pump beam perturbs the materials followed by the time-delayed probe beam to reveal the transient evolution of electronic structures, the imaging capability of the Wolter mirrors can offer the pixel-equivalent femtosecond time delay between the pump and probe beams when their wavefronts are not collinear. In combination with some special sample handing systems, such as liquid jets and droplets, the imaging capability can also be used to study the time-dependent electronic structure of chemical transformation spanning multiple time domains from microseconds to nanoseconds. The proposed Wolter mirrors can also be adopted to the existing soft X-ray spectrometers that use the Hettrick–Underwood optical scheme, expanding their capabilities in materials research.

The composition of occupied and unoccupied electronic states in the vicinity of Fermi energies is vital for all materials and relates to their physical, chemical and mechanical properties. This work demonstrates how the combination of resonant and non-resonant X-ray emission spectroscopies supplemented with theoretical modelling allows for quantitative analysis of electronic states in 5d transition metal and metal-oxide materials. Application of X-rays provides element selectivity that, in combination with the penetrating properties of hard X-rays, allows determination of the composition of electronic states under working conditions, i.e. non-vacuum environment. Tungsten metal and tungsten oxide are evaluated to show the capability to simultaneously assess composition of around-band-gap electronic states as well as the character and magnitude of the crystal field splitting.

Time-resolved X-ray absorption spectroscopy (XAS) offers the possibility to monitor the state of materials during chemical reactions. While this technique has been established for transmission measurements for a number of years, XAS measurements in fluorescence mode are challenging because of limitations in signal collection as well as detectors. Nevertheless, measurements in fluorescence mode are often the only option to study complex materials containing heavy matrices or in samples where the element of interest is in low concentration. Here, it has been demonstrated that high-quality quick-scanning full extended X-ray absorption fine-structure data can be readily obtained with sub-second time resolution in fluorescence mode, even for highly diluted samples. It has also been demonstrated that in challenging samples, where transmission measurements are not feasible, quick fluorescence can yield significant insight in reaction kinetics. By studying the fast high-temperature oxidation of a reduced LaFe0.8Ni0.8O3 perovskite type, an example where the perovskite matrix elements prevent measurements in fluorescence, it is shown that it is now possible to follow the state of Ni in situ at a 3 s time resolution.

A scanning soft X-ray spectromicroscope was recently developed based mainly on the photon-in/photon-out measurement scheme for the investigation of local electronic structures on the surfaces and interfaces of advanced materials under conditions ranging from low vacuum to helium atmosphere. The apparatus was installed at the soft X-ray beamline (BL17SU) at SPring-8. The characteristic features of the apparatus are described in detail. The feasibility of this spectromicroscope was demonstrated using soft X-ray undulator radiation. Here, based on these results, element-specific two-dimensional mapping and micro-XAFS (X-ray absorption fine structure) measurements are reported, as well as the observation of magnetic domain structures from using a reference sample of permalloy micro-dot patterns fabricated on a silicon substrate, with modest spatial resolution (e.g. ∼500 nm). Then, the X-ray radiation dose for Nafion® near the fluorine K-edge is discussed as a typical example of material that is not radiation hardened against a focused X-ray beam, for near future experiments.

Bone crystallite chemistry and structure change during bone maturation. However, these properties of bone can also be affected by limited uptake of the chemical constituents of the mineral by the animal. This makes probing the effect of bone-mineralization-related diseases a complicated task. Here it is shown that the combination of vibrational spectroscopy with two-dimensional X-ray diffraction can provide unparalleled information on the changes in bone chemistry and structure associated with different bone pathologies (phosphate deficiency) and/or health conditions (pregnancy, lactation). Using a synergistic analytical approach, it was possible to trace the effect that changes in the remodelling regime have on the bone mineral chemistry and structure in normal and mineral-deficient (hypophosphatemic) mice. The results indicate that hypophosphatemic mice have increased bone remodelling, increased carbonate content and decreased crystallinity of the bone mineral, as well as increased misalignment of crystallites within the bone tissue. Pregnant and lactating mice that are normal and hypophosphatemic showed changes in the chemistry and misalignment of the apatite crystals that can be related to changes in remodelling rates associated with different calcium demand during pregnancy and lactation.

An attempt has been made to combine small-angle scattering of X-rays or neutrons with scanning electron microscopy in reciprocal space, in order to establish a structural analysis method covering a wide range of sizes from micro- to macro-scales.

The proton-conducting material (NH4)4H2(SeO4)3 is examined to check whether its conductivity spectra are sensitive to subtle changes in the crystal structure and proton dynamics caused by external pressure. The AC conductivity was measured using impedance spectroscopy, in the frequency range from 100 Hz to 1 MHz, at temperatures 260 K < T < 400 K and pressures 0.1 MPa < p < 500 MPa. On the basis of the impedance spectra, carefully analyzed at different thermodynamic conditions, the p–T phase diagram of the crystal is constructed. It is found to be linear in the pressure range of the experiment, with the pressure coefficient value dTs/dp = −0.023 K MPa−1. The hydrostatic pressure effect on proton conductivity is also presented and discussed. Measurements of the electrical conductivity versus time were performed at a selected temperature T = 352.3 K and at pressures 0.1 MPa < p < 360 MPa. At fixed thermodynamic conditions (p = 302 MPa, T = 352.3 K), the sluggish solid–solid transformation from low conducting to superionic phase was induced. It is established that the kinetics of this transformation can be described by the Avrami model with an effective Avrami index value of about 4, which corresponds to the classical value associated with the homogeneous nucleation and three-dimensional growth of a new phase.

The proton-conducting crystal (NH4)4H2(SeO4)3 is examined to check whether its conductivity spectra and the phase transition to the superprotonic phase are sensitive to subtle changes in the crystal structure and proton dynamics caused by various thermodynamic conditions. It is established that the kinetics of this transformation can be described using the Avrami model with an effective Avrami index value associated with homogeneous nucleation and three-dimensional growth of a new phase.

The synthesis, characterization and study of structures from a series of bi­phenyls substituted at positions 3, 3', 4 and 4' with groups connected to the bi­phenyl core through oxygen atoms are presented here. The molecular conformation is extensively studied both in the solid as well as in the liquid state, and the effect of different actors (such as packing and chain length) on the torsion angle between aromatic rings is analyzed.

Crystal structure and microscopic optical properties of anthracene derivative compounds have been investigated by single-crystal synchrotron X-ray diffraction, laser confocal microscopy and fluorescence lifetime imaging microscopy.

In the title compound, {[Cu(C14H8O4)(C11H10N4O)(H2O)]·1.25H2O}n, the CuII cations are coordinated in a square-pyramidal fashion by trans carboxylate O-atom donors from two diphenate (dip) ligands, trans pyridyl N-atom donors from two bis(4-pyridyl)urea (bpu) ligands, and a ligated water molecule in the apical position. [Cu(H2O)(dip)(bpu)]n coordination polymer layer motifs are oriented parallel to (overline{1}02). These layer motifs display a standard (4,4) rectangular grid topology and stack in an AAA pattern along the a-axis direction to form the full three-dimensional crystal structure of the title compound, mediated by N—H...O and O—H...O hydrogen bonding patterns involving the water molecules of crystallization.

This article reports conformational polymorphisms of the EF-hand protein MCFD2 which is involved in glycoprotein transport..

Nearly 100 years ago, scientists detected the first signs of cosmic rays—subatomic particles (mostly protons) that zip through space at nearly the speed of light. […]

The post Telescope array finds new evidence that exploding stars are sources of cosmic rays appeared first on Smithsonian Insider.

The way that massive stars form remains mysterious, in part, because massive stars are rare and tend to spend their youth shrouded by dust and gas and hidden from view.

The post Radio telescopes give astronomers rare glimpse at a young protostar’s formation 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.

This innovative facility will be at the front line of Earth defense by searching for "killer" asteroids and comets. It will map large portions of the sky nightly, making it an efficient sleuth for not just asteroids but also supernovae and other variable objects.

The post Super sensitive telescope will detect “killer” asteroids and comets on collision course with Earth appeared first on Smithsonian Insider.

The Panoramic Survey Telescope & Rapid Response System (Pan-STARRS) PS1 telescope has discovered an asteroid about 150 feet in diameter that will come within 4 million miles of Earth in mid-October.

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A new telescope has begun to virtually explore the solar system outback, and already is scoring discoveries.

The post New telescope exploring Solar System’s “outback” appeared first on Smithsonian Insider.

To honor Harvard-Smithsonian astronomer John Huchra, who passed away in October 2010, his friends and colleagues at the Harvard-Smithsonian Center for Astrophysics have created a […]

The post New interactive World Wide Telescope tour chronicles career of Harvard-Smithsonian astronomer John Huchra appeared first on Smithsonian Insider.

Recent work has added dozens of new measurements to star-forming regions in the Milky Way. These measurements have changed the map of the Milky Way, indicating our galaxy has four spiral arms, not two, as previously thought.

The post Very Large Baseline Array telescope is helping Smithsonian astronomers remap Milky Way and Andromeda galaxies appeared first on Smithsonian Insider.

This image of lawyer Clarence S. Darrow (center) talking with group of men in Dayton, Tenn., in July 1925 is one of 10 photographs from […]

The post Scopes Trial photographs released on Web by Smithsonian Archives appeared first on Smithsonian Insider.

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.

Humanity's most complex ground-based astronomy observatory, the Atacama Large Millimeter/submillimeter Array (ALMA), has officially opened for astronomers at its 16,500-foot high desert plateau in northern Chile.

The post Center for Astrophysics project gets first look through new ALMA telescope appeared first on Smithsonian Insider.

The image shows one of the most active and turbulent regions of star birth in our galaxy, a region called Cygnus X.

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For the last 1,000 days the Infrared Array Camera, aboard NASA’s Spitzer Space Telescope, has been operating continuously to probe the universe from its most distant regions to our local solar neighborhood.

The post Top 10 gallery celebrates the Infrared Array Camera aboard the Spitzer Space Telescope appeared first on Smithsonian Insider.

Researchers led by David Nesvorny of Southwest Research Institute and David Kipping of the Harvard-Smithsonian Center for Astrophysics has inferred an unseen planet, this time orbiting a distant star, marking the first success of this technique outside the solar system.

The post Unseen planet’s gravity allows Kepler Telescope to “see” it appeared first on Smithsonian Insider.