The European X-ray Free-Electron Laser (EuXFEL) delivers extremely intense (>1012 photons pulse−1 and up to 27000 pulses s−1), ultrashort (<100 fs) and transversely coherent X-ray radiation, at a repetition rate of up to 4.5 MHz. Its unique X-ray beam parameters enable novel and groundbreaking experiments in ultrafast photochemistry and material sciences at the Femtosecond X-ray Experiments (FXE) scientific instrument. This paper provides an overview of the currently implemented experimental baseline instrumentation and its performance during the commissioning phase, and a preview of planned improvements. FXE's versatile instrumentation combines the simultaneous application of forward X-ray scattering and X-ray spectroscopy techniques with femtosecond time resolution. These methods will eventually permit exploitation of wide-angle X-ray scattering studies and X-ray emission spectroscopy, along with X-ray absorption spectroscopy, including resonant inelastic X-ray scattering and X-ray Raman scattering. A suite of ultrafast optical lasers throughout the UV–visible and near-IR ranges (extending up to mid-IR in the near future) with pulse length down to 15 fs, synchronized to the X-ray source, serve to initiate dynamic changes in the sample. Time-delayed hard X-ray pulses in the 5–20 keV range are used to probe the ensuing dynamic processes using the suite of X-ray probe tools. FXE is equipped with a primary monochromator, a primary and secondary single-shot spectrometer, and a timing tool to correct the residual timing jitter between laser and X-ray pulses.

A new method based on time-resolved X-ray diffraction is proposed in order to measure the elastic strain and stress during ultrasonic fatigue loading experiments. Pure Cu was chosen as an example material for the experiments using a 20 kHz ultrasonic fatigue machine mounted on the six-circle diffractometer available at the DiffAbs beamline on the SOLEIL synchrotron facility in France. A two-dimensional hybrid pixel X-ray detector (XPAD3.2) was triggered by the strain gage signal in a synchronous data acquisition scheme (pump–probe-like). The method enables studying loading cycles with a period of 50 µs, achieving a temporal resolution of 1 µs. This allows a precise reconstruction of the diffraction patterns during the loading cycles. From the diffraction patterns, the position of the peaks, their shifts and their respective broadening can be deduced. The diffraction peak shift allows the elastic lattice strain to be estimated with a resolution of ∼10−5. Stress is calculated by the self-consistent scale-transition model through which the elastic response of the material is estimated. The amplitudes of the cyclic stresses range from 40 to 120 MPa and vary linearly with respect to the displacement applied by the ultrasonic machine. Moreover, the experimental results highlight an increase of the diffraction peak broadening with the number of applied cycles.

Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.

Nanoparticles are essential electrocatalysts in chemical production, water treatment and energy conversion, but engineering efficient and specific catalysts requires understanding complex structure–reactivity relations. Recent experiments have shown that Bragg coherent diffraction imaging might be a powerful tool in this regard. The technique provides three-dimensional lattice strain fields from which surface reactivity maps can be inferred. However, all experiments published so far have investigated particles an order of magnitude larger than those used in practical applications. Studying smaller particles quickly becomes demanding as the diffracted intensity falls. Here, in situ nanodiffraction data from 60 nm Au nanoparticles under electrochemical control collected at the hard X-ray nanoprobe beamline of MAX IV, NanoMAX, are presented. Two-dimensional image reconstructions of these particles are produced, and it is estimated that NanoMAX, which is now open for general users, has the requisites for three-dimensional imaging of particles of a size relevant for catalytic applications. This represents the first demonstration of coherent X-ray diffraction experiments performed at a diffraction-limited storage ring, and illustrates the importance of these new sources for experiments where coherence properties become crucial.

A new Rococo 2 X-ray fluorescence detector was implemented into the cryogenic sample environment at the Hard X-ray Micro/Nano-Probe beamline P06 at PETRA III, DESY, Hamburg, Germany. A four sensor-field cloverleaf design is optimized for the investigation of planar samples and operates in a backscattering geometry resulting in a large solid angle of up to 1.1 steradian. The detector, coupled with the Xspress 3 pulse processor, enables measurements at high count rates of up to 106 counts per second per sensor. The measured energy resolution of ∼129 eV (Mn Kα at 10000 counts s−1) is only minimally impaired at the highest count rates. The resulting high detection sensitivity allows for an accurate determination of trace element distributions such as in thin frozen hydrated biological specimens. First proof-of-principle measurements using continuous-movement 2D scans of frozen hydrated HeLa cells as a model system are reported to demonstrate the potential of the new detection system.

A new setup for picosecond pump–probe X-ray scattering at the Austrian SAXS beamline at Elettra-Sincrotrone Trieste is presented. A high-power/high-repetion-rate laser has been installed on-site, delivering UV/VIS/IR femto­second-pulses in-sync with the storage ring. Data acquisition is achieved by gating a multi-panel detector, capable of discriminating the single X-ray pulse in the dark-gap of the Elettra hybrid filling mode. Specific aspects of laser- and detection-synchronization, on-line beam steering as well protocols for spatial and temporal overlap of laser and X-ray beam are also described. The capabilities of the setup are demonstrated by studying transient heat-transfer in an In/Al/GaAs superlattice structure and results are confirmed by theoretical calculations.

This paper presents a deep learning algorithm for tomographic reconstruction (GANrec). The algorithm uses a generative adversarial network (GAN) to solve the inverse of the Radon transform directly. It works for independent sinograms without additional training steps. The GAN has been developed to fit the input sinogram with the model sinogram generated from the predicted reconstruction. Good quality reconstructions can be obtained during the minimization of the fitting errors. The reconstruction is a self-training procedure based on the physics model, instead of on training data. The algorithm showed significant improvements in the reconstruction accuracy, especially for missing-wedge tomography acquired at less than 180° rotational range. It was also validated by reconstructing a missing-wedge X-ray ptychographic tomography (PXCT) data set of a macroporous zeolite particle, for which only 51 projections over 70° could be collected. The GANrec recovered the 3D pore structure with reasonable quality for further analysis. This reconstruction concept can work universally for most of the ill-posed inverse problems if the forward model is well defined, such as phase retrieval of in-line phase-contrast imaging.

The time evolution of the electron density and the resulting time dependence of the X-ray polarizability of a crystal irradiated by highly intense XFEL femtosecond pulses is investigated theoretically. Rate equations for bound electrons and the Boltzmann equation for the unbound electron gas are used in calculations.

Contributions of experimental and selected theoretical charge-density research to medicinal chemistry are reviewed; combining experimental methods from high-resolution small-molecule and macromolecular crystallography with theory proves to be fruitful.

It has been revealed that in cylindrical nano-confinement, the hydrogen-bonding direction of nylon-12 crystals in the rod could self-assemble to be parallel to the long axis of the rod. The dominant growth direction and hydrogen-bonding direction of the γ-form crystal in the long axis of the rod has been revealed by TEM–SAED and WAXD.

An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs.

Mammalian Munc18 proteins are essential for membrane fusion and human health. Here, we review the literature describing structural and in vitro data, and identify a possible explanation for the conflicting functional roles that have been reported.

An extended analysis of structural ensembles obtained from small-angle X-ray scattering data reveals subclass-specific conformational preferences of IgG antibodies, which are largely determined by the hinge-region structure.

Ripon sinkhole concerns halt Harrogate council homes plans  BBC News

UK government's fracking 'ban' has a convenient loophole  The Conversation UK

Fracking in the UK was doomed a decade ago – Tories have wasted precious time on a fossil fuel fantasy  The Conversation UK

Expert confirms true impact of earthquakes in Devon and Cornwall  Devon Live

Second earthquake recorded this year in Northamptonshire  Northampton Chronicle and Echo

Snowdonia earthquake confirmed by British Geological Survey  Daily Post

Fracking firm Cuadrilla signs secret deal with geological agency to 'destroy confidential documents'  iNews

Gluconate 5-dehydrogenase (Ga5DH; EC 1.1.1.69) from Lentibacter algarum (LaGa5DH) was recombinantly expressed in Escherichia coli and purified to homogeneity. The protein was crystallized and the crystal structure was solved at 2.1 Å resolution. The crystal belonged to the monoclinic system, with space group P1 and unit-cell parameters a = 55.42, b = 55.48, c = 79.16 Å, α = 100.51, β = 105.66, γ = 97.99°. The structure revealed LaGaDH to be a tetramer, with each subunit consisting of six α-helices and three antiparallel β-hairpins. LaGa5DH has high structural similarity to other Ga5DH proteins, demonstrating that this enzyme is highly conserved.

The concept of statistical signal detection by controlling the false-discovery rate (FDR) to aid the atomic model interpretation of cryo-EM density maps is reviewed. The recommended usage of the FDR software tool is presented together with its successful integration into the CCP-EM suite.

In the title bis­chalcone, C17H12Br2O, the olefinic double bonds are almost coplanar with their attached 4-bromo­phenyl rings [torsion angles = −10.2 (4) and −6.2 (4)°], while the carbonyl double bond is in an s-trans conformation with with respect to one of the C=C bonds and an s-cis conformation with respect to the other [C=C—C=O = 160.7 (3) and −15.2 (4)°, respectively]. The dihedral angle between the 4-bromo­phenyl rings is 51.56 (2)°. In the crystal, mol­ecules are linked into a zigzag chain propagating along [001] by weak C—H⋯π inter­actions. The conformations of related bis­chalcones are surveyed and a Hirshfeld surface analysis is used to investigate and qu­antify the inter­molecular contacts.

The synthesis, spectroscopic data and crystal and mol­ecular structures of four 3-(3-phenyl­prop-1-ene-3-one-1-yl)thio­phene derivatives, namely 1-(4-hydroxy­phen­yl)-3-(thio­phen-3-yl)prop-1-en-3-one, C13H10O2S, (1), 1-(4-meth­oxy­phen­yl)-3-(thio­phen-3-yl)prop-1-en-3-one, C14H12O2S, (2), 1-(4-eth­oxy­phen­yl)-3-(thio­phen-3-yl)prop-1-en-3-one, C15H14O2S, (3), and 1-(4-­bromophen­yl)-3-(thio­phen-3-yl)prop-1-en-3-one, C13H9BrOS, (4), are described. The four chalcones have been synthesized by reaction of thio­phene-3-carbaldehyde with an aceto­phenone derivative in an absolute ethanol solution containing potassium hydroxide, and differ in the substituent at the para position of the phenyl ring: –OH for 1, –OCH3 for 2, –OCH2CH3 for 3 and –Br for 4. The thio­phene ring in 4 was found to be disordered over two orientations with occupancies 0.702 (4) and 0.298 (4). The configuration about the C=C bond is E. The thio­phene and phenyl rings are inclined by 4.73 (12) for 1, 12.36 (11) for 2, 17.44 (11) for 3 and 46.1 (6) and 48.6 (6)° for 4, indicating that the –OH derivative is almost planar and the –Br derivative deviates the most from planarity. However, the substituent has no real influence on the bond distances in the α,β-unsaturated carbonyl moiety. The mol­ecular packing of 1 features chain formation in the a-axis direction by O—H⋯O contacts. In the case of 2 and 3, the packing is characterized by dimer formation through C—H⋯O inter­actions. In addition, C—H⋯π(thio­phene) inter­actions in 2 and C—H⋯S(thio­phene) inter­actions in 3 contribute to the three-dimensional architecture. The presence of C—H⋯π(thio­phene) contacts in the crystal of 4 results in chain formation in the c-axis direction. The Hirshfeld surface analysis shows that for all four derivatives, the highest contribution to surface contacts arises from contacts in which H atoms are involved.

The title compound, hexa­kis­(2-methyl-1H-imidazol-3-ium) hepta­molybdate 2-methyl-1H-imidazole disolvate dihydrate, (C4H7N2)6[Mo7O24]·2C4H6N2·2H2O, was prepared from 2-methyl­imidazole and ammonium hepta­molybdate tetra­hydrate in acid solution. The [Mo7O24]6− hepta­molybdate cluster anion is accompanied by six protonated (C4H7N2)+ 2-methyl­imidazolium cations, two neutral C4H6N2 2-methyl­imidazole mol­ecules and two water mol­ecules of crystallization. The cluster consists of seven distorted MoO6 octa­hedra sharing edges or vertices. In the crystal, the components are linked by N—H⋯N, N—H⋯O, O—H⋯O, N—H⋯(O,O) and O—H⋯(O,O) hydrogen bonds, generating a three-dimensional network. Weak C—H⋯O inter­actions consolidate the packing.

The title tetra­nuclear copper complex, [Cu4Cl6O(C6H9N3O3)4] or [Cu4Cl6O­(MET)4] [MET is 1-(2-hy­droxy­eth­yl)-2-methyl-5-nitro-1H-imidazole or metronidazole], contains a tetra­hedral arrangement of copper(II) ions. Each copper atom is also linked to the other three copper atoms in the tetra­hedron via bridging chloride ions. A fifth coordination position on each metal atom is occupied by a nitro­gen atom of the monodentate MET ligand. The result is a distorted CuCl3NO trigonal–bipyramidal coordination polyhedron with the axial positions occupied by oxygen and nitro­gen atoms. The extended structure displays O—H⋯O hydrogen bonding, as well as unusual short O⋯N inter­actions [2.775 (4) Å] between the nitro groups of adjacent clusters that are oriented perpendicular to each other. The scattering contribution of disordered water and methanol solvent mol­ecules was removed using the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–16] in PLATON [Spek (2009). Acta Cryst. D65, 148–155].

Phenanthroline ligands are important metal-binding mol­ecules which have been extensively researched for applications in both material science and medicinal chemistry. Azo­benzene and its derivatives have received significant attention because of their ability to be reversibly switched between the E and Z forms and so could have applications in optical memory and logic devices or as mol­ecular machines. Herein we report the formation and crystal structure of a highly unusual novel diazo-diphenanthroline compound, C24H14N6O2·2CHCl3.

The isostructural title compounds, poly[piperazin-1-ium [di-μ-bromido-caesium]], {(C4H11N2)[CsBr2]}n, and poly[piperazin-1-ium [di-μ-bromido-rubidium]], {(C4H11N2)[RbBr2]}n, contain singly-protonated piperazin-1-ium cations and unusual ABr6 (A = Cs or Rb) trigonal prisms. The prisms are linked into a distinctive `curtain wall' arrangement propagating in the (010) plane by face and edge sharing. In each case, a network of N—H⋯N, N—H⋯Br and N—H⋯(Br,Br) hydrogen bonds consolidates the structure.

Reaction of 2-(anthracen-9-yl)phenol (HOPhAn, 1) with divalent Yb[N(SiMe3)2]2·2THF in THF–toluene mixtures affords the mixed-valence YbII–YbIII dimer {[2-(anthracen-9-yl)phenolato-κO]bis­(tetra­hydro­furan)­ytterbium(III)}-tris­[μ-2-(anthracen-9-yl)phenolato]-κ4O:O;κO:1,2-η,κO-{[2-(anthracen-9-yl)phenolato-κO]ytterbium(II)} toluene tris­olvate, [Yb2(C20H13O)5(C4H8O)2]·3C7H7 or [YbIII(THF)2(OPhAn)](μ-OPhAn)3[YbII(OPhAn)]·3C7H7 (2), as the major product. It crystallized as a toluene tris­olvate. The Yb—O bond lengths in the crystal structure of this dimer clearly identify the YbII and YbIII centres. Inter­estingly, the formally four-coordinate YbII centre shows a close contact with one anthracene C—C bond of a bridging OPhAn ligand, bringing the formal coordination number to five.

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.

The reaction of t-Bu2Si(OH)2 with two equivalents of Cp2Zr(CH3)2 produces the title t-Bu2SiO2-siloxide bridged dimer, [Zr2(CH3)2(C5H5)4(C8H18O2Si)] or [Cp2Zr(CH3)]2[μ-t-Bu2SiO2] (1), where one methyl group is retained per zirconium atom. The same product is obtained at room temperature even when equimolar ratios of the silanediol and Cp2Zr(CH3)2 are used. Attempts to thermally eliminate methane and produce a bridging methyl­ene complex resulted in decomposition. The crystal structure of 1 displays typical Zr—CH3 and Zr—O distances but the Si—O distance [1.628 (2) Å] and O—Si—O angle [110.86 (15)°] are among the largest observed in this family of compounds suggesting steric crowding between the t-Bu substituents of the silicon atom and the cyclo­penta­dienyl groups. The silicon atom lies on a crystallographic twofold axis and both Cp rings are disordered over two orientations of equal occupancy.

In the title compound, (2,2'-bi­pyridine-κ2N,N')bis­(2-meth­oxy­ethyl xanthato-κS)zinc(II), [Zn(C4H7O2S2)2(C10H8N2)], the ZnII ion is coordinated to two N atoms of the 2,2'-bi­pyridine ligand and two S atoms from two 2-meth­oxy­ethyl xanthate ligands. The ZnII ion lies on a crystallographic twofold rotation axis and has distorted tetra­hedral coordination geometry. In the crystal, mol­ecules are linked by weak C—H⋯O hydrogen bonds, forming supramolecular chains propagating along the a-axis direction. Weak intra­molecular C—H⋯S hydrogen bonds are also observed. The inter­molecular contacts in the crystal were further analysed using Hirshfield surface analysis, which indicates that the most significant contacts are H⋯H (36.3%), followed by S⋯H/H⋯S (24.7%), C⋯H/H⋯C (15.1%), O⋯H/H⋯O (14.4%), N⋯H/H⋯N (4.1%) and C⋯C (2.9%).

In the title hydrated hybrid compound C14H14N2OS2·H2O, the planar imidazo[1,2-a]pyridine ring system is linked to the 1,3-di­thiol­ane moiety by an enone bridge. The atoms of the C—C bond in the 1,3-di­thiol­ane ring are disordered over two positions with occupancies of 0.579 (14) and 0.421 (14) and both disordered rings adopt a half-chair conformation. The oxygen atom of the enone bridge is involved in a weak intra­molecular C—H⋯O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, the hybrid mol­ecules are associated in R22(14) dimeric units by weak C—H⋯O inter­actions. O—H⋯O hydrogen bonds link the water mol­ecules, forming infinite self-assembled chains along the b-axis direction to which the dimers are connected via O—H⋯N hydrogen bonding. Analysis of inter­molecular contacts using Hirshfeld surface analysis and contact enrichment ratio descriptors indicate that hydrogen bonds induced by water mol­ecules are the main driving force in the crystal packing formation.

Chalcones of type 4-XC6H4C(O)CH=CHC6H4(OCH2CCH)-4, where X = Cl, Br or MeO, have been converted to the corresponding 4,5-di­hydro­pyrazole-1-carbo­thio­amides using a cyclo­condensation reaction with thio­semicarbazide. The chalcones 1-(4-chloro­phen­yl)-3-[4-(prop-2-yn­yloxy)phen­yl]prop-2-en-1-one, C18H13ClO2, (I), and 1-(4-bromo­phen­yl)-3-[4-(prop-2-yn­yloxy)phen­yl]prop-2-en-1-one, C18H13BrO2, (II), are isomorphous, and their mol­ecules are linked into sheets by two independent C—H⋯π(arene) inter­actions, both involving the same aryl ring with one C—H donor approaching each face. In each of the products (RS)-3-(4-chloro­phen­yl)-5-[4-(prop-2-yn­yloxy)phen­yl]-4,5-di­hydro­pyrazole-1-carbo­thio­amide, C19H16ClN3OS, (IV), (RS)-3-(4-bromo­phen­yl)-5-[4-(prop-2-yn­yloxy)phen­yl]-4,5-di­hydro­pyrazole-1-carbo­thio­amide, C19H16BrN3OS, (V), and (RS)-3-(4-meth­oxy­phen­yl)-5-[4-(prop-2-yn­yloxy)phen­yl]-4,5-di­hydro­pyrazole-1-carbo­thio­amide, C20H19N3O2S, (VI), the reduced pyrazole ring adopts an envelope conformation with the C atom bearing the 4-prop-2-yn­yloxy)phenyl substituent, which occupies the axial site, displaced from the plane of the four ring atoms. Compounds (IV) and (V) are isomorphous and their mol­ecules are linked into chains of edge-fused rings by a combination of N—H⋯S and C—H⋯S hydrogen bonds. The mol­ecules of (VI) are linked into sheets by a combination of N—H⋯S, N—H⋯N and C—H⋯π(arene) hydrogen bonds. Comparisons are made with the structures of some related compounds.

A new conjugated carbazole chalcone compound, (E)-3-[4-(9,9a-di­hydro-8aH-carbazol-9-yl)phen­yl]-1-(4-nitro­phen­yl)prop-2-en-1-one (CPNC), C27H18N2O3, was synthesized using a Claisen–Schmidt condensation reaction. CPNC crystallizes in the monoclinic non-centrosymmetric space group Cc and adopts an s-cis conformation with respect to the ethyl­enic double bonds (C=O and C=C). The crystal packing features C—H⋯O and C—H⋯π inter­actions whose percentage contribution was qu­anti­fied by Hirshfeld surface analysis. Quantum chemistry calculations including geometrical optimization and mol­ecular electrostatic potential (MEP) were analysed by density functional theory (DFT) with a B3LYP/6–311 G++(d,p) basis set.

The title crystal structure is assembled from the superposition of two mol­ecular structures, (E)-1-(5-chloro­thio­phen-2-yl)-3-(3-methyl­thio­phen-2-yl)prop-2-en-1-one, C12H9ClOS2 (93%), and (Z)-1-(5-chloro­thio­phen-2-yl)-3-(3-methyl­thio­phen-2-yl)prop-1-en-1-ol, C12H11ClOS2 (7%), 0.93C12H9ClOS2·0.07C12H11ClOS2. Both were obtained from the reaction of 3-methyl­thio­phene-2-carbaldehyde and 1-(5-chloro­thio­phen-2-yl)ethanone. In the extended structure of the major chalcone component, mol­ecules are linked by a combination of C—H⋯O/S, Cl⋯Cl, Cl⋯π and π–π inter­actions, leading to a compact three-dimensional supra­molecular assembly.

A one-dimensional nickel(II) coordination polymer with the mixed ligands 6-fluoro­nicotinate (6-Fnic) and 4,4'-bi­pyridine (4,4'-bpy), namely, catena-poly[[di­aqua­bis­(6-fluoro­pyridine-3-carboxyl­ato-κO)nickel(II)]-μ-4,4'-bi­pyri­dine-κ2N:N'] trihydrate], {[Ni(6-Fnic)2(4,4'-bpy)(H2O)2]·3H2O}n, (1), was prepared by the reaction of nickel(II) sulfate hepta­hydrate, 6-fluoro­nicotinic acid (C6H4FNO2) and 4,4'-bi­pyridine (C10H8N2) in a mixture of water and ethanol. The nickel(II) ion in 1 is octa­hedrally coordinated by the O atoms of two water mol­ecules, two O atoms from O-monodentate 6-fluoro­nicotinate ligands and two N atoms from bridging 4,4'-bi­pyridine ligands, forming a trans isomer. The bridging 4,4'-bi­pyridine ligands connect symmetry-related nickel(II) ions into infinite one-dimensional polymeric chains running in the [1overline{1}0] direction. In the extended structure of 1, the polymeric chains and lattice water mol­ecules are connected into a three-dimensional hydrogen-bonded network via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of distinct hydrogen-bond ring motifs: octa­meric R88(24) and hexa­meric R86(16) loops.

The syntheses and crystal structures of three mol­ecular salts of protonated 3,4-di­amino­benzoic acid, viz. 2-amino-5-carb­oxy­anilinium chloride, C7H9N2O2+·Cl−, (I), 2-amino-5-carb­oxy­anilinium bromide, C7H9N2O2+·Br−, (II), and 2-amino-5-carb­oxy­anilinium nitrate monohydrate, C7H9N2O2+·NO3−·H2O, (III), are described. The cation is protonated at the meta-N atom (with respect to the carb­oxy group) in each case. In the crystal of (I), carb­oxy­lic acid inversion dimers linked by pairwise O—H⋯O hydrogen bonds are seen and each N—H group forms a hydrogen bond to a chloride ion to result in (100) undulating layers of chloride ions bridged by the inversion dimers into a three-dimensional network. The extended structure of (II) features O—H⋯Br, N—H⋯Br and N—H⋯O hydrogen bonds: the last of these generates C(7) chains of cations. Overall, the packing in (II) features undulating (100) sheets of bromide ions alternating with the organic cations. Inter­molecular inter­actions in the crystal of (III) include O—H⋯O, O—H⋯(O,O), N—H⋯O, N—H⋯N and O—H⋯N links. The cations are linked into (001) sheets, and the nitrate ions and water mol­ecules form undulating chains. Taken together, alternating (001) slabs of organic cations plus anions/water mol­ecules result. Hirshfeld surfaces and fingerprint plots were generated to give further insight into the inter­molecular inter­actions in these structures. The crystal used for the data collection of (II) was twinned by rotation about [100] in reciprocal space in a 0.4896 (15):0.5104 (15) ratio.

A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.

Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer.

A furnace that covers the temperature range from room temperature up to 2000 K has been designed, built and implemented on the D2AM beamline at the ESRF. The QMAX furnace is devoted to the full exploration of the reciprocal hemispace located above the sample surface. It is well suited for symmetric and asymmetric 3D reciprocal space mapping. Owing to the hemispherical design of the furnace, 3D grazing-incidence small- and wide-angle scattering and diffraction measurements are possible. Inert and reactive experiments can be performed at atmospheric pressure under controlled gas flux. It is demonstrated that the QMAX furnace allows monitoring of structural phase transitions as well as microstructural evolution at the nanoscale, such as self-organization processes, crystal growth and strain relaxation. A time-resolved in situ oxidation experiment illustrates the capability to probe the high-temperature reactivity of materials.

Instrumentation for time-resolved small-angle neutron scattering measurements with sub-millisecond time resolution, based on Gähler's TISANE (time-involved small-angle neutron experiments) concept, is in operation at NIST's Center for Neutron Research. This implementation of the technique includes novel electronics for synchronizing the neutron pulses from high-speed counter-rotating choppers with a periodic stimulus applied to a sample. Instrumentation details are described along with measurements demonstrating the utility of the technique for elucidating the reorientation dynamics of anisometric magnetic particles.

Owing to their combined open-framework structures and semiconducting properties, two-dimensional thio­stannates show great potential for catalytic and sensing applications. One such class of crystalline materials consists of porous polymeric [Sn3S72−]n sheets with molecular cations embedded in-between. The compounds are denoted R-SnS-1, where R is the cation. Dependent on the cation, some R-SnS-1 thio­stannates transition into amorphous phases upon dispersion in water. Knowledge about the fundamental chemical properties of the thio­stannates, including their water stability and the nature of the amorphous products, has not yet been established. This paper presents a time-resolved study of the transition from the crystalline to the amorphous phase of two violet-light absorbing thio­stannates, i.e. AEPz-SnS-1 [AEPz = 1-(2-amino­ethyl)­piperazine] and trenH-SnS-1 [tren = tris­(2-amino­ethyl)­amine]. X-ray total scattering data and pair distribution function analysis reveal no change in the local intralayer coordination during the amorphization. However, a rapid decrease in the crystalline domain sizes upon suspension in water is demonstrated. Although scanning electron microscopy shows no significant decrease of the micrometre-sized particles, transmission electron microscopy reveals the formation of small particles (∼200–400 nm) in addition to the larger particles. The amorphization is associated with disorder of the thio­stannate nanosheet stacking. For example, an average decrease in the interlayer distance (from 19.0 to 15.6 Å) is connected to the substantial loss of the organic components as shown by elemental analysis and X-ray photoelectron spectroscopy. Despite the structural changes, the light absorption properties of the amorphisized R-SnS-1 compounds remain intact, which is encouraging for future water-based applications of such materials.

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.

Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.

The X-chromosome-linked inhibitor of apoptosis protein (XIAP) is a multidomain protein whose main function is to block apoptosis by caspase inhibition. XIAP is also involved in other signalling pathways, including NF-κB activation and copper homeostasis. XIAP is overexpressed in tumours, potentiating cell survival and resistance to chemotherapeutics, and has therefore become an important target for the treatment of malignancy. Despite the fact that the structure of each single domain is known, the conformation of the full-length protein has never been determined. Here, the first structural model of the full-length XIAP dimer, determined by an integrated approach using nuclear magnetic resonance, small-angle X-ray scattering and electron paramagnetic resonance data, is presented. It is shown that XIAP adopts a compact and relatively rigid conformation, implying that the spatial arrangement of its domains must be taken into account when studying the interactions with its physiological partners and in developing effective inhibitors.

High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX.

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.

In the past three years, Dirac half-metals (DHMs) have attracted considerable attention and become a high-profile topic in spintronics becuase of their excellent physical properties such as 100% spin polarization and massless Dirac fermions. Two-dimensional DHMs proposed recently have not yet been experimentally synthesized and thus remain theoretical. As a result, their characteristics cannot be experimentally confirmed. In addition, many theoretically predicted Dirac materials have only a single cone, resulting in a nonlinear electromagnetic response with insufficient intensity and inadequate transport carrier efficiency near the Fermi level. Therefore, after several attempts, we have focused on a novel class of DHMs with multiple Dirac crossings to address the above limitations. In particular, we direct our attention to three-dimensional bulk materials. In this study, the discovery via first principles of an experimentally synthesized DHM LaNiO3 with many Dirac cones and complete spin polarization near the Fermi level is reported. It is also shown that the crystal structures of these materials are strongly correlated with their physical properties. The results indicate that many rhombohedral materials with the general formula LnNiO3 (Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) in the space group R3c are potential DHMs with multiple Dirac cones.

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.