id Improving the reliability of small- and wide-angle X-ray scattering measurements of anisotropic precipitates in metallic alloys using sample rotation By journals.iucr.org Published On :: 2024-11-04 Nanometric precipitates in metallic alloys often have highly anisotropic shapes. Given the large grain size and non-random texture typical of these alloys, performing small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on such samples for determining their characteristics (typically size and volume fraction) results in highly anisotropic and irreproducible data. Rotations of flat samples during SAXS/WAXS acquisitions are presented here as a solution to these anisotropy issues. Two aluminium alloys containing anisotropic precipitates are used as examples to validate the approach with a −45°/45° angular range. Clear improvements can be seen on the SAXS I(q) fitting and the consistency between the different SAXS/WAXS measurements. This methodology results in more reliable measurements of the precipitate's characteristics, and thus allows for time- and space-resolved measurements with higher accuracy. Full Article text
id Integrating machine learning interatomic potentials with hybrid reverse Monte Carlo structure refinements in RMCProfile By journals.iucr.org Published On :: 2024-10-29 Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in RMCProfile that grants flexibility to apply potentials supported by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications. Full Article text
id Crystal structures of two polymorphs for fac-bromidotricarbonyl[4-(4-methoxyphenyl)-2-(pyridin-2-yl)thiazole-κ2N,N']rhenium(I) By journals.iucr.org Published On :: 2024-11-08 Crystallization of the title compound, fac-[ReBr(ppt-OMe)(CO)3] (ppt-OMe = C15H12N2OS), from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and orthorhombic (Pna21; β form) space groups. The ReI complex molecules in either polymorph adopt a six-coordinate octahedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitrogen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds. In polymorph α, two types of hydrogen bonds (C—H...O) are found while, in polymorph β, four types of hydrogen bonds (C—H...O and C—H...Br) exist. Full Article text
id Crystal structures and circular dichroism of {2,2'-[(1S,2S)-1,2-diphenylethane-1,2-diylbis(nitrilophenylmethanylylidene)]diphenolato}nickel(II) and its ethanol solvate By journals.iucr.org Published On :: 2024-11-08 The title compound, [Ni(C40H30N2O2)] (1), with an optically active Schiff base ligand derived from 2-hydroxybenzophenone and (1S,2S)-1,2-diphenylethylenediamine, was crystallized as the solvent-free and ethanol solvate forms (1 and 1·2C2H5OH). In both structures, the two phenyl groups on the stereogenic centers of the O,N,N,O-tetradentate ligand are axially oriented, and the conformation of the central diamine chelate ring is λ. The circular dichroism (CD) spectra of 1 and the analogous nickel(II) complex [Ni(C30H26N2O2)] (2) in solution show partially similar patterns in the 350–450 nm range, but are mirror images in the longer wavelength region (450–650 nm). In the latter region, the sign of CD for these complexes is sensitive to the substituents on the C=N carbon atoms (phenyl for 1 and methyl for 2) rather than the diamine chelate ring conformation. Full Article text
id Efficient boundary-guided scanning for high-resolution X-ray ptychography By journals.iucr.org Published On :: 2024-01-01 In the realm of X-ray ptychography experiments, a considerable amount of ptychography scans are typically performed within a field of view encompassing the target sample. While it is crucial to obtain overlapping scans in small increments over the region of interest for achieving high-resolution sample reconstruction, a significant number of these scans often redundantly measure the empty background within the wide field of view. To address this inefficiency, an innovative algorithm is proposed that introduces automatic guidance for data acquisition. The algorithm first directs the scan point to actively search for the object of interest within the field of view. Subsequently, it intelligently scans along the perimeter of the sample, strategically acquiring measurements exclusively within the boundary of the region of interest. By employing this approach, a reduction in the number of measurements required to obtain high-resolution reconstruction images is demonstrated, as compared with conventional raster scanning methods. Furthermore, the automatic guidance provided by the algorithm offers the added advantage of saving valuable time during the reconstruction process. Through practical implementation on real experiments, these findings showcase the efficacy of the proposed algorithm in enhancing the efficiency and accuracy of X-ray ptychography experiments. This novel approach holds immense potential for advancing sample analysis and imaging techniques in various scientific disciplines. Full Article text
id Ultrashort large-bandwidth X-ray free-electron laser generation with a dielectric-lined waveguide By journals.iucr.org Published On :: 2024-02-09 Large-bandwidth pulses produced by cutting-edge X-ray free-electron lasers (FELs) are of great importance in research fields like material science and biology. In this paper, a new method to generate high-power ultrashort FEL pulses with tunable spectral bandwidth with spectral coherence using a dielectric-lined waveguide without interfering operation of linacs is proposed. By exploiting the passive and dephasingless wakefield at terahertz frequency excited by the beam, stable energy modulation can be achieved in the electron beam and large-bandwidth high-intensity soft X-ray radiation can be generated. Three-dimensional start-to-end simulations have been carried out and the results show that coherent radiation pulses with duration of a few femtoseconds and bandwidths ranging from 1.01% to 2.16% can be achieved by changing the undulator taper profile. Full Article text
id Grazing-incidence synchrotron radiation diffraction studies on irradiated Ce-doped and pristine Y-stabilized ZrO2 at the Rossendorf beamline By journals.iucr.org Published On :: 2024-02-16 In this work, Ce-doped yttria-stabilized zirconia (YSZ) and pure YSZ phases were subjected to irradiation with 14 MeV Au ions. Irradiation studies were performed to simulate long-term structural and microstructural damage due to self-irradiation in YSZ phases hosting alpha-active radioactive species. It was found that both the Ce-doped YSZ and the YSZ phases had a reasonable tolerance to irradiation at high ion fluences and the bulk crystallinity was well preserved. Nevertheless, local microstrain increased in all compounds under study after irradiation, with the Ce-doped phases being less affected than pure YSZ. Doping with cerium ions increased the microstructural stability of YSZ phases through a possible reduction in the mobility of oxygen atoms, which limits the formation of structural defects. Doping of YSZ with tetravalent actinide elements is expected to have a similar effect. Thus, YSZ phases are promising for the safe long-term storage of radioactive elements. Using synchrotron radiation diffraction, measurements of the thin irradiated layers of the Ce-YSZ and YSZ samples were performed in grazing incidence (GI) mode. A corresponding module for measurements in GI mode was developed at the Rossendorf Beamline and relevant technical details for sample alignment and data collection are also presented. Full Article text
id Novel correction procedure for compensating thermal contraction errors in the measurement of the magnetic field of superconducting undulator coils in a liquid helium cryostat By journals.iucr.org Published On :: 2024-02-22 Superconducting undulators (SCUs) can offer a much higher on-axis undulator field than state-of-the-art cryogenic permanent-magnet undulators with the same period and vacuum gap. The development of shorter-period and high-field SCUs would allow the free-electron laser and synchrotron radiation source community to reduce both the length of undulators and the dimensions of the accelerator. Magnetic measurements are essential for characterizing the magnetic field quality of undulators for operation in a modern light source. Hall probe scanning is so far the most mature technique for local field characterization of undulators. This article focuses on the systematic error caused by thermal contraction that influences Hall probe measurements carried out in a liquid helium cryostat. A novel procedure, based on the redundant measurement of the magnetic field using multiple Hall probes at known relative distance, is introduced for the correction of such systematic error. Full Article text
id X-ray beam diagnostics at the MID instrument of the European X-ray Free-Electron Laser Facility By journals.iucr.org Published On :: 2024-04-08 The Materials Imaging and Dynamics (MID) instrument at the European X-ray Free-Electron Laser Facility (EuXFEL) is equipped with a multipurpose diagnostic end-station (DES) at the end of the instrument. The imager unit in DES is a key tool for aligning the beam to a standard trajectory and for adjusting optical elements such as focusing lenses or the split-and-delay line. Furthermore, the DES features a bent-diamond-crystal spectrometer to disperse the spectrum of the direct beam to a line detector. This enables pulse-resolved characterization of the EuXFEL spectrum to provide X-ray energy calibration, and the spectrometer is particularly useful in commissioning special modes of the accelerator. Together with diamond-based intensity monitors, the imager and spectrometer form the DES unit which also contains a heavy-duty beamstop at the end of the MID instrument. Here, we describe the setup in detail and provide exemplary beam diagnostic results. Full Article text
id Improving sensitivity of XANES structural fit to the bridged metal–metal coordination By journals.iucr.org Published On :: 2024-03-26 Hard X-ray absorption spectroscopy is a valuable in situ probe for non-destructive diagnostics of metal sites. The low-energy interval of a spectrum (XANES) contains information about the metal oxidation state, ligand type, symmetry and distances in the first coordination shell but shows almost no dependency on the bridged metal–metal bond length. The higher-energy interval (EXAFS), on the contrary, is more sensitive to the coordination numbers and can decouple the contribution from distances in different coordination shells. Supervised machine-learning methods can combine information from different intervals of a spectrum; however, computational approaches for the near-edge region of the spectrum and higher energies are different. This work aims to keep all benefits of XANES and extend its sensitivity towards the interatomic distances in the first and second coordination shells. Using a binuclear bridged copper complex as a case study and cross-validation analysis as a quantitative tool it is shown that the first 170 eV above the edge are already sufficient to balance the contributions of Cu–O/N scattering and Cu–Cu scattering. As a more general outcome this work highlights the trivial but often overlooked importance of using `longer' energy intervals of XANES for structural refinement and machine-learning predictions. The first 200 eV above the absorption edge still do not require parametrization of Debye–Waller damping and can be calculated within full multiple scattering or finite difference approximations with only moderately increased computational costs. Full Article text
id Modelling the power threshold and optimum thermal deformation of indirectly liquid-nitrogen cryo-cooled Si monochromators By journals.iucr.org Published On :: 2024-04-09 Maximizing the performance of crystal monochromators is a key aspect in the design of beamline optics for diffraction-limited synchrotron sources. Temperature and deformation of cryo-cooled crystals, illuminated by high-power beams of X-rays, can be estimated with a purely analytical model. The analysis is based on the thermal properties of cryo-cooled silicon crystals and the cooling geometry. Deformation amplitudes can be obtained, quickly and reliably. In this article the concept of threshold power conditions is introduced and defined analytically. The contribution of parameters such as liquid-nitrogen cooling efficiency, thermal contact conductance and interface contact area of the crystal with the cooling base is evaluated. The optimal crystal illumination and the base temperature are inferred, which help minimize the optics deformation. The model has been examined using finite-element analysis studies performed for several beamlines of the Diamond-II upgrade. Full Article text
id Soft X-ray wavefront sensing at an ellipsoidal mirror shell By journals.iucr.org Published On :: 2024-06-06 A reliable `in situ' method for wavefront sensing in the soft X-ray domain is reported, developed for the characterization of rotationally symmetric optical elements, like an ellipsoidal mirror shell. In a laboratory setup, the mirror sample is irradiated by an electron-excited (4.4 keV), micrometre-sized (∼2 µm) fluorescence source (carbon Kα, 277 eV). Substantially, the three-dimensional intensity distribution I(r) is recorded by a CCD camera (2048 × 512 pixels of 13.5 µm) at two positions along the optical axis, symmetrically displaced by ±21–25% from the focus. The transport-of-intensity equation is interpreted in a geometrical sense from plane to plane and implemented as a ray tracing code, to retrieve the phase Φ(r) from the radial intensity gradient on a sub-pixel scale. For reasons of statistical reliability, five intra-/extra-focal CCD image pairs are evaluated and averaged to an annular two-dimensional map of the wavefront error {cal W}. In units of the test wavelength (C Kα), an r.m.s. value sigma_{cal{W}} = ±10.9λ0 and a peak-to-valley amplitude of ±31.3λ0 are obtained. By means of the wavefront, the focus is first reconstructed with a result for its diameter of 38.4 µm, close to the direct experimental observation of 39.4 µm (FWHM). Secondly, figure and slope errors of the ellipsoid are characterized with an average of ±1.14 µm and ±8.8 arcsec (r.m.s.), respectively, the latter in reasonable agreement with the measured focal intensity distribution. The findings enable, amongst others, the precise alignment of axisymmetric X-ray mirrors or the design of a wavefront corrector for high-resolution X-ray science. Full Article text
id TomoPyUI: a user-friendly tool for rapid tomography alignment and reconstruction By journals.iucr.org Published On :: 2024-06-26 The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c. Full Article text
id Mango wiggler as a novel insertion device providing a large and symmetrical imaging field of view By journals.iucr.org Published On :: 2024-06-21 A novel insertion device is introduced, designated as the Mango wiggler, designed for synchrotron radiation (SR) imaging that provides a large field of view. This innovative device is constructed from two orthogonal planar wigglers with a small difference in their period lengths, eliciting the phase difference of the magnetic fields to incrementally transitions from 0 to π/2. Such a configuration enlarges the vertical divergence of the light source, as with the horizontal divergence. The appellation `Mango wiggler' derives from the distinctive mango-shaped contour of its radiation field. A comprehensive suite of theoretical analyses and simulations has been executed to elucidate the radiation properties of the Mango wiggler, employing SPECTRA and Mathematica as calculation tools. In conjunction with the ongoing construction of the High Energy Photon Source in Beijing a practical Mango wiggler device has been fabricated for utilization in SR imaging applications. Theoretical analyses were applied to this particular Mango wiggler to yield several theoretical conclusions, and several simulations were performed according to the measured magnetic field results. Full Article text
id VUV absorption spectra of water and nitrous oxide by a double-duty differentially pumped gas filter By journals.iucr.org Published On :: 2024-07-23 The differentially pumped rare-gas filter at the end of the VUV beamline of the Swiss Light Source has been adapted to house a windowless absorption cell for gases. Absorption spectra can be recorded from 7 eV to up to 21 eV photon energies routinely, as shown by a new water and nitrous oxide absorption spectrum. By and large, the spectra agree with previously published ones both in terms of resonance energies and absorption cross sections, but that of N2O exhibits a small shift in the { ilde{f D}} band and tentative fine structures that have not yet been fully described. This setup will facilitate the measurement of absorption spectra in the VUV above the absorption edge of LiF and MgF2 windows. It will also allow us to carry out condensed-phase measurements on thin liquid sheets and solid films. Further development options are discussed, including the recording of temperature-dependent absorption spectra, a stationary gas cell for calibration measurements, and the improvement of the photon energy resolution. Full Article text
id The diamond–silicon carbide composite Skeleton® as a promising material for substrates of intense X-ray beam optics By journals.iucr.org Published On :: 2024-08-06 The paper considers the possibility of using the diamond-silicon carbide composite Skeleton® with a technological coating of polycrystalline silicon as a substrate for X-ray mirrors used with powerful synchrotron radiation sources (third+ and fourth generation). Samples were studied after polishing to provide the following surface parameters: root-mean-square flatness ≃ 50 nm, micro-roughness on the frame 2 µm × 2 µm σ ≃ 0.15 nm. The heat capacity, thermal conductivity and coefficient of linear thermal expansion were investigated. For comparison, a monocrystalline silicon sample was studied under the same conditions using the same methods. The value of the coefficient of linear thermal expansion turned out to be higher than that of monocrystalline silicon and amounted to 4.3 × 10−6 K−1, and the values of thermal conductivity (5.0 W cm−1 K−1) and heat capacity (1.2 J K−1 g−1) also exceeded the values for Si. Thermally induced deformations of both Skeleton® and monocrystalline silicon samples under irradiation with a CO2 laser beam have also been experimentally studied. Taking into account the obtained thermophysical constants, the calculation of thermally induced deformation under irradiation with hard (20 keV) X-rays showed almost three times less deformation of the Skeleton® sample than of the monocrystalline silicon sample. Full Article text
id Prediction of the treatment effect of FLASH radiotherapy with synchrotron radiation from the Circular Electron–Positron Collider (CEPC) By journals.iucr.org Published On :: 2024-08-22 The Circular Electron–Positron Collider (CEPC) in China can also work as an excellent powerful synchrotron light source, which can generate high-quality synchrotron radiation. This synchrotron radiation has potential advantages in the medical field as it has a broad spectrum, with energies ranging from visible light to X-rays used in conventional radiotherapy, up to several megaelectronvolts. FLASH radiotherapy is one of the most advanced radiotherapy modalities. It is a radiotherapy method that uses ultra-high dose rate irradiation to achieve the treatment dose in an instant; the ultra-high dose rate used is generally greater than 40 Gy s−1, and this type of radiotherapy can protect normal tissues well. In this paper, the treatment effect of CEPC synchrotron radiation for FLASH radiotherapy was evaluated by simulation. First, a Geant4 simulation was used to build a synchrotron radiation radiotherapy beamline station, and then the dose rate that the CEPC can produce was calculated. A physicochemical model of radiotherapy response kinetics was then established, and a large number of radiotherapy experimental data were comprehensively used to fit and determine the functional relationship between the treatment effect, dose rate and dose. Finally, the macroscopic treatment effect of FLASH radiotherapy was predicted using CEPC synchrotron radiation through the dose rate and the above-mentioned functional relationship. The results show that the synchrotron radiation beam from the CEPC is one of the best beams for FLASH radiotherapy. Full Article text
id Comparing single-shot damage thresholds of boron carbide and silicon at the European XFEL By journals.iucr.org Published On :: 2024-08-25 Xray free-electron lasers (XFELs) enable experiments that would have been impractical or impossible at conventional X-ray laser facilities. Indeed, more XFEL facilities are being built and planned, with their aim to deliver larger pulse energies and higher peak brilliance. While seeking to increase the pulse power, it is quintessential to consider the maximum pulse fluence that a grazing-incidence FEL mirror can withstand. To address this issue, several studies were conducted on grazing-incidence damage by soft X-ray FEL pulses at the European XFEL facility. Boron carbide (B4C) coatings on polished silicon substrate were investigated using 1 keV photon energy, similar to the X-ray mirrors currently installed at the soft X-ray beamlines (SASE3). The purpose of this study is to compare the damage threshold of B4C and Si to determine the advantages, tolerance and limits of using B4C coatings. Full Article text
id trans-Bis[bis(diphenylphosphanyl)methane-κ2P,P']dichloridoruthenium(II): a triclinic polymorph By journals.iucr.org Published On :: 2023-11-14 The title compound, [RuCl2(C25H22P2)2] or [RuCl2(dppm)2] (dppm = bis(diphenylphosphanyl)methane, C25H22P2) crystallizes as two half-molecules (completed by inversion symmetry) in space group Poverline{1} (Z = 2), with the RuII atoms occupying inversion centers at 0,0,0 and 1/2, 1/2, 1/2, respectively. The bidentate phosphane ligands occupy equatorial positions while the chlorido ligands complete the distorted octahedral coordination spheres at axial positions. The bite angles of the phosphane chelates are similar for the two molecules [(P—Ru—P)avg. = 71.1°], while there are significant differences in the twisting of the methylene backbone, with a distance of the methylene C atom from the RuP4 plane of 0.659 (2) and 0.299 (3) Å, respectively, and also for the phenyl substituents for both molecules due to variations in weak C—H⋯Cl interactions. Full Article text
id A second crystalline modification of 2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-ylidene}hydrazinecarbothioamide By journals.iucr.org Published On :: 2023-11-30 A second crystalline modification of the title compound, C12H19N3S [common name: cis-jasmone thiosemicarbazone] was crystallized from tetrahydrofurane at room temperature. There is one crystallographic independent molecule in the asymmetric unit, showing disorder in the cis-jasmone chain [site-occupancy ratio = 0.590 (14):0.410 (14)]. The thiosemicarbazone entity is approximately planar, with the maximum deviation from the mean plane through the N/N/C/S/N atoms being 0.0463 (14) Å [r.m.s.d. = 0.0324 Å], while for the five-membered ring of the jasmone fragment, the maximum deviation from the mean plane through the carbon atoms amounts to 0.0465 (15) Å [r.m.s.d. = 0.0338 Å]. The molecule is not planar due to the dihedral angle between these two fragments, which is 8.93 (1)°, and due to the sp3-hybridized carbon atoms in the jasmone fragment chain. In the crystal, the molecules are connected by N—H⋯S and C—H⋯S interactions, with graph-set motifs R22(8) and R21(7), building mono-periodic hydrogen-bonded ribbons along [010]. A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are H⋯H (67.8%), H⋯S/S⋯H (15.0%), H⋯C/C⋯H (8.5%) and H⋯N/N⋯H (5.6%) [only non-disordered atoms and those with the highest s.o.f. were considered]. This work reports the second crystalline modification of the cis-jasmone thiosemicarbazone structure, the first one being published recently [Orsoni et al. (2020). Int. J. Mol. Sci. 21, 8681–8697] with the crystals obtained in ethanol at 273 K. Full Article text
id 2-{1-[(6R,S)-3,5,5,6,8,8-Hexamethyl-5,6,7,8-tetrahydronaphthalen-2-yl]ethylidene}-N-methylhydrazinecarbothioamide By journals.iucr.org Published On :: 2023-11-30 The reaction between a racemic mixture of (R,S)-fixolide and 4-methylthiosemicarbazide in ethanol with a 1:1 stoichiometric ratio and catalysed with HCl, yielded the title compound, C20H31N3S [common name: (R,S)-fixolide 4-methylthiosemicarbazone]. There is one crystallographically independent molecule in the asymmetric unit, which is disordered over the aliphatic ring [site-occupancy ratio = 0.667 (13):0.333 (13)]. The disorder includes the chiral C atom, the neighbouring methylene group and the methyl H atoms of the methyl group bonded to the chiral C atom. The maximum deviations from the mean plane through the disordered aliphatic ring amount to 0.328 (6) and −0.334 (6) Å [r.m.s.d. = 0.2061 Å], and −0.3677 (12) and 0.3380 (12) Å [r.m.s.d. = 0.2198 Å] for the two different sites. Both fragments show a half-chair conformation. Additionally, the N—N—C(=S)—N entity is approximately planar, with the maximum deviation from the mean plane through the selected atoms being 0.0135 (18) Å [r.m.s.d. = 0.0100 Å]. The molecule is not planar due to the dihedral angle between the thiosemicarbazone entity and the aromatic ring, which amounts to 51.8 (1)°, and due to the sp3-hybridized carbon atoms of the fixolide fragment. In the crystal, the molecules are connected by H⋯S interactions with graph-set motif C(4), forming a mono-periodic hydrogen-bonded ribbon along [100]. The Hirshfeld surface analysis suggests that the major contributions for the crystal cohesion are [(R,S)-isomers considered separately] H⋯H (75.7%), H⋯S/S⋯H (11.6%), H⋯C/C⋯H (8.3% and H⋯N/N⋯H (4.4% for both of them). Full Article text
id Bis[1,3-bis(2,4,6-trimethylphenyl)imidazolium] bis(μ-cis-1,2-diphenylethene-1,2-dithiolato-κ2S,S':κS)bis[(cis-1,2-diphenylethene-1,2-dithiolato-κ2S,S')iron(III)] dimethyl& By journals.iucr.org Published On :: 2023-12-26 The molecular structure of the solvated title salt, (C21H25N2)2[Fe2(C14H10S2)4]·2C3H7NO reveals that the anion is situated on a crystallographic inversion center in the triclinic space group Poverline{1}. The title compound crystallizes utilizing a network of weak π-stacking interactions of phenyl rings pertaining to the dithiolene unit. Moreover, the acidic imidazolium H atoms [N—C(H)—N] display non-classical hydrogen-bonding interactions of the C—H⋯O type to the oxygen atoms of the N,N-dimethyl formamide solvent, and hydrogen atoms on the backbone of imidazolium rings display weak C—H⋯S interactions with the dithiolene sulfur atoms. Full Article text
id meso-α,α-5,15-Bis(o-nicotinamidophenyl)-10,20-diphenylporphyrin n-hexane monosolvate By journals.iucr.org Published On :: 2023-12-22 The structure of the title solvated porphyrin, C56H38N8O2·C6H14, is reported. Two porphyrin molecules, one ordered and one disordered n-hexane solvate molecules are present in its asymmetric unit. The porphyrin macrocycle shows a characteristic saddle-shaped distortion, and the maximum deviation from the mean plane for non-hydrogen atoms is 0.48 Å. N—H⋯N, N—H⋯O, and C—H⋯O hydrogen bonds, as well as π–π interactions, are observed in the crystal structure. Full Article text
id rac-Hydroxyisovaleric acid By journals.iucr.org Published On :: 2024-01-05 The title compound (systematic name: rac-2-hydroxy-3-methylbutanoic acid), C5H10O3, is the constitutional isomer of α-hydroxybutanoic acid. In the crystal, hydrogen bonds involving the alcoholic hydroxyl group give rise to centrosymmetric dimers that are extended to sheets perpendicular to the crystallographic c axis. Full Article text
id 2-{3-Methyl-2-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-ylidene}-N-phenylhydrazinecarbothioamide. Corrigendum By journals.iucr.org Published On :: 2024-01-31 In the paper by Oliveira et al. [IUCrData (2023), 8, x230971], there was an error in the name of the first author. Full Article text
id N-Methyl-2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-ylidene}hydrazinecarbothioamide By journals.iucr.org Published On :: 2024-01-09 The equimolar and hydrochloric acid-catalysed reaction between cis-jasmone and 4-methylthiosemicarbazide in ethanolic solution yields the title compound, C13H21N3S (common name: cis-jasmone 4-methylthiosemicarbazone). Two molecules with all atoms in general positions are present in the asymmetric unit. In one of them, the carbon chain is disordered [site occupancy ratio = 0.821 (3):0.179 (3)]. The thiosemicarbazone entities [N—N—C(=S)—N] are approximately planar, with the maximum deviation from the mean plane through the selected atoms being −0.0115 (16) Å (r.m.s.d. = 0.0078 Å) for the non-disordered molecule and 0.0052 (14) Å (r.m.s.d. = 0.0031 Å) for the disordered one. The molecules are not planar, since the jasmone groups have a chain with sp3-hybridized carbon atoms and, in addition, the thiosemicarbazone fragments are attached to the respective carbon five-membered rings and the dihedral angles between them for each molecule amount to 8.9 (1) and 6.3 (1)°. In the crystal, the molecules are connected through pairs of N—H⋯S and C—H⋯S interactions into crystallographically independent centrosymmetric dimers, in which rings of graph-set motifs R22(8) and R21(7) are observed. A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are from H⋯H (70.6%), H⋯S/S⋯H (16.7%), H⋯C/C⋯H (7.5%) and H⋯N/N⋯H (4.9%) interactions [considering the two crystallographically independent molecules and only the disordered atoms with the highest s.o.f. for the evaluation]. Full Article text
id trans-Dichloridobis[(S)-(−)-1-(4-methylphenyl)ethylamine-κN]palladium(II) By journals.iucr.org Published On :: 2024-01-12 The title complex, [PdCl2(C9H13N)2], comprises a single molecule in the asymmetric unit. The PdII atom is tetracoordinated by two N atoms from two trans-aligned organic ligands and two Cl ligands, forming a square-planar metal coordination environment. The distances from the ortho-H atoms on the phenyl ring to the central PdII atom fall within the range 4.70–5.30 Å, precluding any significant intramolecular Pd⋯H interactions. Full Article text
id Dichlorido(4,7-dimethoxy-1,10-phenanthroline-κ2N,N')zinc(II) By journals.iucr.org Published On :: 2024-01-12 In the title complex, [ZnCl2(C14H12N2O2)], the ZnII atom is located on a twofold rotation axis and is fourfold coordinated by two chlorido ligands and a bidentate 4,7-methoxy-1,10-phenanthroline ligand in a distorted tetrahedral environment. Weak π–π stacking interactions between adjacent 4,7-dimethoxy-1,10-phenanthroline rings [centroid-to-centroid distances = 3.5969 (11) and 3.7738 (11) Å] contribute to the alignment of the complexes in layers parallel to (overline{2}01). Full Article text
id 2-Aminobenzoxazole–oxalic acid (2/1) By journals.iucr.org Published On :: 2024-01-26 In the title compound, 2C7H7N2O+·C2O42−, proton transfer from oxalic acid to the N atom of the heterocycle has occurred to form a 2:1 molecular salt. In the extended structure, N—H⋯O hydrogen bonds link the components into [100] chains, which feature R22(8) and R44(14) loops. Full Article text
id Synthesis and structure of trans-bis(4-amino-3-nitrobenzoato-κO)bis(4-amino-3-nitrobenzoic acid-κO)diaquamanganese(II) dihydrate By journals.iucr.org Published On :: 2024-01-19 The manganese title complex, [Mn(C7H5N2O4)2(C7H6N2O4)2(H2O)2]·2H2O, is one of the first 4-amino 3-nitrobenzoic acid (4 A3NBA) monoligand metal complexes to be synthesized. It crystallizes in the centrosymmetric monoclinic space group P21/n with the complex molecules located on inversion centers. Four 4 A3NBA ligand molecules are monodentately coordinated by the Mn2+ ion through the carboxylic oxygen atoms while the other two positions of the inner coordination sphere are occupied by water molecules, giving rise to a distorted octahedron, and two water molecules are in the outer coordination sphere. There are two intramolecular hydrogen bonds in the complex molecule. The first is of the common N—H⋯O=N type, while the second is a rarely occurring very strong hydrogen bond in which a common proton is shared by two uncoordinated oxygen atoms of neighboring carboxylate groups. In the crystal, an intricate system of intermolecular hydrogen bonds links the complex molecules into a three-dimensional-network. Full Article text
id Bis(2-hydroxy-2,3-dihydro-1H-inden-1-aminium) tetrachloridopalladate(II) hemihydrate By journals.iucr.org Published On :: 2024-01-26 A new square-planar palladium complex salt hydrate, (C9H12NO)2[PdCl4]·0.5H2O, has been characterized. The asymmetric unit of the complex salt comprises two [PdCl4]2− dianions, four 2-hydroxy-2,3-dihydro-1H-inden-1-aminium cations, each derived from (1R,2S)-(+)-1-aminoindan-2-ol, and one water molecule of crystallization. In the crystal, a two-dimensional layer parallel to (001) features a number of O—H⋯O, N—H⋯O, O—H⋯Cl and N—H⋯Cl hydrogen bonds. Full Article text
id (4-Butyl-1-ethyl-1,2,4-triazol-5-ylidene)[(1,2,5,6-η)-cycloocta-1,5-diene](triphenylphosphane)rhodium(I) tetrafluoridoborate By journals.iucr.org Published On :: 2024-01-26 In the title triazole-based N-heterocyclic carbene rhodium(I) cationic complex with a tetrafluoridoborate counter-anion, [Rh(C8H12)(C8H15N3)(C18H15P)]BF4, which crystallizes with two cations and two anions in the asymmetric unit, the Rh center has a distorted square-planar coordination geometry with expected bond distances. Several nonclassical C—H⋯F hydrogen-bonding interactions help to consolidate the packing. Two of the F atoms of one of the anions are disordered over adjacent sites in a 0.814 (4):0.186 (4) ratio. Full Article text
id Bis[2,6-bis(benzimidazol-2-yl)pyridine-κ3N,N',N'']nickel(II) bis(trifluoromethanesulfonate) diethyl ether monosolvate By journals.iucr.org Published On :: 2024-01-31 In the title complex, [Ni(C19H13N5)2](CF3SO3)2·(CH3CH2)2O, the central NiII atom is sixfold coordinated by three nitrogen atoms of each 2,6-bis(2-benzimidazolyl)pyridine ligand in a distorted octahedral geometry with two trifluoromethanesulfonate ions and a molecule of diethyl ether completing the outer coordination sphere of the complex. Hydrogen bonding contributes to the organization of the asymmetric units in columns along the a axis generating a porous supramolecular structure. The structure was refined as a two-component twin with a refined BASF value of 0.4104 (13). Full Article text
id (2,2'-Bipyridine-κ2N,N')(4,4'-dimethoxy-2,2'-bipyridine-κ2N,N')palladium(II) bis(trifluoromethanesulfonate) By journals.iucr.org Published On :: 2024-02-08 In the title complex salt, [Pd(C10H8N2)(C12H12N2O2)](CF3SO3)2, the palladium(II) atom is fourfold coordinated by two chelating ligands, 2,2'-bipyridine and 4,4'-dimethoxy-2,2'-bipyridine, in a distorted square-planar environment. In the crystal, weak π–π stacking interactions between the 2,2'-bipyridine rings [centroid-to-centroid distances = 3.8984 (19) Å] and between the 4,4'-dimethoxy-2,2'-bipyridine rings [centroid-to-centroid distances = 3.747 (18) Å] contribute to the alignment of the complex cations in columns parallel to the b-axis direction. Full Article text
id Aquabis(2,2'-bipyridine-κ2N,N')(isonicotinamide-κN)ruthenium(II) bis(trifluoromethanesulfonate) By journals.iucr.org Published On :: 2024-02-08 In the title complex, [Ru(C10H8N2)2(C6H6N2O)(H2O)](CF3SO3)2, the central RuII atom is sixfold coordinated by two bidentate 2,2'-bipyridine, an isonicotinamide ligand, and a water molecule in a distorted octahedral environment with trifluoromethanesulfonate ions completing the outer coordination sphere of the complex. Hydrogen bonding involving the water molecule and weak π–π stacking interactions between the pyridyl rings in adjacent molecules contribute to the alignment of the complexes in columns parallel to the c axis. Full Article text
id Bis[μ-bis(pyridin-2-yl)methanone oxime-κ3N:,N',N'']bis[diacetato-κ2O,O';κO-zinc(II)] By journals.iucr.org Published On :: 2024-02-16 The structure of the title complex, [Zn2(C2H3O2)4(C11H9N3O)2], is triclinic containing half of the molecule in the asymmetric unit. Each zinc atom is coordinated to a pyridyl and oxime nitrogen from one di-2-pyridyl ketone oxime (dpko) ligand and a third nitrogen from the other dpko pyridyl ring. Additionally, each zinc is coordinated to two acetato anions, one of which is bidentate and the other monodentate. The uncoordinated oxygen of the monodentate acetato group is involved in a hydrogen bond with the oxime hydrogen. The packing in the crystal is assisted by weak C—H⋯O interactions between acetato groups and neighboring pyridyl rings. Full Article text
id Bis[S-octyl 3-(2-methylpropylidene)dithiocarbazato-κ2N3,S]nickel(II) By journals.iucr.org Published On :: 2024-03-06 The central NiII atom in the title complex, [Ni(C13H25N2S2)2], is located on an inversion center and adopts a roughly square-planar coordination environment defined by two chelating N,S donor sets of two symmetry-related ligands in a trans configuration. The Ni—N and Ni—S bond lenghts are 1.9193 (14) and 2.1788 (5) Å, respectively, with a chelating N—Ni—S bond angle of 86.05 (4)°. These data are compared with those measured for similar dithiocarbazato ligands that bear n-octyl or n-hexyl alkyl chains. Slight differences are observed with respect to the phenylethylidene derivative where the ligands are bound cis relative to one another. Full Article text
id cis,cis,cis-Dichloridobis(N4,N4-dimethylpyridin-4-amine-κN1)bis(dimethyl sulfoxide-κS)ruthenium(II) By journals.iucr.org Published On :: 2024-03-06 The structure of the title compound, [RuCl2(C7H10N2)2(C2H6OS)2], has monoclinic (P21/n) symmetry. The Ru—N distances of the coordination compound are influenced by the trans chloride or dimethylsulfoxide-κS ligands. The molecular structure exhibits disorder for two of the terminal methyl groups of a dimethyl sulfoxide ligand. Full Article text
id 4-Fluoro-2-(phenylamino)benzoic acid By journals.iucr.org Published On :: 2024-03-06 The title compound, C13H10FNO2, was obtained by the reaction of 2-bromo-4-fluorobenzoic acid with aniline. There are two independent molecules, A and B, in the asymmetric unit, with slight conformational differences: the dihedral angles between the aromatic rings are 55.63 (5) and 52.65 (5)°. Both molecules feature an intramolecular N—H⋯O hydrogen bond. In the crystal, the molecules are linked by pairwise O—H⋯O hydrogen bonds to form A–B acid–acid dimers and weak C—H⋯F interactions further connect the dimers. Full Article text
id 5-Bromo-2-(phenylamino)benzoic acid By journals.iucr.org Published On :: 2024-03-06 The title compound, C13H10BrNO2, was obtained by the reaction of 2,5-dibromobenzoic acid and aniline. The molecule is twisted with a dihedral angle between the aromatic rings of 45.74 (11)° and an intramolecular N—H⋯O hydrogen bond is seen. In the crystal, pairwise O—H⋯O hydrogen bonds generate carboxylic acid inversion dimers. Full Article text
id {N-[1-(2-Oxidophenyl)ethylidene]-dl-alaninato}(pentane-1,5-diyl)silicon(IV) By journals.iucr.org Published On :: 2024-03-19 The title SiIV complex, C16H21NO3Si, is built up by a tridentate dinegative Schiff base ligand bound to a silacyclohexane unit. The coordination geometry of the pentacoordinated SiIV atom is a distorted trigonal bipyramid. The presence of the silacyclohexane ring in the complex leads to an unusual coordination geometry of the SiIV atom with the N atom from the Schiff base ligand and an alkyl-C atom in apical positions of the trigonal bipyramid. There is a disorder of the methyl group at the imine bond with two orientations resolved for the H atoms [major orientation = 0.55 (3)]. In the crystal, C—H⋯O interactions are found within corrugated layers of molecules parallel to the ab plane. Full Article text
id trans-Dibromidotetrakis(5-methyl-1H-pyrazole-κN2)manganese(II) By journals.iucr.org Published On :: 2024-03-19 The title compound, trans-dibromidotetrakis(5-methyl-1H-pyrazole-κN2)manganese(II), [MnBr2(C4H6N2)4] or [Mn(3-MePzH)4Br2] (1) crystallizes in the triclinic Poverline{1} space group with the cell parameters a = 7.6288 (3), b = 8.7530 (4), c = 9.3794 (4) Å and α = 90.707 (4), β = 106.138 (4), γ = 114.285 (5)°, V = 542.62 (5) Å3, T = 120 K. The asymmetric unit contains only half the molecule with the manganese atom is situated on a crystallographic inversion center. The 3-MePzH ligands are present in an AABB type manner with two methyl groups pointing up and the other two down. The supramolecular architecture is characterized by several intermolecular C—H⋯N, N—H⋯Br, and C—H⋯π interactions. Earlier, a polymorphic structure of [Mn(3-MePzH)4Br2] (2) with a similar geometry and also an AABB arrangement for the pyrazole ligands was described [Reedijk et al. (1971). Inorg. Chem. 10, 2594–2599; a = 8.802 (6), b = 9.695 (5), c = 7.613 (8) Å and α = 105.12 (4), β = 114.98 (4), γ = 92.90 (3)°, V = 558.826 (5) Å3, T = 295 K]. A varying supramolecular pattern was reported, with the structure of 1 featuring a herringbone type pattern while that of structure 2 shows a pillared network type of arrangement along the a axis. A nickel complex [Ni(3-MePzH)4Br2] isomorphic to 1 and the analogous chloro derivatives of FeII, CoII and CuII are also known. Full Article text
id 4-Fluorobenzyl (Z)-2-(2-oxoindolin-3-ylidene)hydrazine-1-carbodithioate By journals.iucr.org Published On :: 2024-03-19 The title compound, C16H12FN3OS, a fluorinated dithiocarbazate imine derivative, was synthesized by the one-pot, multi-component condensation reaction of hydrazine hydrate, carbon disulfide, 4-fluorobenzyl chloride and isatin. The compound demonstrates near-planarity across much of the molecule in the solid state and a Z configuration for the azomethine C=N bond. The Z form is further stabilized by the presence of an intramolecular N—H⋯O hydrogen bond. In the extended structure, molecules are linked into dimers by N—H⋯O hydrogen bonds and further connected into chains along either [2overline{1}0] or [100] by weak C—H⋯S and C—H⋯F hydrogen bonds, which further link into corrugated sheets and in combination form the overall three-dimensional network. Full Article text
id Bis[2,6-bis(1H-benzimidazol-2-yl)pyridine]ruthenium(II) bis(hexafluoridophosphate) diethyl ether trisolvate By journals.iucr.org Published On :: 2024-03-28 The title compound, [Ru(C19H13N5)2](PF6)2·3C4H10O, was obtained from the reaction of Ru(bimpy)Cl3 [bimpy is 2,6-bis(1H-benzimidazol-2-yl)pyridine] and bimpy in refluxing ethanol followed by recrystallization from diethyl ether/acetonitrile. At 125 K the complex has orthorhombic (Pca21) symmetry. It is remarkable that the structure is almost centrosymmetric. However, refinement in space group Pbcn leads to disorder and definitely worse results. It is of interest with respect to potential catalytic reduction of CO2. The structure displays N—H⋯O, N—H⋯F hydrogen bonding and significant π–π stacking and C—H⋯π stacking interactions. Full Article text
id Ethidium benzoate methanol monosolvate By journals.iucr.org Published On :: 2024-04-18 In the title salt solvate (systematic name: 8-amino-5-ethyl-6-phenylphenanthridin-5-ium benzoate methanol monosolvate), C21H20N3+·C6H5CO2−·CH3OH, two ethidium cations, C21H20N3+, dimerize about a twofold axis through π–π interactions [inter-centroid separation = 3.6137 (4) Å]. The benzoate anions are connected through hydrogen bonding with the –NH2 groups of the ethidium cations and the –OH group of the MeOH molecule. The MeOH molecule also accepts a hydrogen bond from the –NH2 group of the ethidium cation. The result is a one-dimensional hydrogen-bonded chain along the b-axis direction. Full Article text
id Bis[2,3-bis(thiophen-2-yl)pyrido[3,4-b]pyrazine]silver(I) perchlorate methanol disolvate By journals.iucr.org Published On :: 2024-04-26 The title compound, [Ag(C15H9N3S2)2]ClO4·2CH3OH, is monoclinic. The AgI atom is coordinated by pyrido N atoms and is two-coordinate; however, the AgI atom has nearby O atoms that can be assumed to be weakly bonded – one from the perchlorate anion and one from the methanol solvate molecule. One of the thienyl groups on a 2,3-bis(thiophen-2-yl)pyrido[3,4-b]pyrazine is flipped disordered and was refined to occupancies of 68.4 (6) and 31.6 (6)%. Full Article text
id Poly[3-methylpyridinium [(μ2-dihydrogen phosphito)bis(μ3-hydrogen phosphito)dizinc]] By journals.iucr.org Published On :: 2024-04-26 In the title compound, {(C6H8N)[Zn2(HPO3)2(H2PO3)]}n, the constituent ZnO4, HPO3 and H2PO3 polyhedra of the inorganic component are linked into (010) sheets by Zn—O—P bonds (mean angle = 134.4°) and the layers are reinforced by O—H⋯O hydrogen bonds. The protonated templates are anchored to the inorganic sheets via bifurcated N—H⋯(O,O) hydrogen bonds. Full Article text
id (SC,RS)-Bromido(N-{4-methyl-1-[(4-methylphenyl)sulfanyl]pentan-2-yl}-N'-(pyridin-2-yl)imidazol-2-ylidene)palladium(II) bromide By journals.iucr.org Published On :: 2024-04-26 The molecule of the title NCNHCS pincer N-heterocyclic carbene palladium(II) complex, [PdBr(C21H25N3S)]Br, exhibits a slightly distorted square-planar coordination at the palladium(II) atom, with the five-membered chelate ring nearly planar. The six-membered chelate ring adopts an envelope conformation. Upon chelation, the sulfur atom becomes a stereogenic centre with an RS configuration induced by the chiral carbon of the precursor imidazolium salt. There are intramolecular C—H⋯Br—Pd hydrogen bonds in the structure. The two interstitial Br atoms, as the counter-anion of the structure, are both located on crystallographic twofold axes and are connected to the complex cations via C—H⋯·Br hydrogen bonds. Full Article text
id 4-(1H-2,3-Dihydronaphtho[1,8-de][1,3,2]diazaborinin-2-yl)-1-ethylpyridin-1-ium iodide By journals.iucr.org Published On :: 2024-04-26 The title compound, C17H17BN3I, is a type of diazaborinane featuring substitution at the 1, 2, and 3 positions of the nitrogen–boron six-membered heterocycle. The organic molecule has a planar structure, the dihedral angle between the pyridyl ring and the fused ring system being 3.46 (4)°. In the crystal, molecules are stacked in a head-to-tail manner. The iodide ion makes close contacts with three organic molecules and supports the alternating stack. Full Article text
id 4-(1H-2,3-Dihydronaphtho[1,8-de][1,3,2]diazaborinin-2-yl)-1-ethylpyridin-1-ium iodide monohydrate By journals.iucr.org Published On :: 2024-04-26 The cation of the title hydrated salt, C17H17BN3+·I−·H2O, is a diazaborinane featuring substitution at the 1, 2, and 3 positions in the nitrogen–boron six-membered heterocycle. The cation is approximately planar with a dihedral angle between the pyridyl ring and the diazaborinane ring system of 5.40 (5)°. In the crystal, the cations stack along [100] in an alternating head-to-tail manner, while the iodide ion and water molecule form one-dimensional hydrogen-bonded chains beside the cation stack. The cation stacks and I−–water chains are crosslinked by N—H⋯I and N—H⋯O hydrogen bonds. Full Article text