Synthesis and structure of 4-{[(E)-(7-methoxy-1,3-benzodioxol-5-yl)methylidene]amino}-1,5-dimethyl-2-phenyl-2,3-dihydro-1H-pyrazol-3-one

In the title compound, C20H19N3O4, the dihedral angles between the central pyrazole ring and the pendant phenyl and substituted benzene rings are 50.95 (8) and 3.25 (12)°, respectively, and an intramolecular C—H...O link generates an S(6) ring. The benzodioxolyl ring adopts a shallow envelope conformation with the methylene C atom as the flap. In the crystal, the molecules are linked by non-classical C—H...O interactions, which generate a three-dimensional network. Solvent-accessible voids run down the c-axis direction and the residual electron density in these voids was modelled during the refinement process using the SQUEEZE algorithm [Spek (2015). Acta Cryst. C71, 9–18] within the structural checking program PLATON.

HAR, TAAM and BODD refinements of model crystal structures using Cu Kα and Mo Kα X-ray diffraction data

The Independent Atom Model (IAM) of electron density is used in routine X-ray data analysis. However, this model does not give a quantitative description of the electron-density distribution. A better model that allows for modelling of aspherical charge density deformations is introduced by the Hansen–Coppens variant of the multipole model of electron density. However, the application of this model requires crystals of excellent quality and high-resolution XRD data which are quite often difficult criteria to fulfil. Therefore, Mo Kα and Cu Kα data of three model compounds (tricyclic imide, xylitol and methyluracil) were refined using IAM and new methods which enabled the refinement and reconstruction of charge density based on the Cu Kα data. These methods were the Bond-Oriented Deformation Density (BODD) model, Hirshfeld Atom Refinement (HAR) and the Transferable Aspherical Atom Model (TAAM). The final results were compared to the model obtained from neutron diffraction experiments. Our results demonstrated not only that Cu Kα data may be refined using BODD, HAR and TAAM methods, but also revealed systematic errors arising from the use of Cu Kα data. These errors were a result of the limited information in the low-resolution data set that manifested as higher values for the anisotropic displacement parameters (ADPs) and smaller maxima and minima of the residual electron density for the Cu Kα data compared to the Mo Kα data. Notably, these systematic errors were much less significant than those found for the IAM. Therefore, the application of BODD, HAR and TAAM on Cu Kα data has a more significant influence on the final results of refinement than for the Mo Kα data.

Bis(μ4-adamantane-1,3-dicarboxylato-1κO 1:2κO 1′:3κO 3:4κO 3′)octacarbonyl-1κ2 C,2κ2 C,3κ2 C,4κ2 C-tetrakis[tris(4-methylphenyl)phosphane]-1κP,2κP,3κP,4κP-tetraosmium(I)(2 Os–Os)

The title complex, [{Os2(CO)4(C21H21P)2}2(C12H14O4)2], is a centrosymmetric molecular loop consisting of two Os—Os sawhorse units linked by two adamantane dicarboxylato bridges. It was synthesized by the microwave-mediated reaction between Os3(CO)12 and adamantane-1,3-dicarboxylic acid. In contrast to the related complex [{Os2(CO)6}2(μ4-adamantane-1,3-diacetate)2], the metal–metal axes within each molecule are oriented parallel rather than perpendicular to one another. The crystal structure exhibits cavities that contain residual electron density peaks, but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using the SQUEEZE (Spek (2015). Acta Cryst. C71, 9–18) routine in PLATON [Spek (2020). Acta Cryst. E76, 1–11]. These solvent molecules are not considered in the given chemical formula and other crystal data.

Tris(Para-Tolyl)Bismuth Bis(Bromodifluoroacetate). Synthesis and Structure Features

The interaction of tri(para-tolyl)bismuth with tert-butyl hydroperoxide and bromodifluoroacetic acid in diethyl ether have synthesized tris(para-tolyl)bismuth bis(bromodifluoroacetate). The X-ray diffraction pattern for the crystal has been obtained at 293 K on an automatic diffractometer D8 Quest Bruker (MoKα-radiation, λ = 0.71073 Å, graphite monochromator), the results are [C25H21O4F4Br2Bi, M 830.22, the triclinic syngony, the symmetry group P–1; cell parameters: a = 10.292(8), b = 11.752(9), c = 12.693(9) Å, α = 89.42(2) degrees, β = 78.04(3) degrees, γ = 78.04(3) degrees; V = 1424.8(18) Å3; the crystal size is 0.73×0.57×0.41 mm; intervals of reflection indexes are –13 ≤ h ≤ 13, –15 ≤ k ≤ 15, –16 ≤ l ≤ 16; total reflections 45443; independent reflections 7096; Rint 0.1030; GOOF 1.049; R1 = 0.0739, wR2 = 0.1834; residual electron density 2.11/–2.78 e/Å3], the bismuth atom have a distorted trigonal-bipyramidal coordination. The OBiO axial angle is 172.2(3) degrees; the sum of the CBiC angles in the equatorial plane is 360.6. The Bi–O and Bi–C bond lengths are 2.275(8), 2.295(8) Å and 2.187(10)–2.212(13) Å. The Bi•••O=С distances are 3.127(10) and 3.159(10) Å, which is less than the sum of the van der Waals radii of bismuth and oxygen (3.59 Å). There are no intermolecular contacts H∙∙∙Hal in the crystal. Complete tables of coordinates of atoms, bond lengths and valence angles for the structure are deposited at the Cambridge Structural Data Bank (no. 1923097; [email protected]; http: //www.ccdc.cam.ac.uk).

6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminium sulfate monohydrate

The title compound, C4H9N5O2+·SO4 2−·H2O, is the monohydrate of the commercially available compound `C4H7N5O·H2SO4·xH2O'. It is obtained by reprecipitation of C4H7N5O·H2SO4·xH2O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-triamino-1,6-dihydropyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R 2C—NH3 +) and one is rearranged to a protonated imine group (R 2C=NH2 +). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated molecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water molecules are linked into a three-dimensional network by N—H...O and O—H...O hydrogen bonds.

Crystal structure of (methanol-κO)[5,10,15,20-tetrakis(2-aminophenyl)porphyrinato-κ4 N]zinc(II)–chloroform–methanol (1/1/1)

In the crystal structure of the title compound, [Zn(C44H32N8)(CH3OH)]·CHCl3·CH3OH, the ZnII cation is coordinated by four porphyrin N and one methanol O atom within a slightly distorted square-pyramidal environment and is shifted out of the porphyrin plane towards the direction of the methanol molecule. The methyl group of the coordinating methanol molecule is disordered over two sets of sites. The porphyrin backbone is nearly planar and the phenyl rings are almost perpendicular to the porphyrin plane. As is typical for picket-fence porphyrins, all four ortho substituents of the meso-phenyl groups (here the amino groups) are facing to the same side of the porphyrin molecule. In the crystal structure, two neighbouring porphyrin complexes form centrosymmetric dimers that are connected via O—H...N hydrogen bonding. With the aid of additional N—H...N and C—H...N hydrogen bonding, these dimers are stacked into columns parallel to [010] that are finally arranged into layers parallel to (001). Between these layers channels are formed where chloroform solvent molecules are located that are connected to the porphyrin complexes by weak C—H...Cl hydrogen bonding. There are additional cavities in the structure where some small residual electron density is found, indicating the presence of disordered methanol molecules, but a reasonable model could not be refined. Therefore the contribution of the electron density associated with the methanol solvent molecule was removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. Nevertheless, the given chemical formula and other crystal data take into account the methanol solvent molecule.

HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure

The resonant-scattering contributions to single-crystal X-ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X-ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant-scattering correction to the X-ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post-refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.

Structural anomalies in tobelite-2M2 explained by high resolution and analytical electron microscopy

A transmission electron microscopy (TEM) investigation was undertaken in order to elucidate the nature of the structural disorder in a tobelite specimen from the sedimentary rocks of the Armorican sandstones (western France). This structural disorder may be the origin of residual electron-density maxima in difference-Fourier maps reported previously in single-crystal XRD studies of tobelite. The TEM investigation of tobelite confirmed that it is the 2M2 polytype in subfamily-B, but the ordered sequence is interrupted by numerous stacking faults parallel to (001), for which the stacking vectors belong to both subfamilies-A and -B of mica polytypes, with a prevalence of the latter. Chemical heterogeneity depending on the Si/Al ratio and Na and Mg concentration was observed at the nanoscale among different mica lamellae in a single crystal. The observed variations are consistent with a change in mica chemistry leading to interlayer vacancies which may cause shortening of the interlayer separation, as revealed by the single-crystal structure refinements.

Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein–cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O...H—N hydrogen bonds was analyzed with respect to the different secondary-structure elements.