met Refining short-range order parameters from the three-dimensional diffuse scattering in single-crystal electron diffraction data By journals.iucr.org Published On :: 2024-01-01 Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Å for the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Å for the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available. Full Article text
met Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion By journals.iucr.org Published On :: 2024-01-13 Highly accurate protein structure prediction can generate accurate models of protein and protein–protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases. Following this strategy, full-length models or the conservative structural domains could be used directly as the starting model, and the phase error and the model bias between the starting model and the real structure would be modified in the direct-methods-based dual-space iteration. Many challenging cases (from CASP14) have been tested for the general applicability of this constructive strategy, and almost complete models have been generated with reasonable statistics. The hybrid strategy therefore provides a meaningful scheme for X-ray structure determination using a predicted model as the starting point. Full Article text
met Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development By journals.iucr.org Published On :: 2024-04-19 Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification. Full Article text
met Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data By journals.iucr.org Published On :: 2024-07-10 Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile. Full Article text
met In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry By journals.iucr.org Published On :: 2024-07-15 The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons. Full Article text
met On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors By journals.iucr.org Published On :: 2024-08-15 This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED. Full Article text
met CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data By journals.iucr.org Published On :: 2024-08-14 Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) is a web based tool that facilitates the interactive validation of MBS in structures determined through X-ray crystallography and cryo-electron microscopy (cryo-EM). Recent updates to CMM have significantly enhanced its capability to efficiently handle large datasets generated from cryo-EM structural analyses. In this study, we address various challenges inherent in validating MBS within both X-ray and cryo-EM structures. Specifically, we examine the difficulties associated with accurately identifying metals and modeling their coordination environments by considering the ongoing reproducibility challenges in structural biology and the critical importance of well annotated, high-quality experimental data. CMM employs a sophisticated framework of rules rooted in the valence bond theory for MBS validation. We explore how CMM validation parameters correlate with the resolution of experimentally derived structures of macromolecules and their complexes. Additionally, we showcase the practical utility of CMM by analyzing a representative cryo-EM structure. Through a comprehensive examination of experimental data, we demonstrate the capability of CMM to advance MBS characterization and identify potential instances of metal misassignment. Full Article text
met From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion By journals.iucr.org Published On :: 2024-08-28 3D electron diffraction (3DED) is increasingly employed to determine molecular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using dichloromethane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations. Full Article text
met Tuning structural modulation and magnetic properties in metal–organic coordination polymers [CH3NH3]CoxNi1−x(HCOO)3 By journals.iucr.org Published On :: 2024-09-24 Three solid solutions of [CH3NH3]CoxNi1−x(HCOO)3, with x = 0.25 (1), x = 0.50 (2) and x = 0.75 (3), were synthesized and their nuclear structures and magnetic properties were characterized using single-crystal neutron diffraction and magnetization measurements. At room temperature, all three compounds crystallize in the Pnma orthorhombic space group, akin to the cobalt and nickel end series members. On cooling, each compound undergoes a distinct series of structural transitions to modulated structures. Compound 1 exhibits a phase transition to a modulated structure analogous to the pure Ni compound [Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. & Petricek, V. (2020). Inorg. Chem. 59, 17896–17905], whereas compound 3 maintains the behaviour observed in the pure Co compound reported previously [Canadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodriguez-Velamazan, J. A. & Rodriguez-Carvajal, J. (2019). IUCrJ, 6, 105–115], although in both cases the temperatures at which the phase transitions occur differ slightly from the pure phases. Monochromatic neutron diffraction measurements showed that the structural evolution of 2 diverges from that of either parent compound, with competing hydrogen bond interactions that drive the modulation throughout the series, producing a unique sequence of phases. It involves two modulated phases below 96 (3) and 59 (3) K, with different q vectors, similar to the pure Co compound (with modulated phases below 128 and 96 K); however, it maintains the modulated phase below magnetic order [at 22.5 (7) K], resembling the pure Ni compound (which presents magnetic order below 34 K), resulting in an improper modulated magnetic structure. Despite these large-scale structural changes, magnetometry data reveal that the bulk magnetic properties of these solid solutions form a linear continuum between the end members. Notably, doping of the metal site in these solid solutions allows for tuning of bulk magnetic properties, including magnetic ordering temperature, transition temperatures and the nature of nuclear phase transitions, through adjustment of metal ratios. Full Article text
met Elastic and inelastic strain in submicron-thick ZnO epilayers grown on r-sapphire substrates by metal–organic vapour phase deposition By journals.iucr.org Published On :: 2024-02-13 A significant part of the present and future of optoelectronic devices lies on thin multilayer heterostructures. Their optical properties depend strongly on strain, being essential to the knowledge of the stress level to optimize the growth process. Here the structural and microstructural characteristics of sub-micron a-ZnO epilayers (12 to 770 nm) grown on r-sapphire by metal–organic chemical vapour deposition are studied. Morphological and structural studies have been made using scanning electron microscopy and high-resolution X-ray diffraction. Plastic unit-cell distortion and corresponding strain have been determined as a function of film thickness. A critical thickness has been observed as separating the non-elastic/elastic states with an experimental value of 150–200 nm. This behaviour has been confirmed from ultraviolet photoelectron spectroscopy, X-ray photoelectron spectroscopy and high-resolution transmission electron microscopy measurements. An equation that gives the balance of strains is proposed as an interesting method to experimentally determine this critical thickness. It is concluded that in the thinnest films an elongation of the Zn—O bond takes place and that the plastic strained ZnO films relax through nucleation of misfit dislocations, which is a consequence of three-dimensional surface morphology. Full Article text
met Search for missing symmetry in the Inorganic Crystal Structure Database (ICSD) By journals.iucr.org Published On :: 2024-09-17 An exhaustive search for missing symmetry was performed for 223 076 entries in the ICSD (2023-2 release). Approximately 0.65% of them can be described with higher symmetry than reported. Out of the identified noncentrosymmetric entries, ∼74% can be described by centrosymmetric space groups; this has implications for compatible physical properties. It is proposed that the information on the correct space group is included in the ICSD. Full Article text
met Crystal structure and Hirshfeld surface analysis of (2Z)-3-oxo-N-phenyl-2-[(1H-pyrrol-2-yl)methylidene]butanamide monohydrate By journals.iucr.org Published On :: 2023-11-14 In the title compound, C15H14N2O2·H2O, the 1H-pyrrole ring makes a dihedral angle of 59.95 (13)° with the phenyl ring. In the crystal, the molecules are connected by C—H⋯O hydrogen bonds into layers parallel to the (020) plane, while two molecules are connected to the water molecule by two N—H⋯O hydrogen bonds and one molecule by an O—H⋯O hydrogen bond. C—H⋯π and π–π interactions further link the molecules into chains extending in the [overline{1}01] direction and stabilize the molecular packing. According to a Hirshfeld surface study, H⋯H (49.4%), C⋯H/H⋯C (23.2%) and O⋯H/H⋯O (20.0%) interactions are the most significant contributors to the crystal packing. Full Article text
met Synthesis, structure and Hirshfeld surface analysis of 1,3-bis[(1-octyl-1H-1,2,3-triazol-4-yl)methyl]-1H-benzo[d]imidazol-2(3H)-one By journals.iucr.org Published On :: 2023-11-21 The title molecule, C29H44N8O, adopts a conformation resembling a two-bladed fan with the octyl chains largely in fully extended conformations. In the crystal, C—H⋯O hydrogen bonds form chains of molecules extending along the b-axis direction, which are linked by weak C—H⋯N hydrogen bonds and C—H⋯π interactions to generate a three-dimensional network. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (68.3%), H⋯N/N⋯H (15.7%) and H⋯C/C⋯H (10.4%) interactions. Full Article text
met Synthesis, crystal structure and Hirshfeld analysis of trans-bis(2-{1-[(6R,S)-3,5,5,6,8,8-hexamethyl-5,6,7,8-tetrahydronaphthalen-2-yl]ethylidene}-N-methylhydrazinecarbothioamidato-κ2N2,S)palladium(II) ethanol mon By journals.iucr.org Published On :: 2023-11-16 The reaction between the (R,S)-fixolide 4-methylthiosemicarbazone and PdII chloride yielded the title compound, [Pd(C20H30N3S)2]·C2H6O {common name: trans-bis[(R,S)-fixolide 4-methylthiosemicarbazonato-κ2N2S]palladium(II) ethanol monosolvate}. The asymmetric unit of the title compound consists of one bis-thiosemicarbazonato PdII complex and one ethanol solvent molecule. The thiosemicarbazononato ligands act as metal chelators with a trans configuration in a distorted square-planar geometry. A C—H⋯S intramolecular interaction, with graph-set motif S(6), is observed and the coordination sphere resembles a hydrogen-bonded macrocyclic environment. Additionally, one C—H⋯Pd anagostic interaction can be suggested. Each ligand is disordered over the aliphatic ring, which adopts a half-chair conformation, and two methyl groups [s.o.f. = 0.624 (2):0.376 (2)]. The disorder includes the chiral carbon atoms and, remarkably, one ligand has the (R)-isomer with the highest s.o.f. value atoms, while the other one shows the opposite, the atoms with the highest s.o.f. value are associated with the (S)-isomer. The N—N—C(=S)—N fragments of the ligands are approximately planar, with the maximum deviations from the mean plane through the selected atoms being 0.0567 (1) and −0.0307 (8) Å (r.m.s.d. = 0.0403 and 0.0269 Å) and the dihedral angle with the respective aromatic rings amount to 46.68 (5) and 50.66 (4)°. In the crystal, the complexes are linked via pairs of N—H⋯S interactions, with graph-set motif R22(8), into centrosymmetric dimers. The dimers are further connected by centrosymmetric pairs of ethanol molecules, building mono-periodic hydrogen-bonded ribbons along [011]. The Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are [atoms with highest/lowest s.o.f.s considered separately]: H⋯H (81.6/82.0%), H⋯C/C⋯H (6.5/6.4%), H⋯N/N⋯H (5.2/5.0%) and H⋯S/S⋯H (5.0/4.9%). Full Article text
met An octanuclear nickel(II) pyrazolate cluster with a cubic Ni8 core and its methyl- and n-octyl-functionalized derivatives By journals.iucr.org Published On :: 2023-11-30 The molecular and crystal structure of a discrete [Ni8(μ4-OH)6(μ-4-Rpz)12]2− (R = H; pz = pyrazolate anion, C3H3N2−) cluster with an unprecedented, perfectly cubic arrangement of its eight Ni centers is reported, along with its lower-symmetry alkyl-functionalized (R = methyl and n-octyl) derivatives. Crystals of the latter two were obtained with two identical counter-ions (Bu4N+), whereas the crystal of the complex with the parent pyrazole ligand has one Me4N+ and one Bu4N+ counter-ion. The methyl derivative incorporates 1,2-dichloroethane solvent molecules in its crystal structure, whereas the other two are solvent-free. The compounds are tetrabutylazanium tetramethylazanium hexa-μ4-hydroxido-dodeca-μ2-pyrazolato-hexahedro-octanickel, (C16H36N)(C4H12N)[Ni8(C3H3N2)12(OH)6] or (Bu4N)(Me4N)[Ni8(μ4-OH)6(μ-pz)12] (1), bis(tetrabutylazanium) hexa-μ4-hydroxido-dodeca-μ2-(4-methylpyrazolato)-hexahedro-octanickel 1,2-dichloroethane 7.196-solvate, (C16H36N)2[Ni8(C4H5N2)12(OH)6]·7.196C2H4Cl2 or (Bu4N)2[Ni8(μ4-OH)6(μ-4-Mepz)12]·7.196(ClCH2CH2Cl) (2), and bis(tetrabutylazanium) hexa-μ4-hydroxido-dodeca-μ2-(4-octylpyrazolato)-hexahedro-octanickel, (C16H36N)2[Ni8(C11H19N2)12(OH)6] or (Bu4N)2[Ni8(μ4-OH)6(μ-4-nOctpz)12] (3). All counter-ions are disordered (with the exception of one Bu4N+ in 3). Some of the octyl chains of 3 (the crystal is twinned by non-merohedry) are also disordered. Various structural features are discussed and contrasted with those of other known [Ni8(μ4-OH)6(μ-4-Rpz)12]2− complexes, including extended three-dimensional metal–organic frameworks. In all three structures, the Ni8 units are lined up in columns. Full Article text
met Crystal structure and antimycobacterial evaluation of 2-(cyclohexylmethyl)-7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one By journals.iucr.org Published On :: 2023-11-30 The title compound, C15H15F3N2O3S, crystallizes in the monoclinic system, space group I2/a, with Z = 8. As expected, the nine-membered heterobicyclic system is virtually planar and the cyclohexyl group adopts a chair conformation. There is structural evidence for intramolecular N—S⋯O chalcogen bonding between the benzisothiazolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N—S bond [N—S⋯O = 162.7 (1)°]. In the crystal, the molecules form centrosymmetric dimers through C—H⋯O weak hydrogen bonding between a C—H group of the electron-deficient benzene ring and the benzothiazolinone carbonyl O atom with an R22(10) motif. In contrast to the previously described N-acyl 7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-ones, the title N-cyclohexylmethyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro. Full Article text
met Synthesis, crystal structure and computational analysis of 2,7-bis(4-chlorophenyl)-3,3-dimethyl-1,4-diazepan-5-one By journals.iucr.org Published On :: 2023-11-30 In the title compound, C19H20Cl2N2O, the seven-membered 1,4-diazepane ring adopts a chair conformation while the 4-chlorophenyl substituents adopt equatorial orientations. The chlorophenyl ring at position 7 is disordered over two positions [site occupancies 0.480 (16):0.520 (16)]. The dihedral angle between the two benzene rings is 63.0 (4)°. The methyl groups at position 3 have an axial and an equatorial orientation. The compound exists as a dimer exhibiting intermolecular N—H⋯O hydrogen bonding with R22(8) graph-set motifs. The crystal structure is further stabilized by C—H⋯O hydrogen bonds together with two C—Cl⋯π (ring) interactions. The geometry was optimized by DFT using the B3LYP/6–31 G(d,p) level basis set. In addition, the HOMO and LUMO energies, chemical reactivity parameters and molecular electrostatic potential were calculated at the same level of theory. Hirshfeld surface analysis indicated that the most important contributions to the crystal packing are from H⋯H (45.6%), Cl⋯H/H⋯Cl (23.8%), H⋯C/C⋯H (12.6%), H⋯O/O⋯H (8.7%) and C⋯Cl/Cl⋯C (7.1%) interactions. Analysis of the interaction energies showed that the dispersion energy is greater than the electrostatic energy. A crystal void volume of 237.16 Å3 is observed. A molecular docking study with the human oestrogen receptor 3ERT protein revealed good docking with a score of −8.9 kcal mol−1. Full Article text
met Crystal structure and Hirshfeld surface analysis of a new benzimidazole compound, 3-{1-[(2-hydroxyphenyl)methyl]-1H-1,3-benzodiazol-2-yl}phenol By journals.iucr.org Published On :: 2024-01-01 The title compound, C20H16N2O2, is composed of two monosubstituted benzene rings and one benzimidazole unit. The benzimidazole moiety subtends dihedral angles of 46.16 (7) and 77.45 (8)° with the benzene rings, which themselves form a dihedral angle of 54.34 (9)°. The crystal structure features O—H⋯N and O—H⋯O hydrogen-bonding interactions, which together lead to the formation of two-dimensional hydrogen-bonded layers parallel to the (101) plane. In addition, π–π interactions also contribute to the crystal cohesion. Hirshfeld surface analysis indicates that the most significant contacts in the crystal packing are: H⋯H (47.5%), O⋯H/H⋯O (12.4%), N⋯H/H⋯N (6.1%), C⋯H/H⋯C (27.6%) and C⋯C (4.6%). Full Article text
met Crystal structure of [1,3-bis(2,4,6-trimethylphenyl)imidazolidin-2-ylidene]dichlorido(2-{[(2-methoxyethyl)(methyl)amino]methyl}benzylidene)ruthenium By journals.iucr.org Published On :: 2024-01-01 The title compound, [RuCl2(C33H43N3O)], is an example of a new generation of N,N-dialkyl ruthenium catalysts with an N—Ru coordination bond as part of a six-membered chelate ring. The Ru atom has an Addison τ parameter of 0.244, which indicates a geometry intermediate between square-based pyramidal and trigonal–bipyramidal. The complex shows the usual trans arrangement of the two chlorides, with Ru—Cl bond lengths of 2.3515 (8) and 2.379 (7) Å, and a Cl—Ru—Cl angle of 158.02 (3)°. One of the chlorine atoms and the atoms of the 2-methoxy-N-methyl-N-[(2-methylphenyl)methyl]ethane-1-amine group of the title complex display disorder over two positions in a 0.889 (2): 0.111 (2) ratio. Full Article text
met The synthesis and structural properties of a chloridobis{N-[(4-methoxyphenyl)imino]pyrrolidine-1-carboxamide}zinc(II) (acetonitrile)trichloridozincate coordination complex By journals.iucr.org Published On :: 2024-01-01 The title complex, [ZnCl(C12H15N3O2)2][ZnCl3(CH3CN)], was synthesized and its structure was fully characterized through single-crystal X-ray diffraction analysis. The complex crystallizes in the orthorhombic system, space group Pbca (61), with a central zinc atom coordinating one chlorine atom and two pyrrolidinyl-4-methoxyphenyl azoformamide ligands in a bidentate manner, utilizing both the nitrogen and oxygen atoms in a 1,3-heterodiene (N=N—C=O) motif for coordinative bonding, yielding an overall positively (+1) charged complex. The complex is accompanied by a [(CH3CN)ZnCl3]− counter-ion. The crystal data show that the harder oxygen atoms in the heterodiene zinc chelate form bonding interactions with distances of 2.002 (3) and 2.012 (3) Å, while nitrogen atoms are coordinated by the central zinc cation with bond lengths of 2.207 (3) and 2.211 (3) Å. To gain further insight into the intermolecular interactions within the crystal, Hirshfeld surface analysis was performed, along with the calculation of two-dimensional fingerprint plots. This analysis revealed that H⋯H (39.9%), Cl⋯H/H⋯Cl (28.2%) and C⋯H/H⋯C (7.2%) interactions are dominant. This unique crystal structure sheds light on arrangement and bonding interactions with azoformamide ligands, and their unique qualities over similar semicarbazone and azothioformamide structures. Full Article text
met Crystal structure of 2-[(5-amino-1-tosyl-1H-pyrazol-3-yl)oxy]-1-(4-methoxyphenyl)ethan-1-one 1,4-dioxane monosolvate By journals.iucr.org Published On :: 2024-01-01 In the structure of the title compound, C19H19N3O5S·C4H8O2, the two independent dioxane molecules each display inversion symmetry. The pyrazole ring is approximately parallel to the aromatic ring of the oxy-ethanone group and approximately perpendicular to the tolyl ring of the sulfonyl substituent. An extensive system of classical and `weak' hydrogen bonds connects the residues to form a layer structure parallel to (201), within which dimeric subunits are conspicuous; neighbouring layers are connected by classical hydrogen bonds to dioxanes and by `weak' hydrogen bonds from Htolyl donors. Full Article text
met Crystal structure and Hirshfeld-surface analysis of diaquabis(5-methyl-1H-1,2,4-triazole-3-carboxylato)copper(II) By journals.iucr.org Published On :: 2024-01-01 The title compound, [Cu(HL)2(H2O)2] or [Cu(C4H4N3O2)2(H2O)2], is a mononuclear octahedral CuII complex based on 5-methyl-1H-1,2,4-triazole-3-carboxylic acid (H2L). [Cu(HL)2(H2O)2] was synthesized by reaction of H2L with copper(II) nitrate hexahydrate (2:1 stoichiometric ratio) in water under ambient conditions to produce clear light-blue crystals. The central Cu atom exhibits an N2O4 coordination environment in an elongated octahedral geometry provided by two bidentate HL− anions in the equatorial plane and two water molecules in the axial positions. Hirshfeld surface analysis revealed that the most important contributions to the surface contacts are from H⋯O/O⋯H (33.1%), H⋯H (29.5%) and H⋯N/N⋯H (19.3%) interactions. Full Article text
met Synthesis, crystal structure and properties of poly[(μ-2-methylpyridine N-oxide-κ2O:O)bis(μ-thiocyanato-κ2N:S)cobalt(II)] By journals.iucr.org Published On :: 2024-01-01 The title compound, [Co(NCS)2(C6H7NO)]n or Co(NCS)2(2-methylpyridine N-oxide), was prepared by the reaction of Co(NCS)2 and 2-methylpyridine N-oxide in methanol. All crystals obtained by this procedure show reticular pseudo-merohedric twinning, but after recrystallization, one crystal was found that had a minor component with only a very few overlapping reflections. The asymmetric unit consists of one CoII cation, two thiocyanate anions and one 2-methylpyridine N-oxide coligand in general positions. The CoII cations are octahedrally coordinated by two O-bonding 2-methylpyridine N-oxide ligands, as well as two S- and two N-bonding thiocyanate anions, and are connected via μ-1,3(N,S)-bridging thiocyanate anions into chains that are linked by μ-1,1(O,O) bridging coligands into layers. No pronounced directional intermolecular interactions are observed between the layers. The 2-methylpyridine coligand is disordered over two orientations and was refined using a split model with restraints. Powder X-ray diffraction (PXRD) indicates that a pure sample was obtained and IR spectroscopy confirms that bridging thiocyanate anions are present. Thermogravimetry and differential thermoanalysis (TG-DTA) shows one poorly resolved mass loss in the TG curve that is accompanied by an exothermic and an endothermic signal in the DTA curve, which indicate the decomposition of the 2-methylpyridine N-oxide coligands. Full Article text
met Crystal structure and Hirshfeld surface analysis of dimethyl 4-hydroxy-5,4'-dimethyl-2'-(toluene-4-sulfonylamino)biphenyl-2,3-dicarboxylate By journals.iucr.org Published On :: 2024-01-01 In the title compound, C25H25NO7S, the molecular conformation is stabilized by intramolecular O—H⋯O and N—H⋯O hydrogen bonds, which form S(6) and S(8) ring motifs, respectively. The molecules are bent at the S atom with a C—SO2—NH—C torsion angle of −70.86 (11)°. In the crystal, molecules are linked by C—H⋯O and N—H⋯O hydrogen bonds, forming molecular layers parallel to the (100) plane. C—H⋯π interactions are observed between these layers. Full Article text
met Crystal structure and Hirshfeld surface analysis of 3-benzyl-2-[bis(1H-pyrrol-2-yl)methyl]thiophene By journals.iucr.org Published On :: 2024-01-01 In the title compound, C20H18N2S, the asymmetric unit comprises two similar molecules (A and B). In molecule A, the central thiophene ring makes dihedral angles of 89.96 (12) and 57.39 (13)° with the 1H-pyrrole rings, which are bent at 83.22 (14)° relative to each other, and makes an angle of 85.98 (11)° with the phenyl ring. In molecule B, the corresponding dihedral angles are 89.49 (13), 54.64 (12)°, 83.62 (14)° and 85.67 (11)°, respectively. In the crystal, molecular pairs are bonded to each other by N—H⋯N interactions. N—H⋯π and C—H⋯π interactions further connect the molecules, forming a three-dimensional network. A Hirshfeld surface analysis indicates that H⋯H (57.1% for molecule A; 57.3% for molecule B), C⋯H/H⋯C (30.7% for molecules A and B) and S⋯H/H⋯S (6.2% for molecule A; 6.4% for molecule B) interactions are the most important contributors to the crystal packing. Full Article text
met Temperature-dependent solid-state phase transition with twinning in the crystal structure of 4-methoxyanilinium chloride By journals.iucr.org Published On :: 2024-01-01 At room temperature, the title salt, C7H10NO+·Cl−, is orthorhombic, space group Pbca with Z' = 1, as previously reported [Zhao (2009). Acta Cryst. E65, o2378]. Between 250 and 200 K, there is a solid-state phase transition to a twinned monoclinic P21/c structure with Z' = 2. We report the high temperature structure at 250 K and the low-temperature structure at 100 K. In the low-temperature structure, the –NH3 hydrogen atoms are ordered and this group has a different orientation in each independent molecule, in keeping with optimizing N—H⋯Cl hydrogen bonding, some of which are bifurcated: these hydrogen bonds have N⋯Cl distances in the range 3.1201 (8)–3.4047 (8) Å. In the single cation of the high-temperature structure, the NH hydrogen atoms are disordered into the average of the two low-temperature positions and the N⋯Cl hydrogen bond distances are in the range 3.1570 (15)–3.3323 (18) Å. At both temperatures, the methoxy group is nearly coplanar with the rest of the molecule, with the C—C—O—C torsion angles being −7.0 (2)° at 250 K and −6.94 (12) and −9.35 (12)° at 100 K. In the extended orthorhombic structure, (001) hydrogen-bonded sheets occur; in the monoclinic structure, the sheets propagate in the (010) plane. Full Article text
met An unexpected tautomer: synthesis and crystal structure of N-[6-amino-4-(methylsulfanyl)-1,2-dihydro-1,3,5-triazin-2-ylidene]benzenesulfonamide By journals.iucr.org Published On :: 2024-01-09 The title compound, C10H11N5O2S2, consists of an unexpected tautomer with a protonated nitrogen atom in the triazine ring and a formal exocyclic double bond C=N to the sulfonamide moiety. The ring angles at the unsubstituted nitrogen atoms are narrow, at 115.57 (12) and 115.19 (12)°, respectively, whereas the angle at the carbon atom between these N atoms is very wide, 127.97 (13)°. The interplanar angle between the two rings is 79.56 (5)°. The molecules are linked by three classical hydrogen bonds, forming a ribbon structure. There are also unusual linkages involving three short contacts (< 3 Å) from a sulfonamide oxygen atom to the C—NH—C part of a triazine ring. Full Article text
met Crystal structure and Hirshfeld surface analysis of (E)-2-[2-(2-amino-1-cyano-2-oxoethylidene)hydrazin-1-yl]benzoic acid N,N-dimethylformamide monosolvate By journals.iucr.org Published On :: 2024-01-05 In the title compound, C10H8N4O3·C3H7NO, the asymmetric unit contains two crystallographically independent molecules A and B, each of which has one DMF solvate molecule. Molecules A and B both feature intramolecular N—H⋯O hydrogen bonds, forming S(6) ring motifs and consolidating the molecular configuration. In the crystal, N—H⋯O and O—H⋯O hydrogen bonds connect molecules A and B, forming R22(8) ring motifs. Weak C—H⋯O interactions link the molecules, forming layers parallel to the (overline{2}12) plane. The DMF solvent molecules are also connected to the main molecules (A and B) by N—H⋯O hydrogen bonds. π–π stacking interactions [centroid-to-centroid distance = 3.8702 (17) Å] between the layers also increase the stability of the molecular structure in the third dimension. According to the Hirshfeld surface study, O⋯H/H⋯O interactions are the most significant contributors to the crystal packing (27.5% for molecule A and 25.1% for molecule B). Full Article text
met {[(E)-(1,3-Benzodioxol-5-yl)methylidene]amino}thiourea By journals.iucr.org Published On :: 2024-01-09 The synthesis and crystallographic analysis of the title compound, C9H9N3O2S, are reported. The compound crystallizes in the monoclinic space group P21/c, revealing characteristic bond lengths and angles typical of thiosemicarbazone groups. The supramolecular organization primarily arises from hydrogen bonding and π–π stacking interactions, leading to distinctive dimeric formations. Full Article text
met Synthesis and crystal structure of N1,N2-dimethylethanedihydrazide By journals.iucr.org Published On :: 2024-01-12 The title compound, N1,N2-dimethylethanedihydrazide, C4H10N4O2, was obtained by the methylation of oxalyl dihydrazide protected with phthalimide. The molecule is essentially non-planar with a dihedral angle between the two planar hydrazide fragments of 86.5 (2)°. This geometry contributes to the formation of a multi-contact three-dimensional supramolecular network via C—H⋯O, N—H⋯O and N—H⋯N hydrogen bonds. Full Article text
met Synthesis, crystal structure and thermal properties of dibromidobis(2-methylpyridine N-oxide-κO)cobalt(II) By journals.iucr.org Published On :: 2024-01-12 Reaction of CoBr2 with 2-methylpyridine N-oxide in n-butanol leads to the formation of the title compound, [CoBr2(C6H7NO)2] or [CoBr2(2-methylpyridine N-oxide)2]. Its asymmetric unit consists of one CoII cation as well as two bromide anions and two 2-methylpyridine N-oxide coligands in general positions. The CoII cations are tetrahedrally coordinated by two bromide anions and two 2-methylpyridine N-oxides, forming discrete complexes. In the crystal structure, these complexes are linked predominantly by weak C–H⋯Br hydrogen bonding into chains that propagate along the crystallographic a-axis. Powder X-ray diffraction (PXRD) measurements indicate that a pure phase was obtained. Thermoanalytical investigations prove that the title compound melts before decomposition; before melting, a further endothermic signal of unknown origin was observed that does not correspond to a phase transition. Full Article text
met Synthesis and crystal structures of boryl ortho-silylaryl trifluoromethanesulfonates By journals.iucr.org Published On :: 2024-01-12 We report the synthesis and structural characterization of three crystalline borylated ortho-silylaryl trifluoromethanesulfonates: 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2-(trimethylsilyl)phenyl trifluoromethanesulfonate, C16H24BF3O5SSi (1a), 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2-(trimethylsilyl)phenyl trifluoromethanesulfonate, C16H24BF3O5SSi (1b), and 2-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-6-(trimethylsilyl)phenyl trifluoromethanesulfonate, C17H26BF3O5SSi (2), which are versatile aryne precursors. For all three compounds, the heteroatom substituents are almost coplanar with the central aromatic moiety. C—heteroatom bonding metrics are unexceptional and fall withing the typical range of C—B, C—Si, and C—O single bonds. Despite numerous electronegative sites, only weak intermolecular interactions are observed in the solid state. Full Article text
met Synthesis and crystal structure of diisothiocyanatotetrakis(4-methylpyridine N-oxide)cobalt(II) and diisothiocyanatotris(4-methylpyridine N-oxide)cobalt(II) showing two different metal coor By journals.iucr.org Published On :: 2024-01-26 The reaction of Co(NCS)2 with 4-methylpyridine N-oxide (C6H7NO) leads to the formation of two compounds, namely, tetrakis(4-methylpyridine N-oxide-κO)bis(thiocyanato-κN)cobalt(II), [Co(NCS)2(C6H7NO)4] (1), and tris(4-methylpyridine N-oxide-κO)bis(thiocyanato-κN)cobalt(II), [Co(NCS)2(C6H7NO)3] (2). The asymmetric unit of 1 consists of one CoII cation located on a centre of inversion, as well as one thiocyanate anion and two 4-methylpyridine N-oxide coligands in general positions. The CoII cations are octahedrally coordinated by two terminal N-bonding thiocyanate anions in trans positions and four 4-methylpyridine N-oxide ligands. In the extended structure, these complexes are linked by C—H⋯O and C—H⋯S interactions. In compound 2, two crystallographically independent complexes are present, which occupy general positions. In each of these complexes, the CoII cations are coordinated in a trigonal–bipyramidal manner by two terminal N-bonding thiocyanate anions in axial positions and by three 4-methylpyridine N-oxide ligands in equatorial positions. In the crystal, these complex molecules are linked by C—H⋯S interactions. For compound 2, a nonmerohedral twin refinement was performed. Powder X-ray diffraction (PXRD) reveals that 2 was nearly obtained as a pure phase, which is not possible for compound 1. Differential thermoanalysis and thermogravimetry data (DTA–TG) show that compound 2 start to decompose at about 518 K. Full Article text
met (E)-N,N-Diethyl-4-{[(4-methoxyphenyl)imino]methyl}aniline: crystal structure, Hirshfeld surface analysis and energy framework By journals.iucr.org Published On :: 2024-01-26 In the title benzylideneaniline Schiff base, C18H22N2O, the aromatic rings are inclined to each other by 46.01 (6)°, while the Car—N= C—Car torsion angle is 176.9 (1)°. In the crystal, the only identifiable directional interaction is a weak C—H⋯π hydrogen bond, which generates inversion dimers that stack along the a-axis direction. Full Article text
met (S)-(+)-1-(4-Bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine and bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II) By journals.iucr.org Published On :: 2024-01-26 The (S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine ligand, C16H16BrNO, (I), was synthesized through the reaction of 4-methoxyanisaldehyde with (S)-(−)-1-(4-bromophenyl)ethylamine. It crystallizes in the orthorhombic space group P212121 belonging to the Sohncke group, featuring a single molecule in the asymmetric unit. The refinement converged successfully, achieving an R factor of 0.0508. The PdII complex bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II), [PdCl2(C16H16BrNO)2], (II), crystallizes in the monoclinic space group P21 belonging to the Sohncke group, with two molecules in the asymmetric unit. The central atom is tetracoordinated by two N atoms and two Cl atoms, resulting in a square-planar configuration. The imine moieties exhibit a trans configuration around the PdII centre, with average Cl—Pd—N angles of approximately 89.95 and 90°. The average distances within the palladium complex for the two molecules are ∼2.031 Å for Pd—N and ∼2.309 Å for Pd—Cl. Full Article text
met Crystal structures and Hirshfeld surface analyses of methyl 4-{2,2-dichloro-1-[(E)-phenyldiazenyl]ethenyl}benzoate, methyl 4-{2,2-dichloro-1-[(E)-(4-methylphenyl)diazenyl]ethenyl}benzoate and methyl 4- By journals.iucr.org Published On :: 2024-01-26 The crystal structures and Hirshfeld surface analyses of three similar azo compounds are reported. Methyl 4-{2,2-dichloro-1-[(E)-phenyldiazenyl]ethenyl}benzoate, C16H12Cl2N2O2, (I), and methyl 4-{2,2-dichloro-1-[(E)-(4-methylphenyl)diazenyl]ethenyl}benzoate, C17H14Cl2N2O2, (II), crystallize in the space group P21/c with Z = 4, and methyl 4-{2,2-dichloro-1-[(E)-(3,4-dimethylphenyl)diazenyl]ethenyl}benzoate, C18H16Cl2N2O2, (III), in the space group Poverline{1} with Z = 2. In the crystal of (I), molecules are linked by C—H⋯N hydrogen bonds, forming chains with C(6) motifs parallel to the b axis. Short intermolecular Cl⋯O contacts of 2.8421 (16) Å and weak van der Waals interactions between these chains stabilize the crystal structure. In (II), molecules are linked by C—H⋯O hydrogen bonds and C—Cl⋯π interactions, forming layers parallel to (010). Weak van der Waals interactions between these layers consolidate the molecular packing. In (III), molecules are linked by C—H⋯π and C—Cl⋯π interactions forming chains parallel to [011]. Furthermore, these chains are connected by C—Cl⋯π interactions parallel to the a axis, forming (0overline{1}1) layers. The stability of the molecular packing is ensured by van der Waals forces between these layers. Full Article text
met Crystal structure, Hirshfeld surface analysis, crystal voids, interaction energy calculations and energy frameworks and DFT calculations of ethyl 2-cyano-3-(3-hydroxy-5-methyl-1H-pyrazol-4-yl)-3-phenylpropanoate By journals.iucr.org Published On :: 2024-01-31 The title compound, C16H17N3O3, is racemic as it crystallizes in a centrosymmetric space group (Poverline{1}), although the trans disposition of substituents about the central C—C bond is established. The five- and six-membered rings are oriented at a dihedral angle of 75.88 (8)°. In the crystal, N—H⋯N hydrogen bonds form chains of molecules extending along the c-axis direction that are connected by inversion-related pairs of O—H⋯N into ribbons. The ribbons are linked by C—H⋯π(ring) interactions, forming layers parallel to the ab plane. A Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (45.9%), H⋯N/N⋯H (23.3%), H⋯C/C⋯H (16.2%) and H⋯O/O⋯H (12.3%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 100.94 Å3 and 13.20%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
met Crystal structure, Hirshfeld surface analysis, crystal voids, interaction energy calculations and energy frameworks, and DFT calculations of 1-(4-methylbenzyl)indoline-2,3-dione By journals.iucr.org Published On :: 2024-01-31 The indoline portion of the title molecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C—H⋯O hydrogen bonds and C—H⋯π(ring), π-stacking and C=O⋯π(ring) interactions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (43.0%), H⋯C/C⋯H (25.0%) and H⋯O/O⋯H (22.8%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined molecular structure in the solid state. Full Article text
met Synthesis, crystal structure and Hirshfeld surface analysis of 2-({5-[(naphthalen-1-yl)methyl]-4-phenyl-4H-1,2,4-triazol-3-yl}sulfanyl)-1-(4-nitrophenyl)ethanone By journals.iucr.org Published On :: 2024-01-26 The title compound, C27H20N4O3S, crystallizes in the monoclinic system, space group P21/n, with Z = 4. The global shape of the molecule is determined by the orientation of the substituents on the central 4H-1,2,4-triazole ring. The nitrophenyl ring, phenyl ring, and naphthalene ring system are oriented at dihedral angles of 82.95 (17), 77.14 (18) and 89.46 (15)°, respectively, with respect to the triazole ring. The crystal packing features chain formation in the b-axis direction by S⋯O interactions. A Hirshfeld surface analysis indicates that the highest contributions to surface contacts arise from contacts in which H atoms are involved. Full Article text
met Crystal structure and Hirshfeld surface analysis of 4-(2-chloroethyl)-5-methyl-1,2-dihydropyrazol-3-one By journals.iucr.org Published On :: 2024-01-31 In the crystal of the title compound, C6H9ClN2O, molecular pairs form dimers with an R22(8) motif through N—H⋯O hydrogen bonds. These dimers are connect into ribbons parallel to the (100) plane with R44(10) motifs by N—H⋯O hydrogen bonds along the c-axis direction. In addition, π–π [centroid-to-centroid distance = 3.4635 (9) Å] and C—Cl⋯π interactions between the ribbons form layers parallel to the (100) plane. The three-dimensional consolidation of the crystal structure is also ensured by Cl⋯H and Cl⋯Cl interactions between these layers. According to a Hirshfeld surface study, H⋯H (43.3%), Cl⋯H/H⋯Cl (22.1%) and O⋯H/H⋯O (18.7%) interactions are the most significant contributors to the crystal packing. Full Article text
met Crystal structure and Hirshfeld surface analysis of (Z)-N-{chloro[(4-ferrocenylphenyl)imino]methyl}-4-ferrocenylaniline N,N-dimethylformamide monosolvate By journals.iucr.org Published On :: 2024-02-02 The title molecule, [Fe2(C5H5)2(C23H17ClN2)]·C3H7NO, is twisted end to end and the central N/C/N unit is disordered. In the crystal, several C—H⋯π(ring) interactions lead to the formation of layers, which are connected by further C—H⋯π(ring) interactions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (60.2%) and H⋯C/C⋯H (27.0%) interactions. Hydrogen bonding, C—H⋯π(ring) interactions and van der Waals interactions dominate the crystal packing. Full Article text
met Structural characterization of a new samarium–sodium heterometallic coordination polymer By journals.iucr.org Published On :: 2024-02-06 Lanthanide-containing materials are of interest in the field of crystal engineering because of their unique properties and distinct structure types. In this context, a new samarium–sodium heterometallic coordination polymer, poly[tetrakis(μ2-2-formyl-6-methoxyphenolato)samarium(III)sodium(I)], {[SmNa(C8H7O3)4]·solvent}n (Sm-1), was synthesized and crystallized via slow evaporation from a mixture of ethanol and acetonitrile. The compound features alternating SmIII and NaI ions, which are linked by ortho-vanillin (o-vanillin) ligands to form a mono-periodic chain-like coordination polymer. The chains propagate along the [001] direction. Residual electron density of disordered solvent molecules in the void space could not be reasonably modeled, thus the SQUEEZE function was applied. The structural, vibrational, and optical properties are reported. Full Article text
met Crystal structures of sulfonamide protected bicyclic guanidines: (S)-8-{[(tert-butyldimethylsilyl)oxy]methyl}-1-[(2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-yl)sulfonyl]-1,3,4,6,7,8-hexa By journals.iucr.org Published On :: 2024-02-20 Two compounds, (S)-8-{[(tert-butyldimethylsilyl)oxy]methyl}-1-[(2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-yl)sulfonyl]-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium trifluoromethanesulfonate, C27H46N3O4SSi+·CF3O3S−, (1) and (S)-8-(iodomethyl)-1-tosyl-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium iodide, C15H21IN3O2S+·I−, (2), have been synthesized and characterized. They are bicyclic guanidinium salts and were synthesized from N-(tert-butoxycarbonyl)-l-methionine (Boc-l-Met-OH). The guanidine is protected by a 2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl (Pbf, 1) or a tosyl (2) group. In the crystals of both compounds, the guanidinium group is almost planar and the N–H forms an intramolecular hydrogen bond in a six-membered ring to the oxygen atom of the sulfonamide protecting group. Full Article text
met Syntheses, characterizations, crystal structures and Hirshfeld surface analyses of methyl 4-[4-(difluoromethoxy)phenyl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, isopropyl 4-[4-(difluoro& By journals.iucr.org Published On :: 2024-02-08 The crystal structures and Hirshfeld surface analyses of three similar compounds are reported. Methyl 4-[4-(difluoromethoxy)phenyl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, (C21H23F2NO4), (I), crystallizes in the monoclinic space group C2/c with Z = 8, while isopropyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, (C23H27F2NO4), (II) and tert-butyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, (C24H29F2NO4), (III) crystallize in the orthorhombic space group Pbca with Z = 8. In the crystal structure of (I), molecules are linked by N—H⋯O and C—H⋯O interactions, forming a tri-periodic network, while molecules of (II) and (III) are linked by N—H⋯O, C—H⋯F and C—H⋯π interactions, forming layers parallel to (002). The cohesion of the molecular packing is ensured by van der Waals forces between these layers. In (I), the atoms of the 4-difluoromethoxyphenyl group are disordered over two sets of sites in a 0.647 (3): 0.353 (3) ratio. In (III), the atoms of the dimethyl group attached to the cyclohexane ring, and the two carbon atoms of the cyclohexane ring are disordered over two sets of sites in a 0.646 (3):0.354 (3) ratio. Full Article text
met Crystal structure of 4-(benzo[d]thiazol-2-yl)-1,2-dimethyl-1H-pyrazol-3(2H)-one By journals.iucr.org Published On :: 2024-02-16 In the title compound, C12H11N3OS, the interplanar angle between the pyrazole and benzothiazole rings is 3.31 (7)°. In the three-dimensional molecular packing, the carbonyl oxygen acts as acceptor to four C—H donors (with one H⋯O as short as 2.25 Å), while one methyl hydrogen is part of the three-centre system H⋯(S, O). A double layer structure parallel to (overline{1}01) can be recognized as a subsection of the packing. Full Article text
met Crystal structure of tetrakis(μ-2-hydroxy-3,5-diisopropylbenzoato)bis[(dimethyl sulfoxide)copper(II)] By journals.iucr.org Published On :: 2024-02-27 Metal complexes of 3,5-diisopropylsalicylate are reported to have anti-inflammatory and anti-convulsant activities. The title binuclear copper complex, [Cu2(C13H17O3)4(C2H6OS)2] or [Cu(II)2(3,5-DIPS)4(DMSO)2], contains two five-coordinate copper atoms that are bridged by four 3,5-diisopropylsalicylate ligands and capped by two axial dimethyl sulfoxide (DMSO) moieties. Each copper atom is attached to four oxygen atoms in an almost square-planar fashion, with the addition of a DMSO ligand in an apical position leading to a square-pyramidal arrangement. The hydroxy group of the diisopropylsalicylate ligands participates in intramolecular O—H⋯O hydrogen-bonding interactions. Full Article text
met Crystal structure of 1-{4-[bis(4-methylphenyl)amino]phenyl}ethene-1,2,2-tricarbonitrile By journals.iucr.org Published On :: 2024-02-29 The title compound, C25H18N4, crystallizes in the centrosymmetric orthorhombic space group Pbca, with eight molecules in the unit cell. The main feature noticeable in the structure is the impact of the tricyanovinyl (TCV) group in forcing partial planarity of the portion of the molecule carrying the TCV group and directing the molecular packing in the solid state, resulting in the formation of π-stacks of dimers within the unit cell. Short π–π stack closest atom-to-atom distances of 3.444 (15) Å are observed. Such motif patterns are favorable as they are thought to be conducive for better charge transport in organic semiconductors, which results in enhanced device performance. Intramolecular charge transfer is evident from the shortening in the observed experimental bond lengths. The nitrogen atoms (of the cyano groups) are involved in extensive short contacts, primarily through C—H⋯NC interactions with distances of 2.637 (17) Å. Full Article text
met CoII-catalysed synthesis of N-(4-methoxyphenyl)-5-(pyridin-4-yl)-1,3,4-oxadiazol-2-amine hemihydrochloride monohydrate By journals.iucr.org Published On :: 2024-03-12 The title compound, C14H12N4O2·0.5HCl·H2O or H(C14H12N4O2)2+·Cl−·2H2O, arose from the unexpected cyclization of isonicotinoyl-N-phenyl hydrazine carbothioamide catalysed by cobalt(II) acetate. The organic molecule is almost planar and a symmetric N⋯H+⋯N hydrogen bond links two of them together, with the H atom lying on a crystallographic twofold axis. The extended structure features N—H⋯O and O—H⋯Cl hydrogen bonds, which generate [001] chains. Weak C—H⋯Cl interactions cross-link the chains. The chloride ion has site symmetry 2. The major contributions to the Hirshfeld surface are from H⋯H (47.1%), Cl⋯H/H⋯Cl (total 10.8%), O⋯H/H⋯O (7.4%) and N⋯H/H⋯N (6.7%) interactions. Full Article text
met Crystal structure of tetraphenyl phosphate tetrakis[dimethyl (2,2,2-trichloroacetyl)phosphoramidato]lutetium(III), PPh4[LuL4] By journals.iucr.org Published On :: 2024-03-12 A lutetium(III) complex based on the anion of the ligand dimethyl (2,2,2-trichloroacetyl)phosphoramidate (HL) and tetraphenylphosphonium, of composition PPh4[LuL4] (L = CAPh = carbacylamidophosphate), or (C24H20)[Lu(C4H6Cl3NO4P)4], has been synthesized and structurally characterized. The X-ray diffraction study of the compound revealed that the lutetium ion is surrounded by four bis-chelating CAPh ligands, forming the complex anion [LuL4]− with a coordination number of 8[O] for LuIII, while PPh4+ serves as a counter-ion. The coordination geometry around the Lu3+ ion was determined to be a nearly perfect triangular dodecahedron. The complex crystallizes in the monoclinic crystal system, space group P21/c, with four molecules in the unit cell. Weak hydrogen bonds O⋯HC(Ph), Cl⋯HC(Ph) and N⋯HC(Ph) are formed between the cations and anions. For a comparative study, HL-based structures were retrieved from the Cambridge Structural Database (CSD) and their geometries and conformations are discussed. A Hirshfeld surface analysis was also performed. Full Article text
met Crystal structure and Hirshfeld surface analysis of 8-benzyl-1-[(4-methylphenyl)sulfonyl]-2,7,8,9-tetrahydro-1H-3,6:10,13-diepoxy-1,8-benzodiazacyclopentadecine ethanol hemisolvate By journals.iucr.org Published On :: 2024-03-26 The asymmetric unit of the title compound, 2C31H28N2O4S·C2H6O, contains a parent molecule and a half molecule of ethanol solvent. The main compound stabilizes its molecular conformation by forming a ring with an R12(7) motif with the ethanol solvent molecule. In the crystal, molecules are connected by C—H⋯O and O—H⋯O hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions also strengthen the molecular packing. Full Article text