rf Crystal structure and Hirshfeld surface analysis of (Z)-4-({[2-(benzo[b]thiophen-3-yl)cyclopent-1-en-1-yl]methyl}(phenyl)amino)-4-oxobut-2-enoic acid By journals.iucr.org Published On :: 2024-04-26 In the title compound, C24H21NO3S, the cyclopentene ring adopts an envelope conformation. In the crystal, molecules are linked by C—H⋯π interactions, forming ribbons along the a axis. Intermolecular C—H⋯O hydrogen bonds connect these ribbons to each other, forming layers parallel to the (0overline{1}1) plane. The molecular packing is strengthened by van der Waals interactions between the layers. The intermolecular contacts were quantified using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be H⋯H 46.0%, C⋯H/H⋯C 21.1%, O⋯H/H⋯O 20.6% and S⋯H/H⋯S 9.0%. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(4-hydroxyphenyl)amino]-5,5-diphenyl-1H-imidazol-4(5H)-one By journals.iucr.org Published On :: 2024-04-26 In the title molecule, C21H17N3O2, the five-membered ring is slightly ruffled and dihedral angles between the pendant six-membered rings and the central, five-membered ring vary between 50.78 (4) and 86.78 (10)°. The exocyclic nitrogen lone pair is involved in conjugated π bonding to the five-membered ring. In the crystal, a layered structure is generated by O—H⋯N and N—H⋯O hydrogen bonds plus C—H⋯π(ring) and weak π-stacking interactions. Full Article text
rf Crystal structure characterization, Hirshfeld surface analysis, and DFT calculation studies of 1-(6-amino-5-nitronaphthalen-2-yl)ethanone By journals.iucr.org Published On :: 2024-05-03 The title compound, C12H10N2O3, was obtained by the deacetylation reaction of 1-(6-amino-5-nitronaphthalen-2-yl)ethanone in a concentrated sulfuric acid methanol solution. The molecule comprises a naphthalene ring system bearing an acetyl group (C-3), an amino group (C-7), and a nitro group (C-8). In the crystal, the molecules are assembled into a two-dimensional network by N⋯H/H⋯N and O⋯H/H⋯O hydrogen-bonding interactions. n–π and π–π stacking interactions are the dominant interactions in the three-dimensional crystal packing. Hirshfeld surface analysis indicates that the most important contributions are from O⋯H/H⋯O (34.9%), H⋯H (33.7%), and C⋯H/H⋯C (11.0%) contacts. The energies of the frontier molecular orbitals were computed using density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-TZVP level of theory and the LUMO–HOMO energy gap of the molecule is 3.765 eV. Full Article text
rf Crystal structure and Hirshfeld surface analysis of (Z)-4-oxo-4-{phenyl[(thiophen-2-yl)methyl]amino}but-2-enoic acid By journals.iucr.org Published On :: 2024-05-10 In the title compound, C15H13NO3S, the molecular conformation is stable with the intramolecular O—H⋯O hydrogen bond forming a S(7) ring motif. In the crystal, molecules are connected by C—H⋯O hydrogen bonds, forming C(8) chains running along the a-axis direction. Cohesion of the packing is provided by weak van der Waals interactions between the chains. A Hirshfeld surface analysis was undertaken to investigate and quantify the intermolecular interactions. The thiophene ring is disordered in a 0.9466 (17):0.0534 (17) ratio over two positions rotated by 180°. Full Article text
rf Crystal structure, Hirshfeld surface analysis, calculations of intermolecular interaction energies and energy frameworks and the DFT-optimized molecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)methyl]-3-(prop-1-en-2-yl)-1H-b By journals.iucr.org Published On :: 2024-05-14 The benzimidazole entity of the title molecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C—H⋯O hydrogen bonds link individual molecules into layers extending parallel to the ac plane. Two weak C—H⋯π(ring) interactions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) interactions. Hydrogen bonding and van der Waals interactions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The molecular structure optimized by density functional theory (DFT) at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined molecular structure in the solid state. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of (3Z)-4-[(4-amino-1,2,5-oxadiazol-3-yl)amino]-3-bromo-1,1,1-trifluorobut-3-en-2-one By journals.iucr.org Published On :: 2024-05-10 In the title compound, C6H4BrF3N4O2, the oxadiazole ring is essentially planar with a maximum deviation of 0.003 (2) Å. In the crystal, molecular pairs are connected by N—H⋯N hydrogen bonds, forming dimers with an R22(8) motif. The dimers are linked into layers parallel to the (10overline{4}) plane by N—H⋯O hydrogen bonds. In addition, C—O⋯π and C—Br⋯π interactions connect the molecules, forming a three-dimensional network. The F atoms of the trifluoromethyl group are disordered over two sites in a 0.515 (6): 0.485 (6) ratio. The intermolecular interactions in the crystal structure were investigated and quantified using Hirshfeld surface analysis. Full Article text
rf Crystal structure and Hirshfeld surface of a pentaaminecopper(II) complex with urea and chloride By journals.iucr.org Published On :: 2024-05-14 The reaction of copper(II) oxalate and hexamethylenetetramine in a deep eutectic solvent made of urea and choline chloride produced crystals of pentaaminecopper(II) dichloride–urea (1/1), [Cu(NH3)5]Cl2·CO(NH2)2, which was characterized by single-crystal X-ray diffraction. The complex contains discrete pentaaminecopper(II) units in a square-based pyramidal geometry. The overall structure of the multi-component crystal is dictated by hydrogen bonding between urea molecules and amine H atoms with chloride anions. Full Article text
rf Crystal structure and Hirshfeld surface analysis of 3,3'-[ethane-1,2-diylbis(oxy)]bis(5,5-dimethylcyclohex-2-en-1-one) including an unknown solvate By journals.iucr.org Published On :: 2024-05-17 The title molecule, C18H26O4, consists of two symmetrical halves related by the inversion centre at the mid-point of the central –C—C– bond. The hexene ring adopts an envelope conformation. In the crystal, the molecules are connected into dimers by C—H⋯O hydrogen bonds with R22(8) ring motifs, forming zigzag ribbons along the b-axis direction. According to a Hirshfeld surface analysis, H⋯H (68.2%) and O⋯H/H⋯O (25.9%) interactions are the most significant contributors to the crystal packing. The contribution of some disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. The solvent contribution was not included in the reported molecular weight and density. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of 1-[3-(2-oxo-3-phenyl-1,2-dihydroquinoxalin-1-yl)propyl]-3-phenyl-1,2-dihydroquinoxalin-2-one By journals.iucr.org Published On :: 2024-05-17 In the title compound, C31H24N4O2, the dihydroquinoxaline units are both essentially planar with the dihedral angle between their mean planes being 64.82 (4)°. The attached phenyl rings differ significantly in their rotational orientations with respect to the dihydroquinoxaline planes. In the crystal, one set of C—H⋯O hydrogen bonds form chains along the b-axis direction, which are connected in pairs by a second set of C—H⋯O hydrogen bonds. Two sets of π-stacking interactions and C—H⋯π(ring) interactions join the double chains into the final three-dimensional structure. Full Article text
rf Crystal structure and Hirshfeld surface analysis of dimethyl 2-oxo-4-(pyridin-2-yl)-6-(thiophen-2-yl)cyclohex-3-ene-1,3-dicarboxylate By journals.iucr.org Published On :: 2024-05-24 In the title compound, C19H17NO5S, the cyclohexene ring adopts nearly an envelope conformation. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions connect the molecules by forming layers parallel to the (010) plane. According to the Hirshfeld surface analysis, H⋯H (36.9%), O⋯H/H⋯O (31.0%), C⋯H/H⋯C (18.9%) and S⋯H/H⋯S (7.9%) interactions are the most significant contributors to the crystal packing. Full Article text
rf The crystal structures and Hirshfeld surface analysis of three new bromo-substituted 3-methyl-1-(phenylsulfonyl)-1H-indole derivatives By journals.iucr.org Published On :: 2024-05-31 Three new 1H-indole derivatives, namely, 2-(bromomethyl)-3-methyl-1-(phenylsulfonyl)-1H-indole, C16H14BrNO2S, (I), 2-[(E)-2-(2-bromo-5-methoxyphenyl)ethenyl]-3-methyl-1-(phenylsulfonyl)-1H-indole, C24H20BrNO3S, (II), and 2-[(E)-2-(2-bromophenyl)ethenyl]-3-methyl-1-(phenylsulfonyl)-1H-indole, C23H18BrNO2S, (III), exhibit nearly orthogonal orientations of their indole ring systems and sulfonyl-bound phenyl rings. Such conformations are favourable for intermolecular bonding involving sets of slipped π–π interactions between the indole systems and mutual C—H⋯π hydrogen bonds, with the generation of two-dimensional monoperiodic patterns. The latter are found in all three structures, in the form of supramolecular columns with every pair of successive molecules related by inversion. The crystal packing of the compounds is additionally stabilized by weaker slipped π–π interactions between the outer phenyl rings (in II and III) and by weak C—H⋯O, C—H⋯Br and C—H⋯π hydrogen bonds. The structural significance of the different kinds of interactions agree with the results of a Hirshfeld surface analysis and the calculated interaction energies. In particular, the largest interaction energies (up to −60.8 kJ mol−1) are associated with pairing of antiparallel indole systems, while the energetics of weak hydrogen bonds and phenyl π–π interactions are comparable and account for 13–34 kJ mol−1. Full Article text
rf Crystal structure and Hirshfeld surface analysis of 6,6'-dimethyl-2,2'-bipyridine-1,1'-diium tetrachloridocobaltate(II) By journals.iucr.org Published On :: 2024-06-11 In the title molecular salt, (C12H14N2)[CoCl4], the dihedral angle between the pyridine rings of the cation is 52.46 (9)° and the N—C—C—N torsion angle is −128.78 (14)°, indicating that the ring nitrogen atoms are in anti-clinal conformation. The Cl—Co—Cl bond angles in the anion span the range 105.46 (3)–117.91 (2)°. In the extended structure, the cations and anions are linked by cation-to-anion N—H⋯Cl and C—H⋯Cl interactions, facilitating the formation of R44(18) and R44(20) ring motifs. Furthermore, the crystal structure features weak anion-to-cation Cl⋯π interactions [Cl⋯π = 3.4891 (12) and 3.5465 (12) Å]. Hirshfeld two-dimensional fingerprint plots revealed that the most significant interactions are Cl⋯H/H⋯Cl (45.5%), H⋯H (29.0%), Cl⋯C/C⋯Cl (7.8%), Cl⋯N/N⋯Cl (3.5%), Cl⋯Cl (1.4) and Co⋯H (1%) contacts. Full Article text
rf A 1:1 flavone cocrystal with cyclic trimeric perfluoro-o-phenylenemercury By journals.iucr.org Published On :: 2024-06-14 The title compound, systematic name tris(μ2-perfluoro-o-phenylene)(μ2-3-phenyl-4H-chromen-4-one)-triangulo-trimercury, [Hg3(C6F4)3(C15H10O2)], crystallizes in the monoclinic P21/n space group with one flavone (FLA) and one cyclic trimeric perfluoro-o-phenylenemercury (TPPM) molecule per asymmetric unit. The FLA molecule is located on one face of the TPPM acceptor and is linked in an asymmetric coordination of its carbonyl oxygen atom with two Hg centers of the TPPM macrocycle. The angular-shaped complexes pack in zigzag chains where they stack via two alternating TPPM–TPPM and FLA–FLA stacking patterns. The distance between the mean planes of the neighboring TPPM macrocycles in the stack is 3.445 (2) Å, and that between the benzo-γ-pyrone moieties of FLA is 3.328 (2) Å. The neighboring stacks are interdigitated through the shortened F⋯F, CH⋯F and CH⋯π contacts, forming a dense crystal structure. Full Article text
rf Crystal structure and Hirshfeld surface analysis of 2-bromoethylammonium bromide – a possible side product upon synthesis of hybrid perovskites By journals.iucr.org Published On :: 2024-06-18 This study presents the synthesis, characterization and Hirshfeld surface analysis of a small organic ammonium salt, C2H7BrN+·Br−. Small cations like the one in the title compound are considered promising components of hybrid perovskites, crucial for optoelectronic and photovoltaic applications. While the incorporation of this organic cation into various hybrid perovskite structures has been explored, its halide salt counterpart remains largely uninvestigated. The obtained structural results are valuable for the synthesis and phase analysis of hybrid perovskites. The title compound crystallizes in the solvent-free form in the centrosymmetric monoclinic space group P21/c, featuring one organic cation and one bromide anion in its asymmetric unit, with a torsion angle of −64.8 (2)° between the ammonium group and the bromine substituent, positioned in a gauche conformation. The crystal packing is predominantly governed by Br⋯H interactions, which constitute 62.6% of the overall close atom contacts. Full Article text
rf Crystal structure and Hirshfeld surface analysis of dimethyl(phenyl)phosphine sulfide By journals.iucr.org Published On :: 2024-06-18 The title compound, C8H11PS, which melts below room temperature, was crystallized at low temperature. The P—S bond length is 1.9623 (5) Å and the major contributors to the Hirshfeld surface are H⋯H (58.1%), S⋯H/H⋯S (13.4%) and C⋯H/H⋯C contacts (11.7%). Full Article text
rf Crystal structure and Hirshfeld surface analysis of a halogen bond between 2-(allylthio)pyridine and 1,2,4,5-tetrafluoro-3,6-diiodobenzene By journals.iucr.org Published On :: 2024-06-21 The crystal structure of the title 2:1 molecular complex between 2-(allylthio)pyridine and 1,2,4,5-tetrafluoro-3,6-diiodobenzene, C6F4I2·2C8H9NS, at 100 K has been determined in the monoclinic space group P21/c. The most noteworthy characteristic of the complex is the halogen bond between iodine and the pyridine ring with a short N⋯I contact [2.8628 (12) Å]. The Hirshfeld surface analysis shows that the hydrogen⋯hydrogen contacts dominate the crystal packing with a contribution of 32.1%. Full Article text
rf Crystal structure and Hirshfeld surface analysis of 1-[6-bromo-2-(4-fluorophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]pyrrolidin-2-one By journals.iucr.org Published On :: 2024-06-25 In the title compound, C19H18BrFN2O, the pyrrolidine ring adopts an envelope conformation. In the crystal, molecules are linked by intermolecular N—H⋯O, C—H⋯O, C—H⋯F and C—H⋯Br hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions connect molecules into ribbons along the b-axis direction, consolidating the molecular packing. The intermolecular interactions in the crystal structure were quantified and analysed using Hirshfeld surface analysis. Full Article text
rf Synthesis, structure and Hirshfeld surface analysis of 2-oxo-2H-chromen-4-yl pentanoate By journals.iucr.org Published On :: 2024-06-21 In the title compound, C14H14O4, the dihedral angle between the coumarin ring system (r.m.s deviation = 0.016 Å) and the pentanoate ring is 36.26 (8)°. A short intramolecular C—H⋯O contact of 2.40 Å is observed. Hirshfeld surface analysis reveals that 46.1% of the intermolecular interactions are from H⋯H contacts, 28.6% are from H⋯O/O⋯H contacts and 14.7% are from H⋯C/C⋯H. Full Article text
rf Crystal structure determination and analyses of Hirshfeld surface, crystal voids, intermolecular interaction energies and energy frameworks of 1-benzyl-4-(methylsulfanyl)-3a,7a-dihydro-1H-pyrazolo[3,4-d]pyrimidine By journals.iucr.org Published On :: 2024-06-25 The pyrazolopyrimidine moiety in the title molecule, C13H12N4S, is planar with the methylsulfanyl substituent lying essentially in the same plane. The benzyl group is rotated well out of this plane by 73.64 (6)°, giving the molecule an approximate L shape. In the crystal, C—H⋯π(ring) interactions and C—H⋯S hydrogen bonds form tubes extending along the a axis. Furthermore, there are π–π interactions between parallel phenyl rings with centroid-to-centroid distances of 3.8418 (12) Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (47.0%), H⋯N/N⋯H (17.6%) and H⋯C/C⋯H (17.0%) interactions. The volume of the crystal voids and the percentage of free space were calculated to be 76.45 Å3 and 6.39%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the cohesion of the crystal structure is dominated by the dispersion energy contributions. Full Article text
rf Synthesis, structural studies and Hirshfeld surface analysis of 2-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]pyridin-1-ium hexakis(nitrato-κ2O,O')thorate(IV) By journals.iucr.org Published On :: 2024-07-05 Reaction of thorium(IV) nitrate with 2-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]pyridine (L) yielded (LH)2[Th(NO3)6] or (C14H13N4)2[Th(NO3)6] (1), instead of the expected mixed-ligand complex [Th(NO3)4L2], which was detected in the mass spectrum of 1. In the structure, the [Th(NO3)6]2− anions display an icosahedral coordination geometry and are connected by LH+ cations through C—H⋯O hydrogen bonds. The LH+ cations interact via N—H⋯N hydrogen bonds. Hirshfeld surface analysis indicates that the most important interactions are O⋯H/H⋯O hydrogen-bonding interactions, which represent a 55.2% contribution. Full Article text
rf Crystal structure determination and Hirshfeld surface analysis of N-acetyl-N-3-methoxyphenyl and N-(2,5-dimethoxyphenyl)-N-phenylsulfonyl derivatives of N-[1-(phenylsulfonyl)-1H-indol-2-yl]methanamine By journals.iucr.org Published On :: 2024-07-09 Two new [1-(phenylsulfonyl)-1H-indol-2-yl]methanamine derivatives, namely, N-(3-methoxyphenyl)-N-{[1-(phenylsulfonyl)-1H-indol-2-yl]methyl}acetamide, C24H22N2O4S, (I), and N-(2,5-dimethoxyphenyl)-N-{[1-(phenylsulfonyl)-1H-indol-2-yl]methyl}benzenesulfonamide, C29H26N2O6S2, (II), reveal a nearly orthogonal orientation of their indole ring systems and sulfonyl-bound phenyl rings. The sulfonyl moieties adopt the anti-periplanar conformation. For both compounds, the crystal packing is dominated by C—H⋯O bonding [C⋯O = 3.312 (4)–3.788 (8) Å], with the structure of II exhibiting a larger number, but weaker bonds of this type. Slipped π–π interactions of antiparallel indole systems are specific for I, whereas the structure of II delivers two kinds of C—H⋯π interactions at both axial sides of the indole moiety. These findings agree with the results of Hirshfeld surface analysis. The primary contributions to the surface areas are associated with the contacts involving H atoms. Although II manifests a larger fraction of the O⋯H/H⋯O contacts (25.8 versus 22.4%), most of them are relatively distal and agree with the corresponding van der Waals separations. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface of ethyl 2-[2-(methylsulfanyl)-5-oxo-4,4-diphenyl-4,5-dihydro-1H-imidazol-1-yl]acetate (thiophenytoin derivative) By journals.iucr.org Published On :: 2024-08-09 The dihydroimidazole ring in the title molecule, C20H20N2O3S, is slightly distorted and the lone pair on the tri-coordinate nitrogen atom is involved in intra-ring π bonding. The methylsulfanyl substituent lies nearly in the plane of the five-membered ring while the ester substituent is rotated well out of that plane. In the crystal, C—H⋯O hydrogen bonds form inversion dimers, which are connected along the a- and c-axis directions by additional C—H⋯O hydrogen bonds, forming layers parallel to the ac plane. The major contributors to the Hirshfeld surface are C⋯H/H⋯C, O⋯H/H⋯O and S⋯H/H⋯S contacts at 20.5%, 14.7% and 4.9%, respectively. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of [1-(4-bromophenyl)-1H-1,2,3-triazol-4-yl]methyl 2-(4-nitrophenoxy)acetate By journals.iucr.org Published On :: 2024-07-31 The title compound, C17H13BrN4O5, was synthesized by a Cu2Br2-catalysed Meldal–Sharpless reaction between 4-nitrophenoxyacetic acid propargyl ether and para-bromophenylazide, and characterized by X-ray structure determination and 1H NMR spectroscopy. The molecules, with a near-perpendicular orientation of the bromophenyl-triazole and nitrophenoxyacetate fragments, are connected into a three-dimensional network by intermolecular C—H⋯O and C—H⋯N hydrogen bonds (confirmed by Hirshfeld surface analysis), π–π and Br–π interactions. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of 1-[(1-octyl-1H-1,2,3-triazol-4-yl)methyl]-3-phenyl-1,2-dihydroquinoxalin-2(1H)-one By journals.iucr.org Published On :: 2024-08-09 In the title molecule, C25H29N5O, the dihydroquinoxaline unit is not quite planar (r.m.s. deviation = 0.030 Å) as there is a dihedral angle of 2.69 (3)° between the mean planes of the constituent rings and the molecule adopts a hairpin conformation. In the crystal, the polar portions of the molecules are associated through C—H⋯O and C—H⋯N hydrogen bonds and C—H⋯π(ring) and C=O⋯π(ring) interactions, forming thick layers parallel to the bc plane and with the n-octyl groups on the outside surfaces. Full Article text
rf Crystal structure and Hirshfeld surface analysis of dichlorido[2-(3-cyclopentyl-1,2,4-triazol-5-yl-κN4)pyridine-κN]palladium(II) dimethylformamide monosolvate By journals.iucr.org Published On :: 2024-08-16 This study presents the synthesis, characterization and Hirshfeld surface analysis of the title mononuclear complex, [PdCl2(C12H14N4)]·C3H7NO. The compound crystalizes in the P21/c space group of the monoclinic system. The asymmetric unit contains one neutral complex Pd(HLc-Pe)Cl2 [HLc-Pe is 2-(3-cyclopentyl-1,2,4-triazol-5-yl)pyridine] and one molecule of DMF as a solvate. The Pd atom has a square-planar coordination. In the crystal, molecules are linked by intermolecular N—H⋯O and C—H⋯N hydrogen bonds, forming layers parallel to the bc plane. A Hirshfeld surface analysis showed that the H⋯H contacts dominate the crystal packing with a contribution of 41.4%. The contribution of the N⋯H/H⋯N and H⋯O/O⋯H interactions is somewhat smaller, amounting to 12.4% and 5%, respectively. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of [Cu(H2L)2(μ-Cl)CuCl3]·H2O [H2L = 2-hydroxy-N'-(propan-2-ylidene)benzohydrazide] By journals.iucr.org Published On :: 2024-08-20 The present study focuses on the synthesis and structural characterization of a novel dinuclear CuII complex, [trichloridocopper(II)]-μ-chlorido-{bis[2-hydroxy-N'-(propan-2-ylidene)benzohydrazide]copper(II)} monohydrate, [Cu2Cl4(C10H12N2O2)2]·H2O or [Cu(H2L)2(μ-Cl)CuCl3]·H2O [H2L = 2-hydroxy-N'-(propan-2-ylidene)benzohydrazide]. The complex crystallizes in the monoclinic space group P21/n with one molecule of water, which forms interactions with the ligands. The first copper ion is penta-coordinated to two benzohydrazine-derived ligands via two nitrogen and two oxygen atoms, and one bridging chloride, which is also coordinated by the second copper ion alongside three terminal chlorines in a distorted tetrahedral geometry. The arrangement around the first copper ion exhibits a distorted geometry intermediate between trigonal bipyramidal and square pyramidal. In the crystal, chains are formed via intermolecular interactions along the a-axis direction, with subsequent layers constructed through hydrogen-bonding interactions parallel to the ac plane, and through slipped π–π stacking interactions parallel to the ab plane, resulting in a three-dimensional network. The intermolecular interactions in the crystal structure were quantified and analysed using Hirshfeld surface analysis. Residual electron density from disordered methanol molecules in the void space could not be reasonably modelled, thus a solvent mask was applied. Full Article text
rf Crystal structure and Hirshfeld surface analysis of 1-[6-bromo-2-(3-bromophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]pyrrolidin-2-one By journals.iucr.org Published On :: 2024-08-30 This study presents the synthesis, characterization and Hirshfeld surface analysis of 1-[6-bromo-2-(3-bromophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]pyrrolidin-2-one, C19H18Br2N2O. In the title compound, the pyrrolidine ring adopts a distorted envelope configuration. In the crystal, molecules are linked by intermolecular N—H⋯O, C—H⋯O and C—H⋯Br hydrogen bonds, forming a three-dimensional network. In addition, pairs of molecules along the c axis are connected by C—H⋯π interactions. According to a Hirshfeld surface study, H⋯H (36.9%), Br⋯H/H⋯Br (28.2%) and C⋯H/H⋯C (24.3%) interactions are the most significant contributors to the crystal packing. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of a new copper(II) complex based on diethyl 2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetate By journals.iucr.org Published On :: 2024-08-30 The title compound, bis[μ-2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetato]bis[diaquacopper(II)] dihydrate, [Cu2(C6H5N3O4)2(H2O)4]·2H2O, is a dinuclear octahedral CuII triazole-based complex. The central copper atoms are hexa-coordinated by two nitrogen atoms in the equatorial positions, two equatorial oxygen atoms of two carboxylate substituents in position 3 and 5 of the 1,2,4-triazole ring, and two axial oxygen atoms of two water molecules. Two additional solvent water molecules are linked to the title molecule by O—H⋯N and O⋯H—O hydrogen bonds. The crystal structure is built up from the parallel packing of discrete supramolecular chains running along the a-axis direction. Hirshfeld surface analysis suggests that the most important contributions to the surface contacts are from H⋯O/O⋯H (53.5%), H⋯H (28.1%), O⋯O (6.3%) and H⋯C/C⋯H (6.2%) interactions. The crystal studied was twinned by a twofold rotation around [100]. Full Article text
rf Crystal structure, Hirshfeld surface analysis, DFT and the molecular docking studies of 3-(2-chloroacetyl)-2,4,6,8-tetraphenyl-3,7-diazabicyclo[3.3.1]nonan-9-one By journals.iucr.org Published On :: 2024-08-30 In the title compound, C33H29ClN2O2, the two piperidine rings of the diazabicyclo moiety adopt distorted-chair conformations. Intermolecular C—H⋯π interactions are mainly responsible for the crystal packing. The intermolecular interactions were quantified and analysed using Hirshfeld surface analysis, revealing that H⋯H interactions contribute most to the crystal packing (52.3%). The molecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–31 G(d,p) level and is compared with the experimentally determined molecular structure in the solid state. Full Article text
rf Crystal structure, Hirshfeld surface analysis, DFT optimized molecular structure and the molecular docking studies of 1-[2-(cyanosulfanyl)acetyl]-3-methyl-2,6-bis(4-methylphenyl)piperidin-4-one By journals.iucr.org Published On :: 2024-09-12 The two molecules in the asymmetric unit of the title compound, C23H24N2O2S, have a structural overlap with an r.m.s. deviation of 0.82 Å. The piperidine rings adopt a distorted boat conformation. Intra- and intermolecular C—H⋯O hydrogen bonds are responsible for the cohesion of the crystal packing. The intermolecular interactions were quantified and analysed using Hirshfeld surface analysis. The molecular structure optimized by density functional theory (DFT) at the B3LYP/6–311++G(d,p)level is compared with the experimentally determined molecular structure in the solid state. Full Article text
rf Synthesis, crystal structure, and Hirshfeld surface analysis of 1,3-dihydro-2H-benzimidazol-2-iminium 3-carboxy-4-hydroxybenzenesulfonate By journals.iucr.org Published On :: 2024-09-06 The asymmetric unit of the title salt, C7H8N3+·C7H5O6S−, comprises two 1,3-dihydro-2H-benzimidazol-2-iminium cations and two 2-hydroxy-5-sulfobenzoate anions (Z' = 2). In the crystal, the molecules interact through N—H⋯O, O—H⋯O hydrogen bonds and C—O⋯π contacts. The hydrogen-bonding interactions lead to the formation of layers parallel to (overline{1}01). Hirshfeld surface analysis revealed that H⋯H contacts contribute to most of the crystal packing with 38.9%, followed by H⋯O contacts with 36.2%. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of 4'-cyano-[1,1'-biphenyl]-4-yl 3-(benzyloxy)benzoate By journals.iucr.org Published On :: 2024-09-12 In the title compound, C27H19O3N, the dihedral angle between the aromatic rings of the biphenyl unit is 38.14 (2)° and the C—O—C—C torsion angle in the benzyloxy benzene fragment is 179.1 (2)°. In the crystal, the molecules are linked by weak C—H⋯O interactions forming S(9) chains propagating along [010]. The most important contributions to the Hirshfeld surface arise from H⋯H (32.4%) and C⋯H/H⋯C (37.0%) contacts. Full Article text
rf Crystal structure, Hirshfeld surface analysis, and calculations of intermolecular interaction energies and energy frameworks of 1-[(1-hexyl-1H-1,2,3-triazol-4-yl)methyl]-3-(1-methylethenyl)-benzimidazol-2-one By journals.iucr.org Published On :: 2024-09-30 The benzimidazole moiety in the title molecule, C19H25N5O, is almost planar and oriented nearly perpendicular to the triazole ring. In the crystal, C—H⋯O hydrogen bonds link the molecules into a network structure. There are no π–π interactions present but two weak C—H⋯π(ring) interactions are observed. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (62.0%), H⋯C/C⋯H (16.1%), H⋯N/N⋯H (13.7%) and H⋯O/O⋯H (7.5%) interactions. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the dispersion energy contributions in the title compound. Full Article text
rf Crystal structure and Hirshfeld surface analysis of (E)-N-(2-styrylphenyl)benzenesulfonamide By journals.iucr.org Published On :: 2024-09-20 The crystal structure of the title compound C20H17NO2S features hydrogen-bonding and C—H⋯π interactions. Hirshfeld surface analysis revealed that H⋯H, C⋯H/H⋯C and O⋯H/H⋯O interactions make a major contribution to the crystal packing. Docking studies were carried out to determine the binding affinity and interaction profile of the title compound with EGFR kinase, a member of the ErbB family of receptor tyrosine kinases, which is crucial for processes such as cell proliferation and differentiation. The title compound shows a strong binding affinity with EGFR kinase, with the most favourable conformation having a binding energy of −8.27 kcal mol−1 and a predicted IC50 of 870.34 nM, indicating its potential as a promising candidate for targeted lung cancer therapy. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of (2-amino-1-methylbenzimidazole-κN3)aquabis(4-oxopent-2-en-2-olato-κ2O,O')nickel(II) ethanol monosolvate By journals.iucr.org Published On :: 2024-10-22 The molecule of the title compound, [Ni(C5H7O2)2(C8H9N3)(H2O)]·C2H5OH, has triclinic (Poverline{1}) symmetry. This compound is of interest for its antimicrobial properties. The asymmetric unit comprises two independent complex molecules, which are linked by N—H⋯O and O—H⋯O hydrogen bonds along [111]. Hirshfeld surface analysis indicates that 71.7% of intermolecular interactions come from H⋯H contacts, 17.7% from C⋯H/H⋯C contacts and 7.6% from O⋯H/H⋯O contacts, with the remaining contribution coming from N⋯H/H⋯N, C⋯N/N⋯C, C⋯C and O⋯O contacts. Full Article text
rf Synthesis, non-spherical structure refinement and Hirshfeld surface analysis of racemic 2,2'-diisobutoxy-1,1'-binaphthalene By journals.iucr.org Published On :: 2024-09-24 In the racemic title compound, C28H30O2, the naphthyl ring systems subtend a dihedral angle of 68.59 (1)° and the molecular conformation is consolidated by a pair of intramolecular C—H⋯π contacts. The crystal packing features a weak C—H⋯π contact and van der Waals forces. A Hirshfeld surface analysis of the crystal structure reveals that the most significant contributions are from H⋯H (73.2%) and C⋯H/H⋯C (21.2%) contacts. Full Article text
rf Crystal structure and Hirshfeld surface analysis of trichlorido(1,10-phenanthroline-κ2N,N')phenyltin(IV) By journals.iucr.org Published On :: 2024-09-24 The title compound, [Sn(C6H5)Cl3(C12H8N2)], which was obtained by the reaction between 1,10-phenanthroline and phenyltin trichloride in methanol, exhibits intramolecular hydrogen-bonding interactions involving the chlorine and hydrogen atoms. Crystal cohesion is ensured by intermolecular C—H⋯Cl hydrogen bonds, as well as Y—X⋯π and π-stacking interactions involving three different aromatic rings with centroid–centroid distances of 3.6605 (13), 3.9327 (14) and 3.6938 (12) Å]. Hirshfeld surface analysis and the associated two-dimensional fingerprint plots reveal significant contributions from H⋯H (30.7%), Cl⋯H/H⋯Cl (32.4%), and C⋯H/H⋯C (24.0%) contacts to the crystal packing while the C⋯C (6.2%), C⋯Cl/Cl⋯C (4.1%), and N⋯H/H⋯N (1.7%) interactions make smaller contributions. Full Article text
rf Crystal structure and Hirshfeld surface analysis of {2-[bis(pyridin-2-ylmethyl)amino]ethane-1-thiolato}chloridocadmium(II) By journals.iucr.org Published On :: 2024-09-30 The title compound, [Cd(C14H16N3S)Cl] or [CdLCl] (1), where LH = 2-[bis(pyridin-2-ylmethyl)amino]ethane-1-thiol, was prepared and structurally characterized. The Cd2+ complex crystallizes in P21/c with a distorted trigonal–bipyramidal metal coordination geometry. Supramolecular interactions in 1 include parallel offset face-to-face interactions between inversion-related pyridyl rings and potential hydrogen bonds with chlorine or sulfur as the acceptor. Additional cooperative pyridyl–pyridyl interactions with roughly 45° tilt angles and centroid–centroid distances of less than 5.5 Å likely also contribute to the overall solid-state stability. Hirshfeld surface analysis indicates that H⋯H (51.2%), Cl⋯H/H⋯Cl (13.9%), C⋯H/H⋯C (12.3%) and S⋯H/H⋯S (11.8%) interactions are dominant in the solid state. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of sulfamethoxazolium methylsulfate monohydrate By journals.iucr.org Published On :: 2024-09-24 The molecular salt sulfamethoxazolium {or 4-[(5-methyl-1,2-oxazol-3-yl)sulfamoyl]anilinium methyl sulfate monohydrate}, C10H12N3O3S+·CH3O4S−·H2O, was prepared by the reaction of sulfamethoxazole and H2SO4 in methanol and crystallized from methanol–ether–water. Protonation takes place at the nitrogen atom of the primary amino group. In the crystal, N—H⋯O hydrogen bonds (water and methylsulfate anion) and intermolecular N—H⋯N interactions involving the sulfonamide and isoxazole nitrogen atoms, link the components into a tri-dimensional network, additional cohesion being provided by face-to-face π–π interactions between the phenyl rings of adjacent molecules. A Hirshfeld surface analysis was used to verify the contributions of the different intermolecular interactions, showing that the three most important contributions for the crystal packing are from H⋯O (54.1%), H⋯H (29.2%) and H⋯N (5.0%) interactions. Full Article text
rf Crystal structure and Hirshfeld surface analyses, crystal voids, intermolecular interaction energies and energy frameworks of 3-benzyl-1-(3-bromopropyl)-5,5-diphenylimidazolidine-2,4-dione By journals.iucr.org Published On :: 2024-10-04 The title molecule, C25H23BrN2O2, adopts a cup shaped conformation with the distinctly ruffled imidazolidine ring as the base. In the crystal, weak C—H⋯O hydrogen bonds and C—H⋯π(ring) interactions form helical chains of molecules extending along the b-axis direction that are linked by additional weak C—H⋯π(ring) interactions across inversion centres. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (51.0%), C⋯H/H⋯C (21.3%), Br⋯H/H⋯Br (12.8%) and O⋯H/H⋯O (12.4%) interactions. The volume of the crystal voids and the percentage of free space were calculated to be 251.24 Å3 and 11.71%, 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. Full Article text
rf Crystal structure and Hirshfeld surface analysis of (nitrato-κ2O,O')(1,4,7,10-tetraazacyclododecane-κ4N)nickel(II) nitrate By journals.iucr.org Published On :: 2024-10-11 The crystal structure of the title compound, [Ni(C8H20N4)(NO3)]NO3, at room temperature, has monoclinic (P21/n) symmetry. The structure displays intermolecular hydrogen bonding. The nickel displays a distorted bipyramidal geometry with the symmetric bidentate bonded nitrate occupying an equatorial site. The 1,4,7,10-tetraazacyclododecane (cyclen) backbone has the [4,8] configuration, with three nitrogen-bound H atoms directed above the plane of the nitrogen atoms towards the offset nickel atom with the fourth nitrogen-bound hydrogen directed below from the plane of the nitrogen atoms. The nitrate anion O atoms are seen to hydrogen bond to the H atoms bound to the N atoms of the ligand. Full Article text
rf Synthesis, structures and Hirshfeld surface analyses of 2-hydroxy-N'-methylacetohydrazide and 2-hydroxy-N-methylacetohydrazide By journals.iucr.org Published On :: 2024-10-15 The structures of the title compounds 2-hydroxy-N'-methylacetohydrazide, 1, and 2-hydroxy-N-methylacetohydrazide, 2, both C3H8N2O2, as regioisomers differ in the position of the methyl group relative to the N atoms in 2-hydroxy-acetohydrazide. In the structure of 1, the 2-hydroxy-acetohydrazide core [OH—C—C(=O)—NH—NH] is almost planar and the methyl group is rotated relative to this plane. As opposed to 1, in the structure of 2 all non-hydrogen atoms lie in the same plane. The hydroxyl and carbonyl groups in structures 1 and 2 are in trans and cis positions, respectively. The methyl amino group and carbonyl group are in the cis position relative to the C—N bond in structure 1, while the amino group and carbonyl group are in the trans position relative to the C—N bond in stucture 2. In the crystal, molecules of 1 are linked by N—H⋯O and O—H⋯N intermolecular hydrogen bonds, forming layers parallel to the ab crystallographic plane. A Hirshfeld surface analysis showed that the H⋯H contacts dominate the crystal packing with a contribution of 55.3%. The contribution of the H⋯O/O⋯H interaction is somewhat smaller, amounting to 30.8%. In the crystal, as a result of the intermolecular O—H⋯O hydrogen bonds, molecules of 2 form dimers, which are linked by N—H⋯O hydrogen bonds and a three-dimensional supramolecular network The major contributors to the Hirshfeld surface are H⋯H (58.5%) and H⋯O/O⋯H contacts (31.7%). Full Article text
rf The crystal structures determination and Hirshfeld surface analysis of N-(4-bromo-3-methoxyphenyl)- and N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}- derivatives of N-{[3-bromo-1-(phenylsulfonyl)-1H-indol- By journals.iucr.org Published On :: 2024-10-04 Two new phenylsulfonylindole derivatives, namely, N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}-N-(4-bromo-3-methoxyphenyl)benzenesulfonamide, C28H22Br2N2O5S2, (I), and N,N-bis{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}benzenesulfonamide, C36H27Br2N3O6S3, (II), reveal the impact of intramolecular π–π interactions of the indole moieties as a factor not only governing the conformation of N,N-bis(1H-indol-2-yl)methyl)amines, but also significantly influencing the crystal patterns. For I, the crystal packing is dominated by C—H⋯π and π–π bonding, with a particular significance of mutual indole–indole interactions. In the case of II, the molecules adopt short intramolecular π–π interactions between two nearly parallel indole ring systems [with the centroids of their pyrrole rings separated by 3.267 (2) Å] accompanied by a set of forced Br⋯O contacts. This provides suppression of similar interactions between the molecules, while the importance of weak C—H⋯O hydrogen bonding to the packing naturally increases. Short contacts of the latter type [C⋯O = 3.389 (6) Å] assemble pairs of molecules into centrosymmetric dimers with a cyclic R22(13) ring motif. These findings are consistent with the results of a Hirshfeld surface analysis and together they suggest a tool for modulating the supramolecular behavior of phenylsulfonylated indoles. Full Article text
rf Crystal structure, Hirshfeld surface analysis, and DFT and molecular docking studies of 6-cyanonaphthalen-2-yl 4-(benzyloxy)benzoate By journals.iucr.org Published On :: 2024-10-22 In the title compound, C25H17NO3, the torsion angle associated with the phenyl benzoate group is −173.7 (2)° and that for the benzyloxy group is −174.8 (2)° establishing an anti-type conformation. The dihedral angles between the ten-membered cyanonaphthalene ring and the aromatic ring of the phenyl benzoate and the benzyloxy fragments are 40.70 (10) and 87.51 (11)°, respectively, whereas the dihedral angle between the aromatic phenyl benzoate and the benzyloxy fragments is 72.30 (13)°. In the crystal, the molecules are linked by weak C—H⋯O interactions forming S(4) chains propagating parallel to [010]. The packing is consolidated by three C—H⋯π interactions and two π–π stacking interactions between the aromatic rings of naphthalene and phenyl benzoate with centroid-to-centroid distances of 3.9698 (15) and 3.8568 (15) Å, respectively. Intermolecular interactions were quantified using Hirshfeld surface analysis. The molecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level, revealing that the energy gap between HOMO and LUMO is 3.17 eV. Molecular docking studies were carried out for the title compound as a ligand and SARS-Covid-2(PDB ID:7QF0) protein as a receptor giving a binding affinity of −9.5 kcal mol−1. Full Article text
rf Synthesis, crystal structure and Hirshfeld surface analysis of 2-{4-[(2-chlorophenyl)methyl]-3-methyl-6-oxopyridazin-1-yl}-N-phenylacetamide By journals.iucr.org Published On :: 2024-10-31 In the title molecule, C20H18ClN3O2, the 2-chlorophenyl group is disordered to a small extent [occupancies 0.875 (2)/0.125 (2)]. The phenylacetamide moiety is nearly planar due to a weak, intramolecular C—H⋯O hydrogen bond. In the crystal, N—H⋯O hydrogen bonds and π-stacking interactions between pyridazine and phenyl rings form helical chains of molecules in the b-axis direction, which are linked by C—H⋯O hydrogen bonds and C—H⋯π(ring) interactions. A Hirshfeld surface analysis was performed, which showed that H⋯H, C⋯H/H⋯C and O⋯H/H⋯O interactions to dominate the intermolecular contacts in the crystal. Full Article text
rf Crystal structure and Hirshfeld surface analysis of the salt 2-iodoethylammonium iodide – a possible side product upon synthesis of hybrid perovskites By journals.iucr.org Published On :: 2024-10-31 The title organic–inorganic hybrid salt, C2H7IN+·I−, is isotypic with its bromine analog, C2H7BrN+·Br− [Semenikhin et al. (2024). Acta Cryst. E80, 738–741]. Its asymmetric unit consists of one 2-iodoethylammonium cation and one iodide anion. The NH3+ group of the organic cation forms weak hydrogen bonds with four neighboring iodide anions, leading to the formation of supramolecular layers propagating parallel to the bc plane. Hirshfeld surface analysis reveals that the most important contribution to the crystal packing is from N—H⋯I interactions (63.8%). The crystal under investigation was twinned by a 180° rotation around [001]. Full Article text
rf Crystal structure and Hirshfeld surface analysis of bis(benzoylacetonato)(ethanol)dioxidouranium(VI) By journals.iucr.org Published On :: 2024-11-05 A new uranium metal–organic complex salt, [U(C10H9O2)2O2(C2H6O)], with benzoyl acetone, namely, bis(benzoylacetonato)(ethanol)dioxidouranium(VI), was synthesized. The compound has monoclinic P21/n symmetry. The geometry of the seven-coordinate U atom is pentagonal bipyramidal, with the uranyl oxygen atoms in apical positions. In the complex, the ligands bind to the metal through oxygen atoms. Additional weak O—H⋯O contacts between the cations and anions consolidate the three-dimensional arrangement of the structure. On the Hirshfeld surface, the largest contributions come from the short contacts such as van der Waals forces, including H⋯H, O⋯H and C⋯H. Interactions including C⋯C and O⋯C contacts were also observed; however, their contribution to the overall cohesion of the crystal structure is minor. A packing analysis was performed to check the strength of the crystal packing. Full Article text
rf Development and testing of a dual-frequency, real-time hardware feedback system for the hard X-ray nanoprobe beamline of the SSRF By journals.iucr.org Published On :: we introduce a novel approach for a real-time dual-frequency feedback system, which has been firstly used at the hard X-ray nanoprobe beamline of SSRF. The BiBEST can then efficiently stabilize X-ray beam position and stability in parallel, making use of different optical systems in the beamline. Full Article text
rf Operation model of a skew-symmetric split-crystal neutron interferometer By journals.iucr.org Published On :: 2024-02-01 The observation of neutron interference using a triple Laue interferometer formed by two separate crystals opens the way to the construction and operation of skew-symmetric interferometers with extended arm separation and length. The specifications necessary for their successful operation are investigated here: most importantly, how the manufacturing tolerance and crystal alignments impact the interference visibility. In contrast with previous studies, both incoherent sources and the three-dimensional operation of the interferometer are considered. It is found that, with a Gaussian Schell model of an incoherent source, the integrated density of the particles leaving the interferometer is the same as that yielded by a coherent Gaussian source having a radius equal to the coherence length. Full Article text
rf Tripling of the scattering vector range of X-ray reflectivity on liquid surfaces using a double-crystal deflector By journals.iucr.org Published On :: 2024-02-16 The maximum range of perpendicular momentum transfer (qz) has been tripled for X-ray scattering from liquid surfaces when using a double-crystal deflector setup to tilt the incident X-ray beam. This is achieved by employing a higher-energy X-ray beam to access Miller indices of reflecting crystal atomic planes that are three times higher than usual. The deviation from the exact Bragg angle condition induced by misalignment between the X-ray beam axis and the main rotation axis of the double-crystal deflector is calculated, and a fast and straightforward procedure to align them is deduced. An experimental method of measuring scattering intensity along the qz direction on liquid surfaces up to qz = 7 Å−1 is presented, with liquid copper serving as a reference system for benchmarking purposes. Full Article text