ir (E)-{[(Butylsulfanyl)methanethioyl]amino}(4-methoxybenzylidene)amine: crystal structure and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2020-01-17 The title hydrazine carbodithioate, C13H18N2OS2, is constructed about a central and almost planar C2N2S2 chromophore (r.m.s. deviation = 0.0263 Å); the terminal methoxybenzene group is close to coplanar with this plane [dihedral angle = 3.92 (11)°]. The n-butyl group has an extended all-trans conformation [torsion angles S—Cm—Cm—Cm = −173.2 (3)° and Cm—Cm—Cm—Cme = 180.0 (4)°; m = methylene and me = methyl]. The most prominent feature of the molecular packing is the formation of centrosymmetric eight-membered {⋯HNCS}2 synthons, as a result of thioamide-N—H⋯S(thioamide) hydrogen bonds; these are linked via methoxy-C–H⋯π(methoxybenzene) interactions to form a linear supramolecular chain propagating along the a-axis direction. An analysis of the calculated Hirshfeld surfaces and two-dimensional fingerprint plots point to the significance of H⋯H (58.4%), S⋯H/H⋯S (17.1%), C⋯H/H⋯C (8.2%) and O⋯H/H⋯O (4.9%) contacts in the packing. The energies of the most significant interactions, i.e. the N—H⋯S and C—H⋯π interactions have their most significant contributions from electrostatic and dispersive components, respectively. The energies of two other identified close contacts at close to van der Waals distances, i.e. a thione–sulfur and methoxybenzene–hydrogen contact (occurring within the chains along the a axis) and between methylene-H atoms (occurring between chains to consolidate the three-dimensional architecture), are largely dispersive in nature. Full Article text
ir The first coordination compound of deprotonated 2-bromonicotinic acid: crystal structure of a dinuclear paddle-wheel copper(II) complex By scripts.iucr.org Published On :: 2020-01-17 A copper(II) dimer with the deprotonated anion of 2-bromonicotinic acid (2-BrnicH), namely, tetrakis(μ-2-bromonicotinato-κ2O:O')bis[aquacopper(II)](Cu—Cu), [Cu2(H2O)2(C6H3BrNO2)4] or [Cu2(H2O)2(2-Brnic)4], (1), was prepared by the reaction of copper(II) chloride dihydrate and 2-bromonicotinic acid in water. The copper(II) ion in 1 has a distorted square-pyramidal coordination environment, achieved by four carboxylate O atoms in the basal plane and the water molecule in the apical position. The pair of symmetry-related copper(II) ions are connected into a centrosymmetric paddle-wheel dinuclear cluster [Cu⋯Cu = 2.6470 (11) Å] via four O,O'-bridging 2-bromonicotinate ligands in the syn-syn coordination mode. In the extended structure of 1, the cluster molecules are assembled into an infinite two-dimensional hydrogen-bonded network lying parallel to the (001) plane via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of various hydrogen-bond ring motifs: dimeric R22(8) and R22(16) loops and a tetrameric R44(16) loop. The Hirshfeld surface analysis was also performed in order to better illustrate the nature and abundance of the intermolecular contacts in the structure of 1. Full Article text
ir Structural characterization and Hirshfeld surface analysis of 2-iodo-4-(pentafluoro-λ6-sulfanyl)benzonitrile By scripts.iucr.org Published On :: 2020-01-17 The title compound, C7H3F5INS, a pentafluorosulfanyl (SF5) containing arene, was synthesized from 4-(pentafluorosulfanyl)benzonitrile and lithium tetramethylpiperidide following a variation to the standard approach, which features simple and mild conditions that allow direct access to tri-substituted SF5 intermediates that have not been demonstrated using previous methods. The molecule displays a planar geometry with the benzene ring in the same plane as its three substituents. It lies on a mirror plane perpendicular to [010] with the iodo, cyano, and the sulfur and axial fluorine atoms of the pentafluorosulfanyl substituent in the plane of the molecule. The equatorial F atoms have symmetry-related counterparts generated by the mirror plane. The pentafluorosulfanyl group exhibits a staggered fashion relative to the ring and the two hydrogen atoms ortho to the substituent. S—F bond lengths of the pentafluorosulfanyl group are unequal: the equatorial bond facing the iodo moiety has a longer distance [1.572 (3) Å] and wider angle compared to that facing the side of the molecules with two hydrogen atoms [1.561 (4) Å]. As expected, the axial S—F bond is the longest [1.582 (5) Å]. In the crystal, in-plane C—H⋯F and N⋯I interactions as well as out-of-plane F⋯C interactions are observed. According to the Hirshfeld analysis, the principal intermolecular contacts for the title compound are F⋯H (29.4%), F⋯I (15.8%), F⋯N (11.4%), F⋯F (6.0%), N⋯I (5.6%) and F⋯C (4.5%). Full Article text
ir [Se(CH2C(O)CH3)3][B12F11NH3]: The first selenium cation with three β-ketone substituents By scripts.iucr.org Published On :: 2020-01-17 The reaction of [Se8][B12F11NH3]2 with acetone and subsequent crystallization from acetone/diethyl ether yielded the selenium cation [Se(CH2C(O)CH3)3]+ as a by-product, which is stabilized by the weakly coordinating undecafluorinated anion [B12F11NH3]−. While attempting to crystallize pure [Se8][B12F11NH3]2, the structure of the isolated product, namely, tris(2-oxopropyl)selenium 1-ammonioundecafluorododecaborate, was surprising. The cation [Se(CH2C(O)CH3)3]+ represents the first example for a cationic selenium compound with three ketone functional groups located in the β-position with respect to the selenium atom. The cation possesses almost trigonal–pyramidal C3 symmetry and forms hydrogen bonds to the ammonio group of the anion. Full Article text
ir Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis(pyridin-4-ylmethyl)ethanediamide and 4-chlorobenzoic acid By scripts.iucr.org Published On :: 2020-01-21 The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half molecules of oxalamide (4LH2), as each is disposed about a centre of inversion, and two molecules of 4-chlorobenzoic acid (CBA), each in general positions. Each 4LH2 molecule has a (+)antiperiplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4LH2 molecules. The anti conformation of the carbonyl groups enables the formation of intramolecular amide-N—H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA molecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-molecule aggregates are formed via carboxylic acid-O—H⋯N(pyridyl) hydrogen bonding. These are connected into a supramolecular tape propagating parallel to [100] through amide-N—H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methylene-C—H⋯O(carbonyl) and CBA-C—H⋯O(amide) interactions. As revealed by a more detailed analysis of the molecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O interactions which provide interaction energies approximately one-quarter of those provided by the amide-N—H⋯O(amide) hydrogen bonding sustaining the supramolecular tape. Full Article text
ir Crystal structures and Hirshfeld surface analysis of trans-bis(thiocyanato-κN)bis{2,4,6-trimethyl-N-[(pyridin-2-yl)methylidene]aniline-κ2N,N'}manganese(II) and trans-bis(thiocyanato-κN)bis{2,4,6-trimethyl-N-[(pyri By scripts.iucr.org Published On :: 2020-01-31 Two new mononuclear metal complexes involving the bidentate Schiff base ligand 2,4,6-trimethyl-N-[(pyridin-2-yl)methylidene]aniline (C15H16N2 or PM-TMA), [Mn(NCS)2(PM-TMA)2] (I) and [Ni(NCS)2(PM-TMA)2] (II), were synthesized and their structures determined by single-crystal X-ray diffraction. Although the title compounds crystallize in different crystal systems [triclinic for (I) and monoclinic for (II)], both asymmetric units consist of one-half of the complex molecule, i.e. one metal(II) cation, one PM-TMA ligand, and one N-bound thiocyanate anion. In both complexes, the metal(II) cation is located on a centre of inversion and adopts a distorted octahedral coordination environment defined by four N atoms from two symmetry-related PM-TMA ligands in the equatorial plane and two N atoms from two symmetry-related NCS− anions in a trans axial arrangement. The trimethylbenzene and pyridine rings of the PM-TMA ligand are oriented at dihedral angles of 74.18 (7) and 77.70 (12)° for (I) and (II), respectively. The subtle change in size of the central metal cations leads to a different crystal packing arrangement for (I) and (II) that is dominated by weak C—H⋯S, C—H⋯π, and π–π interactions. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to quantify these intermolecular contacts, and indicate that the most significant contacts in packing are H⋯H [48.1% for (I) and 54.9% for (II)], followed by H⋯C/C⋯H [24.1% for (I) and 15.7% for (II)], and H⋯S/S⋯H [21.1% for (I) and 21.1% for (II)]. Full Article text
ir Crystal structure, Hirshfeld surface analysis, interaction energy and DFT studies of (2Z)-2-(2,4-dichlorobenzylidene)-4-nonyl-3,4-dihydro-2H-1,4-benzothiazin-3-one By scripts.iucr.org Published On :: 2020-01-31 The title compound, C24H27Cl2NOS, contains 1,4-benzothiazine and 2,4-dichlorophenylmethylidene units in which the dihydrothiazine ring adopts a screw-boat conformation. In the crystal, intermolecular C—HBnz⋯OThz (Bnz = benzene and Thz = thiazine) hydrogen bonds form chains of molecules extending along the a-axis direction, which are connected to their inversion-related counterparts by C—HBnz⋯ClDchlphy (Dchlphy = 2,4-dichlorophenyl) hydrogen bonds and C—HDchlphy⋯π (ring) interactions. These double chains are further linked by C—HDchlphy⋯OThz hydrogen bonds, forming stepped layers approximately parallel to (012). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (44.7%), C⋯H/H⋯C (23.7%), Cl⋯H/H⋯Cl (18.9%), O⋯H/H⋯O (5.0%) and S⋯H/H⋯S (4.8%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—HDchlphy⋯OThz, C—HBnz⋯OThz and C—HBnz⋯ClDchlphy hydrogen-bond energies are 134.3, 71.2 and 34.4 kJ mol−1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. The two carbon atoms at the end of the nonyl chain are disordered in a 0.562 (4)/0.438 (4) ratio. Full Article text
ir Crystal structure, synthesis and thermal properties of bis(4-benzoylpyridine-κN)bis(isothiocyanato-κN)bis(methanol-κN)iron(II) By scripts.iucr.org Published On :: 2020-01-31 In the crystal structure of the title compound, [Fe(NCS)2(C12H9NO)2(CH4O)2], the FeII cations are octahedrally coordinated by two N atoms of 4-benzoylpyridine ligands, two N atoms of two terminal isothiocyanate anions and two methanol molecules into discrete complexes that are located on centres of inversion. These complexes are linked via intermolecular O—H⋯O hydrogen bonds between the methanol O—H H atoms and the carbonyl O atoms of the 4-benzoylpyridine ligands, forming layers parallel to (101). Powder X-ray diffraction proved that a pure sample was obtained but that this compound is unstable and transforms into an unknown crystalline phase within several weeks. However, the solvent molecules can be removed by heating in a thermobalance, which for the aged sample as well as the title compound leads to the formation of a compound with the composition Fe(NCS)2(4-benzoylpyridine)2, which exhibits a powder pattern that is similar to that of Mn(NCS)2(4-benzoylpyridine)2. Full Article text
ir Crystal structure of a nickel compound comprising two nickel(II) complexes with different ligand environments: [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2 By scripts.iucr.org Published On :: 2020-02-06 The title compound, diaqua[tris(2-aminoethyl)amine]nickel(II) hexaaquanickel(II) bis(sulfate), [Ni(C6H18N4)(H2O)2][Ni(H2O)6](SO4)2 or [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2, consists of two octahedral nickel complexes within the same unit cell. These metal complexes are formed from the reaction of [Ni(H2O)6](SO4) and the ligand tris(2-aminoethyl)amine (tren). The crystals of the title compound are purple, different from those of the starting complex [Ni(H2O)6](SO4), which are turquoise. The reaction was performed both in a 1:1 and 1:2 metal–ligand molar ratio, always yielding the co-precipitation of the two types of crystals. The asymmetric unit of the title compound, which crystallizes in the space group Pnma, consists of two half NiII complexes and a sulfate counter-anion. The mononuclear cationic complex [Ni(tren)(H2O)2]2+ comprises an Ni ion, the tren ligand and two water molecules, while the mononuclear complex [Ni(H2O)6]2+ consists of another Ni ion surrounded by six coordinated water molecules. The [Ni(tren)(H2O)2] and [Ni(H2O)6] subunits are connected to the SO42− counter-anions through hydrogen bonding, thus consolidating the crystal structure. Full Article text
ir Crystal structure and Hirshfeld surface analysis of the methanol solvate of sclareol, a labdane-type diterpenoid By scripts.iucr.org Published On :: 2020-02-06 The title compound, C20H36O2·CH3OH [systematic name: (3S)-4-[(S)-3-hydroxy-3-methylpent-4-en-1-yl]-3,4a,8,8-tetramethyldecahydronaphthalen-3-ol methanol monosolvate], is a methanol solvate of sclareol, a diterpene oil isolated from the medicinally important medicinal herb Salvia sclarea, commonly known as clary sage. It crystallizes in space group P1 (No. 1) with Z' = 2. The sclareol molecule comprises two trans-fused cyclohexane rings, each having an equatorially oriented hydroxyl group, and a 3-methylpent-1-en-3-ol side chain. In the crystal, Os—H⋯Os, Os—H⋯Om, Om—H⋯Os and Om—H⋯Om (s = sclareol, m = methanol) hydrogen bonds connect neighboring molecules into infinite [010] chains. The title compound exhibits weak anti-leishmanial activity (IC50 = 66.4 ± 1.0 µM ml−1) against standard miltefosine (IC50 = 25.8 ± 0.2 µM ml−1). Full Article text
ir The crystal structures and Hirshfeld surface analyses of a cadmium(II) and a zinc(II) mononuclear complex of the new tetrakis-substituted pyrazine ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis By scripts.iucr.org Published On :: 2020-02-18 The whole molecule of the cadmium(II) complex, diiodido{N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3N2,N1,N6}cadmium(II), [CdI2(C36H40N6)], (I), of the ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline) (L), is generated by a twofold rotation symmetry; the twofold axis bisects the cadmium atom and the nitrogen atoms of the pyrazine ring. The ligand coordinates in a mono-tridentate manner and the cadmium atom has a fivefold CdN3I2 coordination environment with a distorted shape. In the zinc(II) complex, dichlorido{N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3N2,N1,N6}zinc(II) dichloromethane 0.6-solvate, [ZnCl2(C36H40N6)]·0.6CH2Cl2, (II), ligand L also coordinates in a mono-tridentate manner and the zinc atom has a fivefold ZnN3Cl2 coordination environment with a distorted shape. It crystallized as a partial dichloromethane solvate. In the crystal of I, the complex molecules are linked by weak C—H⋯I contacts, forming ribbons propagating along [100]. In the crystal of II, the complex molecules are linked by a series of C—H⋯π interactions, forming layers lying parallel to the (1overline{1}1) plane. In the crystals of both compounds there are metal–halide⋯π(pyrazine) contacts present. The Hirshfeld analyses confirm the importance of the C—H⋯halide contacts in the crystal packing of both compounds. Full Article text
ir Crystal structure, Hirshfeld surface analysis and DFT studies of 1,3-bis[2-methoxy-4-(prop-2-en-1-yl)phenoxy]propane By scripts.iucr.org Published On :: 2020-02-14 The asymmetric unit of the title compound, C23H28O4, comprises two half-molecules, with the other half of each molecule being completed by the application of twofold rotation symmetry. The two completed molecules both have a V-shaped appearance but differ in their conformations. In the crystal, each independent molecule forms chains extending parallel to the b axis with its symmetry-related counterparts through C—H⋯π(ring) interactions. Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (65.4%), H⋯C/C⋯H (21.8%) and H⋯O/O⋯H (12.3%) interactions. Optimized structures using density functional theory (DFT) at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined molecular structures in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
ir Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 1-(1,3-benzothiazol-2-yl)-3-(2-hydroxyethyl)imidazolidin-2-one By scripts.iucr.org Published On :: 2020-02-14 In the title molecule, C12H13N3O2S, the benzothiazine moiety is slightly non-planar, with the imidazolidine portion twisted only a few degrees out of the mean plane of the former. In the crystal, a layer structure parallel to the bc plane is formed by a combination of O—HHydethy⋯NThz hydrogen bonds and weak C—HImdz⋯OImdz and C—HBnz⋯OImdz (Hydethy = hydroxyethyl, Thz = thiazole, Imdz = imidazolidine and Bnz = benzene) interactions, together with C—HImdz⋯π(ring) and head-to-tail slipped π-stacking [centroid-to-centroid distances = 3.6507 (7) and 3.6866 (7) Å] interactions between thiazole rings. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (47.0%), H⋯O/O⋯H (16.9%), H⋯C/C⋯H (8.0%) and H⋯S/S⋯H (7.6%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—H⋯N and C—H⋯O hydrogen-bond energies are 68.5 (for O—HHydethy⋯NThz), 60.1 (for C—HBnz⋯OImdz) and 41.8 kJ mol−1 (for C—HImdz⋯OImdz). Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. Full Article text
ir Phosphorescent mono- and diiridium(III) complexes cyclometalated by fluorenyl- or phenyl-pyridino ligands with bulky substituents, as prospective OLED dopants By scripts.iucr.org Published On :: 2020-02-18 The crystal structures of tris[9,9-dihexyl-2-(5-methoxypyridin-2-yl-κN)-9H-fluoren-3-yl-κC3]iridium pentane monosolvate, [Ir(C31H38NO)3]·C5H12, (I), di-μ2-chlorido-bis{bis[2-(5-fluoropyridin-2-yl)-9,9-dihexyl-9H-fluoren-3-yl]iridium} pentane 0.3-solvate, [Ir2(C30H35FN)4Cl2]·0.3C5H12, (II), di-μ2-cyanato-bis{bis[9,9-dihexyl-2-(5-methoxypyridin-2-yl)-9H-fluoren-1-yl]iridium} pentane monosolvate, [Ir2(C31H38NO)4(NCO)2(NCO)2]·C5H12, (III), and {μ-N,N'-bis[3,5-bis(trifluoromethyl)phenyl]oxamidato}bis(bis{2-[4-(2,4,6-trimethylphenyl)pyridin-2-yl]phenyl-κ2C1,N'}iridium)–chlorobenzene–pentane (1/2.3/0.4), [Ir2(C20H19N)4(C18H6F12N2O2)]·2.3C6H5Cl·0.4C5H12, (IV), synthesized in the quest for organic light-emitting devices, were determined. The bis-μ2-chloro and bis-μ2-cyanato complexes have ΔΔ and ΛΛ configurations of the distorted octahedral Ir centres in racemic crystals, whereas the oxamido complex has a centrosymmetric (meso) structure with the ΔΛ configuration. The bridging oxamido moiety has a nearly planar anti geometry. All structures show substantial disorder of both host molecules and solvents of crystallization. Full Article text
ir Crystal structure, characterization and Hirshfeld analysis of bis{(E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalen-2-olato}copper(II) dimethyl sulfoxide monosolvate By scripts.iucr.org Published On :: 2020-02-18 In the title compound, [Cu(C16H8Br3N2O)2]·C2H6OS, the CuII atom is tetracoordinated in a square-planar coordination, being surrounded by two N atoms and two O atoms from two N,O-bidentate (E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalen-2-olate ligands. The two N atoms and two O atoms around the metal center are trans to each other, with an O—Cu—O bond angle of 177.90 (16)° and a N—Cu—N bond angle of 177.8 (2)°. The average distances between the CuII atom and the coordinated O and N atoms are 1.892 (4) and 1.976 (4) Å, respectively. In the crystal, complexes are linked by C—H⋯O hydrogen bonds and by π–π interactions involving adjacent naphthalene ring systems [centroid–centroid distance = 3.679 (4) Å]. The disordered DMSO molecules interact weakly with the complex molecules, being positioned in the voids left by the packing arrangement of the square-planar complexes. The DMSO solvent molecule is disordered over two positions with occupancies of 0.70 and 0.30. Full Article text
ir Crystal structure and Hirshfeld surface analysis of (E)-3-(benzylideneamino)-5-phenylthiazolidin-2-iminium bromide By scripts.iucr.org Published On :: 2020-02-21 The central thiazolidine ring of the title salt, C16H16N3S+·Br−, adopts an envelope conformation, with the C atom bearing the phenyl ring as the flap atom. In the crystal, the cations and anions are linked by N—H⋯Br hydrogen bonds, forming chains parallel to the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (46.4%), C⋯H/H⋯C (18.6%) and H⋯Br/Br⋯H (17.5%) interactions. Full Article text
ir Structural, Hirshfeld and DFT studies of conjugated D–π–A carbazole chalcone crystal By scripts.iucr.org Published On :: 2020-02-18 A new conjugated carbazole chalcone compound, (E)-3-[4-(9,9a-dihydro-8aH-carbazol-9-yl)phenyl]-1-(4-nitrophenyl)prop-2-en-1-one (CPNC), C27H18N2O3, was synthesized using a Claisen–Schmidt condensation reaction. CPNC crystallizes in the monoclinic non-centrosymmetric space group Cc and adopts an s-cis conformation with respect to the ethylenic double bonds (C=O and C=C). The crystal packing features C—H⋯O and C—H⋯π interactions whose percentage contribution was quantified by Hirshfeld surface analysis. Quantum chemistry calculations including geometrical optimization and molecular electrostatic potential (MEP) were analysed by density functional theory (DFT) with a B3LYP/6–311 G++(d,p) basis set. Full Article text
ir Crystal structure, Hirshfeld surface analysis and DFT studies of 1-[r-2,c-6-diphenyl-t-3-(propan-2-yl)piperidin-1-yl]ethan-1-one By scripts.iucr.org Published On :: 2020-02-18 In the title compound, C22H27NO, the piperidine ring adopts a chair conformation. The dihedral angles between the mean plane of the piperidine ring and the phenyl rings are 89.78 (7) and 48.30 (8)°. In the crystal, molecules are linked into chains along the b-axis direction by C—H⋯O hydrogen bonds. The DFT/B3LYP/6–311 G(d,p) method was used to determine the HOMO–LUMO energy levels. The molecular electrostatic potential surfaces were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyse the intermolecular interactions in the molecule. Full Article text
ir Crystal structures and Hirshfeld surface analyses of two new tetrakis-substituted pyrazines and a degredation product By scripts.iucr.org Published On :: 2020-02-18 The two new tetrakis-substituted pyrazines, 1,1',1'',1'''-(pyrazine-2,3,5,6-tetrayl) tetrakis(N,N-dimethylmethanamine), C16H32N6, (I) and N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline), C36H40N6, (II), both crystallize with half a molecule in the asymmetric unit; the whole molecules are generated by inversion symmetry. There are weak intramolecular C—H⋯N hydrogen bonds present in both molecules and in (II) the pendant N-methylaniline rings are linked by a C—H⋯π interaction. The degredation product, N,N'-[(6-phenyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazine-2,3-diyl)bis(methylene)]bis(N-methylaniline), C28H29N5, (III), was obtained several times by reacting (II) with different metal salts. Here, the 6-phenyl ring is almost coplanar with the planar pyrrolo[3,4-b]pyrazine unit (r.m.s. deviation = 0.029 Å), with a dihedral angle of 4.41 (10)° between them. The two N-methylaniline rings are inclined to the planar pyrrolo[3,4-b]pyrazine unit by 88.26 (10) and 89.71 (10)°, and to each other by 72.56 (13)°. There are also weak intramolecular C—H⋯N hydrogen bonds present involving the pyrazine ring and the two N-methylaniline groups. In the crystal of (I), there are no significant intermolecular contacts present, while in (II) molecules are linked by a pair of C—H⋯π interactions, forming chains along the c-axis direction. In the crystal of (III), molecules are linked by two pairs of C—H⋯π interactions, forming inversion dimers, which in turn are linked by offset π–π interactions [intercentroid distance = 3.8492 (19) Å], forming ribbons along the b-axis direction. Full Article text
ir Whole-molecule disorder of the Schiff base compound 4-chloro-N-(4-nitrobenzylidene)aniline: crystal structure and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2020-02-18 In the crystal of the title Schiff base compound, C13H9ClN2O2, [CNBA; systematic name: (E)-N-(4-chlorophenyl)-1-(4-nitrophenyl)methanimine], the CNBA molecule shows whole-molecule disorder (occupancy ratio 0.65:0.35), with the disorder components related by a twofold rotation about the shorter axis of the molecule. The aromatic rings are inclined to each other by 39.3 (5)° in the major component and by 35.7 (9)° in the minor component. In the crystal, C—H⋯O hydrogen bonds predominate in linking the major components, while weak C—H⋯Cl interactions predominate in linking the minor components. The result is the formation of corrugated layers lying parallel to the ac plane. The crystal packing was analysed using Hirshfeld surface analysis and compared with related structures. Full Article text
ir Polymorphism of 2-(5-benzyl-6-oxo-3-phenyl-1,6-dihydropyridazin-1-yl)acetic acid with two monoclinic modifications: crystal structures and Hirshfeld surface analyses By scripts.iucr.org Published On :: 2020-02-25 Two polymorphs of the title compound, C19H16N2O3, were obtained from ethanolic (polymorph I) and methanolic solutions (polymorph II), respectively. Both polymorphs crystallize in the monoclinic system with four formula units per cell and a complete molecule in the asymmetric unit. The main difference between the molecules of (I) and (II) is the reversed position of the hydroxy group of the carboxylic function. All other conformational features are found to be similar in the two molecules. The different orientation of the OH group results in different hydrogen-bonding schemes in the crystal structures of (I) and (II). Whereas in (I) intermolecular O—H⋯O hydrogen bonds with the pyridazinone carbonyl O atom as acceptor generate chains with a C(7) motif extending parallel to the b-axis direction, in the crystal of (II) pairs of inversion-related O—H⋯O hydrogen bonds with an R22(8) ring motif between two carboxylic functions are found. The intermolecular interactions in both crystal structures were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 4-allyl-2-methoxy-6-nitrophenol By scripts.iucr.org Published On :: 2020-02-28 The asymmetric unit of the title compound, C10H11NO4, which was synthesized via nitration reaction of eugenol (4-allyl-2-methoxyphenol) with a mixture of nitric acid and sulfuric acid, consists of three independent molecules of similar geometry. Each molecule displays an intramolecular hydrogen bond involving the hydroxide and the nitro group forming an S(6) motif. The crystal cohesion is ensured by intermolecular C—H⋯O hydrogen bonds in addition to π–π stacking interactions between the aromatic rings [centroid–centroid distances = 3.6583 (17)–4.0624 (16) Å]. The Hirshfeld surface analysis and the two-dimensional fingerprint plots show that H⋯H (39.6%), O⋯H/H⋯O (37.7%), C⋯H/H⋯C (12.5%) and C⋯C (4%) are the most important contributors towards the crystal packing. Full Article text
ir Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of (S)-10-propargylpyrrolo[2,1-c][1,4]benzodiazepine-5,11-dione By scripts.iucr.org Published On :: 2020-03-03 The title compound, C15H14N2O2, consists of pyrrole and benzodiazepine units linked to a propargyl moiety, where the pyrrole and diazepine rings adopt half-chair and boat conformations, respectively. The absolute configuration was assigned on the the basis of l-proline, which was used in the synthesis of benzodiazepine. In the crystal, weak C—HBnz⋯ODiazp and C—HProprg⋯ODiazp (Bnz = benzene, Diazp = diazepine and Proprg = propargyl) hydrogen bonds link the molecules into two-dimensional networks parallel to the bc plane, enclosing R44(28) ring motifs, with the networks forming oblique stacks along the a-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.8%), H⋯C/C⋯H (25.7%) and H⋯O/O⋯H (20.1%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—H⋯O hydrogen-bond energies are 38.8 (for C—HBnz⋯ODiazp) and 27.1 (for C—HProprg⋯ODiazp) kJ mol−1. Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are 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
ir Crystal structure and Hirshfeld surface analysis of 3,6-bis(pyrimidin-2-yl)-1,4-dihydro-1,2,4,5-tetrazine dihydrate By scripts.iucr.org Published On :: 2020-03-03 In the title compound, C10H8N8·2H2O or H2bmtz·2H2O [bmtz = 3,6-bis(2'-pyrimidyl)-1,2,4,5-tetrazine], the asymmetric unit consists of one-half molecule of H2bmtz and one water molecule, the whole H2bmtz molecule being generated by a crystallographic twofold rotation axis passing through the middle point of the 1,4-dihydro-1,2,4,5-tetrazine moiety. In the crystal, N—H⋯O, N—H⋯N, O—H⋯O hydrogen bonds and aromatic π–π stacking interactions link the components into a three-dimensional supramolecular network. Hirshfeld surface analysis was used to further investigate the intermolecular interactions in the crystal structure. Full Article text
ir Crystal structure and Hirshfeld surface analysis of (C7H9N4O2)[ZnCl3(H2O)] By scripts.iucr.org Published On :: 2020-03-10 In the title molecular salt, 1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-9-ium aquatrichloridozincate(II), (C7H9N4O2)[ZnCl3(H2O)], the fused ring system of the cation is close to planar, with the largest deviation from the mean plane being 0.037 (3) Å. In the complex anion, the ZnII cation is coordinated by three chloride ions and one oxygen atom from the water ligand in a distorted tetrahedral geometry. In the crystal, inversion dimers between pairs of cations linked by pairwise N—H⋯O hydrogen bonds generate R22(10) rings. The anions are linked into dimers by pairs of O—H⋯Cl hydrogen bonds and the respective dimers are linked by O—H⋯O and N—H⋯Cl hydrogen bonds. Together, these generate a three-dimensional supramolecular network. Hirshfeld surfaces were generated to gain further insight into the packing. Full Article text
ir A redetermination of the crystal structure of the mannitol complex NH4[Mo2O5(C6H11O6)]·H2O: hydrogen-bonding scheme and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2020-03-10 The redetermined structure [for the previous study, see: Godfrey & Waters (1975). Cryst. Struct. Commun. 4, 5–8] of ammonium μ-oxido-μ-[1,5,6-trihydroxyhexane-2,3,4-tris(olato)]bis[dioxidomolybdenum(V)] monohydrate, NH4[Mo2(C6H11O6)O5]·H2O, was obtained from an attempt to prepare a glutamic acid complex from the [Co2Mo10H4O38]6− anion. Subsequent study indicated the complex arose from a substantial impurity of mannitol in the glutamic acid sample used. All hydrogen atoms have been located in the present study and the packing displays N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds. A Hirshfeld surface analysis was also performed. Full Article text
ir Crystal structure, Hirshfeld surface analysis and computational study of 2-chloro-N-[4-(methylsulfanyl)phenyl]acetamide By scripts.iucr.org Published On :: 2020-03-31 In the title compound, C9H10ClNOS, the amide functional group –C(=O)NH– adopts a trans conformation with the four atoms nearly coplanar. This conformation promotes the formation of a C(4) hydrogen-bonded chain propagating along the [010] direction. The central part of the molecule, including the six-membered ring, the S and N atoms, is fairly planar (r.m.s. deviation of 0.014). The terminal methyl group and the C(=O)CH2 group are slightly deviating out-of-plane while the terminal Cl atom is almost in-plane. Hirshfeld surface analysis of the title compound suggests that the most significant contacts in the crystal are H⋯H, H⋯Cl/Cl⋯H, H⋯C/C⋯H, H⋯O/O⋯H and H⋯S/S⋯H. π–π interactions between inversion-related molecules also contribute to the crystal packing. DFT calculations have been performed to optimize the structure of the title compound using the CAM-B3LYP functional and the 6–311 G(d,p) basis set. The theoretical absorption spectrum of the title compound was calculated using the TD–DFT method. The analysis of frontier orbitals revealed that the π–π* electronic transition was the major contributor to the absorption peak in the electronic spectrum. Full Article text
ir The first coordination compound of 6-fluoronicotinate: the crystal structure of a one-dimensional nickel(II) coordination polymer containing the mixed ligands 6-fluoronicotinate and 4,4'-bipyridine By scripts.iucr.org Published On :: 2020-03-10 A one-dimensional nickel(II) coordination polymer with the mixed ligands 6-fluoronicotinate (6-Fnic) and 4,4'-bipyridine (4,4'-bpy), namely, catena-poly[[diaquabis(6-fluoropyridine-3-carboxylato-κO)nickel(II)]-μ-4,4'-bipyridine-κ2N:N'] trihydrate], {[Ni(6-Fnic)2(4,4'-bpy)(H2O)2]·3H2O}n, (1), was prepared by the reaction of nickel(II) sulfate heptahydrate, 6-fluoronicotinic acid (C6H4FNO2) and 4,4'-bipyridine (C10H8N2) in a mixture of water and ethanol. The nickel(II) ion in 1 is octahedrally coordinated by the O atoms of two water molecules, two O atoms from O-monodentate 6-fluoronicotinate ligands and two N atoms from bridging 4,4'-bipyridine ligands, forming a trans isomer. The bridging 4,4'-bipyridine ligands connect symmetry-related nickel(II) ions into infinite one-dimensional polymeric chains running in the [1overline{1}0] direction. In the extended structure of 1, the polymeric chains and lattice water molecules are connected into a three-dimensional hydrogen-bonded network via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of distinct hydrogen-bond ring motifs: octameric R88(24) and hexameric R86(16) loops. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 2-amino-3-hydroxypyridin-1-ium 6-methyl-2,2,4-trioxo-2H,4H-1,2,3-oxathiazin-3-ide By scripts.iucr.org Published On :: 2020-03-27 The asymmetric unit of the title compound, C5H7N2O+·C4H4NO4S−, contains one cation and one anion. The 6-methyl-2,2,4-trioxo-2H,4H-1,2,3-oxathiazin-3-ide anion adopts an envelope conformation with the S atom as the flap. In the crystal, the anions and cations are held together by N—H⋯O, N—H⋯N, O—H⋯O and C—H⋯O hydrogen bonds, thus forming a three-dimensional structure. The Hirshfeld surface analysis and fingerprint plots reveal that the crystal packing is dominated by O⋯H/H⋯O (43.1%) and H⋯H (24.2%) contacts. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 3,4-dihydro-2H-anthra[1,2-b][1,4]dioxepine-8,13-dione By scripts.iucr.org Published On :: 2020-03-27 The title compound, C17H12O4, was synthesized from the dye alizarin. The dihedral angle between the mean plane of the anthraquinone ring system (r.m.s. deviation = 0.039 Å) and the dioxepine ring is 16.29 (8)°. In the crystal, the molecules are linked by C—H⋯O hydrogen bonds, forming sheets lying parallel to the ab plane. The sheets are connected through π–π and C=O⋯π interactions to generate a three-dimensional supramolecular network. Hirshfeld surface analysis was used to investigate intermolecular interactions in the solid-state: the most important contributions are from H⋯H (43.0%), H⋯O/O⋯H (27%), H⋯C/C⋯H (13.8%) and C⋯C (12.4%) contacts. Full Article text
ir Crystal structure, Hirshfeld surface and frontier molecular orbital analysis of 10-benzyl-9-(3-ethoxy-4-hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7,9,10-hexahydroacridine-1,8(2H,5H)-dione By scripts.iucr.org Published On :: 2020-03-27 In the fused ring system of the title compound, C32H37NO4, the central dihydropyridine ring adopts a flattened boat conformation, the mean and maximum deviations of the dihydropyridine ring being 0.1429 (2) and 0.2621 (2) Å, respectively. The two cyclohexenone rings adopt envelope conformations with the tetrasubstituted C atoms as flap atoms. The benzene and phenyl rings form dihedral angles of 85.81 (2) and 88.90 (2)°, respectively, with the mean plane of the dihydropyridine ring. In the crystal, molecules are linked via an O—H⋯O hydrogen bond, forming a helical chain along the b-axis direction. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (65.2%), O⋯H/H⋯O (18.8%) and C⋯H/H⋯C (13.9%) contacts. Quantum chemical calculations for the frontier molecular orbitals were undertake to determine the chemical reactivity of the title compound. Full Article text
ir Crystal structure, Hirshfeld surface analysis and interaction energy, DFT and antibacterial activity studies of ethyl 2-[(2Z)-2-(2-chlorobenzylidene)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl]acetate By scripts.iucr.org Published On :: 2020-04-07 The title compound, C19H16ClNO3S, consists of chlorophenyl methylidene and dihydrobenzothiazine units linked to an acetate moiety, where the thiazine ring adopts a screw-boat conformation. In the crystal, two sets of weak C—HPh⋯ODbt (Ph = phenyl and Dbt = dihydrobenzothiazine) hydrogen bonds form layers of molecules parallel to the bc plane. The layers stack along the a-axis direction with intercalation of the ester chains. The crystal studied was a two component twin with a refined BASF of 0.34961 (5). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (37.5%), H⋯C/C⋯H (24.6%) and H⋯O/O⋯H (16.7%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—HPh⋯ODbt hydrogen bond energies are 38.3 and 30.3 kJ mol−1. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Moreover, the antibacterial activity of the title compound has been evaluated against gram-positive and gram-negative bacteria. Full Article text
ir Crystal structures of (η4-cycloocta-1,5-diene)bis(1,3-dimethylimidazol-2-ylidene)iridium(I) iodide and (η4-cycloocta-1,5-diene)bis(1,3-diethylimidazol-2-ylidene)iridium(I) iodide By scripts.iucr.org Published On :: 2020-04-03 The title complexes, (η4-cycloocta-1,5-diene)bis(1,3-dimethylimidazol-2-ylidene)iridium(I) iodide, [Ir(C5H8N2)2(C8H12)]I, (1) and (η4-cycloocta-1,5-diene)bis(1,3-diethylimidazol-2-ylidene)iridium(I) iodide, [Ir(C7H12N2)2(C8H12)]I, (2), were prepared using a modified literature method. After carrying out the oxidative addition of the amino acid l-proline to [Ir(COD)(IMe)2]I in water and slowly cooling the reaction to room temperature, a suitable crystal of 1 was obtained and analyzed by single-crystal X-ray diffraction at 100 K. Although this crystal structure has previously been reported in the Pbam space group, it was highly disordered and precise atomic coordinates were not calculated. A single crystal of 2 was also obtained by heating the complex in water and letting it slowly cool to room temperature. Complex 1 was found to crystallize in the monoclinic space group C2/m, while 2 crystallizes in the orthorhombic space group Pccn, both with Z = 4. Full Article text
ir Synthesis, crystal structure and Hirshfeld and thermal analysis of bis[benzyl 2-(heptan-4-ylidene)hydrazine-1-carboxylate-κ2N2,O]bis(thiocyanato)nickel(II) By scripts.iucr.org Published On :: 2020-04-07 The title centrosymmetric NiII complex, [Ni(NCS)2(C15H22N2O2)2], crystallizes with one half molecule in the asymmetric unit of the monoclinic unit cell. The complex adopts an octahedral coordination geometry with two mutually trans benzyl-2-(heptan-4-ylidene)hydrazine-1-carboxylate ligands in the equatorial plane with the axial positions occupied by N-bound thiocyanato ligands. The overall conformation of the molecule is also affected by two, inversion-related, intramolecular C—H⋯O hydrogen bonds. The crystal structure features N—H⋯S, C—H⋯S and C—H⋯N hydrogen bonds together with C—H⋯π contacts that stack the complexes along the b-axis direction. The packing was further explored by Hirshfeld surface analysis. The thermal properties of the complex were also investigated by simultaneous TGA–DTA analyses. Full Article text
ir Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 2-(2,3-dihydro-1H-perimidin-2-yl)-6-methoxyphenol By scripts.iucr.org Published On :: 2020-04-03 The title compound, C18H16N2O2, consists of perimidine and methoxyphenol units, where the tricyclic perimidine unit contains a naphthalene ring system and a non-planar C4N2 ring adopting an envelope conformation with the NCN group hinged by 47.44 (7)° with respect to the best plane of the other five atoms. In the crystal, O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl (Phnl = phenol and Prmdn = perimidine) hydrogen bonds link the molecules into infinite chains along the b-axis direction. Weak C—H⋯π interactions may further stabilize the crystal structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.0%), H⋯C/C⋯H (35.8%) and H⋯O/O⋯H (12.0%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, the O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl hydrogen-bond energies are 58.4 and 38.0 kJ mol−1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are 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
ir Crystal structure and Hirshfeld surface analysis of hexyl 1-hexyl-2-oxo-1,2-dihydroquinoline-4-carboxylate By scripts.iucr.org Published On :: 2020-04-09 The asymmetric unit of the title compound, C22H31NO3, comprises of one molecule. The molecule is not planar, with the carboxylate ester group inclined by 33.47 (4)° to the heterocyclic ring. Individual molecules are linked by aromaticC—H⋯Ocarbonyl hydrogen bonds into chains running parallel to [001]. Slipped π–π stacking interactions between quinoline moieties link these chains into layers extending parallel to (100). Hirshfeld surface analysis, two-dimensional fingerprint plots and molecular electrostatic potential surfaces were used to quantify the intermolecular interactions present in the crystal, indicating that the most important contributions for the crystal packing are from H⋯H (72%), O⋯H/H⋯O (14.5%) and C⋯H/H⋯C (5.6%) interactions. Full Article text
ir Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of 3-butyl-2,6-bis(4-fluorophenyl)piperidin-4-one By scripts.iucr.org Published On :: 2020-04-09 The title compound, C21H23F2NO, consists of two fluorophenyl groups and one butyl group equatorially oriented on a piperidine ring, which adopts a chair conformation. The dihedral angle between the mean planes of the phenyl rings is 72.1 (1)°. In the crystal, N—H⋯O and weak C—H⋯F interactions, which form R22[14] motifs, link the molecules into infinite C(6) chains propagating along [001]. A weak C—H⋯π interaction is also observed. A Hirshfeld surface analysis of the crystal structure indicates that the most significant contributions to the crystal packing are from H⋯H (53.3%), H⋯C/C⋯H (19.1%), H⋯F/F⋯H (15.7%) and H⋯O/O⋯H (7.7%) contacts. Density functional theory geometry-optimized calculations were compared to the experimentally determined structure in the solid state and used to determine the HOMO–LUMO energy gap and compare it to the UV–vis experimental spectrum. Full Article text
ir 2-[(2,4,6-Trimethylbenzene)sulfonyl]phthalazin-1(2H)-one: crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-04-21 The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-trimethylbenzene)sulfonyl]-1,2-dihydrophthalazin-1-one}, features a tetrahedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the molecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supramolecular tape along the a-axis direction; tapes assemble without directional interactions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking interactions but, also H⋯H and C—H⋯C contacts. The calculation of the interaction energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking interactions. Full Article text
ir Crystal structure, Hirshfeld surface analysis and DFT studies of 6-bromo-3-(12-bromododecyl)-2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine By scripts.iucr.org Published On :: 2020-04-21 The title compound, C24H30Br2N4O2, consists of a 2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine entity with a 12-bromododecyl substituent attached to the pyridine N atom. The middle eight-carbon portion of the side chain is planar to within 0.09 (1) Å and makes a dihedral angle of 21.9 (8)° with the mean plane of the imidazolopyridine moiety, giving the molecule a V-shape. In the crystal, the imidazolopyridine units are associated through slipped π–π stacking interactions together with weak C—HPyr⋯ONtr and C—HBrmdcyl⋯ONtr (Pyr = pyridine, Ntr = nitro and Brmdcyl = bromododecyl) hydrogen bonds. The 12-bromododecyl chains overlap with each other between the stacks. The terminal –CH2Br group of the side chain shows disorder over two resolved sites in a 0.902 (3):0.098 (3) ratio. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (48.1%), H⋯Br/Br⋯H (15.0%) and H⋯O/O⋯H (12.8%) interactions. The optimized molecular structure, using density functional theory at the B3LYP/ 6–311 G(d,p) level, is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 2-phenyl-1H-phenanthro[9,10-d]imidazol-3-ium benzoate By scripts.iucr.org Published On :: 2020-04-24 In the title compound, C21H15N2+·C7H5O2−, 2-phenyl-1H-phenanthro[9,10-d]imidazole and benzoic acid form an ion pair complex. The system is consolidated by hydrogen bonds along with π–π interactions and N—H⋯π interactions between the constituent units. For a better understanding of the crystal structure and intermolecular interactions, a Hirshfeld surface analysis was performed. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)methyl]amino}benzoic acid dimethylformamide monosolvate By scripts.iucr.org Published On :: 2020-04-24 The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a dimethylformamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic molecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Caryl—CH2—NH—Caryl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supramolecular network, resulting from hydrogen-bonding interactions between the carboxylic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carboxylic group and additional C—H⋯π interactions. Hirshfeld surface analysis was performed to quantify the intermolecular interactions. Full Article text
ir Crystal structure and Hirshfeld surface analysis of 6-benzoyl-3,5-diphenylcyclohex-2-en-1-one By scripts.iucr.org Published On :: 2020-04-21 In the title compound, C25H20O2, the central cyclohexenone ring adopts an envelope conformation. The mean plane of the cyclohexenone ring makes dihedral angles of 87.66 (11) and 23.76 (12)°, respectively, with the two attached phenyl rings, while it is inclined by 69.55 (11)° to the phenyl ring of the benzoyl group. In the crystal, the molecules are linked by C—H⋯O and C—H⋯π interactions, forming a three-dimensional network. Full Article text
ir Synthesis, crystal structure and Hirshfeld surface analysis of N-(4-chlorophenyl)-5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxamide By scripts.iucr.org Published On :: 2020-04-30 The title compound, C19H17ClN4O2, was obtained via a two-step synthesis involving the enol-mediated click Dimroth reaction of 4-azidoanisole with methyl 3-cyclopropyl-3-oxopropanoate leading to the 5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxylic acid and subsequent acid amidation with 4-chloroaniline by 1,1'-carbonyldiimidazole (CDI). It crystallizes in space group P21/n, with one molecule in the asymmetric unit. In the extended structure, two molecules arranged in a near coplanar fashion relative to the triazole ring planes are interconnected by N—H⋯N and C—H⋯N hydrogen bonds into a homodimer. The formation of dimers is a consequence of the above interaction and the edge-to-face stacking of aromatic rings, which are turned by 58.0 (3)° relative to each other. The dimers are linked by C—H⋯O interactions into ribbons. DFT calculations demonstrate that the frontier molecular orbitals are well separated in energy and the HOMO is largely localized on the 4-chlorophenyl amide motif while the LUMO is associated with aryltriazole grouping. A Hirshfeld surface analysis was performed to further analyse the intermolecular interactions. Full Article text
ir Handbook of Industrial Crystallization. Third edition. Edited by Allan S. Myerson, Deniz Erdemir and Alfred Y. Lee. Cambridge University Press, 2019. Pp. 538. Price GBP 145 (hardcover). ISBN 9780521196185. By scripts.iucr.org Published On :: 2020-04-14 Full Article text
ir Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements By scripts.iucr.org Published On :: 2019-07-15 In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) – together with X-ray wavefunction refinement (XWR) – are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures – the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions. Full Article text
ir Cryo-EM structure of Neurospora crassa respiratory complex IV By scripts.iucr.org Published On :: 2019-06-26 In fungi, the mitochondrial respiratory chain complexes (complexes I–IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from Neurospora crassa in lipid nanodiscs as cytochrome c oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from Saccharomyces cerevisiae. Its ten subunits are conserved in S. cerevisiae and Bos taurus, but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to N. crassa. Full Article text
ir Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder By scripts.iucr.org Published On :: 2019-06-20 Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation. Full Article text
ir Magnetic field-induced magnetostructural transition and huge tensile superelasticity in an oligocrystalline Ni–Cu–Co–Mn–In microwire By scripts.iucr.org Published On :: 2019-07-11 Meta-magnetic shape-memory alloys combine ferroelastic order with ferromagnetic order and exhibit attractive multifunctional properties, but they are extremely brittle, showing hardly any tensile deformability, which impedes their practical application. Here, for the first time, an Ni–Cu–Co–Mn–In microwire has been developed that simultaneously exhibits a magnetic field-induced first-order meta-magnetic phase transition and huge tensile superelasticity. A temperature-dependent in situ synchrotron high-energy X-ray diffraction investigation reveals that the martensite of this Ni43.7Cu1.5Co5.1Mn36.7In13 microwire shows a monoclinic six-layered modulated structure and the austenite shows a cubic structure. This microwire exhibits an oligocrystalline structure with bamboo grains, which remarkably reduces the strain incompatibility during deformation and martensitic transformation. As a result, huge tensile superelasticity with a recoverable strain of 13% is achieved in the microwire. This huge tensile superelasticity is in agreement with our theoretical calculations based on the crystal structure and lattice correspondence of austenite and martensite and the crystallographic orientation of the grains. Owing to the large magnetization difference between austenite and martensite, a pronounced magnetic field-induced magnetostructural transition is achieved in the microwire, which could give rise to a variety of magnetically driven functional properties. For example, a large magnetocaloric effect with an isothermal entropy change of 12.7 J kg−1 K−1 (under 5 T) is obtained. The realization of magnetic-field- and tensile-stress-induced structural transformations in the microwire may pave the way for exploiting the multifunctional properties under the coupling of magnetic field and stress for applications in miniature multifunctional devices. Full Article text
ir MicroED with the Falcon III direct electron detector By scripts.iucr.org Published On :: 2019-08-17 Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements. Full Article text
ir R3c-type LnNiO3 (Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) half-metals with multiple Dirac cones: a potential class of advanced spintronic materials By scripts.iucr.org Published On :: 2019-10-16 In the past three years, Dirac half-metals (DHMs) have attracted considerable attention and become a high-profile topic in spintronics becuase of their excellent physical properties such as 100% spin polarization and massless Dirac fermions. Two-dimensional DHMs proposed recently have not yet been experimentally synthesized and thus remain theoretical. As a result, their characteristics cannot be experimentally confirmed. In addition, many theoretically predicted Dirac materials have only a single cone, resulting in a nonlinear electromagnetic response with insufficient intensity and inadequate transport carrier efficiency near the Fermi level. Therefore, after several attempts, we have focused on a novel class of DHMs with multiple Dirac crossings to address the above limitations. In particular, we direct our attention to three-dimensional bulk materials. In this study, the discovery via first principles of an experimentally synthesized DHM LaNiO3 with many Dirac cones and complete spin polarization near the Fermi level is reported. It is also shown that the crystal structures of these materials are strongly correlated with their physical properties. The results indicate that many rhombohedral materials with the general formula LnNiO3 (Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) in the space group R3c are potential DHMs with multiple Dirac cones. Full Article text