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Propane-1,3-diaminium squarate dihydrate, C3H12N22+·C4O42−·2H2O, results from the proton-transfer reaction of propane-1,3-di amine with squaric acid and subsequent crystallization from aqueous medium. The title compound crystallizes in the tetragonal crystal system (space group P4bm) with Z = 2. The squarate dianion belongs to the point group D4h and contains a crystallographic fourfold axis. The propane-1,3-diaminium dication exhibits a C2v-symmetric all-anti conformation and resides on a special position with mm2 site symmetry. The orientation of the propane-1,3-diaminium ions makes the crystal structure polar in the c-axis direction. The solid-state supramolecular structure features a triperiodic network of strong hydrogen bonds of the N—H⋯O and O—H⋯O types. [ABSTRACT FROM AUTHOR]

The title compound, 3‐[(benzo‐1,3‐dioxol‐5‐yl)amino]‐4‐methoxycyclobut‐3‐ene‐1,2‐dione, C12H9NO5 (3), is a precursor to an antimycobacterial squaramide. Block‐shaped crystals of a monoclinic form (3‐I, space group P21/c, Z = 8, Z′ = 2) and needle‐shaped crystals of a triclinic form (3‐II, space group P‐1, Z = 4, Z′ = 2) were found to crystallize concomitantly. In both crystal forms, R22(10) dimers assemble through N—H...O=C hydrogen bonds. These dimers are formed from crystallographically unique molecules in 3‐I, but exhibit crystallographic Ci symmetry in 3‐II. Twinning by pseudomerohedry was encountered in the crystals of 3‐II. The conformations of 3 in the solid forms 3‐I and 3‐II are different from one another but are similar for the unique molecules in each polymorph. Density functional theory (DFT) calculations on the free molecule of 3 indicate that a nearly planar conformation is preferred. [ABSTRACT FROM AUTHOR]

4-(4-nitrophenyl)thiomorpholine, the title compound, has been used as a precursor for the corresponding 4-thiomorpholinoaniline, which is a useful building block in medicinal chemistry. The crystal and molecular structures of the title compound, however, have not been described thus far. We synthesized the title compound by means of a nucleophilic aromatic substitution reaction of 4-fluoronitrobenzene and thiomorpholine and structurally characterized it by X-ray crystallography, DFT calculations, and Hirshfeld surface analysis. In the crystal, the molecule exhibits an approximately CS-symmetric structure, with the nitrogen-bound 4-nitrophenyl group in a quasi axial position on the six-membered thiomorpholine ring in a low-energy chair conformation. The solid-state structure of the title compound is markedly different from that of its morpholine analogue. This can be ascribed to the formation of centrosymmetric dimers through intermolecular C–H···O weak hydrogen bonds involving the methylene groups adjacent to the sulfur atom and face-to-face aromatic stacking. [ABSTRACT FROM AUTHOR]

Betaines of squaric acid have gained research interest because of their structural and spectral properties. We elucidated the crystal and molecular structure of the triethylammonium betaine of squaric acid (1) by X-ray crystallography, IR, and NMR spectroscopy augmented by Hirshfeld surface analysis and DFT calculations. The crystal structure determination using Hirshfeld atom refinement reveals that the resonance hybrid structure with partial enolate character of the two lateral squaric acid C=O groups describes 1 best. The solid-state supramolecular structure features weak intermolecular C−H···O hydrogen bonds. The number of C=O bands in the IR spectrum in the solid-state is consistent with local C2v symmetry of the squaric acid residue in 1. The 13C NMR signals of this group in solution were assigned based on 2D NMR experiments and computational prediction using the Gauge-Independent Atom Orbital (GIAO) method. The present study provides the first structural characterization of a betaine of squaric acid containing a four-coordinate nitrogen atom directly attached to the four-membered ring. [ABSTRACT FROM AUTHOR]

Trehalose conjugates of 3-hydroxychromone (3HC) dyes have previously been utilized as fluorescence labels to detect metabolically active mycobacteria with a view to facilitating point-of-care detection of mycobacterial pathogens, especially Mycobacterium tuberculosis. We subjected the 3HC dye 2-(6-(diethylamino)benzofuran-2-yl)-3-hydroxy-4H-chromen-4-one (3HC-2) to a combined X-ray crystallography and density functional theory (DFT) study, and conducted preliminary fluorescence labelling experiments with the model organism Mycobacterium aurum. In the crystal, 3HC-2 exhibits an s-cis conformation of the chromone and the benzofuran moieties about the central C–C bond. According to DFT calculations, the s-cis conformer is about 1.8 kcal mol−1 lower in energy than the s-trans conformer. The solid-state supramolecular structure features hydrogen-bonded dimers and π...π stacking. Fluorescence microscopy revealed fluorescence of M. aurum cells treated with the dye trehalose conjugate 3HC-2-Tre in the GFP channel. It was concluded that s-cis is the preferred conformation of 3HC-2 and that the generally considered non-pathogenic M. aurum can be labelled with the fluorescence probe 3HC-2-Tre for convenient in vitro drug screening of new antimycobacterial agents. [ABSTRACT FROM AUTHOR]

1,3-Benzo­thia­zin-4-ones (BTZs) are a promising new class of anti-tuberculosis drug candidates, some of which have reached clinical trials. The title compound, the benzamide derivative [2-chloro-3-nitro-5-(tri­fluoro­meth­yl)phen­yl](piper­id­in-1-yl)methanone, C13H12ClF3N2O3, occurs as a side product as a result of competitive reaction pathways in the nucleophilic attack during the synthesis of the BTZ 8-nitro-2-(piperidin-1-yl)-6-(tri­fluoro­meth­yl)-1,3-benzo­thia­zin-4-one, following the original synthetic route, whereby the corresponding benzoyl iso­thio­cyanate is reacted with piperidine as secondary amine. In the title compound, the nitro group and the nearly planar amide group are significantly twisted out of the plane of the benzene ring. The piperidine ring adopts a chair conformation. The tri­fluoro­methyl group exhibits slight rotational disorder with a refined ratio of occupancies of 0.972 (2):0.028 (2). There is structural evidence for inter­molecular weak C—HO hydrogen bonds. [ABSTRACT FROM AUTHOR]

The synthesis of ethyl 2-[(4-methyl­pyridin-2-yl)amino)-4-(pyridin-2-yl)thia­zole- 5-carboxyl­ate via the Hantzsch reaction and partial in situ transesterification during recrystallization from methanol-d4 to the d3-methyl ester, resulting in the title solid solution, ethyl 2-[(4-methyl­pyridin-2-yl)amino)-4-(pyridin-2-yl)thia­zole-5-carboxyl­ate–d3-methyl 2-[(4-methyl­pyridin-2-yl)amino)-4-(pyridin-2-yl)thia­zole-5-carboxyl­ate (0.88/0.12), 0.88C17H16N4O2S·0.12C16D3H11N4O2S, is reported. The refined ratio of ethyl to d3-methyl ester in the crystal is 0.880 (6):0.120 (6). The pyridine ring is significantly twisted out of the plane of the approximately planar picoline thia­zole ester moiety. N—H...N hydrogen bonds between the secondary amino group and the pyridine nitro­gen atom of an adjacent symmetry-related mol­ecule link the mol­ecules into polymeric hydrogen-bonded zigzag tapes extending by glide symmetry in the [001] direction. There is structural evidence for intra­molecular NS chalcogen bonding and inter­molecular weak C—H...O hydrogen bonds between adjacent zigzag tapes. [ABSTRACT FROM AUTHOR]

Abstract: The crystal and molecular structure of [Cu2(H2valdien)2](NO3)2 (1), whereby H2valdien is the known Schiff base ligand N1,N3-bis(3-methoxysalicylidene)diethylenetriamine, is reported. In 1, two H2valdien ligands join two CuII ions in a chelate-spacer-chelate mode, in which the protonated aliphatic secondary amine moieties represent the spacers, to form a double helix. Both CuII ions in the homodinuclear cationic complex exhibit similar distorted square-planar N2O2 coordination spheres. The axially chiral molecular structure of the [Cu2(H2valdien)2]2+ complex features intramolecular π···π stacking and N-H⋯O hydrogen bonds in the crystal. Compound 1 crystallizes in the Sohncke space group P21, with a = 14.165(3), b = 13.7755(13), c = 21.1185(4) Å, β = 102.199(4)°, and with two enantiomeric molecules in the asymmetric unit (Z′ = 2). The two crystallographically unique [Cu2(H2valdien)2]2+ enantiomers are related by pseudo inversion symmetry.Graphical Abstract: The pseudo centrosymmetric chiral Z′ = 2 crystal structure (space group P21) of [Cu2(H2valdien)2](NO3)2, whereby H2valdien is the known Schiff base ligand N1,N3-bis(3-methoxysalicylidene)diethylenetriamine, is reported. [ABSTRACT FROM AUTHOR]

• The solid-state structures of lepidine (4-methylquinoline) and three mineral acid salts are reported. • The molecules of lepidine and the lepidinium cations in the salts are π⋅⋅⋅π-stacked in the crystal structures. • N−H⋅⋅⋅Cl or N−H⋅⋅⋅O hydrogen bonding is observed in the crystal structures of the salts. The crystal and molecular structures of free-base lepidine (4-methylquinoline, 1) and the mineral acid salts lepidinium chloride (2), nitrate (3) and dihydrogen phosphate (4) are reported. Compound 1 was studied by differential scanning calorimetry and in situ capillary cryocrystallography. In the crystal structures, the molecules of free-base lepidine in 1 and the lepidinium cations in 2 – 4 are face-to-face π⋅⋅⋅π-stacked. The quinoline nitrogen atom is not involved in directional intermolecular interactions such as weak hydrogen bonds in 1. In the salts 2 – 4 , proton transfer to the quinoline nitrogen atom and N−H⋅⋅⋅Cl (in 2) and N−H⋅⋅⋅O (in 3 and 4) hydrogen bonding is observed. Hirshfeld surface analysis reveals that lepidinium salts 2 and 3 form hydrogen-bonded dimers in the crystal and confirms that the packing of 4 is dominated by hydrogen-bonded dihydrogen phosphate anion chains. [Display omitted] [ABSTRACT FROM AUTHOR]

The crystal structures of 5,10,15,20-tetra(4-hydroxyphenyl)-21,23H-porphyrin nitrobenzene hexasolvate (1), 5,10,15,20-tetra(4-hydroxyphenyl)porphyrinatonickel(II) nitrobenzene hexasolvate (2) and 5,10,15,20- tetra(4-hydroxyphenyl)porphyrinatocopper(II) nitrobenzene hexasolvate (3) are described. Compounds 1-3 crystallise isomorphously in the non-centrosymmetric tetragonal space group P4cc with Z = 8. There are three crystallographically distinct porphyrin molecules, two of which contain fourfold axes perpendicular to the porphyrin plane. The remaining one contains a twofold axis perpendicular to the porphyrin ring system. The porphyrin building blocks are joined into a three-dimensional network through self-complementary O-H...O hydrogen bonding interactions between 4-hydroxyphenyl groups of adjacent molecules. The space occupied by the nitrobenzene solvent molecules is remarkably large at ca. 61.5% of the unit cell volume in 1-3. [ABSTRACT FROM AUTHOR]

The title compound, [Zn(SiF6)(C12H8N2)2]·CH3OH, contains a neutral heteroleptic tris-chelate ZnII complex, viz. [Zn(SiF6)(phen)2] (phen is 1,10-phenanthroline), exhibiting approximate molecular C2 point-group symmetry. The ZnII cation adopts a severely distorted octahedral coordination. As far as can be ascertained, the title complex represents the first structurally characterized example of a ZnII complex bearing a bidentate-bound hexafluorosilicate ligand. A density functional theory study of the isolated [Zn(SiF6)(phen)2] complex was undertaken to reveal the influence of crystal packing on the molecular structure of the complex. In the crystal structure, the methanol solvent molecule forms a hydrogen bond to one F atom of the hexafluorosilicate ligand. The hydrogen-bonded assemblies so formed are tightly packed in the crystal, as indicated by a high packing coefficient (74.1%). [ABSTRACT FROM AUTHOR]

Abstract: The crystal and molecular structure of (E)-N,N′-dicyclohexylacetamidine (1) is described. Crystalline material of 1 was obtained by sublimation. Single-crystal X-ray analysis revealed a centrosymmetric triclinic structure (space group ) with six molecules in the asymmetric unit (Z′=6). The six crystallographically distinct molecules all exhibit an E-syn structure, but differ in the orientation of the cyclohexyl groups about the central acetamidine moiety. In the crystal, the molecules form polymeric helices via NN hydrogen bonds. The crystal structure comprises two crystallographically distinct helices of opposite handedness (P and M form). The characterisation of 1 in the solid-state is augmented by powder X-ray diffraction, infrared spectroscopy and thermal analysis. Density functional theory (DFT) structure optimisation and frequency calculation were performed at the B3LYP/cc-pVTZ level. The DFT results for the isolated molecule are compared with the experimental results for the solid-state. [Copyright &y& Elsevier]

Abstract: Racemic forms of 1,1′-bi-(2-naphthol) (BINOL) monopivalate (rac-1) and its 6-nitro substitute (rac-2) were structurally characterized by X-ray crystallography. Molecules of opposite chirality form dimers in the crystalline state of rac-1 through OO hydrogen-bonds between the free hydroxy and the pivalate carbonyl group. In contrast, polymeric hydrogen-bonded homo chiral chains were encountered for rac-2. In both rac-1 and rac-2, the dihedral angle between the naphthyl systems shows a significant deviation compared to the approximate 90° angle of BINOL. As expected, compound rac-1 exhibits an increased angle (108.80(4)° and 102.09(4)°) as one of the hydroxy groups in BINOL is replaced by the sterically demanding pivaloyl ester. In contrast, the angle is decreased to 72.0(2)° in the nitro derivative rac-2. [ABSTRACT FROM AUTHOR]

We report the synthesis, spectroscopic and structural elucidation of two prolinamide derivatives of squaric acid, i.e. prolinamide ester amide of squaric acid ethyl ester (1) and prolinamide diamide of squaric acid dihydrate (2). Both compounds crystallize in non-centrosymmetric space groups, monoclinic P21 (1) and orthorhombic P212121 (2), respectively. For first time in the literature the crystal structure of homodiamide of amino acid amide of squaric acid is reported. The data for heterodiamides is also absent. Supramolecular zig-zag chains by hydrogen bonds of H2N–C=O⋯HNH (3.020 Å) and HNH⋯O=C(Sq) (2.972 Å) types with the participation of amide and squaric acid (Sq) fragments, –C=O–NH2 and O=C(Sq) are refined in (1). A helix supramolecular structure is formed in (2) by moderate intermolecular HNH⋯O=C(NH2) hydrogen bond with length of 2.947 Å. The two crystallographical non-equivalent water molecules stabilized the helix by interactions of types HOH⋯O=C(Sq) (2.917 Å), HOH⋯O=C(NH2) (2.899 Å), H2O⋯NH2(C=O) (2.972 Å), respectively. Optical and magnetic properties are investigated with a view to explain the correlation structure-properties of the newly synthesized molecules. [Copyright &y& Elsevier]

Abstract: (E)-4-(Hydroxyiminomethyl)-pyridinium hydrogenoxalate (1) and bis((E)-4-(hydroxyiminomethyl)-pyridinium) squarate (2) were synthesized and their crystal structures determined by means of single crystal X-ray diffraction. The structures of (1) and (2) consist of infinite layers and chains, respectively, formed by (1): N–H···O (2.852(2), 2.827(2)Å) and O–H···O (2.665(2)Å) and (2): N–H···O (2.620(2)Å) and O–H···O (2.600(1)Å) intermolecular hydrogen bonds between the cations and anions. Hydrogenoxalate ions form chains within the infinite layers by strong interanionic O–H···O interactions (2.583(2)Å). Antiperiplanar conformations of the cations for (1) and (2) (CCOH) dihedral angle of 178.9(1)° (1) and 179.4(1)° (2) are observed. Spectroscopic properties both in solution and in the solid state were elucidated by means of 1H- and 13C-NMR, UV-spectroscopy and conventional and linear polarized IR- (IR-LD) spectroscopy. Quantum chemical calculations at the DFT, MP2 and CIS level of theory and the 6-31++G∗∗ basis set were employed for predicting and supporting experimentally observed optical propertied and electronic structures of the protonated (E)-4-(hydroxyiminomethyl)-pyridine. [Copyright &y& Elsevier]

The simplest alkyl aryl ether, anisole (methoxybenzene), C7H8O, is a feedstock chemical and is widely used in the pharmaceutical industry. The structure of anisole at 100 K, as determined by single-crystal X-ray analysis, is reported. A crystal (m.p. 236 K) suitable for X-ray diffraction was obtained from the melt. The title compound crystallizes in the centrosymmetric space group P21/ c with two molecules in the asymmetric unit ( Z′ = 2). Both crystallographically distinct molecules adopt a virtually flat ( Cs-symmetric) conformation. The arrangement of the molecules in the solid state appears to be governed by close packing. No face-to-face π-π stacking of the molecules is observed, but rather edge-to-face interactions result in a herringbone packing motif. [ABSTRACT FROM AUTHOR]

• The crystal structure of L-serinium hydrogensquarate (CSD refcode: HUQNIT), published in this journal very recently is revised. • Problems are due to assignment of the absolute configuration and placement of disordered hydrogen atoms. • HUQNIT actually represents the CSD entry PAZCUO, published more than 20 years ago. The crystal structure of L-serinium hydrogensquarate (CSD refcode: HUQNIT), published in this journal very recently [Tyagi et al., J. Mol. Struct. 1224 (2021) 129190], is revised. Problems arise from the assignment of the absolute configuration of the serinium cation and the positioning of disordered hydrogen atoms of the hydrogensquarate anion. The correct structure of L-serinium hydrogensquarate was published more than 20 years ago [CSD refcode: PAZCUO; Kolev et al., Z. Kristallogr. NCS 213 (1998) 169-170]. [ABSTRACT FROM AUTHOR]

Abstract: The title compound was synthesized and characterized by single crystal X-ray diffraction and solid-state polarized IR-spectroscopy of oriented colloids in a nematic host. The compound crystallizes in the monoclinic space group P21/c and its structure consists of a 3D supramolecular network of tyrammonium cations, water and sulfate anions directed by intermolecular hydrogen bonding interactions. Two non-equivalent tyrammonium cations are observed with pseudo T and T trans configurations, respectively. The vibrational characteristics of the non-equivalent molecules are assigned using solid-state polarized IR-spectroscopy. The structural and spectroscopic data are compared with theoretical calculations at the MP2/6-31++G∗ level of theory and basis set using the tyrammonium cation heptahydrate as a model system. [Copyright &y& Elsevier]

The components of the title compound, C6H14N+·C4HO4-·- 0.5H2O, are connected by moderate intermolecular N—H⋯O hydrogen bonds between the anions and cations into infinite three-dimensional networks. The cyclohexylammonium cation interacts with the solvent molecule by means of an N—H⋯O hydrogen bond. The hydrogensquarate anions form α chains through strong O—H⋯O interactions. [ABSTRACT FROM AUTHOR]