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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]

Abstract: A combined X-ray and density functional theory (DFT) study on the structure of 5,10,15,20-tetra(3-pyridyl)porphyrin (1) has been undertaken. Single-crystal X-ray diffraction revealed molecules of 1 in the ααββ conformation with molecular and crystallographic C i point group symmetry. The porphyrin macrocycle shows no marked deviation from planarity. Positional disorder of the pyrrole NH atoms is discussed. The crystal packing of 1 is achieved through common off-set stacking of the porphyrin entities. Bulk material of 1 was further investigated by scanning electron microscopy (SEM) and powder X-ray diffraction (PXRD). The crystal and molecular structure of 1 is compared to the known structures of the unsolvated free-base 2- and 4-pyridyl isomers. The molecular structure of 1 in solution has been investigated by variable temperature 1H NMR spectroscopy in CDCl3. [Copyright &y& Elsevier]

• BTZ043 crystallizes with two diastereomeric conformers featuring pseudo symmetry. • VT 13C NMR in CDCl 3 indicates a rotational barrier of ΔG ǂ = 14.6 ± 1 kcal mol−1. • DFT calculations reveal two barriers to rotation about the C2 BTZ −N piperidine bond. A structural study of (S)-2-(2-methyl-1,4-dioxa-8-azaspiro[4.5]decan-8-yl)-8-nitro-6-(trifluoromethyl)-4 H -benzo[ e ][1,3]thiazin-4-one (BTZ043), a promising antitubercular drug candidate, is reported. The chiral compound crystallizes in the triclinic system (space group P 1) with two molecules in the asymmetric unit (Z ' = 2), which are related by pseudo inversion symmetry. The two crystallographically distinct molecules represent diastereomeric conformers, which can be transformed to one another by an approximate 180° rotation about the C2 BTZ −N piperidine bond connecting the (S)-2-methyl-1,4-dioxa-8-azaspiro[4.5]decane side chain to C2 of the benzothiazinone (BTZ) scaffold. Variable temperature 13C NMR measurements of BTZ043 in CDCl 3 in the range 248-333 K indicate a rotational barrier of E a = 17.1 ± 1 kcal mol−1 and ΔG ǂ = 14.6 ± 1 kcal mol−1. DFT calculations reveal two barriers to rotation about the C2 BTZ −N piperidine bond, one larger than the other by 4.1 kcal mol−1. [Display omitted] [ABSTRACT FROM AUTHOR]