William T. A. Harrison

The crystal structures of two hydrochloride salts of pyridoxal–N-acylhydrazone–Q (Q = heterocyclic aromatic ring) derivatives, viz. (E)-3-hydroxy-5-(hydroxymethyl)-2-methyl-4-{[(pyridin-4-ylformamido)imino]methyl}pyridin-1-ium chloride dihydrate, C₁₄H₁₅N₄O₃ ⁺·Cl⁻·2H₂O, (I), and (E)-3-hydroxy-5-(hydroxymethyl)-2-methyl-4-{[(pyrimidin-2-ylformamido)imino]methyl}pyridin-1-ium chloride dihydrate, C₁₃H₁₄N₅O₃ ⁺·Cl⁻·2H₂O, (II) are described. The cations, which are protonated at the pyridine N atom of the pyridoxal ring, have similar overall conformations: the dihedral angles between the pyridoxal ring and the terminal aromatic ring are 12.63 (12) and 6.11 (15)° for (I) and (II), respectively. Each cation features an intramolecular O—H...N hydrogen bond, which closes an S(6) ring, but a difference arises in the conformation of the C—C—C—O fragment terminated by the the ring carbon atom bonded to the side chain and the O atom of the hydroxymethyl group: gauche for (I) and anti for (II). The extended structures of (I) and (II) feature numerous strong (N—H and O—H donors) and weak (C—H donor) hydrogen bonds. In (I), the NH_p (pyridine) grouping links to the terminal N atom of the pendant unprotonated pyridine ring of an adjacent cation to generate [010] chains, whereas the NH_h (hydrazide) and OH_hm (hydroxymethyl) moieties link to chloride ion acceptors. In (II), the NH_p and OH_hm groupings bond to chloride anions whereas NH_h bonds to a water molecule. Hydrogen-bonded chains of water molecules occur in (I) and centrosymmetric tetramers in (II). The Hirshfeld surfaces of (I) and (II) are computed and the structures of related compounds are briefly compared.

The ethanol–water layered syntheses and crystal structures of the coordination polymers [Cd(C₁₇H₂₂N₂)₂(H₂O)₂]·2(ClO₄)·C₁₇H₂₂N₂·C₂H₅OH 2 and [Cd(C₁₇H₂₂N₂)₂(NO₃)₂] 3 are reported, where C₁₇H₂₂N₂ is a flexible spacer, 1,7-bis(4-pyridyl)heptane. In compound 2, trans-CdO₂N₄ octahedral nodes are linked by pairs of bridging ligands to result in [001] looped polymeric chains. The chains stack in the [100] direction to form (010) pseudo layers. Sandwiched between them are secondary sheets of free ligands, perchlorate ions and ethanol solvent molecules. Hydrogen bonds between these species help to consolidate the structure. Compound 3 contains trans-CdO₂N₄ octahedral nodes as parts of regular 4⁴ nets, which propagate in the (103) plane. Three independent nets are interpenetrated.

Different supramolecular motifs are formed by the crystallisation of amino-substituted derivatives of quinoxaline, pyrimidine and pyridazine. These were made from the corresponding mono- or dichlorinated heterocycles by a nucleophilic displacement reaction. The pyridine-type nitrogen atoms activate the chlorine atoms because they can stabilise a negative charge, which forms when the amine attacks the ring. One amino group can be attached under mild conditions in hot ethanol or acetonitrile, but the first then deactivates the ring so the second requires more forceful conditions using a pressure vessel at 150 °C. Butylamine is frequently used because it reduces the polarity of the product, making it easier to purify and isolate. The extended structure of the quinoxaline derivatives 16–18 show a common ‘pincer’ hydrogen-bond motif, with a quinoxaline nitrogen atom accepting two N–H···N hydrogen bonds, giving a spiral or helical axis. The chain symmetries are 4₁, 2₁ and 3₁, respectively, depending on the substituents. A stereoview of each is shown. The pyrimidine derivatives 19, 12, 20, 14 and 21 form hydrogen-bonded tapes and compound 20 forms inversion dimers.

Building blocks have been identified that can be functionalised by sequential nucleophilic aromatic substitution. Some examples are reported that involve the formation of cyclic benzodioxin and phenoxathiine derivatives from 4,5-difluoro-1,2-dinitrobenzene, racemic quinoxaline thioethers, and sulfones from 2,3-dichloroquinoxaline and (2-aminophenylethane)-2,5-dithiophenyl-4-nitrobenzene from 1-(2-aminophenylethane)-2-fluoro-4,5-dinitrobenzene. Four X-ray single-crystal structure determinations are reported, two of which show short intermolecular N–O^…N “π hole” contacts.

Microorganisms are a valuable source of pharmaceutically active chemicals, serving as scaffolds for synthesis as well as lead structures. Investigating novel biomes frequently yields intriguing chemistry; the Atacama Desert in Chile is one such example. This study reports the isolation of a new reduced anthracycline-related compound from the Atacama Desert-derived bacterium Saccharothrix S26. Structural characterisation was achieved by one-dimensional and two-dimensional NMR, HR-LCMS, and X-ray crystallography. The compound was tested against the ESKAPE pathogens, bovine mastitis-related pathogens, and the fungal strain Cryptococcus neoformans, but no antimicrobial activity was observed.

In the title compound, {(C6H8N)[Zn2(HPO3)2(H2PO3)]}n, the constituent ZnO4, HPO3 and H2PO3 polyhedra of the inorganic component are linked into (010) sheets by Zn—O—P bonds (mean angle = 134.4°) and the layers are reinforced by O—H⋯O hydrogen bonds. The protonated templates are anchored to the inorganic sheets via bifurcated N—H⋯(O,O) hydrogen bonds.

The absolute configuration and stability of two thianthrene chiral sulfoxides has been determined by means of X-ray single-crystal structure determinations. The analyses and configurations allow verification that the diastereomeric sulfoxides are stable in solution and are not interconverting, which has been suggested in some studies of sulfoxides. The two thianthrene sulfoxides have slightly different R_f values, which allowed their separation using flash chromatography on silica. The spots run back-to-back, which posed a challenge for their separation. The pure, separated compounds in solution remain as separate, single spots on a Thin Layer Chromatography (TLC) plate.

The reaction of either 2-aminophenol or 2-(N-methylamino)-phenol with 1,2-difluoro-4,5-dinitrobenzene and sodium carbonate in EtOH gives 2,3-dinitrophenoxazines. One nitro group, conjugated to the aryl ether, was displaced from 2,3-dinitro-10-methylphenoxazine with different nucleophiles: BuNH2, KOEt, and KOH. The reaction of 2-aminothiophenol with 1,2-difluoro-4,5-dinitrobenzene under the same conditions gives 2,3-dinitrophenothiazine. This reacted with BuNH2 forming 2-butylamino-3-nitrophenothiazine. The dihedral angles of the different compounds are compared.

A porous structure formed from sheets with cavities and two close packed structures were crystallised from building blocks prepared from 2,4-difluoronitrobenzene, a diamine linker and n-butylamine. The porous structure crystallised from a flexible building block prepared using 1,4-diaminobutane as linker. The close packed structures were prepared using either piperazine or 1,4-bis(aminomethyl)benzene as a linker and have less conformational freedom.