Synthesis, crystal structure and conformational analysis of an unexpected [1,5]dithiocine product of aminopyridine and thiovanillin

The condensation reaction of 2-mercapto-3-methoxybenzaldehyde with 3-aminopyridine afforded an unexpected N-alkylated [1,5]dithiocine instead of the N-salicylideneaniline. The proposed mechanism for this condensation involves a strong intramolecular hydrogen bond between the thiol and the amine groups, leading to a second condensation. The corresponding product, i.e. 4,10-dimethoxy-13-(pyridin-3-yl)-6H,12H-6,12-epiminodibenzo[b,f][1,5]dithiocine methanol 0.463-solvate, C21H18N2O2S2·0.463CH3OH, was characterized by single-crystal X-ray diffraction analysis. The supramolecular structure shows π-π stacking and S⋯S interactions in the crystal packing. Within the asymmetric unit, two geometries of the N atom are observed. Although a planar geometry should be expected, a pyramidal one is observed due to the crystal packing. The presence of the two geometries was further supported by density functional theory (DFT) calculations that show an electronic energy difference of less than 2 kJ mol ^-1 between the two conformers.