Fluorinated enamines of nucleobases as precursors of nucleoside analogues. Synthesis, spectroscopic and structural studiesThis article is part of a themed issue on Biophosphates, and is dedicated to Professor Wojciech J. Stec on the occasion of his 70th birthday.Electronic supplementary information (ESI) available: Crystal data and structure refinement, shortest intramolecular and intermolecular contacts for (Z)-9b; NMR spectra of compounds. CCDC reference number 716978. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/b9nj00617f

The 1H and 19F NMR spectra of N-α-fluoro-β-trifluoromethylenamines and isostructural N-β-fluoro-β-trifluoromethylenamines of nucleobases dissolved in CDCl3and DMSO-d6have shown distinct differences associated with the conformational conversion between the Zand Estereoisomers. In the Estereoisomer the tetrafluoropropenyl group is rotated relative to the heteroring plane, whereas the Zstereoisomer assumes the most planar structure. The flat conformation of the Zstereoisomer is stabilised by internal hydrogen bonding between Cα–H and the carbonyl oxygen (pyrimidinic bases) or the endocyclic nitrogen (purinic bases). Large variations in the magnitudes of the chemical shifts of Cβ–H, Cα–F, C6–H and C8–H were observed, i.e.the chemical shift increased with increasing polarity and ability of DMSO-d6to establish intermolecular hydrogen bonds in competition with intramolecular hydrogen bonds. The (Z)-N4-benzoyl-N1-(1,3,3,3-tetrafluoroprop-1-enyl)cytosine crystals undergo a phase transition at 230 K induced by the tetrafluoropropenyl substituent reorientations. Between 300 and 230 K the molecules are present in two conformations, and below 230 K the molecules gradually assume five conformations, remaining in a stable equilibrium with intermolecular forces, evidenced by single-crystal X-ray diffraction. [ABSTRACT FROM AUTHOR]