N 6-Substituted 2-amino-4-chloro-5-formylpyrimidines: puckered versus planar pyrimidine rings, and hydrogen-bonded aggregation in zero, one, two and three dimensions

Abstract

The structures of 12 new N 6-substituted 2-amino-4-chloro-5-formylpyrimidines, where the N 6 substituent is of the type NHR or NR 1 R 2, have been determined. The intramolecular dimensions provide strong evidence for the development of polarized, charge-separated molecular-electronic structures, with the positive charge delocalized over the two exocyclic amino N atoms and with negative charge on the formyl O atom. This polarization appears to be independent of the significant puckering, in seven of the compounds, of the pyrimidine rings from planarity towards boat, twist-boat or screw-boat conformations. In 11 of the compounds studied here, N—H...N hydrogen bonds link pairs of molecules into centrosymmetric R_2^2(8) dimer units, and their overall crystal structures are determined by the patterns of hydrogen bonds by which these units are further linked. Examples are reported in which no further hydrogen bonding occurs; in which the R_2^2(8) dimers are linked into chains of rings, or into sheets; and in which sheets are formed by the π-stacking of hydrogen-bonded chains of rings. In the sole structure lacking the R_2^2(8) dimer motif, N—H...O and N—H...N hydrogen bonds cooperate to generate a three-dimensional framework structure.