The unusual (syn-/ anti-)2 conformation of a di-meth-oxy-pyrimidyl-based tennimide

Acta Crystallogr E Crystallogr Commun. 2023 Aug 23;79(Pt 9):837-841. doi: 10.1107/S2056989023006837. eCollection 2023 Sep 1.

Abstract

The tennimide macrocycle, (I) (C52H40N16O16.0.167H2O), was synthesized from 2-amino-4,6-di-meth-oxy-pyrimidine and pyridine-2,6-dicarbonyl dichloride. Compound (I) represents the first tennimide incorporating pyridine rings in the macrocycle scaffold. In the macrocycle ring, the carbonyl groups at each successive dicarbon-yl(pyridine) moiety adopt the (syn/anti)2 conformation. This contrasts with all previously reported tetra-imide macrocycles, which exhibit the (syn)4 conformation. The effect is to close any potential cavity or niche by having two of the central pyridine C5N rings aligned close to each other [with closest pyridine CgCg ring centroid separations of 3.5775 (19) Å; closest C⋯C = 3.467 (5) Å]. A partial occupancy water mol-ecule (with s.o.f. = 0.167), resides with its oxygen atom on a twofold axis at hydrogen-bonding distances to the carbonyl O atom, in a mol-ecular niche between two pyridine rings. Macrocyles of (I) have all six C=O groups and all eight meth-oxy O atoms present on the macrocycle surface. However, all twelve N atoms are effectively shielded on steric grounds from any potential inter-molecular inter-actions. The remaining two C=O O atoms inter-act with the partial occupancy water mol-ecule via two O-H⋯O=C hydrogen bonds. Macrocycles of (I) stack as one-dimensional chains along the b-axis direction with primary inter-molecular inter-actions involving weak C-H⋯O=C/OCH3/H2O contacts. Chains inter-lock weakly via meth-oxy-meth-oxy C-H⋯O inter-actions into two-dimensional sheets.

Keywords: conformation; crystal structure; macrocycle; meth­oxy; pyridine; pyrimidine; tennimide; tetra­mer.

Grants and funding

Funding for this research was provided by: Dublin City University.