Synthesis, C-13 NMR, and X-ray crystal structure of N6,N9-octamethylenepurinecyclophane

Abstract

The synthesis and structure determination of N6,N9-octamethylenepurine cyclophane by single crystal X-ray diffraction is reported. The cyclophane was prepared from 6-chloropurine and 8-aminooctanoic acid as starting materials. The aminooctyl fragment was first attached to N9 of 6-chloropurine by means of the Mitsunobu reaction and cyclization to the cyclophane effected by nucleophilic attack of the amino group at the C6 position and displacement of chloride ion. Reversing the reaction strategy did not result in formation of the cyclophane. Crystals of the cyclophane were monoclinic, P2/n, a = 9.620(3), b = 12.266(3), c = 11.994(2), Å, β = 111.25(2)°, Z = 4. Intensities were measured with a Nicolet P3 diffractometer and MoKα radiation at room temperature. The structure was solved by direct methods and refined to R = 0.0683, Rw = 0.0493 based on 1730 reflections. The molecule shows some strain, but bond lengths and angles are normal. Attempts to relieve the strain are made by a small distortion of the purine rings and bending of the N6 and C8′ atoms out of the planes to which they are attached (0.314(4), 0.459(5) Å). Further, the N6,H6,Cl′ group is twisted by 30° from the pyrimidine plane and the torsion angles in the aliphatic chain are distorted from the idealized 60, 120, 180° (average, 13.6°; range 5.1–24.9°). These distortions result in some weakening of the π-bonding in the adenine moiety. Keywords: purinophane synthesis, nucleophilic aromatic substitution, conformational analysis, crystal structure.