Structure Investigations of Molecular Crystals Containing the Ring System Cyclo-tris(2,6-pyridylformamidine) by Means of X-ray Powder Diffraction and Force-Field-Constrained Rietveld Refinement

Abstract

A new heterocyclic compound, cyclo-tris(2,6-pyridylformamidine), was synthesized as a highly crystalline powder-like substance from which very small whiskers were produced by a sublimation technique. By rotatingcrystal and powder diffraction measurements, a set of structural data were obtained which were ®tted mathematically to a structural model. The ®tting procedure included geometry optimization by ab initio calculations, crystal structure and X-ray diffraction pattern simulation as well as structure re®nement based on the newly developed Rietveld algorithm BGMN 1 under force-®eld constraints. A single-crystal structure re®nement could not be carried out because of the small size of the whiskers. In order to obtain the atomic coordinates a new procedure incorporating a powder diffraction pattern re®nement was used. Cyclo-tris(2,6pyridylformamidine) crystallizes in a monoclinic unit cell with a = 28.18 (1), b = 14.67 (1), c = 4.428 (1) A Ê , = 90.10 (2) . The symmetry was determined as P2 1 /a. The expected threefold symmetry of the cyclic compound was disturbed in the crystallized state, in agreement with solid-state NMR investigations. The best approximation was obtained when water molecules were additionally packed into the unit cell. ² Present address: HU È LS Silicone GmbH, Friedrich-von-Heyden-Platz 1, D-01610 Nu È nchritz, Germany.Fig. 1. One of the boundary structures of an isolated trimer molecule (note that positions numbered 12, 14, 32, 34, 52 and 54 are each occupied by an H atom).

Polymers containing formamidine groups. VI. Structural influences on the formation of cyclic trimers

“…A symmetric and an asymmetric isomer could be observed in solution at low temperatures. X‐ray powder‐diffraction investigations also confirmed the structure 22. One important conclusion drawn from our investigations is that the amidine groups adopt E ‐syn conformation in the cyclic trimer.…”

“…An unexpected result was obtained with 2,6‐diaminopyridine as the monomer. Its conversion with TEOF resulted almost quantitatively in the formation of a defined cyclic trimer 20, 22…”

Hydrogen bond directed synthesis of pyridazine and naphthyridine containing macrocycles

“…Macrocycle 2 adopts a near planar structure in a manner that points the formamidine C-H hydrogen atoms towards the interior of Interestingly, the crystal structure of macrocycle 2 indicates that the formamidine groups have asymmetric orientations. 17,18 Macrocycle 2 packs into an interdigitated columnar structure with face-to-face aromatic p-stacking (ESI{). It is believed that both hydrogen bonding and steric interactions are involved in macrocyclization and that the formation of these intramolecular H-bonds in the transition state directs the irreversible macrocyclic ring closing reaction to occur at such high yields in the absence of a template.…”

NMR Studies of the Tautomerism of Cyclo-tris(4-R-2,6-pyridylformamidine) in Solution and in the Solid State

“…However, from model considerations we cannot exclude conformational mobility allowing the formation of such dimers as a source of proton exchange. Small deviations from a planar ring were reported by Friedel et al for Ia in the solid state . A larger twist of the pyridine moieties out of the plane of the amidine groups seems possible in solution.…”

“…Some examples are given in Figure . For Ia , a structure analysis by combined X-ray powder diffraction and force-field-constrained Rietveld refinement proposed a nonplanar structure similar to A (Figure ) …”