X-ray structural and conformational studies of [5'-(tryptaminocarbonyl)-2'-deoxyribofuranosyl]thymine, a model compound for the study of the interaction between indole and thymine rings.

The crystal structure of [5'-(tryptaminocarbonyl)-2'-deoxyribofuranosyl]-thymine was determined by an X-ray method in order to elucidate a fundamental feature of interaction between indole and thymine rings. Refinement resulted in a conventional R value of 0.043. The bond lengths and angles are in good agreement with those of the related compounds. The deoxyribose unit has a C2'-endo envelope conformation, and orientation of the thymine base with respect to the sugar is anti. In the crystal, the double layers of the thymidine moieties are formed by the hydrogen bonds around a two-fold screw axis and a single layer of the indole moieties is held together by van der Waals contact, and they are alternately packed parallel to the bc-plane. The conformation of the molecule is an extended form, and the intra- and intermolecular interactions between the indole and thymine rings are not observed in the crystal because the dihedral angle of both rings is approximately a right angle (95.8 degrees), and there is no hydrogen bond or short contact between these rings. It was, however, suggested from the ultraviolet spectroscopic study in dilute solution and from the conformational analysis by energy calculation that the most stable conformation is a folded form with the intramolecular stacking interaction between indole and thymine rings. Therefore, the extended form observed in the crystal might be caused by the packing interaction between the neighboring molecules.