5-Ethynyl-2 `-deoxycytidine: a DNA building block with a `clickable' side chain

Abstract

The title compound [systematic name: 4-amino-1-(2-deoxy-beta -D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C11H13N3O4, shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with chi = -149.2 (1)degrees for conformer (I-1) and -151.4 (1)degrees for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation (E-2, S-type), with P = 164.7 (1)degrees and tau(m) = 36.9 (1)degrees, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, T-3(2), S-type), with P = 189.2 (1)degrees and tau(m) = 33.3 (1)degrees. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.