Unusual ribose conformation in a ternary copper(II) 2′deoxyribonucleotide complex

Abstract

The ternary metal deoxyribonucleotide complex [Cu(bzim)(5′-dGMP)(H₂O)₃](bzim = benzimidazole, 5′-dGMP = 2′-deoxyguanosine 5′-monophosphate) has been prepared and the structure analysed by X-ray diffraction. The compound crystallizes in the space group P1 with a= 7.069(6), b= 13.959(10), c= 14.204(12)Å, α= 75.12(6), β= 94.15(6), γ= 97.98(6)° and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least-squares procedures on the basis of 2813 observed [I 3σ(I)] reflections to final R and R′ values of 0.050 and 0.052 respectively. There are two independent molecules in the asymmetric unit and both copper(II) centres have square-pyramidal co-ordination geometry. An unusual feature of the structure is the co-ordination of the metal by N(7) of the base, in the presence of a π-aromatic amine, bzim. The structure is stabilized by intermolecular base–bzim stacking. The nucleotides of both the molecules have an anti conformation about the glycosyl bond, and a gauche-gauche conformation about the C(4′)–C(5′) bond. A feature of particular interest is the unusual sugar conformation. The base furanose rings of the two nucleotide molecules adopt C(3′)-exo/C(2′)-endo pucker and C(3′)-exo pucker respectively.