Molecular structure of the cis-syn photodimer of d(TpT) (cyanoethyl ester)

The three-dimensional structure was determined by x-ray crystallography for d(Tp](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C₂₃H₃₀N₅O₁₂P · 2H₂O belong to the orthorhombic space group P2₁2₁2₁ (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for Tp] and in parentheses p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ?: 141° (86°). These represent half-chairs designated as ⁶H₁ (Tp]) and ₆H⁵ (p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The Tp] segment has the syn glycosyl conformation, a ²T₃ sugar pucker, and gauche^? conformation at C4′-C5′; the p]T segment is anti, ³T₄, trans. The C5′-O5′ torsion of the p]T unit is –124.5°, and the C3′-O3′ torsion of the Tp] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.