The crystal structures of 2'-deoxy-2'-fluorocytidine and 2'-deoxy-2'-fluorouridine

Abstract Two crystal structures of 2'-deoxy-2'-fluoronucleosides as determined from three dimensional X-ray data are reported. 2'-Deoxy-2'-fluorocytidine (dCfl) crystallises with two water molecules per nucleoside in space group P 2 1 ,2 1 ,2 1 , with a = 6.973(6), b = 26.307(15), c = 6.679(6) A, Z = 4. 2'-Deoxy-2'-fluorouridine (dUfl) crystallises in the same space group with a = 5.266(6), b = 9.426(8), c = 20.449(13) A, Z = 4. Both structures were solved by direct methods and refined to agreement indices R = 0.035 for dCfl and R = 0.041 for dUfl. The molecular conformation of dCfl was found to be very similar to that of cytidine: the orientation of the base with respect to the sugar is anti x = 28.90°, the conformation around the C(4')-C(5') bond is gauche-gauche , and the sugar ring exhibits the usual ribonucleoside puckering C(3')-endo with phase angle P = 22.14° and τ m = 39.20° . Hydrogen bonds extend throughout the crystal as infinite homodromic arrays along both a and c axes. Despite the presence of two water molecules, the fluorine atom is not involved in intermolecular bonding. In contrast to dCfl, dUfl differs significantly from uridine by its unusual sugar puckering C(4')- exo , O(1')- endo with P = 70.84° and τ m = 38.20°. This conformation appears to be stabilised by a close contact between the fluorine atom and the neighbour O(3') proton. Other structural parameters are in the usual range of ribonucleosides: the base is oriented as anti x = 54.40° and the C(4')-C(5') bond orientation is gauche-gauche .