X-ray crystal and ab initio structures of 3′,5′-di-O-acetyl-N(4)-hydroxy-2′-deoxycytidine and its 5-fluoro analogue:: Models of the N(4)-OH-dCMP and N(4)-OH-FdCMP molecules interacting with thymidylate synthase

The crystal and molecular structures of the 3',5'-di-O-acetyl-N(4)-hydroxy-2'-deoxycytidine molecule and its 5-fluoro congener have been determined by X-ray single crystal diffraction. The 3',5'-di-O-acetyl-N(4)-hydroxy-5-fluoro-2'-deoxycytidine molecule crystallizes in the space group C2 with the following unit cell parameters: a = 21.72 angstrom , b = 8.72 angstrom, c = 8.61 angstrom , and beta = 90.42 degrees. 3',5'-di-O-acetyl-N(4)-hydroxy-2'-deoxycytidine also belongs to the monoclinic space group C2 and the unit cell parameters are: a = 39.54 angstrom, b = 8.72 S angstrom, c = 22.89 angstrom , and beta = 95.26 degrees. The non-fluorine analogue demonstrates a rare example of crystal structure with five symmetry-independent molecules in the unit cell. All the molecules in both crystal structures have the sugar residue anti oriented with respect to the base, as well as have the N(4)-OH residue in cis conformation relatively to the N(3)-nitrogen atom. In addition to the molecular geometries from X-ray experiment, the optimized molecular geometries have been obtained with the use of theoretical ab initio calculations at the RHF/6-31G(d) level. The corresponding geometric parameters in the molecules of 3',5'-di-O-acetyl-N(4)-hydroxy-2'-deoxycytidine and its 5-fluoro congener have been compared. The differences including the C(5)=C(6) bond shortening and C(4)-C(5)-C(6) angle widening in the fluorine analogue are discussed in this paper in relation to the molecular mechanism of enzyme, thymidylate synthase, inhibition by N(4)-hydroxy-2'-deoxycytidine monophosphate and its 5-fluoro congener.