Intercalation of water molecules between pyrimidine bases Crystal structure of 1-methyl-5-nitrouracil monohydrate

Abstract

The crystal structure of 1-methyl-5-nitrouracil monohydrate exhibits a novel intercalation of water molecules between pyrimidine bases that are stacked 6.2 Å apart. There is no direct hydrogen bonding along individual stacks, but a water molecule in one stack is hydrogen-bonded to three neighboring bases from adjacent stacks. These three bases are located in the same plane as the water molecule to which they are hydrogen-bonded. This mode of hydrogen bonding leads to infinite planes of parallel sheets of bases and water molecules at layers y ≈ 0 and $\text{1}\text{2}$ with no inter-sheet hydrogen bonding. On the basis of this intercalation and our model building studies, it is suggested that it would be stereochemically possible for a water molecule to act as a ‘spacer’ and stabilize the DNA helix, should a base be turned outside due to dynamical fluctuations of the DNA helix or non-complementary base opposition. Crystals of the title compound are monoclinic, space group C2, with cell constants a = 14.676(1), b = 6.243(1), c = 8.363(1)A, β = 100.88(2)°, Z = 4. Using 950 diffractometer data, the crystal structure of 1-methyl-5-nitrouracil monohydrate was determined by a direct inspection of the (|E|² − 1) Patterson function and refined to an R of 0.062.