"Sandwiched" water molecule between pyrimidine bases and intra-molecular C-H ... Q hydrogen bonding in 5-nitro-1-(beta-D-ribosyluronic acid)-uracil monohydrate.

Abstract

IN the structure of crystalline 5-nitro-l-(β-D-ribosyluronic acid)-uracil monohydrate we have found a novel disposition of a water molecule—‘sandwiched’ between two parallel pyrimidine rings stacked 6.55 A apart. The water molecule is held in its place between these rings by a short O–H … OW (2.589 A) hydrogen bond from the carboxyl group of a uronic acid molecule belonging to an adjacent stack. We have also found that nitro groups adjacent to C–H bonds in the heterocyclic ring of nucleic acid bases apparently polarise these bonds and cause them to take part in strong hydrogen bonds to appropriate donors. The polarisation effect of the nitro group adjacent to the C–H bonds in pyrimidine is perhaps analogous to that of a positive charge adjacent to the C–H bonds in purines1.