Visualization of host-guest interactions between a modified nucleoside andorganic moieties. Crystal structures of 2 '-deoxy 5 '-O-trityluridine and 2 '-deoxy 5'-O-tritylthymidine with benzene, toluene, xylene, trimethylbenzene, cyclohexane and water

This paper describes the crystal structures of 2'-deoxy 5'-O-trityluridine( 5'-TU) and 2'-deoxy 5'-O-tritylthymidine (5'-TT) containing different organ ic moieties. There are two crystallographically independent nucleoside mole cules present in the asymmetric units of all the structures. Uracil and thy mine bases of the 2'-deoxy 5'-trityl uridine(5'-TU) and all the 2'-deoxy 5' -tritylthymidine structures are in an anti conformation with respect to the ir furanose rings. Thymine bases of molecules A and B form symmetric self p airs through N(3)-O(2) hydrogen bonds, whereas uracil bases are not engaged in hydrogen bonding between themselves. Ribose moieties of both molecules of 2'-deoxy 5'-trityithymidine with benzene and toluene are in the C(2')- e ndo conformations while molecules A and B of 2'-deoxy 5'-tritylthymidine co ntaining xylene, trimethylbenzene, cyclohexane and water are in the C(3')- endo and C(1')- exo conformations, respectively. Both ribose moieties of 5' -TU show C(3')- endo puckering. The conformation about the C(4')-C(5') bond for all the 2'-deoxy 5'-tritylthymidine structures is g(+), contrasting wi th the g(-) for the 5'-TU structure. Benzene and toluene molecules stack be tween TT base pairs, while xylene, trimethylbenzene and cyclohexane are ori ented obliquely to the base pairs. 2'-Deoxy 5'-tritylthymidine containing t oluene shows a type V C-H ...pi interaction between the methyl group of tol uene and the thymine base. Remarkably, the 2'-deoxy 5'-tritylthymidine-cont aining xylene, trimethylbenzene, cyclohexane and water structures demonstra te a strong type I O-H ...pi interaction between the ribose O(3') and the t hymine base seen only in 1.25% of the structures. Molecular packing and hyd rogen bonding are discussed.