Visualization of Host--Guest Interactions Between a Modified Nucleoside and Organic Moieties. Crystal Structures of 2'-Deoxy 5'-O-trityluridine and 2'-Deoxy 5'-O-tritylthymidine with Benzene, Toluene, Xylene, Trimethylbenzene, Cyclohexane and Water

• Published in: Journal of Inclusion Phenomena and Macrocyclic Chemistry 2000-05, Vol.37 (1-4), p.281-298
• Main Authors: Prahadeeswaran, D, Kolappan, S, Krishnan, R, Seshadri, T P
• Format: Article
• Language: English
• ISSN: 0923-0750; 1573-1111
• DOI: 10.1023/A:1008158711587

This paper describes the crystal structures of 2'-deoxy 5'-O-trityluridine(5'-TU) and 2'-deoxy 5'-O-tritylthymidine (5'-TT) containing different organic moieties. There are two crystallographically independent nucleoside molecules present in the asymmetric units of all the structures. Uracil and thymine 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 their furanose rings. Thymine bases of molecules A and B form symmetric self pairs 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')-endo conformations while molecules A and B of 2'-deoxy 5'-tritylthymidine containing xylene, trimethylbenzene, cyclohexane and water are in the C(3')-endo and C(1')-exoconformations, 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 with the g for the 5'-TU structure. Benzene and toluene molecules stack between TT base pairs, while xylene, trimethylbenzene and cyclohexane are oriented obliquely to the base pairs. 2'-Deoxy 5'-tritylthymidine containing toluene shows a type V C---H{/content/l37j331hwx0x5q72/xxlarge946.gif} {/content/l37j331hwx0x5q72/xxlarge960.gif} interaction between the methyl group of toluene and the thymine base. Remarkably, the 2'-deoxy 5'-tritylthymidine-containing xylene, trimethylbenzene, cyclohexane and water structures demonstrate a strong type I O---H{/content/l37j331hwx0x5q72/xxlarge946.gif} {/content/l37j331hwx0x5q72/xxlarge960.gif} interaction between the ribose O(3') and the thymine base seen only in 1.25% of the structures. Molecular packing and hydrogen bonding are discussed.