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

Prahadeeswaran, D and Kolappan, S and Krishnan, R and Seshadri, TP (2000) 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. In: Journal of Inclusion Phenomena and Macrocyclic Chemistry, 37 (1-4). pp. 281-297.

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Abstract

This paper describes the crystal structures of 2’-deoxy 5’-O-trityluridine(5’-TU) and20-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 20-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’)-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 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…\pi 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…\pi 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.

Item Type:	Journal Article
Publication:	Journal of Inclusion Phenomena and Macrocyclic Chemistry
Publisher:	Springer
Additional Information:	Copright of this article belongs to Springer.
Keywords:	modified nucleosides;conformation;DNA;RNA.
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	30 Jul 2008
Last Modified:	19 Sep 2010 04:48
URI:	http://eprints.iisc.ac.in/id/eprint/15370

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