An electron density study on cis-1-(2-hydroxymethyl-cyclopentenyl)uracils

A topological charge electron density analysis using the Atoms in Molecules (AIM) theory on B3LYP/6-31++G**//B3LYP/6-31G* charge densities was performed for the series of the five cis-1-(2-hydroxymethyl-Δn-cyclopentenyl))uraciles (n=1–5). These compounds are carbocyclic analogues of nucleosides that belong to an important class of antiviral or antitumoral compounds where the hydroxymethyl group and the heterocyclic base are bonded to adjacent carbons of a cyclopentene ring. The change of position of the double bond within the cyclopentene ring does not significantly affect the electron distribution of the base (that always carries a substantial negative charge), but alters the orientation of the base and the hydroxymethyl group (3-, and 4-cyclopentenyl derivarives being the exception as they present very similar conformations).