Site selectivity of halogen oxygen bonding in 5- and 6-haloderivatives of uracil
Seven 5-and 6-halogenated derivatives of uracil or 1-methyluracil (halogen = Cl, Br, I) were
studied by single crystal X-ray diffraction. In contrast with pure 5-halouracils, where the presence
of N-H…O and C-H…O hydrogen bonds prevents the formation of other intermolecular interactions,
the general ability of pyrimidine nucleobases to provide electron donating groups to halogen
bonding was confirmed in three crystals and cocrystals containing uracil with the halogen atom at
the C6 position. In the latter compounds, among the two nucleophilic oxygen atoms in the C=O
moiety, only the urea carbonyl oxygen O1 can act as halogen bond acceptor, being not saturated by
conventional hydrogen bonds. The halogen bonds in pure 6-halouracils are all rather weak, as
supported by Hirshfeld surface analysis. The strongest interaction was found in the structure of 6-
iodouracil, which displayed the largest (13%) reduction of the sum of van der Waals (vdW) radii for
the contact atoms. Despite this, halogen bonding plays a role