Charge-separated modified nucleobases.: On π-interactions and hydrogen bonding of self-complementary cationic and betainic uracils

Depending on the conditions, reaction of 6-chloropyrimidine-2,4(1H,3H)-dione 1 with heteroaromatics such as 4-(dimethylamino)pyridine, 4-(pyrrolidin-1-yl)pyridine, pyridine, and 1-methylimidazole, respectively, results in the formation of uracil-6-ylhetarenium salts or cross-conjugated uracilylbetaines, the intramolecular interactions of which are examined. In addition, 1 forms uncharged 1:1 pi-stacks with DMAP and PPY, the electronic properties of which are inverted in relation to natural nucleobase-heteroaromatic systems. The geometry of the ct-complexes is governed by steric effects as well as by the frontier orbitals of the uracil and the heteroaromatic, whereas the dipole moments are almost completey uncoupled. 1H NMR experiments in DMSO-dB at room temperature as well as ESI- and MALDIMS prove homo-intramolecular hydrogen bonding of the uracilylhetarenium salts and the uracilylbetaines, respectively. An X-ray single-crystal analysis shows the uracilylbetaine 7 associated with a second molecule via two strong hydrogen bonds, thus forming a centrosymmetric dimer. In contrast to the Watson-Crick pairing mode of natural pyrimidine nucleobases, O(2) and N(3)-H of the uracilylbetaines are involved in hydrogen bonding. This geometry of the dimer 7=7 gives rise to a coupling of the semiempirically calculated dipole moments of the monomeric cross-conjugated betaines.