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

Depending on the conditions, reaction of 6-chloropyrimidine-2,4(1H,3H)-dion e 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 uracilylbetai nes, 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 syst ems. 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 DM SO-dB at room temperature as well as ESI- and MALDIMS prove homo-intramolec ular hydrogen bonding of the uracilylhetarenium salts and the uracilylbetai nes, respectively. An X-ray single-crystal analysis shows the uracilylbetai ne 7 associated with a second molecule via two strong hydrogen bonds, thus forming a centrosymmetric dimer. In contrast to the Watson-Crick pairing mo de of natural pyrimidine nucleobases, O(2) and N(3)-H of the uracilylbetain es are involved in hydrogen bonding. This geometry of the dimer 7=7 gives r ise to a coupling of the semiempirically calculated dipole moments of the m onomeric cross-conjugated betaines.