Alkali metal cations control over nucleophilic substitutions on aromatic fused pyrimidine-2,4-[1H,3H]-diones: towards new PNA monomers

In this paper we report synthesis of a series of aromatic fused pyrimidine-2,4(3H)-dione-1-yl acetic acid and new PNA monomers containing these polycyclic nucleobase analogues. Introduction of a fused aromatic ring onto the 5,6-positions of the pyrimidine-2,4-[1H,3H]-diones brings about the steric effects and the charge delocalization, both weakening the nucleophilic substitutions on the 1- and 3-positions. We found that alkali metal cations play an important role in this alkylation reaction. LiOH brings out a much more efficient alkylation than NaOH does, while KOH nearly does not work on this reaction. Such influences from the alkali metal cations are probably due to that the charge-pairing interactions between the pyrimidine-2,4-dioxide anions and the alkali metal cations rearrange the charge distribution around the whole aromatic system and increase the negative charge distribution on the 1- and 3-nitrogen atoms, which then strengthens the nucleophilic reactivity on these positions.