Crystal structures of deprotonated nucleobases from an expanded DNA alphabet

Reported here is the crystal structure of a heterocycle that implements a donor–donor–acceptor hydrogen‐bonding pattern, as found in the Z component 6‐amino‐5‐nitropyridin‐2(1H)‐one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely polyaqua(μ₆‐2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ido)sodium]–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1)], denoted Z‐Sod, {Na(C₅H₄N₃O₃)(H₂O)]·C₅H₅N₃O₃·H₂O}_n, and ammonium 2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ide–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1), denoted Z‐Am, NH₄⁺·C₅H₄N₃O₃⁻·C₅H₅N₃O₃·H₂O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.