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 poly[[aqua(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. 6‐Amino‐5‐nitropyridin‐2(1H)‐one crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair. The pair resembles the known intercalated cytosine pair. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.