Isomorphic repeat units for putative information-bearing H-bonded duplexes. Part I. Pyrimidine base pairs with polyamide backbone

Abstract

Abstract Synthetic information-bearing macromolecular H-bonded duplexes built up from suitable sub-units are the aim of many attempts in design and synthesis. Repeat units for such duplexes had been earlier designed computationally, consisting of two isomorphic H-bonded pyrimidine base pairs with information-storing potential like the DNA base pairs. A backbone for this set of four pyrimidine bases is now designed to make complete repeat units suitable for incorporation into the putative polymeric duplex. Each strand of the duplex has the repetitive form (-CH2-CHB-CO-NH-)n with B as a pyrimidine base, so the backbone has a polyamide structure. Each backboned monomer is thus defined as NH2-CH2-CHB-COOH (2-amino-1-pyrimidylpropionic acid). The four monomeric units are paired through H-bonding to yield two backboned pairs, studied using density functional theory at the ωB97XD/6-311++G(d,p) level. Parallel and antiparallel backbone orientations are considered, each yielding two backboned H-bonded pairs. The results predict these H-bonded repeat unit pairs to be isomorphic and stable, suggesting a periodic structure for the putative H-bonded macromolecular duplex, which would possess the same information-bearing capacity as DNA.