Theoretical study of hydrogen bonds and electronic properties in hexagonal arrangements composed of self-assembled DNA analogues

Abstract

Aminopyrimidine, triaminopyrimidine, and cyanuric acid as artificial bases can be used to design and prepare multi-stranded DNA structures. In this manuscript, we theoretically investigate the stability of hydrogen-bonded hexagonal structures arising from the self-assembly of aminopyrimidine and cyanuric acid, as well as triaminopyrimidine and cyanuric acid in gas phase and in water. The influence of hydrogen bonds on the stability of hexagonal arrangements is examined by atoms in molecules and natural bond orbital analyses. Moreover, the mutual effects of hydrogen bonds on each other are also evaluated in the hexagonal structures using cooperative energy. Whereas the self-assembly of the hydrogen-bonded hexagonal arrangements may be considered to form new nanostructures, metal sensors, and ion channels, some electronic properties such as band gap, first ionization energy, electron affinity, electronegativity, electronic chemical potential, electrophilicity index, global chemical hardness, and chemical softness are theoretically estimated at M06-2X/6-311++G(d,p) level.