Stability of Nucleobases and Base Pairs Adsorbed on Graphyne and Graphdiyne

Abstract

A theoretical understanding of the structure and energetics of the interaction of nucleobases (NBs) and amino acids with extended carbon-based network structures is crucial for understanding phenomena occurring at the nanobio interface. Herein, we investigate the adsorption of NBs and base pairs (BPs) on the new network materials in the carbon family, graphyne (GY), and graphdiyne (GDY) using dispersion-corrected density functional theory (ωB97XD functional) with a basis set of triple-ζ quality. Systematic investigations on the orientation dependence of the interaction of each of the NBs with a series of model compounds along with their superstructures reveal that the binding strengths of NBs on GY and GDY follow the order G > A > C > T > U, while those of BPs follow the order GC > AT > AU. The NBs and the BPs are found to adsorb at distances of ∼3 Å from the GY and GDY sheets, and the adsorption strengths are higher for GY than GDY. The small decrease in the hydrogen bond energies of the BPs subsequent to adsorption suggests that GY and GDY can serve as promising templates for the self-assembly of DNA and RNA. Our first-principles studies on how the NBs interact with GY and GDY can serve as a first and significant step toward the aim of understanding the interactions of DNA and RNA with GY and GDY as well as designing biomolecular devices based on GY and GDY. We believe that our findings will motivate several studies toward understanding the interface of biology and the nanoworld.