Design Rules for the Generation of Stable Quartet Phases of Nucleobases over Two-Dimensional Materials

Abstract

Out of the quest to decipher the nature of self-assembly and the underlying thermodynamics for the formation of nucleobase quartets on two-dimensional (2D) materials, molecular dynamics simulations and free-energy calculations are performed for three nucleobases, namely guanine, xanthine, and hypoxanthine. Graphene, hexagonal boron nitride (h-BN), and black phosphorene (black Pn) are shown to maintain all quartet structures over wide ranges of temperatures, and their thermal stabilities follow the order hypoxanthine > guanine > xanthine. Disruption of the structural integrity for quartets is studied at various temperatures employing a careful hydrogen bond analyses protocol. Decay profile for a quartet on different surfaces decreases in the order h-BN > graphene > black Pn. The thermal stability of a single quartet is governed by the free energy gained through quartet formation (ΔΔGsQ), whereas the decay rates in an assembly are influenced by interquartet interactions during collision and ΔΔGsQ. h2D-C2N, a novel 2D porous material is demonstrated to disrupt all types of quartets because of extensive hydrogen bonding with the polar surface. It is revealed that 2D materials, which stabilize nucleobases through π–π stacking and have small corrugation in the free-energy landscape for in-plane molecular translation, are able to stabilize quartets, whereas the presence of localized electron density and hydrogen bond donor sites along with large free-energy barriers for translocation lead to quartet disruption.