Capturing concentration-induced aggregation of nucleobases on a graphene surface through polarizable force field simulations

Abstract

Nucleobases have attracted significant attention from the scientific community as a viable candidate for the formation of supramolecular assemblies. Significant research interest has been turned toward developing novel molecules based on nucleobase synthons for applications in a wide spectrum of disciplines. Self-assemblies of nucleobases on a solid support have been observed in experimental studies, but they have not been accurately captured by generalized additive force field molecular dynamics simulations. We show that a polarizable force field can accurately capture the spontaneous self-assembly of higher-order structures in cytosine nucleobases that cannot be captured by nonpolarizable force fields. A gradual transition from an ordered 2D network to a sizable disordered network of hydrogen-bonded structures was observed upon increasing the concentration of nucleobases from 0.25 to 0.75 M. A graphene sheet was found to exert a significant influence on the stabilization of self-assemblies formed by cytosine nucleobases mediated by the π-π interactions. This methodology can be extended to investigate the self-assemblies of other small molecules on graphene-based solid supports.