Interaction and Biocompatibility Analysis of Monolayer Quasi-Hexagonal-Phase Fullerene with DNA: Molecular Dynamics Simulations

The rapid advancement of nanotechnology in biomedicine has spurred widespread interest in the interactions between 2D carbon nanomaterials and biological macromolecules. Monolayer quasi-hexagonal-phase fullerene (qHP-C₆₀), which shares structural and functional similarities with C₆₀ fullerene derivatives, is regarded as a promising yet underexplored platform. In this study, all-atom molecular dynamics simulations were employed to systematically investigate the interactions of monolayer qHP-C₆₀ with both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The results revealed two distinct binding modes. ssDNA underwent spontaneous and strong adsorption onto the qHP-C₆₀ surface, adopting a flattened conformation with a highly favorable binding free energy, which led to significant structural disruption. In contrast, dsDNA interacted only weakly via terminal base pairs, maintaining a perpendicular orientation that preserved the integrity of its double-helical structure. Energy decomposition analysis further identified van der Waals interactions, facilitated by π-π stacking, as the primary driving force for adsorption in both systems. This study not only enhances the fundamental understanding of nanomaterial-DNA interactions but also provides theoretical guidance for designing safer two-dimensional fullerene-based materials for biomedical applications.