Comparative investigation of uridine and Hachimoji RNA base interaction with single-walled carbon nanotube

Single-walled carbon nanotubes (SWCNTs) are promising platforms for biosensing because their electronic properties are sensitive to molecular adsorption. While canonical nucleic acid bases have been extensively studied, little is known about how synthetic Hachimoji bases interact with nanotube surfaces. In this study, we investigate the adsorption of uridine (rU) and the Hachimoji base S (rS) on a finite (5,5) SWCNT fragment. The study aims to compare binding strength and electronic effects between canonical and synthetic bases within a finite gas-phase SWCNT model and to examine whether the two bases show distinguishable local adsorption behavior.

All geometries of the isolated molecules and the SWCNT+rU and SWCNT+rS complexes were fully optimized using density functional theory (DFT) with the PBEh-3c composite method in ORCA. The adsorption complexes were analyzed on an 8 Å hydrogen-terminated (5,5) SWCNT fragment, with the bases initially placed approximately parallel to the nanotube sidewall at ~ 3.1 Å. HOMO-LUMO gaps were calculated for each system: rU (~ 7.5 eV), rS (~ 7.7 eV), SWCNT (~ 3.21 eV), SWCNT + rU (~ 3.19 eV), and SWCNT + rS (~ 3.20 eV). Interaction energies of the optimized complexes were computed using the supermolecule approach, yielding - 0.43364 eV for SWCNT+rU and - 0.55405 eV for SWCNT + rS. Mulliken population analysis was performed to quantify fragment charge redistribution, showing only minor net charge transfer.