Importance of Sugar-Phosphate Backbone and Counterions to First-Principles Modeling of Nucleobases

DFT-based first-principles calculations were carried out to understand the electronic structure difference among a backbone-free nucleobase, a backbone-containing Na counterion nucleotide, and a backbone-containing H counterion nucleotide and their difference in the adsorption on graphene and on graphitic-carbon nitride. The study discovered that the inclusion of a sugar-phosphate backbone changes the electron affinity of most nucleobases from electron acceptors to electron donors. The methyl-terminated backbone-free model cannot replicate the steric effect induced by the sugar-phosphate backbone during the adsorption of nucleobases on 2D materials. Overall, we established that the sugar phosphate backbone should be included in the study of DNA nucleobase adsorption on 2D material. We also showed that when it comes to the adsorption on 2D materials, the backbone-containing H counterion model is superior to the Na counterion model because the Na counterion produces a LUMO near the Fermi energy, which may significantly affect the interaction with the 2D material.