Role of graphene in scavenging methyl cations: a DFT study

Abstract

Context: It is known that methylating agents methylate DNA by transferring a methyl cation (CH₃⁺) to the nucleophilic sites in DNA bases and DNA methylation is implicated in cancer and other pathological conditions. Therefore, it is important to scavenge CH₃⁺ ion in order to protect DNA from methylation. Graphene is considered to be a versatile material for use in a wide variety of fields including sensors, antioxidants, drug delivery and DNA sequencing. In this work, we have theoretically investigated the interaction of CH₃⁺ ions with graphene surface with an aim to understand if pristine graphene can be used as a substrate to adsorb CH₃⁺ cations generated from harmful methylating agents. The computed adsorption energies show that adsorption of one, two and three CH₃⁺ ions on graphene is favourable as the adducts thus formed are found to be substantially stable in both gas phase and aqueous media. The Bader charge transfer analysis and density of states (DOS) calculation also indicate a strong interaction between graphene and CH₃⁺ ions. Thus, our results show that pristine graphene can be used as a substrate to scavenge CH₃⁺ ions.

Methods: The spin polarised density functional theory (DFT) calculations employing PBE functional, ultrasoft pseudopotentials and plane wave basis set having kinetic energy cut-offs of 40 Ry and 400 Ry, respectively, for wave functions and charge densities were carried out to study the adsorption of CH₃⁺ ion(s) on the pristine graphene surface. The Grimme's DFT-D2 method was used for the estimation of van der Waals interactions. The 'dipole correction' along z-direction was also applied for adsorption study. The Marzari-Vanderbilt smearing and Monkhorst-Pack k-point grid were employed for the Brillouin zone sampling. A 6 × 6 graphene supercell with a vertical cell dimension of 18 Å was considered for the adsorption study. The charge transfer between the CH₃⁺ ion(s) and graphene was estimated using Bader charge analysis. The implicit solvation model (SCCS) was used to estimate the solvent effect of aqueous media. All the calculations were performed using QUANTUM ESPRESSO package.

Keywords: DFT; DNA methylation; Graphene; Methyl cation; Radical scavenging.