众所周知，甲基化剂通过将甲基阳离子(CH3+)转移到DNA碱基的亲核位点上进行DNA甲基化，而DNA甲基化与癌症和其他病理状况有关。因此，清除CH3+离子以保护DNA不受甲基化是非常重要的。石墨烯被认为是一种多功能材料，可在传感器、抗氧化剂、药物传递和DNA测序等广泛领域中使用。在这项工作中，我们在理论上研究了CH3+离子与石墨烯表面的相互作用，旨在了解原始石墨烯是否可以作为底物吸附由有害甲基化剂产生的CH3+阳离子。计算得到的吸附能表明，一、二和三个CH3+离子在石墨烯上的吸附是有利的，因为形成的加合物在气相和水介质中都具有相当的稳定性。Bader电荷转移分析和态密度(DOS)计算还表明，石墨烯和CH3+离子之间存在着很强的相互作用。因此，我们的结果表明，原始石墨烯可用作清除CH3+离子的底物。我们采用PBE泛函、超软赝势和平面波基组进行自旋极化密度泛函理论(DFT)计算，波函数和电荷密度的动能截断分别为40 Ry和400 Ry，以研究甲基化剂CH3+离子在未修饰石墨烯表面的吸附。使用Grimme的DFT-D2方法来估计范德华力相互作用。还对z方向应用了“偶极矫正”进行吸附研究。采用Marzari-Vanderbilt扩展和Monkhorst-Pack k点网格进行布里渊区采样。在吸附研究中，考虑了一个6×6的石墨烯超单元，垂直单元尺寸为18 Å。使用Bader电荷分析法估计了甲基离子与石墨烯之间的电荷转移。隐式溶剂模型(SCCS)用于估计水介质的溶剂效应。所有计算均使用QUANTUM ESPRESSO软件包进行。©2023. Springer-Verlag GmbH Germany, part of Springer Nature.

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.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.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.