核碱基/寡核苷酸与石墨烯和氧化石墨烯相互作用的建模：石墨烯表面充电和/或氧化的作用
Modeling of nucleobase/oligonucleotide interaction with graphene and graphene oxide: the role of charging and/or oxidizing the graphene surface
摘要：
我们分析了石墨烯（Gr）表面的电荷和氧化程度对其与胞嘧啶和寡核苷酸r（C）10相互作用的影响。这是一个计算研究，涉及DFT计算和分子动力学模拟。结果表明，胞嘧啶与氧化石墨烯（GO）的相互作用比与Gr强，而胞嘧啶与GO的相互作用的能量仅弱地取决于Gr氧化的程度。阴离子寡核苷酸r（C）10在中性和带正电荷的表面上的吸附与范德华相互作用形成的构象具有一定的相似性。此外，对于带电表面，库仑吸引力给出了显着的贡献，总的相互作用能。对于带负电荷的石墨烯表面，Gr表面与带负电荷的寡核苷酸磷酸骨架之间的静电排斥减弱总结合能。库仑排斥和范德华吸引之间的竞争导致形成独特的寡核苷酸构象，其中所有10个胞嘧啶堆叠在GR上。
英文摘要：
We analyze the influence of the charge and the degree of oxidation of the surface of graphene (Gr) on its interaction with cytosine and oligonucleotide r(C)10. This is a computational study involving DFT calculations and molecular dynamics simulations. It is shown that cytosine interacts stronger with graphene oxide (GO) than with Gr, while the energy of the interaction of cytosine with GO only weakly depends on the degree of the Gr oxidation. A correlation between the shifts of vibrational frequencies of cytosine due to complexation with GO and the degree of the Gr oxidation is found. The adsorption of anionic oligonucleotide r(C)10 onto neutral and positively charged surfaces has a certain conformational similarity to conformations formed with similar van der Waals interactions. Also, for charged surfaces, the Coulombic attraction gives a noticeable contribution to the total interaction energy. For a negatively charged graphene surface the electrostatic repulsion between Gr surface and negatively charged phosphate backbone of oligonucleotide weakens the total binding energy. Competition between the Coulombic repulsion and the van der Waals attraction results in formation of a unique oligonucleotide conformation where all 10 cytosines are stacked onto Gr.
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