Kumawat Rameshwar L, Jha Sanjiv K, Tayo Benjamin O, Sherrill C David
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Mathematics and Science Division, GateWay Community College, Maricopa Community Colleges, Phoenix, Arizona 85034, United States.
J Phys Chem B. 2025 Sep 22. doi: 10.1021/acs.jpcb.5c03247.
Graphene, a low-dimensional material, has shown significant promise in bioelectronics over the past two decades. Most research in this field has focused on pristine graphene. However, experimentally fabricated two-dimensional (2D) graphene and one-dimensional (1D) graphene nanoribbons (GNRs) often contain impurities, such as Stone-Wales (sw) and divacancy (dv) defects. In this study, we conducted a comparative analysis of the adsorption behavior of DNA nucleobases-adenine (A), guanine (G), thymine (T), and cytosine (C)─on three types of graphene nanoribbon (GNR) surfaces: pristine (prGNR), divacancy-defected (dvGNR), and Stone-Wales-defected (swGNR). Using semilocal (PBE) and van der Waals-corrected density functional theory methods (vdW-DF2 and PBE-D2), we evaluated the binding energies of the nucleobases on the different GNR surfaces. Our results show that defected GNRs exhibit less negative binding energies for all nucleobases compared to prGNR when dispersion interactions are taken into account. The binding energies calculated using PBE, PBE-D2, and vdW-DF2 methods range from -0.06 to -0.10, -0.55 to -0.80 and -0.59 to -0.78 eV, respectively. The vdW-DF2 method effectively captures vdW interactions, with binding energies following the order G > A > T > C. These interactions result in weak binding between nucleobase and the π-states of the GNR surfaces, inducing a small interfacial dipole and a shift in the energy bandgap. Quantum transport analysis reveals that while pristine GNRs exhibit distinct conduction channels, defects─such as dv and sw configurations─introduce localized states that interact with delocalized ones, generating pronounced characterized by sharp dips in the transmission spectra. Physisorption of DNA nucleobases on different GNR surfaces induces unique resonance peaks in the transmission function, influenced by the type and position of defects. Conductance sensitivity analysis indicates prGNR as a promising candidate for nucleobase detection, leveraging for precise electronic measurements. However, defected GNRs also exhibit significant sensitivity. Furthermore, Current-Voltage (-) analysis identifies dvGNR devices as the most effective for nucleobase detection due to their high current sensitivity and distinct responses across nucleobases. While prGNR devices detect certain nucleobases, they show less consistent performance due to uniform current trends at higher biases. In contrast, swGNR devices effectively differentiate all four nucleobases through distinct current signals in the 0.6-0.8 V range. These findings underscore the potential of defect-engineered GNRs for the next-generation DNA sequencing applications.
石墨烯作为一种低维材料，在过去二十年里在生物电子学领域展现出了巨大的潜力。该领域的大多数研究都集中在原始石墨烯上。然而，通过实验制备的二维（2D）石墨烯和一维（1D）石墨烯纳米带（GNRs）通常含有杂质，如石-威尔士（sw）和双空位（dv）缺陷。在本研究中，我们对DNA核碱基——腺嘌呤（A）、鸟嘌呤（G）、胸腺嘧啶（T）和胞嘧啶（C）——在三种类型的石墨烯纳米带（GNR）表面上的吸附行为进行了比较分析：原始（prGNR）、双空位缺陷（dvGNR）和石-威尔士缺陷（swGNR）。使用半局域（PBE）和范德华校正密度泛函理论方法（vdW-DF2和PBE-D2），我们评估了核碱基在不同GNR表面上的结合能。我们的结果表明，当考虑色散相互作用时，与原始GNR相比，有缺陷的GNR对所有核碱基的结合能负性更小。使用PBE、PBE-D2和vdW-DF2方法计算的结合能分别在-0.06至-0.10、-0.55至-0.80和-0.59至-0.78 eV范围内。vdW-DF2方法有效地捕捉了范德华相互作用，结合能顺序为G > A > T > C。这些相互作用导致核碱基与GNR表面的π态之间的弱结合，诱导出一个小的界面偶极子并使能带隙发生偏移。量子输运分析表明，虽然原始GNR表现出明显的传导通道，但诸如dv和sw构型等缺陷会引入与离域态相互作用的局域态，在传输谱中产生以尖锐下降为特征的明显变化。DNA核碱基在不同GNR表面上的物理吸附在传输函数中诱导出独特的共振峰，这受到缺陷类型和位置的影响。电导灵敏度分析表明，原始GNR作为核碱基检测的有前景的候选材料，可用于精确的电子测量。然而，有缺陷的GNR也表现出显著的灵敏度。此外，电流-电压（I-V）分析确定dvGNR器件由于其高电流灵敏度和对不同核碱基的明显响应而对核碱基检测最为有效。虽然原始GNR器件能检测某些核碱基，但由于在较高偏压下电流趋势均匀，其性能不太一致。相比之下，swGNR器件通过在0.6 - 0.8 V范围内不同的电流信号有效地区分了所有四种核碱基。这些发现强调了缺陷工程化GNR在下一代DNA测序应用中的潜力。
