Binding mechanisms of DNA/RNA nucleobases adsorbed on graphene under charging: first-principles van der Waals study

Gürel, H. Hakan; Salmankurt, Bahadır

doi:10.1088/2053-1591/aa6e67

Cited by 23 publications

(11 citation statements)

References 29 publications

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“…properties, 2D materials have started to be preferred in the sensing of nucleobases. Fo instance, graphene, silicene, germanene, monolayer transition-metal dichalcogenides MXenes, h-BN, and phosphorene are used for the detection of DNA/RNA nucleobase and amino acids [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Gürel

Salmankurt

2021

Biosensors

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Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases’ sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green’s function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.

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Section: Introductionmentioning

confidence: 99%

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Gürel

Salmankurt

2021

Biosensors

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“…As the workhorse in computational material science, standard density functional theory (DFT), , which is implemented in several computational codes, commonly employs approximations for the exchange-correlation (XC) energy functional like the local density approximation , (LDA) or the generalized gradient approximation (GGA). − However, it is well established that the LDA/GGA approximations cannot provide a proper description of the asymptotic decreasing behavior of the long-range van der Waals (vdW) interactions, − which has motivated a large number of theoretical studies. For example, there are several reviews discussing the main challenges, improvements and, in particular, the importance of the vdW interactions for weakly bonded systems such as adsorption phenomena on surfaces, , water properties, , two-dimensional layered-materials, , biomolecules, , DNA, , interfaces, , and etc. Therefore, it is a problem that affects a wide range of applications, and hence, it has attracted great interest in the last years.…”

Section: Introductionmentioning

confidence: 99%

“…5−9 However, it is well established that the LDA/GGA approximations cannot provide a proper description of the asymptotic decreasing behavior of the long-range van der Waals (vdW) interactions, 10−13 which has motivated a large number of theoretical studies. For example, there are several reviews discussing the main challenges, improvements and, in particular, the importance of the vdW interactions for weakly bonded systems such as adsorption phenomena on surfaces, 14,15 water properties, 16,17 two-dimensional layered-materials, 18,19 biomolecules, 20,21 DNA, 22,23 interfaces, 24,25 and etc. Therefore, it is a problem that affects a wide range of applications, and hence, it has attracted great interest in the last years.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the Performance of van der Waals Dispersion Functionals in the Description of Water and Ethanol on Transition Metal Surfaces

et al. 2018

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Pairwise van der Waals (vdW) corrections have been routinely added to density functional theory (DFT) adsorption studies of inorganic or organic molecules on solid surfaces, however, comparative studies of the available pairwise corrections, e.g., D2, D3, D3(BJ), TS, and TS+SCS, are quite scarce. We report DFT calculations within the Perdew− Burke−Ernzerhof (PBE) functional to assess the performance of the mentioned pairwise vdW corrections for well-defined transition-metal (TM) systems, namely, the Cu, Pt, and Au bulks in the face-centered cubic structure, close-packed TM substrates (Cu(111), Pt(111), Au(111), Cu 9 /Pt 9 /Cu(111), Pt 9 /Cu 9 /Cu(111), Au 9 /Pt 9 /Au(111), Pt 9 /Au 9 /Au(111)), and the adsorption of water and ethanol on the selected substrates, which include strained Pt-monolayers, i.e., a good challenge for pairwise vdW corrections. In general, accounting for vdW interactions leads to smaller lattice constants, which is expected due to the attractive nature of the vdW corrections, and the D3, D3(BJ), and TS+SCS improves the DFT-PBE results, in contrast with D2 and TS. Compared with PBE results, the vdW corrections enhance the contraction of the topmost surface layers, which contributes to change the electronic structure, in particular, the d-band center shifts away from the Fermi energy (up to 0.3 eV) in most cases, while the work function changes by about 0.2 eV in the worst cases. As expected, the attractive nature of the vdW corrections helps to enhance adsorption energies by 3−4 times compared with DFT-PBE. However, the adsorption energy trends versus the d-band center are preserved for all vdW corrections, except for the DFT-D2 framework, which deviates substantially from the studied vdW corrections. Therefore, based on our results and analyses, we can conclude that the D3, D3(BJ), and TS+SCS corrections yield the best description for the selected systems.

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“…Adenine ( A ), cytosine ( C ), guanine ( G ), thymine ( T ), and uracil ( U ) are the primary or canonical nucleobases, which are fundamental constituents of the genetic information stored in DNA/RNA. Because it is know that purine ( A and G ) and pyrimidine bases ( C, T , and U ) can self‐assemble onto crystalline solids, the interaction of nucleobases with nanostructured materials has been extensively studied due to its potential biotechnological applications in nanosciences and medicine, this is to develop materials for resembling, sensing and/or sequencing of DNA/RNA constituents, and or to obtain new biological‐friendly interfaces . Among the layered materials, graphene has shown a superior ability to interact with nucleobases, where experimental and theoretical analyses have determined a high adsorption stability in these cases (even in aqueous conditions), and revealing the processes as biomolecules interact at graphene biointerfases …”

Section: Introductionmentioning

confidence: 99%

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

Cortés‐Arriagada

Ortega

2018

Int J of Quantum Chemistry

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In the last years, experimental/theoretical studies have shown that graphene has a strong affinity toward nucleobases, serving as a promising nanomaterial for self-assembly, sensing, and/or sequencing of DNA/RNA constituents. Then, a complete picture of the properties of the nucleobase-graphene systems is required for its use in technological applications. This work describes a detailed quantum chemical analysis of the aromaticity of adsorbed nucleobases on graphene, comparing between aromaticity indexes based on magnetic, geometry, electron density, and electron delocalization properties of graphene-nucleobase systems. Contrary to the stated by magnetic-based aromaticity criteria (such as nucleus-independent chemical shifts), it is proved that the aromatic character of nucleobases is not increased/decreased upon binding on graphene. Therefore, magnetic aromaticity criteria are not recommended to analyze aromaticity in related systems, unless a fragmented scheme be adopted. Finally, these results are expected to expand the knowledge about the understanding of biomolecules-graphene interactions.

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Binding mechanisms of DNA/RNA nucleobases adsorbed on graphene under charging: first-principles van der Waals study

Cited by 23 publications

References 29 publications

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Comparison of the Performance of van der Waals Dispersion Functionals in the Description of Water and Ethanol on Transition Metal Surfaces

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

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