Adsorption Behavior of Nucleobases on Doped MoS₂ Monolayer: A DFT Study

Abstract

Nucleobases detection is important in DNA sequencing, disease testing linked to genes, and disease treatment. In this work, the interactions of nonmetallic element (Si, P, Cl, Se) doped MoS2 monolayer and nucleobases (A, C, G, T, U) have been studied by first-principles based on density functional theory. Their optimal configurations, the corresponding adsorption energies, charge transfer, and electrical properties are calculated. The adsorption strength and charge transfers after doping Si and P are all larger than that of the pristine MoS2. And they are better at distinguishing nucleobases due to the large standard deviations (θ) of five adsorption energies from same substrate. For the Si–MoS2 monolayer, the nucleobases are perpendicular to its surface, with large charge transfer (0.25e to 0.36e) and adsorption energy (−3.16 to −2.43 eV). And the molecules have significant effects on the electrical properties of Si–MoS2, including band dispersion curve and band gap, due to orbital hybridization between the substrate and the molecules. These results show there’s chemical adsorption between them, which suggest that Si–MoS2 monolayer can be used as a potential probe platform to detect biomolecule. While physical adsorption occurs between P–MoS2 and nucleobases with moderate adsorption energy (−1.17 to −0.71 eV) and change transfer (0.13 to 0.34e). After absorbing single nucleobase molecule, the conductivity of P–MoS2 changes, which suggest its distinguishability and sensitivity to these molecules. And the predicted recovery times of A, C, G, T and U are 300 ms, 9 s, 49 s, 5 ms, and 0.09 ms at 400 K, respectively, which indicate that P–MoS2 monolayer has a potential application prospect in DNA/RNA sequencing.

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

“…The preferable adsorption site of the Au and Li atoms on silicene and germanene monolayers is a hollow site, see M. Sadeghi et al [25] showed that the Li atom can improve the binding energy between the nucleobases and, MoS 2 . Song et al [50] showed that the Au atom can increase the binding energy between the aromatic amino acids such as phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) on MoS 2 monolayer. Additionally, Gorkan et al [17] and Kadioglu et al [51] reported that interactions of amino acids and nucleobases with Au clusters supported blue and black phosphorene, respectively.…”

A Peculiar Binding Characterization of DNA (RNA) Nucleobases at MoOS-Based Janus Biosensor: Dissimilar Facets Role on Selectivity and Sensitivity

“…Clearly, nucleobases on both sides of the 1H–MoOS monolayer energetically adopt a parallel orientation. Related to the adsorption of nucleobases on the Janus MoOS Mo–O side (Mo–S side), the order of adsorption energies is G > A > C > T > U, which is very similar to those of 2D pristine MoS 2 [ 45 , 46 , 47 ]. The adsorption energies of A, C, T, and U on the O layer (S layer) are −0.86 (−0.89), −0.81 (−0.82), −0.71 (−0.76), and −0.64 (−0.67) eV, respectively.…”

“…In addition, by exploring the energy decomposition (see Table 1 and Table 2 ), the binding energy is split into destabilized (positive) and minor deformation energies related to G, A, C, T, and U adsorption states, respectively, and stabilized (negative) with predominant interaction energies between nucleobases with oxygen and sulfur layer sides of the Janus MoOS surfaces (vdW interactions). In addition, the reason that G exhibits the largest binding energy or smallest interaction energy in both sides (O layer or S layer) of the Janus MoOS monolayer and other biomaterials [ 7 , 18 , 45 , 48 , 49 , 50 , 51 , 52 ], is relatively associated with high polarizability prior to other nucleobases [ 50 , 52 , 53 ]. This trend is more encouraging by the charge density distributions and molecular interactions (in the supplementary materials see Figure S1 ).…”

Coronene-based quantum dots for the delivery of the doxorubicin anticancer drug: a computational study

“…Therefore, it is recommended to use radiation to speed up drug desorption. 62 It has been well established that in the treatment of cancer, ultrasonic waves that have been used in conjunction with chemotherapy increase the temperature of cancer tissue to 42–45 °C. 63 Accordingly, we have considered the frequency of the ultrasonic wave ( ν 0 = 2 × 10 4 s −1 ) as the attempted frequency for calculations of the recovery time.…”