Phosphorene as a Template Material for Physisorption of DNA/RNA Nucleobases and Resembling of Base Pairs: A Cluster DFT Study and Comparisons with Graphene

Abstract

A quantum chemistry study was performed to study the interaction of single deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases and hydrogen-bonded base pairs onto a phosphorene nanosheet. Adenine (A), cytosine (C), guanine (G), thymine (T), and uracyl (U) were considered as the adsorbates that are physisorbed onto phosphorene in stacking patterns, reaching adsorption energies of 0.64− 0.94 eV and sorting the physisorption stability as G > C > A > T > U. The structure and aromaticity of all the nucleobases are not affected upon complexation. Likewise, the hydrogen-bonded base-pairs (CG, AT, and AU) are adsorbed in the armchair plane of phosphorene with high adsorption energies of 1.28−1.44 eV and sorting the physisorption stability as CG > AT > AU. The hydrogen bond energies of the base pairs are slightly affected by binding on phosphorene, retaining its stability at room temperature (300 K). Furthermore, comparison analyses showed that phosphorene is better suited for physisorption of nucleobases and base pairs than graphene, improving the stability in up to 27%. This improvement is based on the interplay between enhanced dispersion and electrostatic interactions. Otherwise, all the nucleobases behave as mild n-dopants, introducing up to ∼0.1 e/molecule in phosphorene. The charge doping and bandgap changes suggest that the phosphorene conductance could be sensitive to the physisorption of nucleobases and base pairs. Finally, the new insights from this work shed light onto the physisorption phenomena of biomolecules occurring at phosphorene interfaces, indicating that phosphorene emerges as a promising template for self-assembly of nucleobases in nanobiological devices.

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

“…The B3LYP–NL adsorption energies (Table in parentheses) show differences of up to ∼0.06 eV with those at the B3LYP–NL level, indicating the good agreement between the methods. Moreover, the B3LYP‐D3 adsorption energies show low differences (≤0.1 eV) with respect to those reported with the gCP‐PBE‐D3/def2‐TZVP method, which is a reliable method to study the adsorption of aromatic molecules onto graphene nanosheets, even with best results that the B97‐D3 approach . Further comparisons with related works is also included in the Supporting Information (Table S1).…”

The recent advancement of low-dimensional nanostructured materials for drug delivery and drug sensing application: A brief review

“…D. Cortés-Arriagada et al used another graphene-like nanosheet, phosphorene, to investigate the interaction of nucleobases which plays an important role in designing drug molecules [ 397 ]. For the DFT calculations, they have used DFT-D methods with PBE functional and def2-SVP basis sets.…”

Probing the Interaction of Nucleobases and Fluorophore‐Tagged Nucleobases with Graphene Surface: Adsorption and Fluorescence Studies

“…[20][21][22] Computational and exper-imental studies have been investigated on the interaction of the graphene layer with the nucleobases. [21][22][23][24][25][26][27][28][29][30][31][32][33][34] From these reports, the order of stability in nucleobase-graphene systems is commonly sorted as Guanine (G) > Adenine (A) � Cytosine (C) � Thymine (T) > Uracil (U). [27,[35][36][37][38] The stability of (C, A, and T) is largely dependent on different theoretical methodologies.…”

“…Various studies have been reported for the interaction of the proteins, DNA, and nucleobases with the graphene and doped graphene . Computational and experimental studies have been investigated on the interaction of the graphene layer with the nucleobases . From these reports, the order of stability in nucleobase‐graphene systems is commonly sorted as Guanine (G)>Adenine (A)≥Cytosine (C)≥Thymine (T)>Uracil (U) .…”