Interaction mechanism of biomolecules on vacancy defected 2D materials

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

“…Thus, phosphorene is best suited for physisorption of nucleobases and base pairs than graphene. In this regard, the increased sorption performance of phosphorene is different from related layered materials such as graphyne, graphdiyne, tungsten disulfide (WS 2 ), and molybdenum disulfide (MoS 2 ), where the physisorption strength of nucleobases is decreased compared to graphene as determined from DFT calculations. , Note that the order of binding strength on graphene was computed to be G > A ≈ C > T > U, which is in agreement with previous theoretical studies ,,− ,− (see the Supporting Information for details).…”

“…In fact, the in-plane rotation of nucleobases increases the energy by up to ∼8 kcal/mol, decreasing the adsorption energies. Note that the out-of-plane rotations were not computed because the perpendicular orientations of nucleobases onto two-dimensional materials are unfavorable. , Additionally, it is worthy to point out that the structure of the nucleobases is almost unchanged by binding on phosphorene; indeed, the relaxation energies of nucleobases were found to be lower than ∼0.01 eV (total energy difference between the geometry of the nucleobases in its isolated and physisorbed state).…”

“…All the DFT calculations were performed in the ORCA 4.0 program. , The PBE functional was used, which has been widely implemented to characterize the structural, electronic, and sorption properties of phosphorene and graphene. ,,,,, Geometry optimizations were performed with the all-electron def2-SVP basis sets, while all the electronic properties were obtained with the def2-TZVP basis sets; the auxiliary basis def2/J was adopted for the resolution-of-identity procedure in the ORCA program . The DFT-D3 method (including the Becke–Johnson damping function) was used to include the dispersion energy corrections in the SCF energies ( E SCF‑PBE ) and gradients; , the latter results in the PBE-D3 method.…”

“…Theoretical studies have recently explored the interaction of phosphorene with biomolecules (glycine, leucine, glutamic acid, histidine, and phenylalanine), which are physisorbed with a high stability (adsorption energies of up to ∼0.7 eV). , These studies give evidence that phosphorene could be implemented as part of bioinorganic interfaces. , The latter becomes important because phosphorene is a more biologically friendly material than graphene, causing a lower disruption in the structure of proteins. , Furthermore, the high biocompatibility of phosphorene is also addressed by its high stability in water and organic solvents, − in addition to the biocompatibility of its degrading compounds (phosphate and phosphite) . In this regard, nucleobases such as adenine (A), cytosine (C), guanine (G), thymine (T), and uracyl (U) are important biomolecules because they are the fundamental constituents of the deoxyribonucleic (DNA) and ribonucleic (RNA) acids, storing the genetic information.…”

“…In this respect, the interaction of nucleobases with layered materials such as intrinsic and doped graphene, − transition-metal dichalcogenides, graphynes, BC 3 , and boron-nitride sheets has been studied; , these studies allow us to understand the adsorption phenomena at nanobiological interfaces. Taking graphene as a representative class of adsorbent material, experimental and theoretical analyses have shown that nucleobases are highly stable onto its surface (even in aqueous conditions), giving insights into how these biomolecules interact at graphene interfaces. ,,,, The adsorption energies of nucleobases onto graphene are in the range of 0.4–1.1 eV, depending on the different nucleobases and theoretical methodologies. ,,− ,− The order of stability among all the nucleobases follows the order of G > C ≥ A ≥ T > U, where the stability of C, A, and T can change according with the different theoretical aproaches. ,,− ,− Moreover, the high physisorption stability of nucleobases onto graphene indicates that its hydrogen-bonded base pairs can spontaneously self-assemble on its surface, especially because the hydrogen bonds are merely affected by binding on graphene. , Nevertheless, to the best of our knowledge, there are no major reports dealing with the interaction stability of nucleobases with phosphorene.…”