Enhanced Interactions of Amino Acids and Nucleic Acid Bases with Bare Black Phosphorene Monolayer Mediated by Coadsorbed Species

Abstract

In this paper, we characterize amino acids and nucleic acid bases (nucleobases), such as glutamine, histidine, tyrosine, adenine, guanine, cytosine, and thymine, and examine their interaction with bare, as well as with gold cluster and Ti adatom covered, black phosphorene (α-P) monolayers using density functional theory. The binding of these amino acids and nucleobases to the bare α-P monolayer is realized generally through weak van der Waals interaction and comprises only a small amount of charge exchange. Accordingly, the electronic energy structures of adsorbates and underlying substrate are not affected significantly. However, the electronic structure of bare α-P is significantly affected upon adsorption of a gold cluster and a single Ti adatom; depending on the size of the adsorbate and the symmetry of their coverage, the energy band gap can be tuned and permanent magnetic moments can be attained. Additionally, the adsorption of amino acids or nucleobases to these adsorbates on an α-P monolayer results in enhanced binding and hence makes their sustainable fixation on α-P monolayer possible. In particular, a semiconducting Au decorated α-P monolayer undergoes a metal−insulator transition upon the adsorption of tyrosine. This and similar effects favor the α-P monolayer in biosensor applications. In contrast to the situation with adsorbates, the binding of amino acid is not enhanced when it adsorb to patterned vacancy or divacancy sites of the α-P monolayer. Our study shows that the absorbance of the bare α-P monolayer can be enhanced by coating with amino acid and nucleobases. The absorbance spectrum can be further modified by the adsorption of these molecules to gold atoms on the α-P monolayer.

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

“…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

“…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 ).…”

A new high capacity cathode material for Li/Na-ion batteries: dihafnium sulfide (Hf2S)

“…For example, bulk gold, which is known to be as inactive as the noble gases, shows a catalytic effect when it is reduced to nanosizes. 3,4 Especially after the discovery of graphene, two-dimensional (2D) materials have been studied for a variety of fields, such as energy harvesting, 1,5-7 battery applications, 8,9 medical applications, [10][11][12][13] wearable electronics, 14,15 etc. New requirements emerging in next-generation technologies lead scientists to search for new materials.…”