Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS₂in aqueous environment. The ssDNA sequences [T₁₀, G₁₀, A₁₀, C₁₀, U₁₀, (GT)₅, and (AC)₅] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS₂(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS₂surface and facilitate future studies in design of functional DNA/MoS₂structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

On the chirality-dependent adsorption behavior of volatile organic compounds on carbon nanotubes

The capture and removal of volatile organic compounds (VOCs) have received extensive attention due to their toxicity and carcinogenicity. In order to extend the applications of carbon nanotubes (CNTs) in this field, a deep understanding of the interaction mechanism between VOCs and CNTs is crucial. In this article, molecular dynamics simulations are performed to systematically investigate the multi-molecule adsorption behavior of four representative VOC species on CNTs with a variety of chirality indices. Simulation results reveal that different VOC species exhibit significantly different adsorption preferences on CNTs. For both zigzag and armchair CNTs, the adsorption affinity is positively correlated with the hydrophobicity of VOC molecules and follows the order of toluene > ether > acetone > methanol. This adsorption preference is supported by the binding free energy calculations resulting from the umbrella sampling algorithm. Moreover, the adsorption affinity increases with the diameter of both zigzag and armchair CNTs. Furthermore, the effects of diameter become more significant for those VOC species possessing higher hydrophobicity. As for the effects of chirality, zigzag CNTs show greater adsorption affinity than armchair ones with similar diameters. However, simulation results also indicate that the adsorption affinity does not vary monotonically from zigzag to armchair orientations, leading to additional complexities of harvesting and elimination of VOC molecules in terms of CNTs. Results and data analysis presented in this work suggest that CNT chirality is an important factor for controlling the adsorption of harmful VOC molecules on CNT surfaces.