Search

Exploring therapeutic options is crucial in the ongoing COVID-19 pandemic caused by SARS-CoV-2. Nirmatrelvir, which is a potent inhibitor that targets the SARS-CoV-2 Mpro, shows promise as an antiviral treatment. Additionally, Ivermectin, which is a broad-spectrum antiparasitic drug, has demonstrated effectiveness against the virus in laboratory settings. However, its clinical implications are still debated. Using computational methods, such as molecular docking and 100 ns molecular dynamics simulations, we investigated how Nirmatrelvir and Ivermectin interacted with SARS-CoV-2 Mpro(A). Calculations using density functional theory were instrumental in elucidating the behavior of isolated molecules, primarily by analyzing the frontier molecular orbitals. Our analysis revealed distinct binding patterns: Nirmatrelvir formed strong interactions with amino acids, like MET49, MET165, HIS41, HIS163, HIS164, PHE140, CYS145, GLU166, and ASN142, showing stable binding, with a root-mean-square deviation (RMSD) of around 2.0 Å. On the other hand, Ivermectin interacted with THR237, THR239, LEU271, LEU272, and LEU287, displaying an RMSD of 1.87 Å, indicating enduring interactions. Both ligands stabilized Mpro(A), with Ivermectin showing stability and persistent interactions despite forming fewer hydrogen bonds. These findings offer detailed insights into how Nirmatrelvir and Ivermectin bind to the SARS-CoV-2 main protease, providing valuable information for potential therapeutic strategies against COVID-19.

Carbon-based materials have garnered significant attention since the groundbreaking synthesis of graphene. The exploration of novel 2D carbon allotropes has led to the discovery of materials with intrinsic properties distinct from graphene. Within this context, the biphenylene network (BPN) was successfully synthesized. In this study, we used molecular dynamics (MD) simulations with the Reactive Force Field (ReaxFF) to delve into the thermomechanical properties and fracture patterns of biphenylene-based nanotubes (BPN-NTs) exhibiting armchair (AC-BPN-NT) and zigzag (ZZ-BPN-NT) chiralities. Throughout the longitudinal deformation process, we observed significant morphological transformations preceding the structural fracture of the system. These transformations unfolded in distinct inelastic phases. In both cases, AC- and ZZ-BPN-NT, stress accumulation in four-membered rings led to the creation of octagonal structures; however, in AC, this occurs in the fracture region, subsequently causing the presence of nanopores. On the other hand, for ZZ-BPN-NT, stress accumulation in the rectangular rings occurred in bonds parallel to the deformation, with elongated octagonal structures. The Young’s modulus of these nanotubes ranged from 746 to 1259 GPa, with a melting point of around 4000 K. Our results also explore the influence of diameter and curvature, drawing comparisons with BPN monolayers.

A novel 2D carbon allotrope, pentagraphyne (PG-yne), was introduced in a recent theoretical study. This unique structure is derived from pentagraphene by incorporating acetylenic linkages between sp3 and sp2 hybridized carbon atoms. Given its intriguing electronic and structural properties, it is imperative to investigate the mechanical characteristics and thermal responses of PG-yne in both monolayer and nanotube configurations, which encompass different chiralities and diameters. We conducted fully atomistic reactive molecular dynamics (MD) simulations employing the ReaxFF potential to address these aspects. Our findings reveal that Young’s modulus of PG-yne monolayers stands at approximately 51 GPa at room temperature. In contrast, for the studied nanotubes, regardless of their chirality, it hovers around 45 GPa. Furthermore, our observations indicate that PG-yne-based systems feature an extensive and relatively flat plastic region before reaching the point of total fracture, irrespective of their topology. Regarding their thermal properties, we identified a melting point at approximately 3600 K, accompanied by a phase transition around 1100 K.

Abstract Graphene nanoribbons (GNRs) are promising quasi-one-dimensional materials with various technological applications. Recently, methods that allowed for the control of GNR’s topology have been developed, resulting in connected nanoribbons composed of two distinct armchair GNR families. Here, we employed an extended version of the Su-Schrieffer-Heeger model to study the morphological and electronic properties of these novel GNRs. Results demonstrated that charge injection leads to the formation of polarons that localize strictly in the 9-AGNRs segments of the system. Its mobility is highly impaired by the system’s topology. The polaron displaces through hopping between 9-AGNR portions of the system, suggesting this mechanism for charge transport in this material.

Organic compounds have been employed in developing new green energy solutions with good cost-efficiency compromise, such as photovoltaics. The light-harvesting process in these applications is a crucial feature that still needs improvements. Here, we studied natural dyes to propose an alternative for enhancing the light-harvesting capability of photovoltaics. We performed density functional theory calculations to investigate the electronic and optical properties of the four natural dyes found in achiote seeds (Bixa orellana L.). Different DFT functionals, and basis sets, were used to calculate the electronic and optical properties of the bixin, norbixin, and their trans-isomers (molecules present in Bixa orellana L.). We observed that the planarity of the molecules and their similar extension for the conjugation pathways provide substantially delocalized wavefunctions of the frontier orbitals and similar values for their energies. Our findings also revealed a strong absorption peak in the blue region and an absorption band over the visible spectrum. These results indicate that Bixa orellana L. molecules can be good candidates for improving light-harvesting in photovoltaics.