In Silico Comparative Analysis of Ivermectin and Nirmatrelvir Inhibitors Interacting with the SARS-CoV-2 Main Protease.

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.

On the Stabilization of Carbynes Encapsulated in Penta-Graphene Nanotubes: a DFT Study.

We carried out density functional theory calculations to investigate the electronic and structural properties of linear carbon chains (carbynes) encapsulated in armchair and zigzag penta-graphene (PGNT) nanotubes. Results showed that PGNTs-wrapped carbyne can present negative formation energies that tend to stabilize that encapsulated carbon chains. These chains were stabilized in their cumulene and polyyne forms, with slight dependence on tube diameter. As a general trend, the PGNT band structures are kept almost unchanged upon carbyne encapsulation. This finding indicates weak orbital interactions between the PGNT and the carbyne. No net charge was found in chains encapsulated on zigzag PGNTs. Schematic representation of a carbyne encapsulated in a pentagraphene nanotube.

Dynamical Mechanism of Polarons and Bipolarons in Poly(p-Phenylene Vinylene).

Studies on Poly(p-Phenylene Vinylene) (PPV) and derivatives have experienced enormous growth since they were successfully used to fabricate the first efficient prototypes of Polymer Light-Emitting Diodes in the 90s. Despite this rapid progress, understanding the relationship between charge transport and the morphology in these materials remains a challenge. Here, we shed light on the understanding of the transport mechanism of polarons and bipolarons in PPVs by developing a two-dimensional tight-binding approach that includes lattice relaxation effects. Remarkably, the results show that the PPV lattice loses the energy related to its conjugation during time by transferring this amount of energy to electrons. Such a process for energy transfer permits the quasiparticles to overcome the potential barrier imposed by the local lattice deformations, that are formed in the presence of an additional charge and, consequently, their electric field assisted transport takes place. Within the framework of this transport mechanism, a better insight into the origin of the carrier mobility in PPV and derivatives can be achieved and would be a useful guide for improving their chemical structures and morphologies.

Defective graphene domains in boron nitride sheets.

Novel two-dimensional materials have emerged as hybrid structures that combine graphene and hexagonal boron nitride (h-BN) domains. During their growth process, structural defects such as vacancies and change of atoms connectivity are unavoidable. In the present study, we use first-principle calculations to investigate the electronic structure of graphene domains endowed with a single carbon atom vacancy or Stone-Wales defects in h-BN sheets. The results show that both kinds of defects yield localized states within the bandgap. Alongside this change in the bandgap configuration, it occurs a splitting of the spin channels in such a way that electrons with up and down spins populate different energy levels above and below the Fermi level, respectively. Such a spin arrangement is associated to lattice magnetization. Stone-Wales defects solely point to the appearance of new intragap levels. These results demonstrated that vacancies could significantly affect the electronic properties of hybrid graphene/h-BN sheets. Graphical Abstract A Boron-Nitride sheet doped with a vacancy endowed Carbon domain.

Polaron properties in 2D organic molecular crystals: directional dependence of non-local electron-phonon coupling.

In organic molecular crystals, the polaronic hopping model for the charge transport assumes that the carrier lies at one or a small number of molecules. Such a kind of localization suffers the influence of the non-local electron-phonon (e-ph) interactions associated with intermolecular lattice vibrations. Here, we developed a model Hamiltonian for numerically describing the role played by the intermolecular e-ph interactions on the stationary and dynamical properties of polarons in a two-dimensional array of molecules. We allow three types of electron hopping mechanisms and, consequently, for the nonlocal e-ph interactions: horizontal, vertical, and diagonal. Remarkably, our findings show that the stable polarons are not formed for isotropic arrangements of the intermolecular transfer integrals, regardless of the strengths of the e-ph interactions. Interestingly, the diagonal channel for the e-ph interactions changes the transport mechanism by sharing the polaronic charge between parallel molecular lines in a breather-like mode.

Polaron formation at impurity-endowed lattices.

In semiconducting materials, lattice deformities can play the role of localizing the charge carriers. Polarons are understood as attractive interactions between charge and lattice deformations that result in a single structure composed by a charged particle surrounded by a cloud of phonons. These composite quasi-particles are vital structures when it comes to charge transport mechanism in a wide range of semiconducting materials. In the present work, we investigated the drift of an electron and the subsequent polaron formation in impurity-endowed lattices in the framework of a one-dimensional tight-binding model. Primarily, we scrutinized electronic dynamics in lattices containing two sources of disorders: a barrier and a well. The dispersion of the gamma distribution gives an idea of the extension of the disorder region in the lattice. We studied the dynamics of an injected electron interacting with the lattice vibrations where we consider, for a given degree of disorder, different velocities of the incoming particle. Our results show that there are different kinds of propagation/localization for the electron according to the assumed initial velocity. Importantly, we obtained the critical values for the impurity strength to promote the quenching of Bloch oscillations and the localization of polarons.

A DFT study of a set of natural dyes for organic electronics.

We systematically investigate, at density functional theory level, the electronic properties of a set of ten carotenoid molecules with different conjugation length. Ground state geometries were fully optimized using both B3LYP and its long-range corrected version, i.e., the CAM-B3LYP functional. The time-dependent DFT approach (TD-DFT) was also performed for the calculation of the excited states of the optimized geometries and the results were compared to the experimental ones, when available. Our findings indicate a dependence of the transition vertical energies, oscillator strengths, and transition dipole moments on the extension of conjugation, as expected. We also investigate the impact of the intra-molecular vibrations on the absorption spectrum by means of the Franck-Condon (FC) and nuclear ensemble (NE) approach to spectra simulation. Our simulations suggest that the Franck-Condon approximation may not be suitable to appropriately characterize the vibronic progression of these molecules, whereas the NE approach provides a contribution that vary from negligible to meaningful depending on which molecule and energy region is under analysis.

Concentration effects on intrachain polaron recombination in conjugated polymers.

The influence of different charge carrier concentrations on the recombination dynamics between oppositely charged polarons is numerically investigated using a modified version of the Su-Schrieffer-Heeger (SSH) model that includes an external electric field and electron-electron interactions. Our findings show that the external electric field can play the role of avoiding the formation of excited states (polaron-exciton and neutral excitation) leading the system to a dimerized lattice. Interestingly, depending on a suitable balance between the polaron concentration and the electric field strength, the recombination mechanism can form stable polaron-excitons or neutral excitations. These results may provide guidance to improve the electroluminescence efficiency in Polymer Light Emitting Diodes.