Benchmark Density Functional Theory Approach for the Calculation of Bond Dissociation Energies of the M-O2 Bond: A Key Step in Water Splitting Reactions

Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities

The influence of the composition of the functional used for density functional theory computations on one structural parameter (a dihedral angle) and a spectroscopic parameter (absorption wavelength) is assessed in this study on the basis of two molecules (flavonols). In this kind of molecules, these two parameters should be correlated according to the nature of the electronic transition involved. However, it is shown herein that by varying the proportion of true exchange and correlation while building a functional, it is possible to obtain independently a large range of values for these parameters without any relation with the underlying real values. Therefore, it is concluded that the choice of a functional after a benchmark, especially using user-defined functionals, should be carried out with great care to avoid such effects.

Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide

CONTEXT

The Omicron, Kappa, and Delta variants are different strains of the SARS-CoV-2 virus. Graphene oxide quantum dots (GOQDs) represent a burgeoning class of oxygen-enriched, zero-dimensional materials characterized by their sub-20-nm dimensions. Exhibiting pronounced quantum confinement and edge effects, GOQDs manifest exceptional physical-chemical attributes. This study delves into the potential of graphene oxide quantum dots, elucidating their inherent properties pertinent to the surface structures of SARS-CoV-2, employing an integrated computational approach for the repositioning of inhibitory agents.

METHODS

Following rigorous adjustment tests, a spectrum of divergent bonding conformations emerged, with particular emphasis placed on identifying the conformation exhibiting optimal adjustment scores and interactions. The investigation employed molecular docking simulations integrating affinity energy evaluations, electrostatic potential clouds, molecular dynamics encompassing average square root calculations, and the computation of Gibbs-free energy. These values quantify the strength of interaction between GOQDs and SARS-CoV-2 spike protein variants. The receptor structures were optimized using the CHARM-GUI server employing force field AMBERFF14SB. The algorithm embedded in CHARMM offers an efficient interpolation scheme and automatic step size selection, enhancing the efficiency of the optimization process. The 3D structures of the ligands are constructed and optimized with density functional theory (DFT) method based on the most stable conformer of each binder. Autodock Vina Software (ADV) was utilized, where essential parameters were specified. Electrostatic potential maps (MEPs) provide a visual depiction of molecules' charge distributions and related properties. After this, molecular dynamics simulations employing the CHARM36 force field in Gromacs 2022.2 were conducted to investigate GOs' interactions with surface macromolecules of SARS-CoV-2 in an explicit aqueous environment. Furthermore, our investigation suggests that lower values indicate stronger binding. Notably, GO-E consistently showed the most negative values across interactions with different variants, suggesting a higher affinity compared to other GOQDs (GO-A to GO-D).

Comparison of Cu3, Cu5, and Cu7 clusters as potential antioxidants: A theoretical quest

CONTEXT

Herein, we compare and contrast the dual roles of Cun clusters (n = 3, 5, and 7 atoms) in scavenging or generating RO• free radicals from ROH at the theoretical levels (where R = H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). This investigation is performed in water media to mimic the actual environment in the biological system. In the presence of the Cun clusters, bond dissociation energy (BDE) of RO-H and R-OH is reduced. This is clear evidence for the increased possibility of both the RO-H and R-OH bonds breakage and scavenging of RO• radicals. The nature of anchoring bonds responsible for the interaction of Cun clusters with ROH and RO• are interpreted using the quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analysis. The DFT results indicate that the O•⋅⋅⋅•Cu bond is stronger and has more covalent character in RO•⋅⋅⋅•Cun radical complexes than in ROH⋅⋅⋅•Cun. Therefore, the interactions of Cun clusters with RO• radicals (antioxidant) are more pronounced than their interactions with ROH non-radicals (pro-oxidant).

METHODS

The GAMESS software package was utilized in this paper. The B3LYP and M06 functions with the 6-311 +  + G(d,p), and LANL2DZ/SDD basis sets was used to perform the important geometrical parameters of RO•⋅⋅⋅•Cun and ROH⋅⋅⋅•Cun, binding energy (Eb), and bond dissociation energy (BDE).

Origin of Optoelectronic Contradictions in 3,4-Cycloalkyl[c]-chalcogenophenes: A Computational Study

The planar morphology of the backbone significantly contributes to the subtle optoelectronic features of π-conjugated polymers. On the other hand, the atomistic tuning of an otherwise identical π-backbone could also impact optoelectronic properties systematically. In this manuscript, we compare a series of 3,4-cycloalkylchalcogenophenes by tuning them atomistically using group-16 elements. Additionally, the effect of systematically extending these building blocks in the form of oligomers and polymers is studied. The size of the 3,4-substitution affected the morphology of the oligomers. In addition, the heteroatoms contributed to a further alteration in their geometry and resultant optoelectronic properties. The chalcogenophenes, containing smaller 3,4-cycloalkanes, resulted in lower bandgap oligomers or polymers compared to those with larger 3,4-cycloalkanes. Natural bonding orbital (NBO) calculations were performed to understand the disparity alongside the contour maps of frontier molecular orbitals (FMO).

Molecular docking, DFT studies, and anti-inflammatory evaluation of peshawaraquinone isolated from Fernandoa adenophylla

In recent years, there has been growing interest in exploring natural compounds with anti-inflammatory properties for potential therapeutic applications. This study focuses on investigating the anti-inflammatory potential of peshawaraquinone (PAQ), a compound isolated from Fernandoa adenophylla, which is known for its local use in pain relief. We aim to evaluate the efficacy of peshawaraquinone in both in vitro and in vivo models and gain insights into its mode of action. In the in vitro Human red blood cell (HRBC) assay, various concentrations of peshawaraquinone were tested for their ability to inhibit the hemolysis of red blood cells, a well-established indicator of anti-inflammatory activity. The results demonstrated a maximum percent inhibition of 79.69 at a concentration of 100 µM, indicating significant anti-inflammatory potential. Furthermore, the in vivo xylene-induced ear edema model was employed to assess the compound's efficacy in reducing inflammation. Xylene was topically applied to the ear to induce edema, and peshawaraquinone was administered to evaluate its inhibitory effects. The findings revealed a substantial 74.19% reduction in ear edema, accompanied by decreased ear thickness and histopathological improvements, such as inhibited cell infiltration and epidermal hyperplasia. To gain further insights into the compound's mechanism of action, density functional theory (DFT) calculations were performed to investigate its spectroscopic characteristics and geometric properties. Additionally, docking studies were conducted on key targets involved in inflammation, including COX-1 and COX-2. In conclusion, this study showcases the significant anti-inflammatory potential of peshawaraquinone, offering promising prospects for its use as a natural anti-inflammatory agent. The results from both in vitro and in vivo models, as well as the mechanistic insights gained from computational analyses, provide a solid basis for further exploration of peshawaraquinone's therapeutic applications.Communicated by Ramaswamy H. Sarma.