Zinc thiotropolone combinations as inhibitors of the SARS-CoV-2 main protease.

Numerous organic molecules are known to inhibit the main protease of SARS-CoV-2, (SC2Mpro), a key component in viral replication of the 2019 novel coronavirus. We explore the hypothesis that zinc ions, long used as a medicinal supplement and known to support immune function, bind to the SC2Mpro enzyme in combination with lipophilic tropolone and thiotropolone ligands, L, block substrate docking, and inhibit function. This study combines synthetic inorganic chemistry, in vitro protease activity assays, and computational modeling. While the ligands themselves have half maximal inhibition concentrations, IC50, for SC2Mpro in the 8-34 µM range, the IC50 values are ca. 100 nM for Zn(NO3)2 which are further enhanced in Zn-L combinations (59-97 nM). Isolation of the Zn(L)2 binary complexes and characterization of their ability to undergo ligand displacement is the basis for computational modeling of the chemical features of the enzyme inhibition. Blind docking onto the SC2Mpro enzyme surface using a modified Autodock4 protocol found preferential binding into the active site pocket. Such Zn-L combinations orient so as to permit dative bonding of Zn(L)+ to basic active site residues.

Li and Na Adsorption on Graphene and Graphene Oxide Examined by Density Functional Theory, Quantum Theory of Atoms in Molecules, and Electron Localization Function.

Adsorption of Li and Na on pristine and defective graphene and graphene oxide (GO) is studied using density functional theory (DFT) structural and electronic calculations, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF) analyses. DFT calculations show that Li and Na adsorptions on pristine graphene are not stable at all metal coverages examined here. However, the presence of defects on graphene support stabilizes both Li and Na adsorptions. Increased Li and Na coverages cause metal nucleation and weaken adsorption. Defective graphene is associated with the presence of band gaps and, thus, Li and Na adsorptions can be used to tune these gaps. Electronic calculations show that Li⁻ and Na⁻graphene interactions are Coulombic: as Li and Na coverages increase, the metal valences partially hybridize with the graphene bands and weaken metal⁻graphene support interactions. However, for Li adsorption on single vacancy graphene, QTAIM, ELF, and overlap populations calculations show that the Li-C bond has some covalent character. The Li and Na adsorptions on GO are significantly stronger than on graphene and strengthen upon increased coverages. This is due to Li and Na forming bonds with both carbon and oxygen GO atoms. QTAIM and ELF are used to analyze the metal⁻C and metal⁻metal bonds (when metal nucleation is present). The Li and Na clusters may contain both covalent and metallic intra metal⁻metal bonds: This effect is related to the adsorption support selection. ELF bifurcation diagrams show individual metal⁻C and metal⁻metal interactions, as Li and Na are adsorbed on graphene and GO, at the metal coverages examined here.

Electron density topological and adsorbate orbital analyses of water and carbon monoxide co-adsorption on platinum.

The electron density topology of carbon monoxide (CO) on dry and hydrated platinum is evaluated under the quantum theory of atoms in molecules (QTAIM) and by adsorbate orbital approaches. The impact of water co-adsorbate on the electronic, structural, and vibrational properties of CO on Pt are modelled by periodic density functional theory (DFT). At low CO coverage, increased hydration weakens C-O bonds and strengthens C-Pt bonds, as verified by changes in bond lengths and stretching frequencies. These results are consistent with QTAIM, the 5σ donation-2π* backdonation model, and our extended π-attraction σ-repulsion model (extended π-σ model). This work links changes in the non-zero eigenvalues of the electron density Hessian at QTAIM bond critical points to changes in the π and σ C-O bonds with systematic variation of CO/H2O co-adsorbate scenarios. QTAIM invariably shows bond strengths and lengths as being negatively correlated. For atop CO on hydrated Pt, QTAIM and phenomenological models are consistent with a direct correlation between C-O bond strength and CO coverage. However, DFT modelling in the absence of hydration shows that C-O bond lengths are not negatively correlated to their stretching frequencies, in contrast to the Badger rule: When QTAIM and phenomenological models do not agree, the use of the non-zero eigenvalues of the electron density Hessian as inputs to the phenomenological models, aligns them with QTAIM. The C-O and C-Pt bond strengths of bridge and three-fold bound CO on dry and hydrated platinum are also evaluated by QTAIM and adsorbate orbital analyses.