The present work reports a theoretical study of the infrared spectra of chemical structures that are suitable to the description of the surface chemistry of carbon materials. Prior to any consideration, the computational approach was tested and adapted by comparing the predicted IR spectra to those obtained experimentally for various reference compounds. Several models were considered, subsequently accounting for the most relevant functional groups that have been postulated to decorate the edges of graphene layers on carbon materials (i.e., anhydrides, carboxyls, lactones, phenolic, quinones, and pyrones). For each of the previous functional groups, different structures involving a different number of fused rings were considered. This strategy allowed us to establish the effect of conjugation on the shift of the IR frequencies corresponding to a given functional group. Cooperative effects between different functional groups (phenol-carboxyl, phenol-lactone, and so on) were another aspect that revealed itself to be an interesting issue when assigning frequencies in the IR spectra of highly oxidized carbon materials. Thus, it was found that the frequencies of the CdO bonds present in acid functional groups were systematically lowered when phenolic groups were close enough to establish hydrogen bonds. Special attention was also paid to the elucidation of the origin of the 1600-cm -1 band of carbons. It was found that, in the case of acid carbons, this band can be assigned to CdC stretching of carbon rings decorated mainly with phenolic groups. Cyclic ethers in basic carbons would also promote absorption in the 1600-cm -1 region of the IR spectrum. Finally, the predicted assignments are employed to interpret the IR spectra obtained experimentally for several activated carbons.

Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in explicit solvent. After having performed electrostatic p K a calculations on several X-ray structures, we consider both the native (unbound) configuration of the enzyme and its noncovalent complex with a model peptide, Ace-Ala-Val-Leu-Gln∼Ser-Nme, which mimics the polyprotein sequence recognized at the active site. For each configuration, we also study their monomeric and homodimeric forms. The simulations of the unbound systems show that the relative orientation of domain III is not stable in the monomeric form and provide further details about interdomain motions, protomer–protomer interactions, inter-residue contacts, accessibility at the catalytic site, etc. In the presence of the peptide substrate, the monomeric protease exhibits a stable interdomain arrangement, but the relative orientation between the scissile peptide bond and the catalytic dyad is not favorable for catalysis. By means of comparative analysis, we further assess the catalytic impact of the enzyme dimerization, the actual flexibility of the active site region, and other structural effects induced by substrate binding. Overall, our computational results complement previous crystallographic studies on the SARS-CoV-2 enzyme and, together with other simulation studies, should contribute to outline useful structure–activity relationships.

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Quantum chemical optimizations of the small model systems ([Zn(NH 3 ) ) were performed at different levels of quantum mechanical theory (HF/6-31G*, B3LYP/6-31G*, and MP2/6-31G*) to characterize the Znligand bonds for the Zn1 and Zn2 binding sites of metallo-β-lactamases. The nature of the zinc coordination environment was further studied by considering larger mononuclear complexes at the B3LYP/6-31G*//HF/ 6-31G* level of theory ([Zn(Me-Im) ). The structure and properties of a series of binuclear model compounds showing an hydroxy-mediated Zn1‚‚‚Zn2 interaction were also analyzed at the same level of theory. One of the binuclear models with a global charge of +2, reproduces the main structural features of the Bacteroides fragilis active site as determined by X-ray crystallography. The proposed β-lactamase model has a monoprotonated state characterized by a strong H-bond interaction between a zinc-shared water molecule and a Zn2-bound Asp carboxylic group. The theoretical results are discussed in the context of experimental kinetic and structural data on the B. fragilis active site, resulting in insights into the nature of the zinc-ligand interactions, the location of the mechanistically relevant water molecules, and the actual protonation state of the active site. By combining the present results with previous theoretical and experimental work, mechanistic details for the mode of action of zinc β-lactamases are discussed.