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The SARS-CoV-2 main protease (Mpro) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of Mpro (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of encoding PCA progression during the simulations. The hexapeptides formed stable complexes as expected, with reproducible molecular docking of the substrates given the extensiveness of the procedure. Only Lys-Leu-Gln*** (KLQ***) sequence complexes were studied for molecular dynamics. In this subset of complexes, the PCA analysis identified four classifications of protein motions across these sequences. KLQ*** complexes illustrated the effect of changes in substrate on the active site, with implications for understanding the substrate recognition of Mpro and informing the development of small molecule inhibitors. [ABSTRACT FROM AUTHOR]

Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0, and Y+ (Y = Li, Na, K) and Z− (Z = F, Cl, Br) ions using M06-2X, B3LYP and ω B97XD functionals in conjunction with the 6–31 + + G(d,p), aug-cc-pVDZ(-X2C) and 6–311 + + G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation...O and cation-π interactions, while Z− anions generally establish anion...H–O contacts. Predicted binding energies at the M06-2X/6–311 + + G(d,p) level range between − 26.6 and − 70.2 kcal/mol for cationic complexes and − 20.4 and − 62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O...cation...O interactions where the cation is trapped between O37 and O38 atoms of TXA0. Anions do not behave uniformly towards TXA0: while the fluoride anion F− induces the deprotonation of TXA0, Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0...Y+ and TXA0...Z− complexes are mainly stabilized by electrostatic and inductive effects, whose combined contributions account for more than 60 percent of the total interaction energy. [ABSTRACT FROM AUTHOR]

The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computations suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO-3G) model, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-off between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the effect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces underpinning the process of cycloadduct formation. [ABSTRACT FROM AUTHOR]

The ambident reactivity of small-sized XAHs (X=H, F, Cl, Br, CH3, and A=S, Se, Te) molecules towards the imidazole molecule (IMZ) has been investigated using wave function (MP2) and Density Functional Theory (B3LYP, B3LYP-D3). Molecular electrostatic potentials (MEPs) and frontier molecular orbitals of monomers are computed to rationalise the regioselectivity of IMZ towards XAHs. The chemical bonding of each complex is described in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) paradigms. The symmetry-adapted perturbation theory (SAPT) is employed to assess the physical nature of the interactions. Our findings suggest that XAHs mainly bind to IMZ through H-bonding and chalcogen-bonding interactions of weak to moderate strength, with binding energies ranging from −3.1 to −17.6 kcal/mol at the MP2/aug-cc-pVDZ(-PP) level. Topological QTAIM descriptors reveal all H-bonds between IMZ and XAHs to be purely noncovalent contacts, while chalcogen bonds of halogenated XAHs (X = F, Cl, Br) show a partial covalent character. SAPT2 calculations indicate that both H-bonded and chalcogen-bonded complexes are mainly stabilised by electrostatic interactions. Insights drawn from this study are expected to constitute the bedrock for further investigations about noncovalent interaction between middle to big-sized chalcogen-containing molecules and imidazole derivatives. [ABSTRACT FROM AUTHOR]