Insights from in silico study of receptor energetics of SARS-CoV-2 variants.

The emergence of new variants of the novel coronavirus SARS-CoV-2 with increased infectivity, superior virulence, high transmissibility, and unmatched immune escape has demonstrated the adaptability and evolutionary fitness of the virus. The subject of relative order of the binding affinity of SARS-CoV-2 variants with the human ACE2 (hACE2) receptor is hotly debated and its resolution has implications for drug design and development. In this work, we have investigated the energetics of the binding of receptor binding domain (RBD) of SARS-CoV-2 variants of concern (VOCs): Beta (B.1.351), Delta (B.1.617.2), Omicron (B.1.1.529), variant of interest (VOI): Kappa (B.1.617.1), and Delta Plus (B.1.617.2.1) variant with the human ACE2 receptor by using the umbrella sampling (US) method. Our work indicates that Delta and Delta Plus variants have greater values of the US binding free energy than Wild-type (WT), whereas Beta, Kappa, and Omicron variants have lower values. Further analysis of hydrogen bonding, salt bridges, non-bonded interaction energy, and contact surface area at the RBD-hACE2 interface establish Delta as the variant with the highest binding affinity among these variants.

First-Principles Study on the Selective Separation of Toxic Gases by Mg-MOF-74.

This study primarily focused on the detection and separation of toxic gases such as CO, H2S, SO2, NH3, NO, and NO2 by Mg-MOF-74, as well as assessing the stability of those toxic gases on it. The calculations were performed by using density functional theory as implemented in the Gaussian-09 and Quantum ESPRESSO suites of the program. GGA-type PBE-D2 functionals with a plane wave basis set were used in the optimization of the Mg-MOF-74 crystal, and hybrid-type B3LYP and M06 functionals with the 6-31G*basis set were used in cluster calculation. The binding energies of CO and H2S with MOF were found to be in the physisorption range, whereas the energies of SO2, NH3, NO, and NO2 were found to be in the chemisorption range. Based on binding energy, hardness, and softness studies, it was found that NO and NO2 molecules were more stable in Mg-MOF-74, suggesting that Mg-MOF-74 is a good detector for NO and NO2 molecules.

Adsorption of methane on single metal atoms supported on graphene: Role of electron back-donation in binding and activation.

We consider single metal atoms supported on graphene as possible candidate systems for on-board vehicular storage of methane or for methane activation. We use density functional theory to study the adsorption of one and two molecules of methane on such graphene-supported single atoms, where the metal atom M is a 3d-transition metal (Sc to Zn). Our results suggest that M = Sc, Ti, and V are the best candidates for gas storage applications, while Ni and Co seem particularly promising with respect to activation of the C-H bond in methane. We find a strong and linear correlation between the adsorption energy of methane and the degree of back-donation of electrons from occupied metal d-states to antibonding methane states. A similar correlation is found between the elongation of C-H bonds and electron back-donation. An important role is played by the graphene substrate in enhancing the binding of methane on metal atoms, compared to the negligible binding observed on isolated metal atoms.