Dataset for Modelling Reaction Mechanisms Using Density Functional Theory: Mechanism of ortho-Hydroxylation by High-Valent Iron-Oxo Species

Modelling reaction mechanisms using density functional theory is one of the popular routes to underpin the course of a chemical reaction. Although numerous publications have come out in this area, the pitfall of modelling such reactions and explicitly publishing the entire data set (structures, energies, coordinates, spin densities, etc.) which lead to the conclusions are scarce. Here we have attempted to set a trend wherein all the computed data to underpin the reaction mechanism of ortho-hydroxylation of aromatic compounds by high-valent iron-oxo complexes (FeIII–OOH, FeIV=O, and FeV=O) are collected. Since the structure, energetics and other details of the calculations can be employed in future to probe/understand the reactivity pattern of such species, establishing the data set is justified. Here by analysing the presented results we also discuss in brief the presented results

Theoretical exploration on structures, bonding aspects and molecular docking of α -aminophosphonate ligated copper complexes against SARS-CoV-2 proteases

Recent years have witnessed a growing interest in the biological activity of metal complexes of α-aminophosphonates. Here for the first time, a detailed DFT study on five α-aminophosphonate ligated mononuclear/dinuclear CuII complexes is reported using the dispersion corrected density functional (B3LYP-D2) method. The electronic structures spin densities, FMO analysis, energetic description of spin states, and theoretical reactivity behaviour using molecular electrostatic potential (MEP) maps of all five species are reported. All possible spin states of the dinuclear species were computed and their ground state S values were determined along with the computation of their magnetic coupling constants. NBO analysis was also performed to provide details on stabilization energies. A molecular docking study was performed for the five complexes against two SARS-CoV-2 coronavirus protein targets (PDB ID: 6LU7 and 7T9K). The docking results indicated that the mononuclear species had a higher binding affinity for the targets compared to the dinuclear species. Among the species investigated, species I showed the highest binding affinity with the SARS-CoV-2 Omicron protease. NPA charge analysis showed that the heteroatoms of model species III had a more nucleophilic nature. A comparative study was performed to observe any variations and/or correlations in properties among all species

The emergence of the circulating vaccine-derived poliovirus type 2 in multiple countries requires active surveillance : current scenario and counteracting strategies

Dear Editor, On April 11, 2022, a child less than two years old living in the Tamanrasset province of South Algeria showed signs of acute flaccid paralysis (AFP). On July 8, 2022, this was notified by the WHO through the Global Polio Laboratory Network (GPLN) as a case of circulating vaccine-derived poliovirus type 2 (cVDPV2) [1]. In the past few months, several genetically-linked Sabin-like type 2 (SL-2) poliovirus isolates have been detected numerous times in the US and the UK [2]. Since last February, the GPLN in London has been consistently detecting SL-2 isolates in sewage samples. The latter showed enough mutations to be classified as type 2 vaccine-derived poliovirus (VDPV2) and, due to the evidence of community transmission, were classified as circulating VDPV2 (cVDPV2) [2]. No human cases of VDPV2 have been documented in the UK as of September 5, 2022. Only one case of VDPV2 was reported in an unvaccinated paralytic individual. This was the first poliomyelitis case reported in that country since 2013 that was not linked to recent international travel. In the US, the virus isolates detected in environmental samples were found to be genetically-related to those reported in the sewage samples from London and those from Jerusalem, Israel [2]. In the case of the child who showed AFP in Algeria, the cVDPV2 isolates were detected in the stool samples. This was the first case of cVDPV2 in that country. Genome sequencing showed that the isolated virus was genetically-related to one strain previously isolated in Kano, Nigeria. The child had not received the polio vaccine and had never travelled outside the Tamanrasset province. Public health investigations are currently underway in that region to identify any more AFP cases [1]

Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action

A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) of SARS-CoV-2 S-protein, Papain-like protein of SARS-CoV-2 (PLpro), reverse transcriptase of SARS-CoV-2 (RdRp) were chosen for in silico study. A set of previously synthesized compounds (1–5) were docked into the active sites of the targets. Based on the docking score, ligand efficiency, binding free energy, and dissociation constants for a definite conformational position of the ligand, inhibitory potentials of the compounds were measured. The stability of the protein–ligand (P-L) complex was validated in silico by using molecular dynamics simulations using the YASARA suit. Moreover, the pharmacokinetic properties, FMO and NBO analysis were performed for ranking the potentiality of the compounds as drug. The geometry optimizations and electronic structures were investigated using DFT. As per the study, compound-5 has the best binding affinity against all four targets. Moreover, compounds 1, 3 and 5 are less toxic and can be considered for oral consumption

Mechanistic insights into the allylic oxidation of aliphatic compounds by tetraamido iron(<scp>v</scp>) species: A C–H <i>vs.</i> O–H bond activation

This work is based on a deep insight into a comparative study of C–H vs. O–H bond activation of allylic compound by the high valent iron complex. Our theoretical findings can help to design catalysts with better efficiency for catalytic reactions.</p

Effect of the ring size of TMC ligands in controlling C–H bond activation by metal-superoxo species

This work is based on deep insight into the role of the ring size of ligands during C–H bond activation. Our findings can help design catalysts with better catalytic reactions.</jats:p

Oxidation of methane by an N-bridged high-valent diiron–oxo species: electronic structure implications on the reactivity

Methane activation by dinuclear high-valent iron–oxo species: do we need two metals to activate such inert bonds? Our theoretical study using DFT methods where electronic structure details and mechanistic aspects are established answers this intriguing question.</p