Use of DFT-based reactivity descriptors for rationalizing radical addition reactions: applicability and difficulties

Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator

The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general-purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz-Singh-Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions.

Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase

The QM/MM simulations followed by electron density feature analysis are carried out to deepen the understanding of the reaction mechanism of cephalosporin hydrolysis in the active site of the L1 metallo-β-lactamase. The differences in reactivity of ten similar cephalosporin compounds are explained by using an extended set of bonding descriptors. The limiting step of the reaction is characterized by the proton transfer to the nitrogen atom of the cephalosporin thiazine ring accompanied with formation of the C₄ Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> C₃ double bond in its N–C₄–C₃ fragment. The temporary N⋯H–O_w hydrogen bond, which is formed in the transition state of the limiting step of the reaction was recognized as a key atomic interaction governing the reactivity of various cephalosporins. Non-local real-space bonding descriptors show that different extent of localization of electron lone pair at N atom in the transition state affect the reactivity of compounds: smaller electron localization is typical for the less reactive species. In particular, the Fermi hole analysis shows how exchange electron correlation in the N⋯H–O_w fragment control electron lone pair localization. Delocalization tensor, linear response kernel and source function indicate that features of electron delocalization in the N–C₄–C₃ fragment of cephalosporins in the transition state complexes determine the differences in C₄–C₃ bond for substrates with high and low rate constants. The C₄–C₃ bond of the N–C₄–C₃ fragment at the transition state is similar to that of the preceding intermediate for the less reactive species and resembles the features of the enzyme–product complex for more reactive compounds. The power and limitations of the descriptors applied for solving the problem are discussed and the generality of approach is stressed.

Combination of QM/MM and modern bonding descriptors explains different reactivity of cephalosporins in the active site of the L1 metallo-β-lactamase.

Functional insights of a molecular complex pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid on infectious agents and ctDNA - A comparative biological screening and complementary theoretical calculations

Systematic identification and quantification of active radical sites in a small molecule, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid as well as in the stable free radical (DPPH^•) were carried out by Fukui functions calculation using DFT functional with B3LYP/6-311++G(d,p) level of basis set. Bioactive Lewis acid-base compound, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid (PDNB:DNBA) has been synthesized and crystallized by slow evaporation - solution method at 30 °C. Various functional groups and the structural arrangements were ascertained from spectral and XRD analyses, respectively. UV-vis spectral analysis was used to find out the stability of the anticipated drug for about 60 min using methanol as a solvent. Stabilization of the compound was linked to the presence of enormous N-H…O, O-H…O and C-H…O hydrogen bonding interactions identified through Hirshfeld surface analysis. Chemical stability and reactivity of the drug were validated from theoretical optimization and HOMO-LUMO analysis. Active nucleophilic, electrophilic and radical sites of PDNB:DNBA were also identified from molecular electrostatic potential analysis. Inhibition of growth of pathogens in screening experiments by the proposed drug attests its suitability in biological applications. Antioxidant activity of the compound, PDNB:DNBA, endorses its aptness for scavenging reactive radicals. Fluorimetry experiments confirm hyperchromism in DNA binding analysis proving groove mode of binding. Molecular docking explored the various modes of intermolecular interactions of the drug with microbes as well as DNA.

Bioactivity of a radical scavenger bis(pyrazolium p-toluenesulphonate) on ctDNA and certain microbes: a combined experimental and theoretical analysis

A small organic molecule, bis(pyrazolium p-toluenesulphonate) (BPPTS), was crystallized, characterized and used to scavenge free radicals in biological systems. SXRD and spectroscopic analyses were used to confirm the structure of BPPTS. Methanolic and ethanolic solutions of BPPTS were used to assess the stability of the proposed drug using the UV-vis spectrophotometric technique. Optimization of the molecular structure was carried out by DFT with B3LYP/6-311++G(d,p) level of basis set. MEP and Fukui functions that elaborate theoretically the predominant electrophilic, nucleophilic and radical sites in BPPTS were correlated with experimental biological screening. BPPTS exhibits strong activity against Bacillus subtilis and Escherichia coli, comparable with all other analyzed pathogens. The free radical scavenging activity of BPPTS was assessed by both experimental studies and theoretical calculations. The binding sites of DPPH, which can bind to BPPTS, were also predicted by Fukui functions. DNA binding of BPPTS in UV-vis studies revealed the groove mode of binding due to the occurrence of hyperchromism. The phenomenon of hyperchromism was established by the Hirshfeld surface analysis of BPPTS, which confirmed the presence of π···π interactions (2.4%). Molecular docking established a positive correlation between experimental bio-screening reports and simulated data. ADMET properties were also calculated.

B-Hb⋯π interactions in benzene–borazine sandwich and multidecker complexes: a DFT study

Multidecker complexes of benzene/borazine can be formed through B-H_b⋯π interactions.

Thermal stability of phenolic resin: new insights based on bond dissociation energy and reactivity of functional groups

Based on bisphenol-F-like model molecules, the bond dissociation energies and Fukui function were calculated to interpret the relationship between the atomistic structure and thermal properties of the phenolic resin.

Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study

The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.

Evaluation of the antiradical activity of hyperjovinol-A utilizing donor-acceptor maps

Hyperjovinol-A ((2-methyl-1-(2,4,6-trihydroxy-3-(3-hydroxy-3,7-dimethyloct-6-enyl)phen yl)propan-1-one) is an acylated phloroglucinol isolated from Hypericum Jovis and exhibiting good antioxidant activity. The study investigates the compound’s antiradical ability on the basis of the electron-donor and electron-acceptor abilities of its conformers, deriving donor and acceptor indexes and mapping them in terms of donor-acceptor maps (DAM). The DAMs of vitamins C and E and of carotene astaxantine are used as comparison references. Calculations were performed at the DFT/BPW91/6-311+G(d,p) level, with optimizations on fully relaxed geometries to obtain the conformers of the neutral molecule in vacuo, and single point calculations to obtain the energies of the cationic and anionic species in vacuo and of the neutral, cationic, and anionic species in water, ethanol, and pentylethanoate. The calculations in solution utilized the polarizable continuum model (PCM). The results indicate that hyperjovinol-A may have better antiradical activity than vitamin C. This is in agreement with experimental results, showing that the antioxidant activity of hyperjovinol-A is comparable with that of the best drugs currently in clinical use. The activity is maintained in solution. The Fukui function f(·) was also calculated for all the conformers of hyperjovinol-A, to identify the regions of highest reactivity.

The Utility of the HSAB Principle via the Fukui Function in Biological Systems

The hard/soft acid-base principle has long been known to be an excellent predictor of chemical reactivity. The Fukui function, a reactivity descriptor from conceptual density functional theory, has been shown to be related to the local softness of a system. The usefulness of the Fukui function is explored and demonstrated herein for three common biological problems: ligand docking, active site detection, and protein folding. In each type of study, a scoring function is developed based on the local HSAB principle using atomic Fukui indices. Even with necessary approximations for its use in large systems, the Fukui function remains a useful descriptor for predicting chemical reactivity and understanding chemical systems.