Computer-aided design of caffeic acid derivatives: free radical scavenging activity and reaction force.

Context: Antioxidants are known to play a beneficial role in human health. Caffeic acid has been previously recognized as efficient in this context. However, such a capability can be enhanced through structural modification.

Radical scavenging activity of bromophenol analogs: analysis of kinetics and mechanisms.

Context: This theoretical study explores the antioxidant activity of five bromophenol analogs, with a particular focus on their interaction with different solvent environments of varying polarities. Key findings include the correlation between increased solvent polarity and enhanced antioxidant activity of these analogs, comparable in some instances to ascorbic acid. Notably, compound 5, developed by our research team, demonstrates superior antioxidant activity in both lipid and aqueous solutions, surpassing that of ascorbic acid and other tested analogs.

Strategic design, theoretical insights, synthesis, and unveiling antioxidant potential in a novel ascorbic acid analog.

Context: In this study, we investigated the antioxidant potential of a novel ascorbic acid analog, DsD, assessing its interactions with the methylperoxyl (CH3OO·) radical in aqueous and lipid environments. Our focus was on understanding the acid-base equilibrium and how pH affects DsD's primary reaction mechanisms. Our findings indicate a marked preference for hydrogen atom transfer in lipid media, contrasting with sequential proton loss electron transfer (SPLET) in aqueous solutions.

Identifying the Transients and Transformation Products in Hydroxyl Radical-Methimazole Reactions Using DFT and UPLC-Q-TOF MS/MS Approaches.

Oxidative reactions of the hydroxyl radical (·OH) with methimazole (MMI), an antithyroid drug, are crucial for understanding its fate in oxidizing environments. By synergistically integrating density functional theory and ultraperformance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF MS/MS) techniques, we elucidated the transients and transformation products (TPs) arising from the ·OH-MMI reactions. We probed two hydrogen-atom abstraction (HA) reactions, three radical adduct formation reactions, and single electron transfer (SET) at the M06-2/6-311++G(d,p)/SMD(water) level.

Role of Imidazole and Chelate Ring Size in Copper Oxidation Catalysts: An Experimental and Theoretical Study.

In this work, the structural, solution, electrochemical, and catalytic properties of the complexes with ligands derived from imidazole and pyridines were studied. A comparative study of five bioinspired copper catalysts with or without coordinated imidazole and with different chelate ring sizes is presented. Catalytic efficiency on the oxidation of 3,5-di-butylcatechol (DTBC) and -aminophenol (OAP) in a MeOH/HO medium was assessed by means of the Michaelis-Menten model.

Functional impact and molecular binding modes of drugs that target the PI3K isoform p110δ.

Targeting the PI3K isoform p110δ against B cell malignancies is at the mainstay of PI3K inhibitor (PI3Ki) development. Therefore, we generated isogenic cell lines, which express wild type or mutant p110δ, for assessing the potency, isoform-selectivity and molecular interactions of various PI3Ki chemotypes. The affinity pocket mutation I777M maintains p110δ activity in the presence of idelalisib, as indicated by intracellular AKT phosphorylation, and rescues cell functions such as p110δ-dependent cell viability.

The Synergy between Glutathione and Phenols-Phenolic Antioxidants Repair Glutathione: Closing the Virtuous Circle-A Theoretical Insight.

Glutathione (GSH) and phenols are well-known antioxidants, and previous research has suggested that their combination can enhance antioxidant activity. In this study, we used Quantum Chemistry and computational kinetics to investigate how this synergy occurs and elucidate the underlying reaction mechanisms. Our results showed that phenolic antioxidants could repair GSH through sequential proton loss electron transfer (SPLET) in aqueous media, with rate constants ranging from 3.

Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics.

Thiophenols are chemical species with multiple desirable biological properties, including their primary and secondary antioxidant capacity. In this work, the repairing antioxidant activity of eight different thiophenols has been investigated for damaged leucine and tryptophane. The investigation was carried out employing quantum mechanical and transition state methods to calculate the thermodynamic and kinetic data of the reactions involved, while simulating the biological conditions at physiological pH and aqueous and lipidic medium.

Insights into the Mechanism of Hydroxyl Radical Mediated Oxidations of 2-Aminopurine: A Computational and Sonochemical Product Analysis Study.

Mechanistic details of hydroxyl radical (OH) mediated oxidations of 2-aminopurine (2AP) in the aqueous phase have been established in this study via a combination of DFT calculations (at the M05-2X/6-311+G(d,p) level with SMD solvation) and sonochemical end product analyses by the LC-Q-TOF-MS/MS method. Rate constants and branching ratios for single electron transfer (SET), two H-abstractions (HA), and seven radical adduct formation (RAF) reactions of OH with 2AP were evaluated using transition state theory (TST). The RAF at the C8-position of 2AP is noted as the dominant process, which constitutes almost 46.

Computationally Designed Sesamol Derivatives Proposed as Potent Antioxidants.

Oxidative stress has been recognized to play an important role in several diseases, such as Parkinson's and Alzheimer's disease, which justifies the beneficial effects of antioxidants in ameliorating the deleterious effects of these health disorders. Sesamol, in particular, has been investigated for the treatment of several conditions because of its antioxidant properties. This article reports a rational computational design of new sesamol derivatives.

The Antioxidant Capability of Higenamine: Insights from Theory.

Density functional theory was employed to highlight the antioxidant working mechanism of higenamine in aqueous and lipid-like environments. Different reaction mechanisms were considered for the reaction of higenamine with the OOH radical. The pH values and the molar fraction at physiological pH were determined in aqueous solution.

Theoretical Study of the Reactivity and Selectivity of Various Free Radicals with Cysteine Residues.

Radicals in biochemical environments can lead to protein damage. Theoretical studies can help us to understand the observed radical selectivity. In this work, the kinetics and thermodynamics of the hydrogen-transfer (HT) and single-electron transfer (SET) reactions between a cysteine derivative and 17 free radicals of biological significance have been theoretically investigated in aqueous and lipid media.

Thiophenols, Promising Scavengers of Peroxyl Radicals: Mechanisms and kinetics.

The activity of 12 thiophenols as primary antioxidants in aqueous solution has been studied using density functional theory. Twelve different substituted thiophenols were tested as peroxyl radicals scavengers. Single electron transfer (SET) and formal hydrogen transfer (FHT) were investigated.

Reinvestigation of Acetophenones Oxidation by Performic Acid in Formic Acid.

The Baeyer-Villiger (BV) reaction of acetophenones R-COCH (R = phenyl, 4-methylphenyl, 3,4-dimethoxyphenyl) with performic acid (PFA) in formic acid (FA) as the catalyst and solvent was reinvestigated using the MPWB1K functional in conjunction with the 6-311G(d,p) and 6-311++G(d,p) basis sets. For the acid-catalyzed addition step, we used the eight-membered ring transition structure proposed in our previous work. The calculated and experimental results obtained for the BV reaction under the mentioned conditions lead to the conclusion that our mechanism is more reliable than the one reported by Liu and co-workers, in which the acid-catalyzed first step involves a transition state with a six-membered ring structure.

The other side of the superoxide radical anion: its ability to chemically repair DNA oxidized sites.

The superoxide radical anion can repair oxidative damage. In particular, it was demonstrated that O2˙- can repair oxidized DNA by electron transfer, restoring the original structure of this important molecule. Acid-base equilibria have been considered, and the influence of the pH on the main reaction mechanism has been explored.

Melatonin and its metabolites as chemical agents capable of directly repairing oxidized DNA.

Oxidative stress mediates chemical damage to DNA yielding a wide variety of products. In this work, the potential capability of melatonin and several of its metabolites to repair directly (chemically) oxidative lesions in DNA was explored. It was found that all the investigated molecules are capable of repairing guanine-centered radical cations by electron transfer at very high rates, that is, diffusion-limited.

Comprehensive Investigation of the Antioxidant and Pro-oxidant Effects of Phenolic Compounds: A Double-Edged Sword in the Context of Oxidative Stress?

Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs) within the framework of the density functional theory and based on kinetic data.

Chemical Insights into the Antioxidant Mechanisms of Alkylseleno and Alkyltelluro Phenols: Periodic Relatives Behaving Differently.

The possible antioxidant reaction mechanisms of recently synthesized and tested alkylseleno (telluro) phenols have been explored using density functional theory by considering two solvents physiologically relevant, water and pentylethanoate (PE). In addition, the possible pathway for the antioxidant regeneration with ascorbic acid has been investigated. Results show that selenium and tellurium systems follow different chemical behaviors.

Radical-trapping and preventive antioxidant effects of 2-hydroxymelatonin and 4-hydroxymelatonin: Contributions to the melatonin protection against oxidative stress.

Background: Melatonin is well known for its antioxidant capacity, which has been attributed to the combined protective effects of the parent molecule and its metabolites. However, the potential role of 2-hydroxymelatonin (2OHM) and 4-hydroxymelatonin (4OHM) in such protection has not been previously investigated.

Methods: The calculations were performed using the Density Functional Theory, with the M05-2X and M05 functionals, the 6-311+G(d,p) basis set and the solvation model based on density (SMD).

The role of acid-base equilibria in formal hydrogen transfer reactions: tryptophan radical repair by uric acid as a paradigmatic case.

The results presented in this work demonstrate the high complexity of chemical reactions involving species with multiple acid-base equilibria. For the case study investigated here, it was necessary to consider two radical species for tryptophan (Trp˙ and Trp˙) and three fractions for uric acid (HUr, HUr and HUr) in order to properly reproduce the experimental results. At pH = 7.

Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor.

DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model.

Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil.

2-Thiocytosine (TC) and 2-thiouracil (TU) were subjected to hydrated electron (e), formate radical (CO˙) and 2-hydroxypropan-2-yl radical ((CH)˙COH) reactions in aqueous medium. Transients were characterized by absorption spectroscopy and the experimental findings were rationalized by DFT calculations at LC-ωPBE and M06-2X levels using a 6-311+G(d,p) basis set and SMD solvation. In e reactions, a ring N-atom protonated radical of TC and an exocyclic O-atom protonated radical of TU were observed via addition of e and subsequent protonation by solvent molecules.

Empirically Fitted Parameters for Calculating pKa Values with Small Deviations from Experiments Using a Simple Computational Strategy.

Two empirically fitted parameters have been derived for 74 levels of theory. They allow fast and reliable pKa calculations using only the Gibbs energy difference between an acid and its conjugated base in aqueous solution (ΔGs(BA)). The parameters were obtained by least-squares fits of ΔGs(BA) vs experimental pKa values for phenols, carboxylic acids, and amines using training sets of 20 molecules for each chemical family.

Coumarin-Chalcone Hybrids as Peroxyl Radical Scavengers: Kinetics and Mechanisms.

The primary antioxidant activity of coumarin-chalcone hybrids has been investigated using the density functional and the conventional transition state theories. Their peroxyl radical scavenging ability was studied in solvents of different polarity and taking into account different reaction mechanisms. It was found that the activity of the hybrids increases with the polarity of the environment and the number of phenolic sites.