Antioxidative Potency and UV–Vis spectra features of the compounds resulting from the chelation of Fe2+ by Caffeic Acid Phenethyl Ester and two of its derivatives

Molecular dynamics, molecular docking, DFT, and ADMET investigations of the Co(II), Cu(II), and Zn(II) chelating on the antioxidant activity and SARS-CoV-2 main protease inhibition of quercetin

The natural flavonol quercetin (Q) is found in many vegetables, fruits, and beverages, and it is known as a strong antioxidant. Its metal ion chelation may increase its antioxidant activity. The present study aims to explore the Co(II), Cu(II), and Zn(II) chelating on the antioxidant effectiveness and severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) main protease (Mpro) inhibitory of quercetin using Density-functional theory (DFT), molecular docking, and molecular dynamics simulations (MD). DFT calculations at the B3LYP/LanL2DZ reveal that the high antioxidant activity of the metal-chelated quercetin complexes is mainly returned to their lower ionization potentials (IPs) compared with the one of the free quercetin. Molecular docking of quercetin and its Co(II), Cu(II), and Zn(II) chelates into the active binding sites of peroxiredoxin 5 and SARS-CoV-2 main protease (Mpro) were performed using Lamarckian Genetic Algorithm method. The docked quercetin and its metal chelates fit well into the binding site of the target proteins, and their binding affinity is strongly influenced by the type of the chelated metals Co(II), Cu(II), and Zn(II), and molar ratio metal: ligand, i.e. 1:2 and 2:1. Further, the binding stability of QZn2 and QCu2 in peroxiredoxin 5 and SARS-CoV-2 main protease targets is evaluated using MD simulation conducted for 100 ns simulations at natural room temperature conditions, and the obtained results showed that all chelates remain bound to the ligand binding groove of protein except for 1HD2_QZn2 complex. Finally, the adsorption, distribution, metabolism, excretion, and toxicity (ADMET) and drug-likeness properties of quercetin and cobalt(II)-quercetin (QCo2(II)) were investigated.

Theoretical Study of Antioxidant and Prooxidant Potency of Protocatechuic Aldehyde

In this study, the antioxidant and prooxidant potency of protocatechuic aldehyde (PCA) was evaluated using density functional theory (DFT). The potency of direct scavenging of hydroperoxyl (HOO•) and lipid peroxyl radicals (modeled by vinyl peroxyl, H2C=CHOO•) involved in lipid peroxidation was estimated. The repair of oxidative damage in biomolecules (lipids, proteins and nucleic acids) and the prooxidant ability of PCA phenoxyl radicals were considered. The repairing potency of PCA was investigated for damaged tryptophan, cysteine, leucine, DNA base guanine and linolenic acid. The thermodynamics and kinetics of the single electron transfer (SET) and formal hydrogen atom transfer (fHAT) mechanisms underlying the studied processes were investigated under physiological conditions in aqueous and lipid environments using the SMD/M06-2X/6-311++G(d,p) level of theory. Sequestration of catalytic Fe2+ and Fe3+ ions by PCA, which prevents HO• production via Fenton-like reactions, was modeled. Molecular docking was used to study the inhibitory capability of PCA against xanthine oxidase (XO), one of the enzymes producing reactive oxygen species. The attained results show that PCA has the capability to scavenge lipid peroxyl radicals, repair damaged tryptophan, leucine and guanine, chelate catalytic iron ions and inhibit XO. Thus, PCA could be considered a possible multifunctional antioxidant.

Solvation energies of the ferrous ion in water and in ammonia at various temperatures

CONTEXT

The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion.

METHOD

All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.

Use of vinasse and coffee waste as chelating agent of photo-Fenton landfill leachate treatment

This research studies the use of vinasse (VS) coming from Pisco and caffeic acid (Caa) from solid coffee waste as chelating agents of this process, to carry out a photo-Fenton process using UVc lamps of 254-nm wavelength for 60 min, at the natural pH of the landfill leachate (8.9). Without the chelating agent, there was a removal of UV 254 and COD of 54.2% and 54.7%, respectively, when the photo-Fenton reaction was carried out at pH 3; at pH 6, the removal of UV 254 and COD was 13.1% and 39.2%, respectively, and at pH 8.9, the elimination of UV 254 and COD was 10.8% and 16.1%, respectively. When Caa was used in the landfill leachate (LL) for the photo-catalytic processes carried out at pH 8.9, a removal of 24.1%, 43.0%, and 47.4% of UV 254 was obtained using 5 mg/L, 50 mg/L, and 100 mg/L of Caa. The removal of UV 254 was 27.3%, 30.7%, and 36.3% using 5 mg/L, 50 mg/L, and 100 mg/L of VS, respectively, and the removal of COD was 32.2%, 35.4%, and 39.2% using 5 mg/L, 50 mg/L, and 100 mg/L of VS, respectively. When Caa was used in the LL at pH 8.9, the concentration of total Fe went from 37.5 to 33.2, from 40.2 to 36.8, and from 45.2 to 42.1, using 5 mg/L, 50 mg/L, and 100 mg/L of caffeic acid, respectively. Using VS in the LL at pH 8.9, the concentration of total Fe along the run went from 35.1 to 32.2, from 39.4 to 34.8, and from 42.1 to 40.2, using 5 mg/L, 50 mg/L, and 100 mg/L of VS, respectively. As a result of these processes, it was noted that the use of Caa and VS increases the solubility of Fe at a higher pH.

Mactanamide and lariciresinol as radical scavengers and Fe2+ ion chelators - A DFT study

A DFT based kinetic study of OOH radical scavenging potency of mactanamide (MA) and lariciresinol (LA), two natural polyphenols, indicates their nearly equal potential via the proton coupled electron transfer (PCET) mechanism in lipid media. Contribution of C-H bond breaking to this potency is negligible compared to O-H bond breaking, contrary to recent claims. The predicted potency of both compounds is not sufficient to protect biological molecules from oxidative damage in lipid media. In aqueous media, the scavenging potency of MA and LA phenoxide anions via the single electron transfer (SET) mechanism is much higher and may contribute to the protection of lipids, proteins, and DNA from OOH radical damage. Also, MA and LA have the potential to chelate catalytic Fe2+ ions, thus suppressing the formation of dangerous OH radicals via Fenton-type reactions. The monoanionic species of MA and LA show stronger monodentate chelating ability with Fe2+ ion compared to its neutral form. The dianionic specie LA2- exhibited the highest chelation ability with Fe2+ ion via bidentate 1:2 coordination. However, direct radical scavenging and metal chelation could be rarely operative in vivo because MA and LA presumably achieve very low concentrations in systemic circulation.

Discovery of Novel 3-Hydroxyquinazoline-2,4(1H,3H)-Dione Derivatives: A Series of Metal Ion Chelators with Potent Anti-HCV Activities

Millions of people worldwide suffer from acute or chronic liver inflammation caused by the hepatitis C virus (HCV). Metal ion chelators have achieved widespread success in the development of antiviral drugs. Some inhibitors with metal ion chelating structures have been proven to have good inhibitory activities on non-structural protein 5B (NS5B) polymerase. However, most of the reported metal ion chelators showed poor anti-HCV potency at the cellular level. Hence, we designed and synthesized a series of 3-hydroxyquinazoline-2,4(1H,3H)-dione derivatives with novel metal ion chelating structures. Typical compounds such as 21h, 21k, and 21t showed better anti-HCV activities than ribavirin with EC50 values less than 10 μM. 21t is currently known as one of the metal ion chelators with the best anti-HCV potency (EC50 = 2.0 μM) at the cellular level and has a better therapeutic index (TI > 25) as compared to ribavirin and the reported compound 6. In the thermal shift assay, the representative compounds 21e and 21k increased the melting temperature (Tm) of NS5B protein solution by 1.6 °C and 2.1 °C, respectively, at the test concentration, indicating that these compounds may exert an anti-HCV effect by targeting NS5B. This speculation was also supported by our molecular docking studies and ultraviolet-visible (UV-Vis) spectrophotometry assay, in which the possibility of binding of 3-hydroxyquinazoline-2,4(1H,3H)-diones with Mg2+ in the NS5B catalytic center was observed.

Theoretical Study of Radical Inactivation, LOX Inhibition, and Iron Chelation: The Role of Ferulic Acid in Skin Protection against UVA Induced Oxidative Stress

Ferulic acid (FA) is used in skin formulations for protection against the damaging actions of the reactive oxygen species (ROS) produced by UVA radiation. Possible underlying protective mechanisms are not fully elucidated. By considering the kinetics of proton-coupled electron transfer (PCET) and radical-radical coupling (RRC) mechanisms, it appears that direct scavenging could be operative, providing that a high local concentration of FA is present at the place of ^•OH generation. The resulting FA phenoxyl radical, after the scavenging of a second ^•OH and keto-enol tautomerization of the intermediate, produces 5-hydroxyferulic acid (5OHFA). Inhibition of the lipoxygenase (LOX) enzyme, one of the enzymes that catalyse free radical production, by FA and 5OHFA were analysed. Results of molecular docking calculations indicate favourable binding interactions of FA and 5OHFA with the LOX active site. The exergonicity of chelation reactions of the catalytic Fe²⁺ ion with FA and 5OHFA indicate the potency of these chelators to prevent the formation of ^•OH radicals via Fenton-like reactions. The inhibition of the prooxidant LOX enzyme could be more relevant mechanism of skin protection against UVA induced oxidative stress than iron chelation and assumed direct scavenging of ROS.

Theoretical study of the impact of metal complexation on the reactivity properties of Curcumin and its diacetylated derivative as antioxidant agents

The chemical behavior of Curcumin and its derivatives as antioxidant and metal chelator has become the subject of intense experimental research. In this work, a theoretical study was conducted with the aim to investigate whether the acetylation of the aromatic group in Curcumin, which makes it more lipophilic, will alter its biological activities. Also, we selected from the literature metal complexes of Curcumin and its diacetylated derivative with Ga(III) and In(III), in order to discriminate the molecular active sites of the investigated molecules in which the oxidative process occurs and to obtain information about their antioxidation mechanisms. The geometrical structures and electronic properties of these compounds have been obtained using the density functional theory (DFT) method, known for its accurate results. As our other objective is to understand the factors driving biological behavior of all the studied compounds as well as the impact of the metal complexation of Curcumin and its diacetylated derivative, we provided here evidences to explain experimental observations from a molecular reactivity perspective.

Temperature-dependent oxidation of BSCAPE molecule in methanol medium

Temperature-dependent solvation free energy and oxidation by free energy of ionization of 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) in methanol medium are the concerns of the present work. This molecule is a relevant phenolic acid enclosing multiple bioactivities. The explicit, implicit and discrete-continuum models of solvation were used. The methanol molecules were coordinated to this acid to form cluster complexes. The dual method M06-2X/6-31++G(d,p)//B3LYP/6-31G(d) was employed along with basis set superposition error correction. The results show that, the free energy of coordination and solvation are distant. Both quantities increase with temperature. From discrete-continuum treatment, there is non-spontaneity of solvation process, while coordination yielded spontaneity and non-spontaneity at cold and hot room temperatures, respectively. The ionization potential in gas phase, decreases with temperature. All the solvation models yielded lower ionization potential than that of gas phase. Thus, it follows that, the increase of temperature and methanol medium favours the oxidation of BSCAPE. Consequently, this favours its metabolism processes.

Insight of UV-vis spectra and atmospheric implication for the reaction of ˙OH radical towards glyphosate herbicide and its hydrates

The rate constant of the reactions of ˙OH radicals with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K. The results served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP). The calculations yielded an atmospheric lifetime of 2.34 hours and a POCP of 24.7 for GPS. Upon addition of water molecules, there is an increase of lifetime and decrease of POCP for water monomer and water dimer. The POCP for water trimer is slightly above the gaseous GPS. However, the POCPs of GPS and its hydrates are comparable to that of alkanes. The GPS and its hydrates were found to be a potential reservoir of CO₂. The acidification potential (AP) of GPS was found to be 0.189 and decreases upon addition of water molecules. This shows negligible contribution to rain acidification as the AP is less than that of SO₂. The UV-vis spectra were attained using the M06-L/6-311++G(3df,3pd) method and cover the range 160–260 nm which fits well with experiment.

The rate constant of the reactions of ˙OH radical with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K.

Infrared spectra of PEHA molecule and its resistance to oxidation in water and methanol media at 298.15 K: solvent cluster size dependency

The present work investigates the infrared spectra and solvation free energies (SE) of PEHA ((E)-2-(Pyridin-2-yl) ethyl 3-(3,4-dihydroxyphenyl) acrylate) and their impact on the oxidation. The latter was examined through the ionization potential parameter (IP). These investigations were carried out by the DFT method at B3LYP/6-31G(d) for optimization and frequency calculations and corrected for BSSE. X3LYP/6-311++G(2d,2p) was employed for single-point energy calculations. Water and methanol cluster sizes were used for solvation through the explicit solvent model. Thus, the infrared spectra show that the overview frequencies of PEHA compare well with the experimental results. The intense infrared absorptions of complexes are due to the stretching of O-H bonds of solvent clusters in the range 2600-3850 cm^-1. The binding energy per solvent molecule of complexes was calculated and shows that water and methanol clusters mimic the liquid state as from 5 to 10 solvent molecules. The SE of PEHA increases with the increase of the cluster size of water and methanol in the direction of the limit. The latter was censured by the solvation done using the combined explicit-implicit solvent model. As for IP parameter, the results are largely above the IP limit and lower than the IP from gas phase. Thus, water and methanol media have an effect of lowering the IP of PEHA compound. Consequently, both media favour the oxidation of PEHA molecule, which facilitates its metabolism in human organism.

Antioxidant Properties of Lapachol and Its Derivatives and Their Ability to Chelate Iron (II) Cation: DFT and QTAIM Studies

The elucidation of the complexation of lapachol and its derivatives to Fe²⁺ cation has been done using the density functional theory (DFT). This complexation has been limited to bidentate and tridentate to Fe²⁺ cation. Geometry optimizations have been implemented in gas and solution phase (water, acetonitrile, chlorobenzene, benzene, and toluene) for ligands at B3LYP/6-311++G (d,p) level of theory using B3LYP/6-31+G(d,p) optimized data as starting point. But, the geometrical optimizations in solution phase of the 22 complexes analyzed of lapachol and its derivatives to Fe²⁺ cation were restricted to acetonitrile and benzene. The complexation energy and the metal ion affinity (MIA) have also been calculated using the B3LYP method. The results obtained indicated a proportionality between the MIA values and the retained charge on Fe²⁺ cation for k²-(O₁,O₂) modes. But, an inverse proportionality has been yielded between these two parameters for k³-(O₂, C=C) tridentate modes. For k³-(O₃,C=C) tridentate mode coordination, the higher stability has been obtained. In this latter tridentate coordination in gas phase, the topological analysis of complexes exhibits the fact that the electron density is concentrated between the O₃ oxygen atom of the ligand attached to Fe²⁺ and this metal cation. Moreover, the hydrogen bond strength calculated for isolated ligands (situated between 23.92 and 30.15 kJ/mol) is in the range of normal HBs. Collectively, all the complexation processes have shown to be highly exothermic. Our results have also shown that the electron extraction from Fe²⁺...La_i complexes is more difficult compared to that from free ligands.

Thermodynamic of solvation, solute - Solvent electron transfer and ionization potential of BSCAPE molecule and its UV-vis spectra in aqueous solution

The molecular system 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) is a phenolic acid that covers a large spectrum of biological properties. The investigations of solvation and oxidation processes of BSCAPE molecule by computational means were the challenge of this present work. Water was required for solvation throughout the work. The explicit H₂O were sequentially added to form the complexes BSCAPE(H₂O)_n=0-11. The discrete - continuum model was at the heart of this work. DFT and TD-DFT both associated to the continuum model SMD were required. Hence, the structures, the solvation energies, the energies of solute - solvent electron transfer (SSET), the ionisation potential (IP), and the UV-vis spectra were studied. It comes out that, the structure of the CAPE part included in BSCAPE agrees well with the available experimental values of CAPE but with a minor influence due to the presence of benzensulfonyl group. The enthalpy and free energy of solvation increase linearly with nH₂O. The global reactivity indexes were assessed to appreciate the oxidation of BSCAPE. The latter quality was strongly assessed by the enthalpy and free energy of SSET and IP. The SSET potential increase with nH₂O and the size of water clusters. The values 723.16 and 711.62 kJ/mol were found for enthalpy and free energy of IP respectively. Then in aqueous solution, the results fall down and upon addition of nH₂O, they approach gas phase value for 11H₂O and still are not stabilized. Therefore, the resistance to oxidation starts to raise at this level. Elsewhere, the UV-vis spectra of BSCAPE present four important peaks about 279.3, 234.8, 208.4 and 199.4 nm in gaseous state. The excitation shifts to the red as the number of H₂O increase. Their oscillator strengths also increase with solvation.

A DFT Study of Structural and Bonding Properties of Complexes Obtained from First-Row Transition Metal Chelation by 3-Alkyl-4-phenylacetylamino-4,5-dihydro-1H-1,2,4-triazol-5-one and Its Derivatives

Density functional calculations were used to explore the complexation of 3-alkyl-4-phenylacetylamino-4,5-dihydro-1h-1,2,4-triazol-5-one (ADPHT) derivatives by first-row transition metal cations. Neutral ADPHT ligand and mono deprotonated ligands have been used. Geometry optimizations have been performed in gas-phase and solution-phase (water, benzene, and N,N-dimethylformamide (DMF)) with B3LYP/Mixed I (LanL2DZ for metal atom and 6-31+G(d,p) for C, N, O, and H atoms) and with B3LYP/Mixed II (6-31G(d) for metal atom and 6-31+G(d,p) for C, N, O, and H atoms) especially in the gas-phase. Single points have also been carried out at CCSD(T) level. The B3LYP/Mixed I method was used to calculate thermodynamic energies (energies, enthalpies, and Gibb energies) of the formation of the complexes analyzed. The B3LYP/Mixed I complexation energies in the gas phase are therefore compared to those obtained using B3LYP/Mixed II and CCSD(T) calculations. Our results pointed out that the deprotonation of the ligand increases the binding affinity independently of the metal cation used. The topological parameters yielded from Quantum Theory of Atom in Molecules (QTAIM) indicate that metal-ligand bonds are partly covalent. The significant reduction of the proton affinity (PA) observed when passing from ligands to complexes in gas-phase confirms the notable enhancement of antioxidant activities of neutral ligands.

Quantum Chemical Investigation on the Antioxidant Activity of Neutral and Anionic Forms of Juglone: Metal Chelation and Its Effect on Radical Scavenging Activity

The chelation ability of divalent Mg, Ca, Fe, Co, Ni, Cu, Zn, and monovalent Cu ions by neutral and anionic forms of juglone has been investigated at DFT/B3LYP/6-31+G(d,p) level of theory in gas and aqueous phases. It is noteworthy that only the 1 : 1 stoichiometry was considered herein. The effects of these metals on the radical scavenging activity of neutral juglone were evaluated via the usual descriptors of hydrogen atom transfer. According to our results, metal chelation by the two forms of juglone was spontaneous and exothermic in both media. Based on the binding energies, Cu(II) ion showed the highest affinity for the ligands. QTAIM analyses identified the metal-ligand bonds as intermediate type interactions in all the chelates, except those of Ca and Mg. It was also found that the chelates were better radical scavengers than the ligands. In the gas phase, the scavenging activity of the compounds was found to be governed by direct hydrogen atom transfer, the Co(II) chelate being the most reactive. In the aqueous phase also, the sequential proton loss electron transfer was preferred by all the molecules, while the Cu(II) chelates were the most reactive.

Structural and Antioxidant Properties of Compounds Obtained from Fe2+ Chelation by Juglone and Two of Its Derivatives: DFT, QTAIM, and NBO Studies

The chelating ability of juglone and two of its derivatives towards Fe²⁺ion and the antioxidant activity (AOA) of the resulting chelates and complexes (in the presence of H₂O and CH₃OH as ligands) in gas phase is reported via bond dissociation enthalpy, ionization potential, proton dissociation enthalpy, proton affinity, and electron transfer enthalpy. The DFT/B3LYP level of theory associated with the 6-31+G(d,p) and 6-31G(d) Pople-style basis sets on the atoms of the ligands and the central Fe(II), respectively, was used. Negative chelation free energies obtained revealed that juglone derivatives possessing the O-H substituent (L₂) have the greatest ability to chelate Fe²⁺ ion. Apart from 1B, thermodynamic descriptors of the AOA showed that the direct hydrogen atom transfer is the preferred mechanism of the studied molecules. NBO analysis showed that the Fe-ligand bonds are all formed through metal to ligand charge transfer. QTAIM studies revealed that among all the Fe-ligand bonds, the O₁-Fe bond of 1A is purely covalent. The aforementioned results show that the ligands can be used to fight against Fe(II) toxicity, thus preserving human health, and fight against the deterioration of industrial products. In addition, most of the complexes studied have shown a better AOA than their corresponding ligands.