The radical scavenging activity of monocaffeoylquinic acids: the role of neighboring hydroxyl groups and pH levels.

Caffeoylquinic acids (CQAs) are well-known antioxidants. However, a key aspect of their radical scavenging activity - the mechanism of action - has not been addressed in detail thus far. Here we report on a computational study of the mechanism of activity of CQAs in scavenging hydroperoxyl radicals. In water at physiological pH, the CQAs demonstrated ≈ 104 times higher HOO˙ antiradical activity than in lipid medium (k(lipid) ≈ 104 M-1 s-1). The activity in the aqueous solution was determined by the hydrogen transfer mechanism of the adjacent hydroxyl group (O6'-H) of the dianion states (Γ = 93.2-95.2%), while the single electron transfer reaction of these species contributed 4.8-6.8% to the total rate constants. The kinetics estimated by the calculations are consistent with experimental findings in water (pH = 7.5), yielding a kcalculated/kexperimental = 2.4, reinforcing the reliability and precision of the computational method and demonstrating its utility for evaluating radical reactions in silico. The results also revealed the pH dependence of the HOO˙ scavenging activity of the CQAs; activity was comparable for all compounds below pH 3, however at higher pH values 5CQA reacted with the HOO˙ with lower activity than 3CQA or 4CQA. It was also found that CQAs are less active than Trolox below pH 4.7, however over pH 5.0 they showed higher activity than the reference. The CQAs had the best HOO˙ antiradical activity at pH values between 5.0 and 8.6. Therefore, in the physiological environment, the hydroperoxyl antiradical capacity of CQAs exhibits similarity to renowned natural antioxidants including resveratrol, ascorbic acid, and Trolox.

The Theoretical and Experimental Insights into the Radical Scavenging Activity of Rubiadin.

Rubiadin (RBD), an anthraquinone derivative, is obtained from Rubia cordifolia, a plant species classified under the Rubiaceae family. Rubiadin has proven beneficial properties, such as anticancer, neuroprotective, anti-inflammatory, and antidiabetic activity. The antioxidant activity of this molecule was suggested by some experimental results but has not been clearly established thus far. In this study, we employ DFT calculations to comprehensively assess the mechanism and kinetics of the HO•/HOO• radical scavenging activity of this compound in relation to solvents. RBD showed moderate HO• radical scavenging activity, with rate constants of 2.95 × 108 and 1.82 × 1010 M-1 s-1 in lipid and polar media, respectively. In the aqueous solution, the compound exhibited remarkable superoxide anion radical scavenging activity (k = 4.93 × 108 M-1 s-1) but modest HOO• antiradical activity. RBD also showed promising antiradical activity against a variety of radicals (CCl3O•, CCl3OO•, NO2, SO4•-, and N3•), while experimental and computational results confirmed that RBD has moderate activity in DPPH/ABTS•+ assays. Thus, RBD is predicted to be a good, albeit selective, radical scavenger.

A Comprehensive Study of the Radical Scavenging Activity of Rosmarinic Acid.

Rosmarinic acid (RA) is reported in separate studies to be either an inducer or reliever of oxidative stress, and this contradiction has not been resolved. In this study, we present a comprehensive examination of the radical scavenging activity of RA using density functional theory calculations in comparison with experimental data. In model physiological media, RA exhibited strong HO• radical scavenging activity with overall rate constant values of 2.89 × 1010 and 3.86 × 109 M-1 s-1. RA is anticipated to exhibit excellent scavenging properties for HOO• in an aqueous environment (koverall = 3.18 × 108 M-1 s-1, ≈2446 times of Trolox) following the hydrogen transfer and single electron transfer pathways of the dianion state. The neutral form of the activity is equally noteworthy in a lipid environment (koverall = 3.16 × 104 M-1 s-1) by the formal hydrogen transfer mechanism of the O6(7,15,16)-H bonds. Chelation with RA may prevent Cu(II) from reduction by the ascorbic acid anion (AA-), hence blocking the OIL-1 pathway, suggesting that RA in an aqueous environment also serves as an OIL-1 antioxidant. The computational findings exhibit strong concurrence with the experimental observations, indicating that RA possesses a significant efficacy as a radical scavenger in physiological environments.

Antiradical Activity of Lignans from Cleistanthus sumatranus: Theoretical Insights into the Mechanism, Kinetics, and Solvent Effects.

Sumatranus lignans (SL) isolated from Cleistanthus sumatranus have demonstrated bioactivities, e.g., they were shown to exhibit immunosuppressive properties in previous research. Their structure suggests potential antioxidant activity that has not attracted any attention thus far. Consistently, a comprehensive analysis of the antioxidant activity of these compounds is highly desirable with the view of prospective medical applications. In this work, the mechanism and kinetics of the antiradical properties of SL against hydroperoxyl radicals were studied by using calculations based on density functional theory (DFT). In the lipid medium, it was discovered that SL reacted with HOO• through the formal hydrogen transfer mechanism with a rate constant of 101-105 M-1 s-1, whereas in aqueous media, the activity primarily occurred through the sequential proton loss electron transfer mechanism with rate constants of 102-108 M-1 s-1. In both lipidic and aqueous environments, the antiradical activity of compounds 6 and 7 exceeds that of resveratrol, ascorbic acid, and Trolox. These substances are therefore predicted to be good radical scavengers in physiological environments.

Controllable hierarchical self-assembly: systematic study forming metallosupramolecular frameworks on the basis of helical beta-oligoamides.

Self-assembly is a key guiding principle for the design of complex nanostructures. Substituted beta oligoamides offer versatile building blocks that can have inherent folding characteristics, offering geometrically defined functionalities that can specifically bind and assemble with predefined morphological characteristics. In this work hierarchical self-assembly is implemented based on metal coordinating helical beta-oligoamides crosslinked with transition metals selected for their favourable coordination geometries, Fe2+, Cu2+, Ni2+, Co2+, Zn2+, and two metalates, MoO42-, and WO42-. The oligoamide Ac-ß3Aß3Vß3S-αHαHαH-ß3Aß3Vß3A (3H) was designed to allow crosslinking via three distinct faces of the helical unit, with a possibility of forming three dimensional framework structures. Atomic force microscopy (AFM) confirmed the formation of specific morphologies that differ characteristically with each metal. X-Ray photoelectron spectroscopy (XPS) results reveal that the metal centres can be reduced in the final structures, confirming strong chemical interaction. Time of flight secondary ion mass spectrometry (ToF-SIMS) confirmed the spatial distribution of metals within the self-assembled networks, also revealing molecular fragments that confirm coordination to histidine and carboxyl moieties. The metalates MoO42- and WO42- were also able to induce the formation of specific superstructure morphologies. It was observed that assembly with either of nickel, copper, and molybdate form thin films, while cobalt, zinc, and tungstate produced specific three dimensional networks of oligoamides. Iron was found to form both a thin film and a complex hierarchical assembly with the 3H simultaneously. The design of the 3H substituted beta oligoamide to readily form metallosupramolecular frameworks was demonstrated with a range of metals and metalates with a degree of control over layer thicknesses as a function of the metal/metalate. The results validate and broaden the metallosupramolecular framework concept and establish a platform technology for the design of functional thin layer materials.

The alkoxy radical polymerization of N-vinylpyrrolidone in organic solvents: theoretical insight into the mechanism and kinetics.

Poly(N-vinylpyrrolidone) (PVP) is a polymer with many applications in cosmetic, pharmaceutical, and biomedical formulations due to its minimal toxicity. PVP can be synthesized through radical polymerization in organic solvents; this well-known industrial process is thoroughly characterized experimentally, however, quantum chemical modeling of the process is scarce: the mechanism and kinetics have not been thoroughly investigated yet. In this work, the mechanism and kinetics of the alkoxy radical polymerization of N-vinylpyrrolidone in organic solvents, namely isopropanol (IP) and toluene (TL), were successfully modeled by computational chemistry. The initiator radicals di-tert-butyl peroxide (TBO˙) and dicumyl peroxide (CMO˙) as well as the solvents isopropanol and toluene, were shown to be capable of assisting in the initiation reactions. The rate constant was influenced by the combination of initiators and solvent and the values of the rate constant of propagation were approximately 101-103 M-1 s-1. The radical polymerization of NVP with dicumyl peroxide as an initiator was comparable to that of di-tert-butyl peroxide in all of the examined organic solvents, whereas the solvents had less of an effect.

Study of the Mechanism and Kinetics of the Radical Scavenging Activity of 2-Mercaptoimidazole.

2-Mercaptoimidazole (2MI) is related to natural ovothiols that are recognized as powerful radical scavengers. Yet, despite early reports of its potent antioxidant properties, 2MI received little attention. Specifically, its radical scavenging activity against typical free radicals like HO• and HOO• has not yet been studied in terms of its mechanism and kinetics. In this project, density functional theory (DFT) simulations were used to assess the antiradical activity of 2MI. Calculations indicate that 2MI can demonstrate anti-HO• activity in both lipid and aqueous environments (koverall of 1.05 × 1010 and 2.07 × 1010 M-1 s-1, respectively). The calculated kinetics is extremely close to the experimental data in water (pH = 7.0), resulting in a kcalculated/kexperimental ratio of 1.73, validating the accuracy of the computational method and its usefulness for assessing radical scavenging activity in silico. In lipid media, the HOO• radical scavenging activity of 2MI is faster than that of common typical natural scavengers such as ascorbic acid, Trolox, and trans-resveratrol; hence, 2MI is a powerful radical scavenger in nonpolar media.

Feruloylmonotropeins: promising natural antioxidants in Paederia scandens.

Paederia scandens (Lour.) is a widely used medicinal herb in Vietnam, China, India, and Japan for the treatment of a variety of conditions, including toothache, chest pains, piles, and spleen inflammation. There is broad interest in identifying the composition of its extracts and confirming their numerous biological activities, including anti-nociceptive, antiviral, and anticancer properties. Two iridoid glucosides obtained from the MeOH extract of P. scandens, 6'-O-E-feruloylmonotropein (6-FMT) and 10'-O-E-feruloylmonotropein (10-FMT), are potential antioxidants based on their structure. In this study, the hydroperoxyl scavenging activity of 6-FMT and 10-FMT was examined in silico by using density functional theory. These FMTs are predicted to be weak antioxidants in non-polar environments, whereas a good HOO˙ scavenging activity is expected in polar environments (pH = 7.4) with k overall = 3.66 × 107 M-1 s-1 and 9.45 × 106 M-1 s-1, respectively. This activity is better than many common antioxidants such as trolox and nearly equivalent to ascorbic acid and resveratrol. The hydroperoxyl scavenging activity was exerted mainly by the di-anion form of FMTs in water at physiological pH following the single electron transfer mechanism. The results suggest that FMTs are promising natural antioxidants in aqueous physiological environments.

Membrane binding properties of plant defensins.

The membrane interaction characteristics of five antifungal plant defensin peptides: NaD1, and the related HXP4 and L5, as well as NaD2 and the related ZmD32 were studied. These peptides were chosen to cover a broad range of cationic charges with little structural variations, allowing for assessment of the role of charge in their membrane interactions. Membrane permeabilizing activity against C. albicans was confirmed and quantified for benchmarking purposes. Viscoelastic characteristics of the membrane interactions were studied in typical neutral and charged model membranes using quartz crystal microbalance with dissipation (QCM-D. Frequency-dissipation fingerprinting analysis of the QCM-D results revealed that all of the peptides were able to bind to all studied model membranes albeit with slightly different viscoelastic character for each membrane type. However, characteristic disruption patterns were not observed suggesting that the membrane disrupting activity of these defensins is mostly specific to fungal membranes, and that increasing the peptide charge does not enhance their action. The results also show that the presence of specific sterols has a profound effect on the ability of the peptides to disrupt the membrane.

The radical scavenging activity of glycozolidol in physiological environments: a quantum chemical study.

Glycozolidol was isolated from the root of Glycosmis pentaphylla (6-hydroxy-2-methoxy-3-methylcarbazole, GLD). This molecule attracted considerable interest due to its beneficial biological activities that likely stem from its antioxidant activity; yet, the radical scavenging action of GLD has not been investigated thus far. In this study, DFT calculations were used to estimate the radical scavenging activity of GLD against a variety of biologically significant radical species in physiological environments. The findings demonstrated that GLD exerts significant antiradical activity in water at pH = 7.40 and in pentyl ethanoate (as a model of lipidic media) with k overall = 8.23 × 106 and 3.53 × 104 M-1 s-1, respectively. In aqueous solution, the sequential proton-loss electron transfer mechanism made the highest contribution to the activity, whereas in nonpolar solvents the formal hydrogen transfer mechanism dominated the activity. GLD is predicted to have strong antiradical activity against CH3O˙, CH3OO˙, CCl3OO˙, NO2, SO4˙-, DPPH and ABTS+˙ k app ≈ 109 M-1 s-1 and k f ≈ 106 M-1 s-1. The results suggest that GLD is a good radical scavenger in physiological environments.

Large-Scale Synthesis of Nanosilica from Silica Sand for Plant Stimulant Applications.

Nanosilica is a versatile nanomaterial suitable as, e.g., drug carriers in medicine, fillers in polymers, and fertilizer/pesticide carriers and potentially a bioavailable source of silicon in agriculture. The enhanced biological activity of nanosilica over quartz sand has been noted before; it is directly related to the altered physicochemical properties of the nanoparticles compared to those of the bulk material. Therefore, it is feasible to use nanosilica as a form of plant stimulant. Nanosilica synthesis is a relatively cheap routine process on the laboratory scale; however, it is not easily scalable. Largely for this reason, studies of nanosilica fertilizers are scarce. This study will focus on industrial-scale silica nanoparticle production and the application of nanosilica as a plant stimulant in maize. A variant of the sol-gel method is used to successfully synthesize nanosilica particles starting from silica sand. The resulting particles are in the size range of 16-37 nm with great purity. The potential of nanosilica as a plant stimulant is demonstrated with the increased quantity and quality of maize crops.

Synthesis and evaluation of the antioxidant activity of 3-pyrroline-2-ones: experimental and theoretical insights.

The heterocyclic γ-lactam ring 2-pyrrolidinone has four carbon atoms and one nitrogen atom. Among the group of derivatives of 2-pyrrolidinones, 1,5-dihydro-2H-pyrrol-2-ones, also known as 3-pyrroline-2-ones, play a significant structural role in a variety of bioactive natural compounds. In this study, three-component reactions were used to successfully synthesize six polysubstituted 3-hydroxy-3-pyrroline-2-one derivatives. The antioxidant activity of the compounds was tested by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, identifying 4-ethoxycarbonyl-3-hydroxy-5-(4-methylphenyl)-1-phenyl-3-pyrroline-2-one (4b) as the most promising radical scavenger. Quantum chemistry calculations of the thermodynamics and kinetics of the radical scavenging activity also suggest that 4b is an effective HO˙ radical scavenger, with k overall values of 2.05 × 109 and 1.54 × 1010 M-1 s-1 in pentyl ethanoate and water, respectively. On the other hand, 4b could not scavenge hydroperoxyl radicals in either media. The ability of 4b to scavenge hydroxyl radicals in polar and non-polar environments is comparable to that of conventional antioxidants such as melatonin, gallic acid, indole-3-carbinol, ramalin, or Trolox. Thus 4b may be classed as a promising HO˙ radical scavenger in the physiological environment.

A Potent Antioxidant Sesquiterpene, Abelsaginol, from Abelmoschus sagittifolius: Experimental and Theoretical Insights.

The sesquiterpenoid compound abelsaginol (AS) was successfully isolated from Abelmoschus sagittifolius for the first time. The compound was identified using NMR and MS data. The antioxidant activity of AS was also evaluated both theoretically and experimentally. AS was found to be a weak HOO• radical scavenger in organic solvents such as pentyl ethanoate and dimethyl sulfoxide (k overall = ∼ 102 M-1 s-1), in a good agreement with the results of the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assay. However, AS exhibited good HOO• antiradical activity in water at pH 7.40 (k overall = 9.00 × 106 M-1 s-1) through the single-electron transfer mechanism of the anion state. Further calculations also demonstrated that AS could exert good to moderate activity against CH3O•, CH3OO•, CCl3OO•, NO2, and SO4 •- radicals, with k f values from 4.00 × 103 to 1.52 × 107 M-1 s-1. However, AS exerted much lower activity against HO•, CCl3O•, NO, O2 •-, and N3 • radicals under the studied conditions. In general, the activity of AS in water at pH 7.40 is higher than that of Trolox or butylated hydroxytoluene, which are common reference antioxidants. Thus, in an aqueous physiological milieu, AS is a promising natural antioxidant.

Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods.

In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X-H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08-HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2-1.5 kcal mol-1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX-H (X=C, N, O, S) bonds.

The hydroperoxyl radical scavenging activity of natural hydroxybenzoic acids in oil and aqueous environments: Insights into the mechanism and kinetics.

Foods that contain hydroxybenzoic acid derivatives (HBA) include red fruits, black radish, onion, and potato peel. HBA are widely known for their anti-inflammatory, anti-cancer, and especially antioxidant capabilities; however, a comprehensive study of the mechanism and kinetics of the antiradical action of these compounds has not been performed. Here, we report a study on the mechanisms and kinetics of hydroperoxyl radical scavenging activity of HBA by density functional theory (DFT) calculations. According to the results, HBA exert low HOO• antiradical activity in the nonpolar environment with overall rate constants in the range of koverall = 5.90 × 10-6 - 4.10 × 103 M-1 s-1. However, most HBA exhibit significant HOO• antiradical activity (koverall = 105 - 108 M-1 s-1) by the single electron transfer (SET) reaction of the phenoxide anions in water at physiological pH. The overall rate constant increases with increasing pH values in the majority of the substances studied. At pH ≤ 4, gentisic acid had the best HOO• antiradical activity (log(koverall) = 3.7-4.8), however at pH > 4, the largest HOO• radical scavenging activity (log(koverall) = 4.8-9.8) was almost exclusively found for gallic and syringic acids. Salicylic and 5-sulphosalicylic acids have the lowest antiradical activity across most of the pH range. The activities of the majority of the acids in this study are faster than the reference compound Trolox. Thus, in the aqueous physiological environment, these HBA are good natural antioxidants.

7-O-Galloyltricetifavan: a promising natural radical scavenger.

7-O-Galloyltricetifavan (7OGT), a natural flavonoid, is isolated from the leaves of Pithecellobium clypearia. The compound exhibits a variety of biological activities. This study details the evaluation of the HOO• antiradical activity of 7OGT by quantum chemistry calculations. The HOO• trapping activity of 7OGT in the gas phase (reference state) was discovered to follow the formal hydrogen transfer mechanism with a rate constant of k = 4.58 × 108 M-1 s-1. In physiological environments, 7OGT is predicted to be an excellent HOO• radical scavenger with k overall = 2.65 × 108 and 1.40 × 104 M-1 s-1 in water and pentyl ethanoate solvents, respectively. The HOO• antiradical activity of 7OGT in water at physiological pH is approximately 2000 times that of Trolox and substantially higher than that of other well-known natural antioxidants such as trans-resveratrol or ascorbic acid. Thus, 7OGT is an excellent natural antioxidant in polar environments.

Oxoberberine: a promising natural antioxidant in physiological environments.

Oxoberberine (OB, 2,10-dihydroxy-3,9-dimethoxy-8-oxo-protoberberine, artathomsonine), which was isolated from Artabotrys thomsonii, was shown to exhibit potent antioxidant activity in vitro, however that is the only reported evidence of the radical scavenging activity of this compound thus far. In the present study, thermodynamic and kinetic calculations were used to determine the free radical scavenging activity of OB against a range of biologically important species, under physiological conditions. In the first part the activity is calculated against the HOO˙ radical that is both biologically important and a reference radical for comparison. It was found that OB has high antiradical capacity against HOO˙ in both lipid medium and water at physiological pH with k overall = 1.33 × 105 and 1.73 × 106 M-1 s-1, respectively. The formal hydrogen transfer mechanism defined the activity in nonpolar environments, whereas in the aqueous solution the single electron transfer competes with the hydrogen transfer pathway. The results showed that, in lipid medium, the HOO˙ trapping capability of OB is better than typical antioxidants such as Trolox, BHT, resveratrol and ascorbic acid. Similarly, the activity of OB in water at pH 7.4 is roughly 19 and 7 times faster than those of Trolox and BHT, respectively, but slightly lower than the activities of resveratrol or ascorbic acid. In the second part, it was found that OB also exhibits high activity against other typical free radicals such as CH3O˙, CH3OO˙, CCl3OO˙, NO2, SO4˙-, DPPH and ABTS˙+ with k f ranging from 2.03 × 105 to 5.74 × 107 M-1 s-1. Hence, it is concluded that OB is a promising radical scavenger in the physiological environment.

Protocol for using artificial lipid droplets to study the binding affinity of lipid droplet-associated proteins.

Here, we present a protocol to construct artificial lipid droplets to study the binding affinity of lipid droplet-associated proteins. We provide procedures to construct adiposomes and prepare recombinant lipid droplet-associated proteins. Then we describe approaches to measure the number density of perilipin 2 on natural lipid droplets, construct artificial lipid droplets, and determine the binding affinity of perilipin 2 on artificial lipid droplets. This protocol can be adapted to determine the binding properties of various lipid droplet-associated proteins. For complete details on the use and execution of this protocol, please refer to Ma et al. (2021).

Theoretical insights into the antiradical activity and copper-catalysed oxidative damage of mexidol in the physiological environment.

Mexidol (MD, 2-ethyl-6-methyl-3-hydroxypyridine) is a registered therapeutic agent for the treatment of anxiety disorders. The chemical structure suggests that MD may also act as an antioxidant. In this study, the hydroperoxyl radical scavenging activity of MD was studied to establish baseline antioxidant activity, followed by an investigation of the effect of MD on the copper-catalysed oxidative damage in biological systems, using computational methods. It was found that MD exhibits moderate radical scavenging activity against HOO• in water and pentyl ethanoate solvents following the single electron transfer and formal hydrogen transfer mechanisms, respectively. MD can chelate Cu(II), forming complexes that are much harder to reduce than free Cu(II): MD chelation completely quenches the Cu(II) reduction by ascorbic acid and suppresses the rate of reduction reaction by O 2 ⋅ - that are the main reductants of Cu(II) in biological environments. Therefore, MD exerts its anti-HO• activity primarily as an OIL-1 inhibitor.

Mechanistic and Kinetic Studies of the Radical Scavenging Activity of 5-O-Methylnorbergenin: Theoretical and Experimental Insights.

5-O-Methylnorbergenin (5-OMB), a natural compound isolated from Rourea harmandiana, is a compound with potential antioxidant activity based on its chemical structure; however, this activity has not been investigated thus far. In this study, the antioxidant activity of 5-OMB was evaluated by experimental and computational methods. 5-OMB exhibited high activity in DPPH (IC50 = 7.25 ± 0.94 µM) and ABTS•+ (IC50 = 4.23 ± 0.12 µM) assays, higher than the reference compound Trolox. The computational results consistently show that 5-OMB is an excellent HOO• radical scavenger (koverall = 8.14 × 108 M-1 s-1) in water at physiological pH, however it only exerts weak activity in lipid medium (koverall = 3.02 × 102 M-1 s-1). The reaction follows the formal hydrogen transfer mechanism in nonpolar solvents, whereas both the sequential proton loss electron transfer and the formal hydrogen transfer pathways contribute to the activity in aqueous solution. There is a good agreement between experimental and computational data, suggesting that 5-OMB is a promising natural radical scavenger in aqueous physiological environment.