Oxidative stress, a result of overproduction of reactive oxygen/nitrogen/chlorine species and/or impairment in the cellular antioxidative defense system, has been considered as an important mechanism of cyto- and genotoxicity. There is a growing interest in searching for exogenous natural and synthetic antioxidants as therapeutic and pharmacological agents [1–5]. Flavonoids, a large group of secondary plant phenolic metabolites (phenolic acids, phenolic diterpenes, flavonoids, tannins, and coumarins being among them), are important natural antioxidants, free radical scavengers and regulators of cellular redox balance and redox signaling cascades [1–6]. Flavonoids are abundant components of human diet and about 10,000 flavonoids have been found in different natural plant sources. The total amount of flavonoids consumed is estimated at hundreds of mg/day . The basic flavonoid structure consists of two phenyl groups joined by a three carbon atom bridge. Flavonoids are classified into flavonols, flavones, flavanones, isoflavones, catechins, anthocyanidins, and chalcones according to their chemical structures.
The molecular structure and mechanisms of antioxidative, cytoprotective and regulative activities of flavonoids as well as their potential use (tested both ex vivo and in vivo) are widely discussed [1–7]. Several mechanisms of action are involved in biological properties of flavonoids such as direct free radical scavenging, transition metal ion chelation, indirect upregulation of cellular antioxidant defense enzymes (such as glutathione S-transferase or UDP-glucuronosyl transferase), activation of survival genes, regulation of a number of signaling pathways and mitochondrial function, modulation of inflammatory responses, and anti-microbial action [5, 6]. Flavonoids directly bind many proteins and activate, inhibit, upregulate, or downregulate such cascades as protein kinases, AMPK, MAPK, NF-kB, the TGFβ-2/PI3K/AKT pathways, p53-mediated apoptotic events, the NF-E2-related transcription factor (NRF2)-mediated activation of genes (the Nrf2-Keap1 pathway), the major regulator of cytoprotective responses to oxidative stress [7, 8]. The flavonoids quercetin, kaempferol, and epicatechin, weak acids with a hydrophobic character, considerably prevent cellular reactive oxygen species (ROS) production by mitochondria (IC50 ≈ 1–2 µM), inhibit redox enzymes, NAD(P)H oxidases, xanthine oxidases, monooxygenases, cyclooxygenases, and lipooxygenases .
Direct antiradical/antioxidant capacities of flavonoids are related to the redox properties of their easily oxidized phenolic hydroxyl groups and conjugated rings. Bors et al. were the first to claim three partial structures contributing to the radical-scavenging activity of flavonoids: the 3’,4’ - ortho-dihydroxyl structure in the B ring (catechol structure) as a radical target site (a), the C2 = C3-double bond with conjugation to the 4-oxo group in the C ring which is necessary for delocalization of an unpaired electron from the B ring (b), and the hydroxyl substituent at position 3 of the C ring which is necessary for enhancement of radical-scavenging activity (c)  (Fig. 1). The important role of intramolecular H-bonding was simultaneously claimed (d) [11, 12]. Quercetin, which belongs to the class of flavonols, contains all the four chemical structures that determine high antioxidant activity .
Recently we suggested that the biochemical effects of some flavonoids (quercetin, catechin, naringenin) were partially connected with modification of the membrane bilayer structure, fluidity, and hydration, as well as with flavonoid ability to regulate mitochondrial membrane permeability and to prevent oxidative stress in membrane compartments [14, 15]. In our experiments, the flavonoids considerably inhibited membrane lipid peroxidation (the IC50 values were equal to 9.7 ± 0.8 µM, 8.8 ± 0.7 µM, and 46.8 ± 4.4 µM in the case of quercetin, catechin and naringenin, respectively) and decreased glutathione oxidation in mitochondria and erythrocytes treated with tert-butyl hydroperoxide [14, 15]. The capacity of flavonoids (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate, and scutellarein,) to inhibit key proteins involved in coronavirus infective cycle has recently been reviewed .
The mechanisms of direct antioxidant activity of polyphenols may be clarified via: 1. hydrogen atom transfer (HAT) and proton-coupled electron transfer (PCET) (the proton and electron are simultaneously transferred to the radical in one kinetic step), 2. single electron transfer followed by-proton transfer (SET-PT) (it is a two-step mechanism), 3. sequential proton loss electron transfer (SPLET) (it is a reverse mechanism with respect to SET-PT, relatively stable polyphenol anion formation after the proton loss is the first step of this mechanism), and 4. formation of stable adducts with radicals [17, 18]. In nonpolar environments (e.g., lipid bilayer), PCET is the only active process of free radical scavenging by flavonoids, and under nonacidic conditions, SPLET is the major mechanism and both the mechanisms take place in reactions against peroxyl or DPPH radicals [11, 19]. Simultaneously, flavonoids display pro-oxidant toxic effects associated with ROS generation via the catechol group oxidation to semiquinone radicals and quinones. The semiquinone radicals and quinones arylate protein thiols and form adducts with reduced glytathione .
Earlier the calculations of the structure and thermochemical parameters of flavonoids were widely performed using the methods of quantum chemistry [8, 17, 20–22]. The more reactive sites in quercetin molecule (Fig. 1), one of the most abundant and studied flavonoids, are the 4’- and 3’-OH groups (the catechol group) of the ring B, as well as the 3-OH group of the ring C through direct H-atom transfer were found. Participation of the 7-OH group, as an orientator of the reaction and not as a direct H-donor in radical scavenging, was revealed. The o-quinone (for quercetin unhydrate) and o-quinone and p-quinone (for quercetin dehydrate) derived from the 3’- and 4’- OH groups were suggested as the main oxidation products of quercetin . It was supposed that the quercetin semiquinone radical arising after removal of the hydrogen atom of the 4’-OH group was the most stable radical and favored to deactivate other radicals via proton and/or electron transfer .
Since the electronic and molecular parameters are crucial for biochemical activity, the present study addressed parallel evaluation of the optimal molecular geometry and electronic properties of flavonoids and their reactions with free radicals/oxidants in the model systems of stable DPPH radical reduction and flavonoid autoxidations and chlorinations by hypochlorous acid. For analysis of the structure/activity relationships, we compared three flavonoid molecules representing different classes that are most abundant and possess high biochemical activity: quercetin (flavonols), catechin (flavanols or flavan-3-ols), and naringenin (flavanones) (Fig. 1). The chemical structure of lipophilic quercetin is characterized by the catechol (3’, 4’o-dihydroxy) group in the B ring, and the double bond in the C ring between C-2 and C-3 in conjunction with the 4-carbonyl group, as well as the 3-, 5- and 7- hydroxyl groups. The water - soluble catechin molecule does not have the 2, 3 double bond in conjunction with the 4-carbonyl group in the C ring and naringenin is a flavanon differing from the quercetin structure by the absence of the C2 = C3 double bond in the C ring and hydroxyl groups at the 3- position on the C ring and at the 3’- position on the B ring (Fig. 1). The parameters of quercetin, catechin, and naringenin molecules extend to a great number of flavonoid subclasses.