Conformational transitions of the quercetin molecule via the rotations of its rings: a comprehensive theoretical study

Biodegradation of flavonoids - Influences of structural features

Flavonoids, a class of natural products with a variety of applications in nutrition, pharmacy and as biopesticides, could substitute more harmful synthetic chemicals that persist in the environment. To gain a better understanding of the biodegradability of flavonoids and the influence of structural features, firstly, the ultimate biodegradation of 19 flavonoids was investigated with the Closed Bottle Test according to the OECD guideline 301 D. Secondly, regarding the fast abiotic degradation reported for several flavonoids with severe concentration decrease within hours and its possible impacts on the processes behind the ultimate biodegradation, primary degradation of 4 selected flavonoids was compared at conditions representing biodegradation, abiotic degradation, and mixed substrates by monitoring the flavonoids' concentrations with HPLC-UV/vis. Our results showed that 17 out of the 19 tested flavonoids were readily biodegradable. Structural features like a hydroxy group at C3, the C2-C3 bond order, a methoxy group in the B ring, and the position of the B ring in regard to the chromene core did not affect biodegradation of the tested flavonoids. Only flavone without any hydroxy groups and morin with an uncommon 2',4' pattern of hydroxy groups were non-readily biodegradable. Monitoring the concentration of 4 selected flavonoids by HPLC-UV/vis revealed that biodegradation occurred faster than abiotic degradation at CBT conditions with no other carbon sources present. The presence of an alternative carbon source tends to increase lag phases and decrease biodegradation rates. At this condition, abiotic degradation contributed to the degradation of unstable flavonoids. Overall, as a first tier to assess the environmental fate, our results indicate low risks for persistence of most flavonoids. Thus, flavonoids could represent benign substitutes for persistent synthetic chemicals.

Manifestations of intramolecular H-bonds of CH… O and OH… C type in quercetin molecule: Analysis of IR spectra by mean of density functional theory

The IR spectra of 48 conformers of quercetin which represent full conformation space of its tautomers have been modeled at B3LYP/6-311++G(d,p) level of the density functional theory. The presence of intramolecular H-bonds C2'H/C6'H…O3 and O3H…C2'/C6' was characterized by their spectral manifestations. The C2'H/C6'H…O3 contacts were found to have a spectral blue-shift. The O3H…C2'/C6' contacts were mostly red-shifted. The stretching vibrations of H-bonds C2'H/C6'H…O3 demonstrate an increase in the intensity of the modes of stretching vibrations ν(C2'H)/ν(C6'H) and an increase in the frequency of their out-of-plane vibrations γ(C2'H)/γ(C6'H). Most of the spectral parameters correlate a little with the energy of the H-bonds.

Natural dihydroisobenzofuran derivatives as a template for promising radical scavengers: theoretical insights into structure–activity relationships, thermochemistry and kinetics

Dihydroisobenzofuran heterocycle is a structural motif found in a number of medications with anti-tumour, anti-diabetic, and antibacterial activities. It is also found in a slew of natural substances, most notably fungus metabolites, which have been shown to possess credible radical scavenging activity. Density functional theory studies on three different derivatives were conducted to investigate their electronic structures as well as thermochemical and kinetic behaviour against ·OOH, ·OH, and ·OCH3 in biologically relevant solvents, with the goal of elucidating structure–activity relationships and discussing the potential role of the scaffolds as a template for new semisynthetic antioxidants. The importance of resonance and inductive effects, and also hydrogen bonding, has been underlined, but most importantly, it has been demonstrated that all structures have considerable scavenging potential against all studied radicals, with reactions rates close to the diffusion limit.

Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity

The antioxidative nature of chemicals is now routinely studied using computational quantum chemistry. Scientists are constantly proposing new approaches to investigate those methods, and the subject is evolving at a rapid pace. The goal of this review is to collect, consolidate, and present current trends in a clear, methodical, and reference-rich manner. This paper is divided into several sections, each of which corresponds to a different stage of elaborations: preliminary concerns, electronic structure analysis, and general reactivity (thermochemistry and kinetics). The sections are further subdivided based on methodologies used. Concluding remarks and future perspectives are presented based on the remaining elements.

Extrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents

Discovery of potential lead molecule is a challenging, and complex process which require lots of money, patience, and manpower. Human beings are using natural products, predominantly secondary metabolites, for this purpose since ancient time and they are still working on them as a potent source for drug discovery due to their wide structural diversity. Phenolic phytochemicals such as hydroxytyrosol and tyrosol are natural antioxidant and involved in many biological disease cure. Herein, we have carried out the quantum chemical calculations for conformational analysis, geometry optimization and computation of electronic as well as optical properties of hydroxytyrosol and its analogues (1a-1k) in terms of density functional theory by using Gaussian 09 program suite. The eventual charge transfer within the molecules has been confirmed by the analysis of frontier molecular orbitals. The molecular docking studies of 1a-1k with cyclooxygenase-2 showed the noticeable binding affinity as compared to other nonsteroidal anti-inflammatory drugs viz. aspirin, naproxen and celecoxib. Computation of pharmacokinetics and pharmacological properties confirmed the lead/drug like potential of these screened molecules. Furthermore, the molecular dynamics simulation of best three docked ligands (1f, 1h and 1k)-receptor complex and their binding free energy calculations reveals that these molecules bind in the catalytic cavity of cyclooxygenase-2 and found stable during the 100 ns of simulation. Communicated by Ramaswamy H. Sarma.

A Never-Ending Conformational Story of the Quercetin Molecule: Quantum-Mechanical Investigation of the O3′H and O4′H Hydroxyl Groups Rotations

The quercetin molecule is known to be an effective pharmaceutical compound of a plant origin. Its chemical structure represents two aromatic A and B rings linked through the C ring containing oxygen and five OH hydroxyl groups attached to the 3, 3′, 4′, 5, and 7 positions. In this study, a novel conformational mobility of the quercetin molecule was explored due to the turnings of the O3′H and O4′H hydroxyl groups, belonging to the B ring, around the exocyclic C-O bonds. It was established that the presence of only three degrees of freedom of the conformational mobility of the O3′H and O4′H hydroxyl groups is connected with their concerted behavior, which is controlled by the non-planar (in the case of the interconverting planar conformers) or locally non-planar (in other cases) TSsO3′H/O4′H transition states, in which O3′H and O4′H hydroxyl groups are oriented by the hydrogen atoms towards each other. We also explored the number of the physico-chemical and electron-topological characteristics of all intramolecular-specific contacts—hydrogen bonds and attractive van der Waals contacts at the conformers and also at the transition states. Long-terms perspectives for the investigations of the structural bases of the biological activity of this legendary molecule have been shortly described.

A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

Intramolecular tautomerization of the quercetin molecule due to the proton transfer: QM computational study

Quercetin molecule (3, 3', 4', 5, 7-pentahydroxyflavone, C15H10O7) is an important flavonoid compound of natural origin, consisting of two aromatic A and B rings linked through the C ring with endocyclic oxygen atom and five hydroxyl groups attached to the 3, 3', 4', 5 and 7 positions. This molecule is found in many foods and plants, and is known to have a wide range of therapeutic properties, like an anti-oxidant, anti-toxic, anti-inflammatory etc. In this study for the first time we have revealed and investigated the pathways of the tautomeric transformations for the most stable conformers of the isolated quercetin molecule (Brovarets' & Hovorun, 2019) via the intramolecular proton transfer. Energetic, structural, dynamical and polar characteristics of these transitions, in particular relative Gibbs free and electronic energies, characteristics of the intramolecular specific interactions-H-bonds and attractive van der Waals contacts, have been analysed in details. It was demonstrated that the most probable process among all investigated is the proton transfer from the O3H hydroxyl group of the C ring to the C2' carbon atom of the C2'H group of the B ring along the intramolecular O3H…C2' H-bond with the further formation of the C2'H2 group. It was established that the proton transfer from the hydroxyl groups to the carbon atoms of the neighboring CH groups is assisted at the transition states by the strong intramolecular HCH…O H-bond (~28.5 kcal∙mol-1). The least probable path of the proton transfer-from the C8H group to the endocyclic O1 oxygen atom-causes the decyclization of the C ring in some cases. It is shortly discussed the biological importance of the obtained results.