Structural Determination of Antioxidant and Anticancer Flavonoid Rutin in Solution through DFT Calculations of 1H NMR Chemical Shifts

Computational studies on a selection of phosphite esters as antioxidants for polymeric materials

CONTEXT

Phosphite esters, a class of organo-phosphorus compounds, are widely used as non-discolouring antioxidants in many polymeric products. Apart from normal radical scavenging, they prevent the splitting of hydroperoxides (ROOH), one of the initial products of autoxidation, from forming extremely reactive free radicals such as alkoxy (RO.) and hydroxy (.OH) radicals. The inherent molecular properties of antioxidants and the chemistry of their action are essential for researchers working in this field of science. Four organo-phosphorous compounds well-known for their antioxidant activity are selected here for theoretical analysis: Tri(m-methylphenyl) phosphite (m-TMPP), Tri(4-methyl-2,6-di-tert-butylphenyl) phosphite (TMdtBPP), Tri(allylphenyl) phosphite (TAPP) and Tri(mercaptobenzothiazoyl) thiophosphate (TMBTTP). The antioxidant activity exhibited by these compounds is theoretically verified, and the results are consistent with the available experimental data. Such theoretical predictions offer advantages in scientific research, particularly when researchers need to select certain molecules as antioxidants for experiments from a pool of molecular systems.

METHODS

The chemical computations presented in this report are done in Gaussian 16 program package. The procedure of density functional theory (DFT) with the model chemistry B3LYP/6-31G(d,p) is used to generate computational data. Global reactivity indices, thermochemical data, Fukui functions, molecular electrostatic potential and NMR spectra are computed for the chosen molecular systems from their optimized geometries.

On the use OF 1H-NMR chemical shifts and thermodynamic data for the prediction of the predominant conformation of organic molecules in solution: the example of the flavonoid rutin

Conformational analyses of organic compounds in solution still represent a challenge to be overcome. The traditional methodology uses the relative energies of the conformations to decide which one is most likely to exist in the experimental sample. The goal of this work was to deepen the approach of conformational analysis of flavonoid rutin (a well-known antioxidant agent) in DMSO solution. The methodology we used in this paper involves expanding the sample configuration space to a total of 44 possible geometries, using Molecular Dynamics (MD) simulations, which accesses structures that would hardly be considered with our chemical perception, followed by DFT geometry optimizations using the ωB97X-D/6-31G(d,p) - PCM level of theory. Spectroscopic and thermodynamic analyses were done, by calculating the relative energies and nuclear magnetic resonance (1H-NMR) chemical shifts, comparing the theoretical and experimental 1H-NMR spectra (DMSO-d 6) and evaluating Mean Absolute Error (MAE). The essence of this procedure lies in searching for patterns, like those found in traditional DNA tests common in healthcare. Here, the theoretical spectrum plays the role of the analyzed human sample, while the experimental spectrum acts as the reference standard. In solution, it is natural for the solute to dynamically alter its geometry, going through various conformations (simulated here by MD). However, our DFT/PCM results show that a structure named 32 with torsion angles ϕ 1 and ϕ 2 manually rotated by approx. 20° showed the best theoretical-experimental agreement of 1H-NMR spectra (in DMSO-d 6). Relative energies benchmarking involving 16 DFT functionals revealed that the ωB97X-D is very adequate for estimating energies of organic compounds with dispersion of charge (MAE < 1.0 kcal mol-1, using ab initio post-Hartree-Fock MP2 method as reference). To describe the stability of the conformations, calculations of Natural Bonding Orbitals (NBO) were made, aiming to reveal possible intramolecular hydrogen bonds that stabilize the structures. Since van der Waals (vdW) interactions are difficult to be identified by NBO donations, the Reduced Density Gradient (RDG) were calculated, which provides 2D plots and 3D surfaces that describe Non-Covalent Interactions (NCI). These data allowed us to analyze the effect of dispersion interactions on the relative stability of the rutin conformations. Our results strongly indicate that a combination of DFT (ωB97X-D)-PCM relative energies and NMR spectroscopic criterion is a more efficient strategy in conformational analysis of organic compounds in solution.

Quantum chemical investigation of predominant conformation of the antibiotic azithromycin in water and DMSO solutions: thermodynamic and NMR analysis

Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH … N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.

Theoretical study of Gibbs free energy and NMR chemical shifts, of the effect of methyl substituents on the isomers of (E)-1-(α,Ꞵ-Dimethylbenzyliden)-2,2-diphenylhydrazine

A theoretical analysis of free Gibbs Energy and NMR 1H 13C chemical shifts of the effect of introduce methyl groups on diphenyl rings, to produce different isomers of (E)-1-(α,Ꞵ-dimethylbenzylidene)-2,2-diphenylhydrazine, is presented. IR vibrational frequencies, Mulliken charges, molecular electrostatic potential (MEP), Gibbs free energy (G) and 1H- and 13C-NMR chemical shifts were obtained by theoretical calculations. In this analysis it was found that the position of the methyl group affects the values of the 1H- and 13C-NMR chemical shifts and the ∆G and ∆H thermodynamic properties of formation and reaction, these properties vary with the same trend, for the isomers studied. Gibbs free energy calculations show that the theoretical (E)-1-(3,4-Dimethylbenzylidene)-2,2-diphenylhydrazine isomer is the most stable, which explains the success of the experimental synthesis of this compound among the other isomers. For this molecule, the C of the HC=N group is the most nucleophilic and the H is the least acidic. The 1H-NMR chemical shifts of protons show a strong correlation with the C=N distance. It was also observed that methyl affects the ν(C=N) frequencies, the C=N distance increases when the inductive effect of the methyl groups is in the structure.

Why Do Dietary Flavonoids Have a Promising Effect as Enhancers of Anthracyclines? Hydroxyl Substituents, Bioavailability and Biological Activity

Anthracyclines currently play a key role in the treatment of many cancers, but the limiting factor of their use is the widespread phenomenon of drug resistance and untargeted toxicity. Flavonoids have pleiotropic, beneficial effects on human health that, apart from antioxidant activity, are currently considered small molecules-starting structures for drug development and enhancers of conventional therapeutics. This paper is a review of the current and most important data on the participation of a selected series of flavonoids: chrysin, apigenin, kaempferol, quercetin and myricetin, which differ in the presence of an additional hydroxyl group, in the formation of a synergistic effect with anthracycline antibiotics. The review includes a characterization of the mechanism of action of flavonoids, as well as insight into the physicochemical parameters determining their bioavailability in vitro. The crosstalk between flavonoids and the molecular activity of anthracyclines discussed in the article covers the most important common areas of action, such as (1) disruption of DNA integrity (genotoxic effect), (2) modulation of antioxidant response pathways, and (3) inhibition of the activity of membrane proteins responsible for the active transport of drugs and xenobiotics. The increase in knowledge about the relationship between the molecular structure of flavonoids and their biological effect makes it possible to more effectively search for derivatives with a synergistic effect with anthracyclines and to develop better therapeutic strategies in the treatment of cancer.

1H-NMR and LC-MS Based Metabolomics Analysis of Potato (Solanum tuberosum L.) Cultivars Irrigated with Fly Ash Treated Acid Mine Drainage

1H NMR and LC-MS, commonly used metabolomics analytical platforms, were used to annotate the metabolites found in potato (Solanum tuberosum L.) irrigated with four different treatments based on FA to AMD ratios, namely: control (0% AMD; tap water), 1:1 (50% AMD), 3:1 (75% AMD is 75% FA: AMD), and 100% AMD (untreated). The effects of stress on plants were illustrated by the primary metabolite shifts in the region from δH 0.0 to δH 4.0 and secondary metabolites peaks were prominent in the region ranging from δH 4.5 to δH 8.0. The 1:3 irrigation treatment enabled, in two potato cultivars, the production of significantly high concentrations of secondary metabolites due to the 75% FA: AMD content in the irrigation mixture, which induced stress. The findings suggested that 1:1 irrigation treatment induced production of lower amounts of secondary metabolites in all crops compared to crops irrigated with untreated acid mine drainage treatment and with other FA-treated AMD solutions.

Relationships between Structure and Antioxidant Capacity and Activity of Glycosylated Flavonols

The antioxidant capacity (AC) and antioxidant activity (AA) of three flavonols (FLV), aglycones and their glycosylated derivatives were evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays in various solvents. Findings confirmed that the glycosylation at the 3-position (3-glycosylation) always decreased the AC under most conditions due to substitution of the 3-position hydroxyl group and glycoside disruption in the molecular planarity. The 7-glycosylated derivatives did not have the above effects, thus generally exhibited ACs similar to their aglycones. Glycosylation decreased the AA of kaempferol and isorhamnetin for both assays in methanol, 3-glycosylation inhibited quercetin AA in the ABTS assay. In the DPPH assay, the AA of 3-glycosylated quercetin was significantly higher than quercetin. Using LC–MS/MS analysis, we found that quercetin and quercetin-7-glucoside underwent dimerization during the antioxidant reaction, potentially leading to a decline in AAs. However, 3-glycoside substitution may have hindered dimer formation, thereby allowing the FLVs to retain strong free radical scavenging abilities.

Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of 1H NMR Chemical Shifts

Chloroquine (CQ) and hydroxychloroquine (HCQ) have been standard antimalarial drugs since the early 1950s, and very recently, the possibility of their use for the treatment of COVID-19 patients has been considered. To understand the drug mode of action at the submicroscopic level (atoms and molecules), molecular modeling studies with the aid of computational chemistry methods have been of great help. A fundamental step in such theoretical investigations is the knowledge of the predominant drug molecular structure in solution, which is the real environment for the interaction with biological targets. Our strategy to access this valuable information is to perform density functional theory (DFT) calculations of ¹H NMR chemical shifts for several plausible molecular conformers and then find the best match with experimental NMR profile in solution (since it is extremely sensitive to conformational changes). Through this procedure, after optimizing 30 trial distinct molecular structures (ωB97x-D/6-31G(d,p)-PCM level of calculation), which may be considered representative conformations, we concluded that the global minimum (named M24), stabilized by an intramolecular N-H hydrogen bond, is not likely to be observed in water, chloroform, and dimethyl sulfoxide (DMSO) solution. Among fully optimized conformations (named M1 to M30, and MD1 and MD2), we found M12 (having no intramolecular H-bond) as the most probable structure of CQ and HCQ in water solution, which is a good approximate starting geometry in drug-receptor interaction simulations. On the other hand, the preferred CQ and HCQ structure in chloroform (and CQ in DMSO-d₆) solution was assigned as M8, showing the solvent effects on conformational preferences. We believe that the analysis of ¹H NMR data in solution can establish the connection between the macro level (experimental) and the sub-micro level (theoretical), which is not so apparent to us and appears to be more appropriate than the thermodynamic stability criterion in conformational analysis studies.

Analysis of Conformational, Structural, Magnetic, and Electronic Properties Related to Antioxidant Activity: Revisiting Flavan, Anthocyanidin, Flavanone, Flavonol, Isoflavone, Flavone, and Flavan-3-ol

Understanding the antioxidant activity of flavonoids is important to investigate their biological activities as well as to design novel molecules with low toxicity and high activity. Aromaticity is a chemical property found in cyclic structures that plays an important role in their stability and reactivity, and its investigation can help us to understand the antioxidant activity of some heterocyclic compounds. In the present study, we applied the density functional theory (DFT) to investigate the properties of seven flavonoid structures with well-reported antioxidant activity: flavan, anthocyanidin, flavanone, flavonol, isoflavone, flavone, and flavan-3-ol. Conformational, structural, magnetic, and electronic analyses were performed using nuclear magnetic resonance, ionization potentials, electron affinity, bond dissociation energy, proton affinity, frontier molecular orbitals (highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO)), and aromaticity through nucleus-independent chemical shifts to analyze these seven flavonoid structures. We revised the influence of hydroxyl groups on the properties of flavonoids and also investigated the influence of the aromaticity of these seven flavonoids on the antioxidant activity.

Current methodologies to refine bioavailability, delivery, and therapeutic efficacy of plant flavonoids in cancer treatment

Over the last two decades, several advancements have been made to improve the therapeutic efficacy of plant flavonoids, especially in cancer treatment. Factors such as low bioavailability, poor flavonoid stability and solubility, ineffective targeted delivery, and chemo-resistance hinder the application of flavonoids in anti-cancer therapy. Many anti-cancer compounds failed in the clinical trials because of unexpected altered clearance of flavonoids, poor absorption after administration, low efficacy, and/or adverse effects. Hence, the current research strategies are focused on improving the therapeutic efficacy of plant flavonoids, especially by enhancing their bioavailability through combination therapy, engineering gut microbiota, regulating flavonoids interaction with adenosine triphosphate binding cassette efflux transporters, and efficient delivery using nanocrystal and encapsulation technologies. This review aims to discuss different methodologies with examples from reported dietary flavonoids that showed an enhanced anti-cancer efficacy in both in vitro and in vivo models. Further, the review discusses the recent progress in biochemical modifications of flavonoids to improve bioavailability, solubility, and therapeutic efficacy.

Quantum chemical investigation of beta-CD–catechin flavonoid encapsulation in solution through NMR analysis: an adequate controlled drug-delivery system

DFT–PCM–water calculations of ¹H NMR chemical shifts for 28 optimized catechin–beta-CD complex structures revealed that adsorption mode of complexion should be predominant in aqueous media, with full-inclusion 1 : 1 structure being in total disagreement with experimental ¹H NMR profile (D₂O).

Conformational Analysis of 5,4'-Dihydroxy-7,5',3'-trimethoxyisoflavone in Solution Using 1H NMR: A Density Functional Theory Approach

Among 20 compounds isolated from the extracts of Ouratea ferruginea the 5,4'-dihydroxy-7,5',3'-trimethoxyisoflavone (9) showed the best inhibitory effect on glutathione S-transferase (GST) and so deserves our attention. In this work we investigated the preferred molecular structure of 9 in chloroform solution using the density functional theory (DFT) and molecular dynamics simulation. Comparison between experimental ¹H NMR data in CDCl₃ solution and calculated chemical shifts enabled us to precisely determine the conformation adopted by 9 in solution, which can be used in further theoretical studies involving interaction with biological targets. Moreover, the experimental NMR data were used as reference to assess the ability of DFT based methods to predict ¹H NMR spectrum in solution for organic compounds. Among various DFT functionals the hybrid B3LYP was the most adequate for the calculation of chemical shifts in what CH_n protons are concerned. Regarding the OH hydrogen, inclusion of explicit CHCl₃ solvent molecules adequately placed around the solute led to good agreement with the experimental chemical shifts (in CDCl₃). It is a well-known fact that theoretical prediction of chemical shifts for OH hydrogens poses as a challenge and also revealed that the way the solvent effects are included in the DFT calculations is crucial for the right prediction of the whole ¹H NMR spectrum. It was found in this work that a supermolecule solute-solvent calculation with a minimum of four CHCl₃ molecules is enough to correctly reproduce the ¹H NMR experimental profile observed in solution, revealing that the calculated solvated structure used to reproduce the NMR chemical shifts is not unique.

Determination of Anticancer Zn(II)-Rutin Complex Structures in Solution through Density Functional Theory Calculations of 1H NMR and UV-VIS Spectra

Coordination compounds formed by flavonoid ligands are recognized as promising candidates as novel drugs with enhanced antioxidant and anticancer activity. Zn(II)-Rutin complexes have been described in the literature and distinct coordination modes proposed based on ¹H NMR/MS and IR/UV-VIS experimental spectroscopic data: 1:1/1:2 (Zn(II) binding to A-C rings) and 2:1 (Zn(II) binding to A-C-B rings) stoichiometry. Aiming to clarify these experimental findings and provide some physical insights into the process of complex formation in solution, we carried out density functional theory calculations of NMR and UV-VIS spectra for 25 plausible Zn(II)-Rutin molecular structures including solvent effect using the polarizable continuum model approach. The studied complexes in this work have 1:1, 1:2, 2:1, and 3:1 metal-ligand stoichiometry for all relevant Zn(II)-Rutin configurations. The least deviation between theoretical and experimental spectroscopic data was used as an initial criterion to select the probable candidate structures. Our theoretical spectroscopic results strongly indicate that the experimentally suggested modes of coordination (1:2 and 2:1) are likely to exist in solution, supporting the two distinct experimental findings in DMSO and methanol solution, which may be seen as an interesting result. Our predicted 1:2 and 2:1 metal complexes are in agreement with the experimental stoichiometry; however, they differ from the proposed structure. Besides the prediction of the coordination site and molecular structure in solution, an important contribution of this work is the determination of the OH-C5 deprotonation state of rutin due to metal complexation at the experimental conditions (pH = 6.7 and 7.20). We found that, in the two independent synthesis of metal complexes, distinct forms of rutin (OH-C5 and O^(-)-C5) are present, which are rather difficult to be assessed experimentally.

Structure of the flavonoid catechin in solution: NMR and quantum chemical investigations

DFT-PCM statistical index scan curves and ¹H-NMR profiles reveal conformational changes when a solid catechin sample is dissolved in acetone solvent.

Structural Determination of Antioxidant and Anticancer Flavonoid Rutin in Solution through DFT Calculations of 1H NMR Chemical Shifts

As the knowledge of the predominant molecular structure of antioxidant and anticancer flavonoid rutin in solution is very important for understanding the mechanism of action, a quantum chemical investigation of plausible rutin structures including solvent effects is of relevance. In this work, DFT calculations were performed to find possible minimum energy structures for the rutin molecule. ¹H NMR chemical shift DFT calculations were carried out in DMSO solution using the polarizable continuum model (PCM) to simulate the solvent effect. Analysis of the experimental and theoretical ¹H NMR chemical shift profiles offers a powerful fingerprint criterion to determine the predominant molecular structure in solution. Therefore, our aim is to find the best match between experimental (in DMSO‐d) and theoretical (PCM–DMSO) ¹H NMR spectrum profiles. Among 34 optimized structures located on the potential energy surface, we found that structure 32, with a B‐ring deviated 30° from a planar configuration (geometry usually assumed for polyphenols), showed an almost perfect agreement with experimental the ¹H NMR pattern when compared to the corresponding fully optimized planar geometry. This structure is also predicted as the global minimum based on room‐temperature Gibbs free energy calculations in solution and, therefore, should be experimentally observed. This is new and valuable structural information regarding structure–activity relationship studies, and such information is hard to obtain by experimentalists without the aid of the X‐ray diffraction technique.