Solvent Effects are Important in Elucidating Radical-Scavenging Mechanisms of Antioxidants. A Case Study on Genistein

Abstract

In two recent researches on antioxidant mechanisms of flavonoids and isoflavonoids, quantum chemical method was employed to calculate the proton dissociation energies, the bond dissociation energies and the ionization potentials for the phenols and derived radicals to help determine the radical-scavenging mechanisms. As the solvent effect was left out of consideration, the conclusion drawn from the calculation incurred some controversies. In the current study, we re-calculated the parameters for genistein and its anion by employing a B3LYP/6–311+G(d,p)//6–31G(d,p) method with solvent effect. Accordingly, a more reasonable explanation on the experimentally observed behavior of genistein as a radical scavenger was obtained. Therefore, solvent effect should be considered in the investigation of radical-scavenging mechanisms of antioxidants in polar solvents.     

Why B-ring is the active center for genistein to scavenge peroxyl radical: a DFT study

The structure-activity relationship for genistein to scavenge peroxyl radical was clarified by density functional theory (DFT) calculations using the B3LYP/6-31G(d,p) method. It was revealed that the conjugation of an electron-withdrawing 1,4-pyrone group with A-ring of genistein was not beneficial to enhance the radical-scavenging activities. Thus, hydroxyl in B-ring became the active center of genistein to scavenge peroxyl radical.     

Proton dissociation is important to understanding structure-activity relationships of gallic acid antioxidants

Gallic acid derivatives (GADs) can efficiently scavenge free radicals, which is partially responsible for their neuroprotective effects. As GADs tend to deprotonate to give birth to GAD anions, which has big influence on the radical-scavenging behaviors of GADs, to understand the structure-activity relationships (SARs) of GAD antioxidants, the anions should be taken into consideration. In this paper, a combined density functional theory method, labeled as (RO)B3LYP/6-311+G(2d,2p)//AM1/AM1, was employed to calculate homolytic O-H bond dissociation enthalpies and adiabatic ionization potentials for GADs and derived anions in solvent (ethanol), by which the experimentally observed SARs of GADs were better elucidated.     

Unexpected role of 5-OH in DPPH radical-scavenging activity of 4-thiaflavans. Revealed by theoretical calculations

The O-H bond dissociation enthalpies (BDEs) of 4-thiaflavans were calculated by a combined density functional theory method (RO)B3LYP/6-311 + G(2d,2p)//AM1/AM1. The calculated BDEs not only gave a reasonable explanation on the DPPH radical-scavenging activity difference of 4-thiaflavans, but also revealed the unexpected role of 5-OH in enhancing the antioxidant activity of A-ring.     

三种黑米花色苷自由基清除能力的理论评价

用一种组合的密度泛函理论方法计算了三种黑米花色苷的O-H键解离焓和电离势,以此作为理论指标评价其自由基清除能力。计算结果发现花色苷的电离势和总抗氧化能力存在良好的线性关系,提示电离势表征的质子转移伴随电子转移的反应机制在清除自由基的过程中发挥着重要作用。     

Theoretical ab initio study of the effects of methylation on structure and stability of G:C Watson-Crick base pair

Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single-point calculations have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.     

A DFT study on the mechanisms for the cycloaddition reactions between 1−aza-2-azoniaallene cations and acetylenes

The mechanisms of cycloaddition reactions between 1-aza-2-azoniaallene cations 1 and acetylenes 2 have been investigated using the global electrophilicity and nucleophilicity of the corresponding reactants as global reactivity indexes defined within the conceptual density functional theory. The reactivity and regioselectivity of these reactions were predicted by analysis of the energies, geometries, and electronic nature of the transition state structures. The theoretical results revealed that the reaction features a tandem process: an ionic 1,3-dipolar cycloaddition to produce the cycloadducts 3?H-pyrazolium salts 3 followed by a [1,2]-shift affording the thermodynamically more stable adducts 4 or 5. The mechanism of the cycloaddition reactions can be described as an asynchronous concerted pathway with reverse electron demand. The model reaction has also been investigated at the QCISD/6-31++G(d,p) and CCSD(T)/6-31++G(d,p)//B3LYP/6-31++G(d,p) levels as well as by the DFT. The polarizable continuum model, at the B3LYP/6-31++G(d,p) level of theory, was used to study solvent effects on all the studied reactions. In solvent dichloromethane, all the initial cycloadducts 3 were obtained via direct ionic process as the result of the solvent effect. The consecutive [1,2]-shift reaction, in which intermediates 3 are rearranged to the five-membered heterocycles 4/5, is proved to be a kinetically controlled reaction, and the regioselectivity can be modulated by varying the migrant. The LOL function and RDG function based on localized electron analysis were used to analysis the covalent bond and noncovalent interactions in order to unravel the mechanism of the title reactions.     

Lignin-derived oak phenolics: a theoretical examination of additional potential health benefits of red wine

Lignin-derived phenolic compounds can be extracted from oak barrels during the aging of red wine, and it is hypothesized that these compounds may contribute to the health benefits of red wine by their antioxidant, radical-scavenging, or chemopreventive activities. Density functional calculations (B3LYP/6-311++G**) support the radical-scavenging abilities of the oak phenolics. Sinapaldehyde, syringaldehyde, syringol, and syringylacetone all have bond dissociation energies that are lower than resveratrol and comparable to the flavonoid catechin. Molecular docking studies of the oak phenolics with known resveratrol protein targets also show that these compounds dock favorably to the protein targets. Thus, lignin-derived oak phenolics, although found in small concentrations, may contribute to the beneficial antioxidant, chemopreventive, and cardioprotective effects of red wine.     

Theoretical study on isomerization and peptide bond cleavage at aspartic residue

Isomerization and peptide bond cleavage at aspartic residue (Asp) in peptide models have been reported. In this study, the mechanisms and energies concerning the isomerization and peptide bond cleavage at Asp residue were investigated by the density functional theory (DFT) at B3LYP/6-311++G(d,p). The integral equation formalism-polarizable continuum model (IEF-PCM) was utilized to calculate solvation effect by single-point calculation of the gas-phase B3LYP/6-311++G(d,p)-optimized structure. Mechanisms and energies of the dehydration in isomerization reaction of Asp residue were comparatively analyzed with the deamidation reaction of Asn residue. The results show that the succinimide intermediate was formed preferentially through the step-wise reaction via the tetrahedral intermediate. The cleavage at C-terminus is more preferential than those at N-terminus. In comparison to isomerization, peptide bond cleavage is ～20 kcal mol^?1 and lower in activation barrier than the isomerization. So, in this case, the isomerization of Asp is inhibited by the peptide bond cleavage.     

Dehydration of a polyether type extraction agent and of the corresponding K+ complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods

In this paper we report a quantum chemical study performed at the B3LYP/6-311G++(d,p) level of theory on structural and energetic aspects of the sequential dehydration of a tetra-hydrated polyethylene-glycol type podand (1,2-bis-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-benzene, hereafter b33) and its complex with the K(+) cation. Thermodynamical parameters were determined by hessian quantum calculations performed using a self-consistent reaction field (SCRF) method, taking into account solvent (dichloromethane) effects. The results allowed the estimation of dehydration enthalpies, entropies and free energies for the hydrated free b33 podand and its corresponding K(+) cation complex in dichloromethane. The low absolute values found for the dehydration free energies as well as the structural features found for the optimized structures and the corresponding basis superposition calculated interaction energies, support the hypothesis of an interfacial complexation type mechanism governing the assisted extraction of K(+) from an aqueous toward an organic phase, in liquid/liquid extraction.     

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH₃NO₂ → CH₃ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C?NO₂ bond axis, the barriers of the isomerization are lower than the C–NO₂ bond dissociation energies, leading to the preferences of the isomerization over the C?NO₂ bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C–NO₂ bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.     

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.     

Fluoro-substitution effects in deoxyfluoro-D-glucose derivatives: random conformational search and quantum chemical calculation

The effect of substitution by the fluorine atom at different positions of D-glucose was investigated by quantum chemical calculation of the low-energy conformers. These were obtained through the Random conformational search method. The geometries of conformers were optimized at the RHF/6-31(d) level, then reoptimization and vibrational analysis were performed at the B3LYP/6-31+G(d) level. Single-point energies were calculated at the B3LYP/6-311++G(2d,2p) level. The free energies of solvation in water were calculated utilizing the AM1-SM5.4 solvation model. For all substitution positions, the ring conformation does not change much, and the pyranoid 4C1 conformers are dominant, while variations in the substitution site result in different effects in the network of hydrogen bonds, anomeric effect, the solvation free energy, and the ratio of alpha- and beta-anomers.     

Comparative theoretical studies of energetic pyrazole-pyridine derivatives

The pyrazole-pyridine derivatives were optimized to obtain their molecular geometries and electronic structures at the DFT-B3LYP/6-31G(d,p) and DFT-B3P86/6-31G(d,p) levels. Molecular mechanics (MM) calculations were performed for the title compounds. Heats of formation (HOFs) were predicted through designed isodesmic reactions. Detonation performance was evaluated by using the Kamlet-Jacobs equations based on the calculated densities and heats of formation. The thermal stability of the title compounds was investigated via the bond dissociation energies (BDEs). The simulation results reveal that the compound with one pyrazole ring that is fully nitro-substituted performs similarly to the famous explosive HMX, and the compound with two pyrazole rings that are fully nitro-substituted outperforms HMX. According to the quantitative standard of energetics and stability as high energy density materials (HEDMs), the compound with two pyrazole rings that are fully nitro-substituted essentially satisfies this requirement.     

Tautomeric energetics of xanthine oxidase substrates: xanthine, 2-oxo-6-methylpurine, and lumazine

The stability of the tautomers of each of the three important substrates of xanthine oxidase, xanthine, 2-oxo-6-methylpurine, and lumazine, was examined by quantum mechanical calculations. The geometries of these tautomers were optimized at the AM1, Hartree-Fock (HF/6-31G), and hybrid Hartree-Fock/density functional theory (B3LYP/6-31G(d)) levels of theory. The single point energies of some of the more stable tautomers for each of the substrates were calculated at the B3LYP/6-311 +G(2d,p) level of theory. The Conductor Polarized Continuum Model (CPCM) was used to evaluate the solvent effects on the relative stabilities of these tautomers. The calculations clearly identify the lowest energy tautomeric form for xanthine and lumazine. On the other hand, there appear to be three tautomers for 2-oxo-6-methylpurine, with only minor energetic differences in vacuo. In water, however, only one of them predominates. The lowest energy tautomers presumably represent the predominant tautomeric forms at the molybdenum center of xanthine oxidase during catalysis. Implications of these computational results are discussed in the context of enzyme catalysis.     

Density functional computational studies on (E)-2-[(2-Hydroxy-5-nitrophenyl)-iminiomethyl]-4-nitrophenolate

Density functional calculations of the structure, atomic charges, molecular electrostatic potential and thermodynamic functions have been performed at B3LYP/6-31G(d,p) level of theory for the title compound (E)-2-[(2-hydroxy-5-nitrophenyl)-iminiomethyl]-4-nitrophenolate. The results show that the phenolate oxygen atom and all of the nitro group oxygen atoms have bigger negative charges, and the coordination ability of these atoms differs in different solvents. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6-31G(d,p) basis set by applying the Onsager method and the isodensity polarized continuum model (IPCM). The results obtained with these methods reveal that the IPCM method yielded a more stable structure than Onsager’s method. In addition, natural bond orbital and frontier molecular orbital analysis of the title compound were performed using the B3LYP/6-31G(d,p) method.     

Hydrophilic interaction liquid chromatography and accurate mass measurement for quantification and confirmation of morphine, codeine and their glucuronide conjugates in human urine

A hydrophilic interaction liquid chromatography-time-of-flight mass spectrometry (HILIC-TOFMS) method for the quantification and confirmation of morphine (M), codeine (C), morphine-3-glucuronide (M3G), morphine-6-glucuronide (M6G) and codeine-6-glucuronide (C6G) is presented. The method was validated in terms of specificity, selectivity, extraction recovery, accuracy, repeatability, linearity and matrix effect. After a straightforward sample preparation by solid phase extraction (SPE) the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The HILIC technique provided good chromatographic separation which was critical for isomers M3G and M6G. The analytes were detected after electrospray ionization (ESI) in positive mode with mass accuracies below 2 mDa using a 5-mDa window. A measurement range of 50-5000 ng/ml was applied for calibration using deuterated analogs as internal standards. The precision of the method was 5.7% and 10.2% (RSD) within and between days, respectively. The applicability of the method was demonstrated with authentic urine samples known to contain codeine and/or morphine and their intact glucuronide conjugates. Identification of the analytes was based on in-source collision induced dissociation (ISCID), applying three diagnostic ions with accurate mass.     

Conformational preferences of α,α-trehalose in gas phase and aqueous solution

This work presents an investigation on the conformational preferences of α,α-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer’s stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM.     

Theoretical investigation of the effect of sugar substitution on the antioxidant properties of flavonoids

Natural flavonoids are secondary phenolic plant metabolites known for their bioactivity as antioxidants. The evaluation of this property is generally done by the estimation of their direct free radical-scavenging activity as hydrogen or electron donating compounds. This paper reviews experimental results available in the literature for a selection of flavonoids and compares them with calculated quantities characteristic of the hydrogen or electron donation. For that purpose, bond dissociation energies, ionization potentials and electron transfer enthalpies are computed by using DFT methods and the ONIOM procedure implemented in the ab initio program Gaussian. This process has been chosen because it can be extended to the study of large molecules. When acid dissociation and interaction with the solvent are taken into account, the results present very good concordance with experimental results, enlightening the complexity of the processes involved in the classical assays which measure the ability of compounds to scavenge the (2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt) radical cation (ABTS (+)) or the 2,2-diphenyl-1-picryl-hydrazyl radical (DPPH(·)). This study demonstrates the good accuracy of theoretical calculations in obtaining the relative energies involved in free radical scavenging abilities and its capacity for predictive behaviour. It also highlights the necessity to take into account the pK(a) of the compounds and the solvent interaction. The ability of the method to calculate the antioxidant properties of larger molecules are tested on glycosylated flavonoids and the effects of sugar substitution on the antioxidant properties of flavonoids are investigated, pointing out the importance of the charges on the oxygen atoms.