Radical sites in humic acids: A theoretical study on protocatechuic and gallic acids

Persulfate-based remediation of organic-contaminated soil: Insight into the impacts of natural iron ions and humic acids with complexation/redox functionality

The use of persulfate (PDS) for in-situ chemical oxidation of organic contaminants in soils has garnered significant interest. However, the presence of naturally occurring iron-containing substances and humic acid (HA) in environmental compartments can potentially influence the effectiveness of soil remediation. Thus, this study aimed to investigate the role of key functional groups (adjacent phenolic hydroxyl (Ar-OH) and carboxyl groups (-COOH)) in HA that interact with iron. Modified HAs were used to confirm the significance of these moieties in iron interaction. Additionally, the mechanism by which specific functional groups affect Fe complexation and redox was explored through contaminant degradation experiments, pH-dependent investigations, HA by-products analysis, and theoretical calculations using six specific hydroxybenzoic acids as HA model compounds. The results showed a strong positive correlation between accessible Ar-OH and -COOH groups and Fe3+/Fe2+ redox. This was attributed to HA undergoing a conversion process to a semiquinone-containing radical form, followed by a quinone-containing intermediate, while Fe3+ acted as an electron shuttle between HA and PDS, with Fe3+ leaching facilitated by generated H+ ions. Although the stability of HA-Fe3+ complexes with -COOH as the primary binding sites was slightly higher at neutral/alkaline conditions compared to acidic conditions, the buffering properties of the soil and acidification of the PDS solution played a greater role in determining the Ar-OH groups as the primary binding site in most cases. Therefore, the availability of Ar-OH groups on HA created a trade-off between accelerated Fe3+/Fe2+ redox and quenching reactions. Appropriate HA and iron contents were found to favor PDS activation, while excessive HA could lead to intense competition for reactive oxygen species (ROS), inhibiting pollutant degradation in soil. The findings provide valuable insights into the interaction of HA and Fe-containing substances in persulfate oxidation, offering useful information for the development of in-situ remediation strategies for organic-contaminated soil.

Degradation of Sulfamethoxazole by Manganese(IV) Oxide in the Presence of Humic Acid: Role of Stabilized Semiquinone Radicals

In this work, we demonstrate for the first time the abatement of sulfamethoxazole (SMX) induced by stabilized ortho-semiquinone radicals (o-SQ•-) in the MnO2-mediated system in the presence of humic acid. To evaluate the performance of different MnO2/mediator systems, 16 mediators are examined for their effects on MnO2 reactions with SMX. The key role of the bidentate Mn(II)-o-SQ• complex and MnO2 surface in stabilizing SQ•- is revealed. To illustrate the formation of the Mn(II)-o-SQ• complex, electron spin resonance, cyclic voltammetry, and mass spectra were used. To demonstrate the presence of o-SQ• on the MnO2 surface, EDTA was used to quench Mn(II)-o-SQ•. The high stability of o-SQ•- on the MnO2 surface is attributed to the higher potential of o-SQ•- (0.9643 V) than the MnO2 surface (0.8598 V) at pH 7.0. The SMX removal rate constant by different stabilized o-SQ• at pH 7.0 ranges from 0.0098 to 0.2252 min-1. The favorable model is the rate constant ln (kobs, 7.0) = 6.002EHOMO(o-Qred) + 33.744(ELUMO(o-Q) - EHOMO(o-Qred)) - 32.800, whose parameters represent the generation and reactivity of o-SQ•, respectively. Moreover, aniline and cystine are competitive substrates for SMX in coupling o-SQ•-. Due to the abundance of humic constituents in aquatic environments, this finding sheds light on the low-oxidant-demand, low-carbon, and highly selective removal of sulfonamide antibiotics.

Kinetics and mechanisms for sulfamethoxazole transformation in the phenolic acid-laccase (Trametes versicolor) system

Oxidation of phenolic acids (PCs) by laccase could produce various kinds of reactive oxygen species (ROS), which is expected to have substantial impact on the transformation of antibiotics like sulfamethoxazole (SMX) in soil and aquatic environments. In this study, the formation of semiquinones radical (SQ^●-), superoxide anion radical (O₂^●-), hydrogen peroxide (H₂O₂), hydroxyl radical (^●OH), and singlet oxygen (¹O₂) in a laccase-gallic acid (GA) reaction system was confirmed. Meanwhile, GA would be transformed to its monomeric quinone and quinones of di- and tri-polymers. Transformation of SMX by laccase alone is negligible, while which was greatly enhanced in the presence of GA at the optimal pH of 5.5. The dissolved O₂ was the requisite for transformation of SMX due to its fundamental role in the formation of SQ^●-, the key species initializing the chain reactions for the generation of other ROS. The quenching experiments indicated O₂^●- and ¹O₂ were the main ROS responsible for SMX transformation. A total of thirteen products were proposed for the SMX transformation, with the pathways including the breaking of S-N bond, the cleavage of oxazole ring, electrophilic substitution, Michael addition, and condensation reactions. Moreover, the existence of electron-withdrawing substitution group on the benzene ring of PCs and less stability of SQ^●- was believed to be favorable for the transformation of SMX. The results above expand our understanding on the role of oxidation of PCs by laccase in the SMX transformation in environments and are of significance in relation to use of laccase in dealing with SMX pollution.

Enhanced transformation of sulfamethoxazole by birnessite in the presence of gallic acid: Kinetics and pathways

The emergence of antibiotic agents like sulfamethoxazole (SMX) in soils and surface water can cause serious threat to human and animal health. In this work, mechanisms for the promotive effect of gallic acid (GA) on the transformation of SMX by birnessite were studied. In the absence of GA, the observed pseudo-first-order reaction constants (k_obs) decreased as the pH increased from 4.0 to 8.0, in agreement with the decrease in redox potential of birnessite with increasing pH. The changes in chemical state of surface Mn atoms suggested that Mn(IV) played a major role in SMX transformation. SMX was transformed mainly by the bond cleavage of SN and SC, NH oxidation, and self- or cross-coupling reactions, with the formation of seven transformation products. The presence of GA could significantly promote the transformation of SMX, which was more pronounced at pH 6.0 comparing to the effect observed at 4.0. This promotive effect was attributed to both the addition reactions between SMX and GA quinones and the condensation reactions between -COOH of quinones and -NH₂ of SMX or its transformation products. Moreover, the addition reaction between SMX and OH coming from the GA oxidation by birnessite was also proposed, while its contribution to SMX transformation was small. Furthermore, pyrogallol and methyl gallate that do not contain electron-withdrawing substituent like -COOH group are less effective in promoting SMX transformation than GA, suggesting the electron-density of β‑carbon is key to the occurrence of addition reaction. Our results demonstrate the important role of birnessite and naturally occurring phenolic acids in abiotic transformation SMX, which will profoundly affect its mobility and bioavailability in environments.

o-Semiquinone radical anion isolated as an amorphous porous solid

The use of metal cations is a commonly applied strategy to create S > 1/2 stable molecular systems containing semiquinone radicals. Persistent mono-semiquinonato complexes of diamagnetic metal ions (S = 1/2) have been hitherto less common and mostly limited to the complexes of heavy metal ions. In this work, a mono-semiquinonato complex of aluminum, derived from 1,2-dihydroxybenzene, is obtained using a surprisingly short and uncomplicated procedure. The isolated product is an amorphous and porous solid that exhibits very good stability under ambient conditions. To characterise its molecular and electronic structure, 9.7, 34 and 406 GHz EPR spectroscopy was used in concert with computational techniques (DFT and DLPNO-CCSD). It was revealed that the radical complex is composed of two chemically equivalent aluminum cations and two catechol-like ligands with the unpaired electron uniformly distributed between the two organic molecules. The good stability and porous structure make this complex applicable in heterogeneous aerobic reactions.

Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

Hydroxybenzoic acids, like gallic acid and protocatechuic acid, are highly abundant natural compounds. In biotechnology, they serve as critical precursors for various molecules in heterologous production pathways, but a major bottleneck is these acids’ non-oxidative decarboxylation to hydroxybenzenes. Optimizing this step by pathway and enzyme engineering is tedious, partly because of the complicating cofactor dependencies of the commonly used prFMN-dependent decarboxylases. Here, we report the crystal structures (1.5–1.9 Å) of two homologous fungal decarboxylases, AGDC1 from Arxula adenivorans, and PPP2 from Madurella mycetomatis. Remarkably, both decarboxylases are cofactor independent and are superior to prFMN-dependent decarboxylases when heterologously expressed in Saccharomyces cerevisiae. The organization of their active site, together with mutational studies, suggests a novel decarboxylation mechanism that combines acid–base catalysis and transition state stabilization. Both enzymes are trimers, with a central potassium binding site. In each monomer, potassium introduces a local twist in a β-sheet close to the active site, which primes the critical H86-D40 dyad for catalysis. A conserved pair of tryptophans, W35 and W61, acts like a clamp that destabilizes the substrate by twisting its carboxyl group relative to the phenol moiety. These findings reveal AGDC1 and PPP2 as founding members of a so far overlooked group of cofactor independent decarboxylases and suggest strategies to engineer their unique chemistry for a wide variety of biotechnological applications.

Benchmarking Antioxidant-Related Properties for Gallic Acid through the Use of DFT, MP2, CCSD, and CCSD(T) Approaches

We present a benchmark investigation on the O-H bond dissociation enthalpies (BDEs) and ionization potential (IP) for gallic acid (GA), a widely known polyphenolic antioxidant. These properties were determined in the gas-phase and in water through the use of density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2), coupled-cluster with single and double excitations (CCSD), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The 6-311++G(df,p), cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were used. Regarding DFT functionals, the M06-2X provided the best agreement for the BDEs when compared to the corresponding CCSD(T)/aug-cc-pVTZ results; M06-2X was also found to be the most suitable for probing the IP for the protonated forms of GA while LC-ωPBE was the most reliable in the case of deprotonated GA. Given that these properties represent important descriptors for examining mechanisms related to the antioxidant potential of a given polyphenol, we hope that the present work can serve as a guide for computational chemists venturing in the field.

Molecular characteristics of leonardite humic acid and the effect of its fractionations on sulfamethoxazole photodegradation

The widespread occurrence of synthetic antibiotic sulfamethoxazole (SMX)- poses a potential risk to aquatic ecosystems where dissolved organic matter (DOM) may affect its photolysis. In this study, the elimination of SMX by solar photolysis was investigated in the presence of leonardite humic acid (LHA) and its fractions. Fourier transform ion cyclotron resonance mass (FT-ICR-MS) spectra showed that LHA has high aromaticity. van Krevelen diagrams demonstrated highly unsaturated and phenolic compounds. The photolytic degradation of SMX was impeded by all DOM, mainly due to the competition of photons and scavenging or quenching of reactive oxygen species (ROS). The evaluation of isolated fractions of LHA suggested that fractions with MW < 3500, 14000-25,000 and > 100,000 had the greatest negative effects on sulfamethoxazole photodegradation; their inhibitory activities could reach up to 56.2%, 52.9% and 50.5%, respectively. The characterization of DOM at the molecular level will provide further insights into the assessment of photolysis for antibiotic elimination in natural waters where DOM exists ubiquitously.

Differential absorbance study of interactions between europium, soil and aquatic NOM and model compounds

This study compared the binding of europium by soil and aquatic natural organic matter (NOM) exemplified by Pahokee Peat humic acid (PPHA) and Northern Reservoir NOM, respectively. NOM/Eu³⁺ interactions were measured based on the differential absorbance approach. The experimental results show that the binding of Eu³⁺ by humic acid isolated from agricultural soil results in several features of the differential spectra that are distinct from those observed for aquatic NOM. These features may be associated with the presence in soil NOM of functional groups similar to gallic acid. The binding of Eu³⁺ by NOM was modeled using a phenomenological approach that accounted for the involvement of dissimilar metal-binding functionalities. This study also introduced the concept of integrated differential absorbance; the use of that parameter allowed achieving a close fit between the experimental and model data. This study presents an alternative approach to ascertain mechanisms of, and differences in the interactions of europium with model compounds and natural organic matter with the provenance from soil and surface water.

Can Carbamates Undergo Radical Oxidation in the Soil Environment? A Case Study on Carbaryl and Carbofuran

Radical oxidation of carbamate insecticides, namely carbaryl and carbofuran, was investigated with spectroscopic (electron paramagnetic resonance [EPR] and UV-vis) and theoretical (density functional theory [DFT] and ab initio orbital-optimized spin-component scaled MP2 [OO-SCS-MP2]) methods. The two carbamates were subjected to reaction with ^•OH, persistent DPPH^• and galvinoxyl radical, as well as indigenous radicals of humic acids. The influence of fulvic acids on carbamate oxidation was also tested. The results obtained with EPR and UV-vis spectroscopy indicate that carbamates can undergo direct reactions with various radical species, oxidizing themselves into radicals in the process. Hence, they are prone to participate in the prolongation step of the radical chain reactions occurring in the soil environment. Theoretical calculations revealed that from the thermodynamic point of view hydrogen atom transfer is the preferred mechanism in the reactions of the two carbamates with the radicals. The activity of carbofuran was determined experimentally (using pseudo-first-order kinetics) and theoretically to be noticeably higher in comparison with carbaryl and comparable with gallic acid. The findings of this study suggest that the radicals present in soil can play an important role in natural remediation mechanisms of carbamates.

Toward an Understanding of the Ambiguous Electron Paramagnetic Resonance Spectra of the Iminoxy Radical from o-Fluorobenzaldehyde Oxime: Density Functional Theory and ab Initio Studies

Iminoxy radicals (R1R2C═N—O•) possess an inherent ability to exist as E and Z isomers. Although isotropic hyperfine couplings for the species with R1 = H allow one to distinguish between E and Z, unequivocal assignment of the parameters observed in the EPR spectra of the radicals without the hydrogen atom at the azomethine carbon to the right isomer is not a simple task. The iminoxyl derived from o-fluoroacetophenone oxime (R1 = CH3 and R2 = o-FC6H5) appears to be a case in point. Moreover, for its two isomers the rotation of the o-FC6H5 group brings into existence the syn and anti conformers, depending on the mutual orientation of the F atom and C═N—O• group, making a description of hyperfine couplings to structure even more challenging. To accomplish this, a vast array of theoretical methods (DFT, OO-SCS-MP2, QCISD) was used to calculate the isotropic hyperfine couplings. The comparison between experimental and theoretical values revealed that the E isomer is the dominant radical form, for which a fast interconversion between anti and syn conformers is expected. In addition, the origin of the significant AF increase with solvent polarity was analyzed.

High-Field Electron Paramagnetic Resonance and Density Functional Theory Study of Stable Organic Radicals in Lignin: Influence of the Extraction Process, Botanical Origin, and Protonation Reactions on the Radical g Tensor

The radical concentrations and g factors of stable organic radicals in different lignin preparations were determined by X-band EPR at 9 GHz. We observed that the g factors of these radicals are largely determined by the extraction process and not by the botanical origin of the lignin. The parameter mostly influencing the g factor is the pH value during lignin extraction. This effect was studied in depth using high-field EPR spectroscopy at 263 GHz. We were able to determine the gxx, gyy, and gzz components of the g tensor of the stable organic radicals in lignin. With the enhanced resolution of high-field EPR, distinct radical species could be found in this complex polymer. The radical species are assigned to substituted o-semiquinone radicals and can exist in different protonation states SH3+, SH2, SH1-, and S2-. The proposed model structures are supported by DFT calculations. The g principal values of the proposed structure were all in reasonable agreement with the experiments.

Theoretical Characterisation of Phosphinyl Radicals and Their Magnetic Properties: g Matrix

The g matrices (g tensors) of various phosphinyl radicals (R2 P(.) ) were calculated using the DFT and multireference configuration interaction (MRCI) methods. The g matrices were distinctly dependent on the molecular structure of the radical. To thoroughly examine this dependence, the contributions from individual atoms and excited states were calculated. The former revealed the gain from the phosphorus atom to be preeminent unless PO or PS bonds are present in the radical molecule. The contributions owing to excited states arising from electronic transitions between doubly occupied molecular orbitals and the SOMO were clearly positive, as in the case of semiquinone and niroxide radicals. The transitions from the phosphorus lone pair were of paramount importance. Surprisingly, unlike for semiquinones and nitroxides, a significant negative contribution was observed from excitations from the SOMO to unoccupied molecular orbitals. For radicals with PO bonds, this contribution to the g2 component was dominant.

Gallic acid: a versatile antioxidant with promising therapeutic and industrial applications

Oxidative stress, a result of an overproduction and accumulation of free radicals, is the leading cause of several degenerative diseases such as cancer, atherosclerosis, cardiovascular diseases, ageing and inflammatory diseases.