Modulation of radical and nonradical pathways via modified carbon nanotubes toward efficient oxidation of binary pollutants in water

In order to minimize the knowledge gap between single and binary pollutants degradation by persulfate-based advanced oxidation processes (PS-AOPs), iron-loaded N-doped carbon nanotubes (Fe-NCNT) and its acid-washing sample (Fe-NCNT-W) were synthesized as peroxymonosulfate (PMS) activator for simultaneous oxidation of acid orange 7 (AO7) and electron-rich (phenol/ibuprofen) or electron-deficient pollutants (nitrobenzene/benzoic acid). Mechanistic studies revealed that both radical (HO•, SO4•-) and nonradical (electron-transfer, high-valent iron) pathways involved for organic oxidation in Fe-NCNT/PMS system, while electron-transfer pathway (ETP) and high-valent iron-oxo species accounted for pollutant degradation at the surface and inner space of Fe-NCNT-W, respectively. The oxidation performances in single or binary systems were systematically investigated. In comparison to benchmark radical-based (Fe2+/PMS), nonradical ETP (NCNT/PMS) and mixed (Fe-NCNT/PMS) systems, Fe-NCNT-W/PMS outperformed superior performance toward oxidation of binary pollutants with little inference from solution pH or background substances, which could also be fabricated into membrane reactor for actual dyeing sewage treatment. Such superiorities should be mainly ascribed to the particular selectivity and intensive treatment of nonradical pathways in Fe-NCNT-W/PMS system with nanoconfinement effect. This work affords novel insights into the treatment of combined pollution via PMS activation by engineered nanomaterials.

A highly selective C-rhamnosyltransferase from Viola tricolor and insights into its mechanisms

C-Glycosides are important natural products with various bioactivities. In plant biosynthetic pathways, the C-glycosylation step is usually catalyzed by C-glycosyltransferases (CGTs), and most of them prefer to accept uridine 5'-diphosphate glucose (UDP-Glc) as sugar donor. No CGTs favoring UDP-rhamnose (UDP-Rha) as sugar donor has been reported, thus far. Herein, we report the first selective C-rhamnosyltransferase VtCGTc from the medicinal plant Viola tricolor. VtCGTc could efficiently catalyze C-rhamnosylation of 2-hydroxynaringenin 3-C-glucoside, and exhibited high selectivity towards UDP-Rha. Mechanisms for the sugar donor selectivity of VtCGTc were investigated by molecular dynamics (MD) simulations and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) binding free energy calculations. Val144 played a vital role in recognizing UDP-Rha, and the V144T mutant could efficiently utilize UDP-Glc. This work provides a new and efficient approach to prepare flavonoid C-rhamnosides such as violanthin and iso-violanthin.

Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review

Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.

Supported Mn2O3-based catalysts for NO-SCO: an experimental study

In this paper, the NO-SCO (the selective catalytic oxidation of NO) experiments of single-phase Mn₂O₃, supported Mn₂O₃/Al₂O₃, and the Ce-doped Mn_xCe_y/Al catalyst system were carried out. The physical and chemical properties of the catalysts were analyzed by XRD, BET, XPS, SEM, O₂-TPD, and H₂-TPR. The effects of loading and Ce doping on catalyst activity were studied. The results show that the Mn₂O₃ catalyst exhibited the best activity at 300 ℃, and the NO conversion rate of Mn₂O₃ was 78.2%. The relative content of O_α adsorbed on the surface of the Mn_x/Al catalyst decreased obviously by loading Mn₂O₃ on γ-Al₂O₃, which led to the decrease in catalyst activity. And the temperature window moved to the high-temperature region. After doping Ce, the dispersion of Mn enhanced, and the relative content of oxygen O_α adsorbed on the surface increased. The low-temperature activity and fluidity of oxygen in catalysts were improved. Among them, the Mn_0.2Ce_0.08/Al catalyst obtained a high specific surface area, good pore structure, large oxygen storage capacity, and excellent surface oxygen species. The corresponding NO conversion rate reached 83.5% at 290 ℃. Then, the effects of operating parameters such as space velocity, NO concentration, and O₂ content on the catalytic activity of Mn_0.2Ce_0.08/Al were discussed. The experimental results show that the NO conversion rate of Mn_0.2Ce_0.08/Al decreased with increasing NO concentration and space velocity. The O₂ content had a positive effect on the catalytic activity of the catalyst. However, the NO conversion rate tended to be stable due to the saturation of oxygen adsorbed on the catalyst. Through cycling experiments, we found that Mn₂O₃, Mn_0.2/Al, and Mn_0.2Ce_0.08/Al catalysts showed good oxidation stabilities for NO oxidation. The evaluation of the water and sulfur resistance of the catalyst shows that the toxicity of SO₂ was reduced by the aqueous atmosphere to a certain extent. Through the structural optimization of the basic model and the calculation of the NO-SCO reaction path, the results show that the NO-SCO reaction on the Mn₂O₃ (110) face followed the ER mechanism more. For the Mn₂O₃/Al₂O₃ (110) surface, the LH-MvK hybrid mechanism can greatly reduce the desorption energy barrier of the reaction intermediates, which is more favorable for the NO-SCO reaction. The catalytic mechanisms of the Mn_xCe_y/Al catalysts require further in-depth research.

Elucidation of radical- and oxygenate-driven paths in zeolite-catalysed conversion of methanol and methyl chloride to hydrocarbons

Understanding hydrocarbon generation in the zeolite-catalysed conversions of methanol and methyl chloride requires advanced spectroscopic approaches to distinguish the complex mechanisms governing C-C bond formation, chain growth and the deposition of carbonaceous species. Here operando photoelectron photoion coincidence (PEPICO) spectroscopy enables the isomer-selective identification of pathways to hydrocarbons of up to C₁₄ in size, providing direct experimental evidence of methyl radicals in both reactions and ketene in the methanol-to-hydrocarbons reaction. Both routes converge to C₅ molecules that transform into aromatics. Operando PEPICO highlights distinctions in the prevalence of coke precursors, which is supported by electron paramagnetic resonance measurements, providing evidence of differences in the representative molecular structure, density and distribution of accumulated carbonaceous species. Radical-driven pathways in the methyl chloride-to-hydrocarbons reaction(s) accelerate the formation of extended aromatic systems, leading to fast deactivation. By contrast, the generation of alkylated species through oxygenate-driven pathways in the methanol-to-hydrocarbons reaction extends the catalyst lifetime. The findings demonstrate the potential of the presented methods to provide valuable mechanistic insights into complex reaction networks.

Iron-based metal-organic framework derived pyrolytic materials for effective Fenton-like catalysis: Performance, mechanisms and practicability

In this study, a new catalyst was fabricated by pyrolysis under nitrogen atmosphere with MIL-53(Fe) as the precursor, and was applied to catalyze Fenton-like process. Effects of calcination temperature and pH on decontamination performance, and stability of materials were investigated. Under optimal conditions (calcination temperature of 500 °C and pH of 5.0), the new Fenton-like system remained low iron leaching, and achieved high pseudo-first-order rate constant of 0.0251 min^-1 for bisphenol S (BPS) removal, which is much higher than those in MIL-53(Fe), and nano-Fe₃O₄ catalyzed Fenton-like systems. The superiority of the new catalyst for Fenton-like catalysis was attributed to high specific surface area, as well as formed Fe(II), coordinatively unsaturated iron center and the Fe-O/Fe-C compounds based on the analyses of characterizations. Furthermore, main active species for BPS degradation was identified as hydroxyl radicals, and total hydroxyl radical generation was determined by trapping experiments. The degradation pathways of BPS were also proposed by intermediates monitoring. Moreover, this catalyst showed good potential for practical application, according to the evaluation of reuse, different pollutants degradation, and BPS removal in real wastewater. We believe this study developed a new catalyst with high catalytic activity, high stability and wide application scope, and also sheds light on further development of metal-organic frameworks for Fenton-like catalysis.

Identification and manipulation of active centers on perovskites to enhance catalysis of peroxymonosulfate for degradation of emerging pollutants in water

Perovskites (the general formula of ABO₃) with versatile substrates can serve as desirable catalysts to initiate advanced oxidation processes (AOPs) for environmental remediation. However, the knowledge regarding the active centers remains piecemeal and unclear, such as how the redox metal centers of B site, inert metals of A site, oxygen vacancies, and direct oxidation of catalysts govern the chemical degradation of aqueous pollutants. This study aimed to identify principal alternations in physicochemical and electrical properties of ABO₃-based perovskites modified with partial/overall substitution at A/B sites and synthesized at different conditions. In order to probe varied catalytic activity of these catalysts, ofloxacin (OFX) was used as a model micro-pollutant. Results showed that the OFX degradation by activation of peroxymonosulfate (PMS) with LaFeO₃ perovskite was favored by the Sr substitution at A site, Cu substitution at B site, and increasing calcination temperature. Evolution of ¹O₂, ^•OH and SO₄^•- have proven for efficient OFX oxidation, as evidenced by results from in-situ electron paramagnetic resonance (EPR) analyses and quenching tests. Specifically, the introduction of Sr at A site can facilitate PMS self-decomposition to produce more ¹O₂ due to the increased abundance of surface oxygen vacancies. In contrast, the Cu substitution at B site improved the surface oxygen vacancies, as well as the electrical conductivity, which can further accelerate ^•OH and SO₄^•- generation for the OFX degradation. This study provides deeper insights into the underlying mechanisms governing the catalytic activity of perovskites. These findings build a basis for better decontamination of hazardous environmental organic pollutants.

Critical review of natural iron-based minerals used as heterogeneous catalysts in peroxide activation processes: Characteristics, applications and mechanisms

Recently, an increasing number of works have been reported about iron-based materials applied as catalysts in peroxide activation processes to degrade pollutants in water. Iron-based catalysts include synthetic and natural iron-based materials. However, some synthetic iron-based materials are difficult to scale up in the practical applications due to high cost and serious secondary environmental pollution. In contrast, natural iron-based minerals are more available and cheaper, and also hold a great promise in peroxide activation processes for pollutant degradation. In this review, we classify different natural iron-based materials into two categories: iron oxide minerals (e.g., magnetite, hematite, and goethite,), and iron sulfide minerals (e.g., pyrite and pyrrhotite,). Their overview applications in peroxide activation processes for pollutant degradation in wastewaters are systematically summarized for the first time. Moreover, the peroxide activation mechanisms induced by natural minerals, and the influences of reaction conditions in different systems are discussed. Finally, the application prospects and existing drawbacks of natural iron-based minerals in the peroxide activation processes for wastewater treatment are proposed. We believe this review can shed light on the application of natural iron-based minerals in peroxide activation processes and present better perspectives for future researches.

Mining methods and typical structural mechanisms of terpene cyclases

Terpenoids, formed by cyclization and/or permutation of isoprenes, are the most diverse and abundant class of natural products with a broad range of significant functions. One family of the critical enzymes involved in terpenoid biosynthesis is terpene cyclases (TCs), also known as terpene synthases (TSs), which are responsible for forming the ring structure as a backbone of functionally diverse terpenoids. With the recent advances in biotechnology, the researches on terpene cyclases have gradually shifted from the genomic mining of novel enzyme resources to the analysis of their structures and mechanisms. In this review, we summarize both the new methods for genomic mining and the structural mechanisms of some typical terpene cyclases, which are helpful for the discovery, engineering and application of more and new TCs.

Expanded mesoporous silica-encapsulated ultrasmall Pt nanoclusters as artificial enzymes for tracking hydrogen peroxide secretion from live cells

Design of synthetic structures that possess the similar functions to natural enzymes held great promise in environmental detection and biomedical application. Herein, a new concept for the fabrication of solid-supported catalysts as peroxidase mimic have been proposed to realize high-catalytic activity and stability by utilizing expanded mesoporous silica (EMSN)-encapsulated Pt nanoclusters. Compared with PtNCs, the introduction of amino group modified EMSN would enrich H₂O₂ on the surface of PtNCs and increase the catalytic sites for H₂O₂ decomposition, which gave rise to the higher catalytic activity of EMSN-PtNCs over a broad pH range, especially in weakly acidic and neural solutions. This would facilitate their applications for real-time monitoring the secretion of H₂O₂ from living cancer cells stimulated by various anticancer drugs. Our findings not only pave the way to use porous matrix as the structural component for the design of the biomimetic catalysts, but also provide a simple and reliable platform to monitor H₂O₂ released from living cells in real time, which holds great potential for elucidating the biological roles of H₂O₂ and underlying molecular mechanisms of drug cytotoxicity as well as drug therapeutic effects.

Approaches to the solution of coupled multiexponential transient-state rate kinetic equations: A critical review

The transient-state kinetic approach has failed to reach its full potential despite its advantage over the steady-state approach in its ability to observe mechanistic events directly and in real time. This failure has been due in part to the lack of any rigorously derived and readily applicable body of theory corresponding to that which currently characterizes the steady-state approach. In order to clarify the causes of this discrepancy and to suggest a route to its solution we examine the capabilities and limitations of the various forms of transient-state kinetic approaches to the mathematical resolution of enzymatic reaction mechanisms currently available. We document a lack of validity inherent in their basic assumptions and suggest the need for a potentially more rigorous analytic approach.

Structure of iridoid synthase in complex with NADP(+)/8-oxogeranial reveals the structural basis of its substrate specificity

Iridoid synthase (IS), as a vegetal enzyme belonging to the short-chain dehydrogenase/reductase (SDR) superfamily, produces the ring skeletons for downstream alkaloids with various pharmaceutical activities, including the commercially available antineoplastic agents, vinblastine and vincristine. Here, we present the crystal structures of IS in apo state and in complex with NADP(+)/8-oxogeranial, exhibiting an active center that lacks the classical Tyr/Lys/Ser triad spatially conserved in SDRs, with only the catalytically critical function of triad tyrosine remained in Tyr178. In consistent, mutation of Tyr178 to a phenylalanine residue significantly abolished the catalytic activity of IS. Within the substrate binding pocket, the linear-shaped 8-oxogeranial adopts an entirely extended conformation with its two aldehyde ends hydrogen-bonded to Tyr178-OH and Ser349-OH, respectively. In addition, the intermediate carbon chain of bound substrate is harbored by a well-ordered hydrophobic scaffold, involving residues Ile145, Phe149, Leu203, Met213, Phe342, Ile345 and Leu352. Mutagenesis studies showed that both Ser349 and the hydrophobic residues around are determinant to the substrate specificity and, consequently, the catalytic activity of IS. In contrast, the Gly150-Pro160 loop previously proposed as a factor involved in substrate binding might have very limited contribution, because the deletion of residues Ile151-His161 has only slight influence on the catalytic activity. We believe that the present work will help to elucidate the substrate specificity of IS and to integrate its detailed catalytic mechanism.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

Catalytic mechanisms of metallohydrolases containing two metal ions

At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii) the ability to bind larger substrates, (iv) enhanced electrostatic activation of substrates, and (v) decreased transition-state energies. Among this group of proteins, enzymes that catalyze the hydrolysis of ester and amide bonds form a very prominent family, the metallohydrolases. These enzymes are involved in a multitude of biological functions, and an increasing number of them gain attention for translational research in medicine and biotechnology. Their functional versatility and catalytic proficiency are largely due to the presence of metal ions in their active sites. In this chapter, we thus discuss and compare the reaction mechanisms of several closely related enzymes with a view to highlighting the functional diversity bestowed upon them by their metal ion cofactors.