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1. A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids

   https://doi.org/10.1093/plphys/kiac604  

   Zhang, Bixia; Lewis, Jacob A; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee (December 2022, Plant Physiology)

   Abstract In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress. 

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2. Oxidation of Amino Acids by Peracetic Acid: Reaction Kinetics, Pathways and Theoretical Calculations

   https://doi.org/https://doi.org/10.1016/j.wroa.2018.09.002  

   Du, P.; Liu, W.; Cao, H.; Zhao, H.; Huang, C.-H. (January 2018, Water research. X)

   Peracetic acid (PAA) is a sanitizer with increasing use in food, medical and water treatment industries. Amino acids are important components in targeted foods for PAA treatment and ubiquitous in natural waterbodies and wastewater effluents as the primary form of dissolved organic nitrogen. To better understand the possible reactions, this work investigated the reaction kinetics and transformation pathways of selected amino acids towards PAA. Experimental results demonstrated that most amino acids showed sluggish reactivity to PAA except cysteine (CYS), methionine (MET), and histidine (HIS). CYS showed the highest reactivity with a very rapid reaction rate. Reactions of MET and HIS with PAA followed second-order kinetics with rate constants of 4.6 ± 0.2, and 1.8 ± 0.1 M−1s−1 at pH 7, respectively. The reactions were faster at pH 5 and 7 than at pH 9 due to PAA speciation. Low concentrations of H2O2 coexistent with PAA contributed little to the oxidation of amino acids. The primary oxidation products of amino acids with PAA were [O] addition compounds on the reactive sites at thiol, thioether and imidazole groups. Theoretical calculations were applied to predict the reactivity and regioselectivity of PAA electrophilic attacks on amino acids and improved mechanistic understanding. As an oxidative disinfectant, the reaction of PAA with organics to form byproducts is inevitable; however, this study shows that PAA exhibits lower and more selective reactivity towards biomolecules such as amino acids than other common disinfectants, causing less concern of toxic disinfection byproducts. This attribute may allow greater stability and more targeted actions of PAA in various applications. 

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3. Reaction mechanism for atmospheric pressure plasma treatment of cysteine in solution

   https://doi.org/10.1088/1361-6463/ace196  

   Polito, Jordyn; Herrera Quesada, María J.; Stapelmann, Katharina; Kushner, Mark J. (July 2023, Journal of Physics D: Applied Physics)

   Abstract Mechanisms for the cold atmospheric plasma (CAP) treatment of cells in solution are needed for more optimum design of plasma devices for wound healing, cancer treatment, and bacterial inactivation. However, the complexity of organic molecules on cell membranes makes understanding mechanisms that result in modifications (i.e. oxidation) of such compounds difficult. As a surrogate to these systems, a reaction mechanism for the oxidation of cysteine in CAP activated water was developed and implemented in a 0-dimensional (plug-flow) global plasma chemistry model with the capability of addressing plasma-liquid interactions. Reaction rate coefficients for organic reactions in water were estimated based on available data in the literature or by analogy to gas-phase reactions. The mechanism was validated by comparison to experimental mass-spectrometry data for COST-jets sustained in He/O₂, He/H₂O and He/N₂/O₂mixtures treating cysteine in water. Results from the model were used to determine the consequences of changing COST-jet operating parameters, such as distance from the substrate and inlet gas composition, on cysteine oxidation product formation. Results indicate that operating parameters can be adjusted to select for desired cysteine oxidation products, including nitrosylated products. 

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4. Low-temperature ignition and oxidation mechanisms of tetrahydropyran

   https://doi.org/10.1016/j.proci.2024.105528  

   Hartness, Samuel W; Saab, Marwa; Preußker, Matthias; Mazzotta, Rosalba; Dewey, Nicholas S; Hill, Annabelle W; Vanhove, Guillaume; Fenard, Yann; Heufer, K Alexander; Rotavera, Brandon (June 2024, Proceedings of the Combustion Institute)

   Cyclic ethers are relevant as next-generation biofuels and are also combustion intermediates that follow directly from unimolecular decomposition of hydroperoxyalkyl radicals. Accordingly, cyclic ether reactions are crucial to understanding low-temperature oxidation for advanced compression-ignition applications in combustion where peroxy radials are central to degenerate chain-branching pathways. Reaction mechanisms relevant to low-temperature ignition of cyclic ethers contain intrinsic complexities due to competing reactions of carbon-centered radicals formed in the initiation step undergoing either ring-opening or reactions with O2. To gain insight into mechanisms describing tetrahydropyran combustion, ignition delay time and speciation measurements were conducted. The present work integrates measurements below 1000 K of ignition delay times and species profiles in rapid compression machine experiments from 5 – 20 bar, spanning several equivalence ratios, with jet-stirred reactor experiments at 1 bar and stoichiometric conditions. The experiments are complemented with the development of the first chemical kinetics mechanism for tetrahydropyran that includes peroxy radical reactions, including O2-addition to tetrahydropyranyl (Ṙ), HOȮ-elimination from tetrahydropyranylperoxy (ROȮ) and hydroperoxytetrahydropyranyl (Q̇OOH), bi-cyclic ether formation, β-scission of Q̇OOH, and ketohydroperoxide formation. Negative-temperature coefficient (NTC) behavior is exhibited in the experiments and is reflected in the model predictions, which were within experimental uncertainty for several conditions. Disparities between the model predictions and experiments were analyzed via sensitivity analysis to identify contributing factors from elementary reactions. The analyses examine the role of ring-opening products of tetrahydropyranyl and hydroperoxytetrahydropyranyl isomers to identify reaction mechanisms that may contribute to model uncertainties. The detection of 66 species in the JSR experiments indicates that tetrahydropyran undergoes complex reaction networks, which includes interconnected reactions of aldehyde radicals and alkyl radicals. Primary radicals pentanal-5-yl and butanal-4-yl are derived from ring-opening reactions of tetrahydropyran-1-yl and undergo subsequent decarbonylation to form alkyl radicals (1-butyl and 1-propyl) that undergo reaction with O2 and may contribute to chain-branching, in addition to pathways involving tetrahydropyran-derived ketohydroperoxides. 

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5. Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals

   https://doi.org/10.1016/j.proci.2024.105578  

   Doner, Anna C; Zádor, Judit; Rotavera, Brandon (July 2024, Proceedings of the Combustion Institute)

   Cyclic ethers undergo H-abstraction reactions that yield carbon-centered radicals (Ṙ). The ether functional group introduces a competing set of reaction pathways: ring-opening and reaction with O2 to form peroxy radical adducts, ROȮ, which can result in stereoisomers. ROȮ derived from cyclic ethers can subsequently isomerize into hydroperoxy-substituted carbon-centered radicals, Q̇OOH, which can also undergo ring-opening reactions or pathways prototypical to alkyl oxidation. The balance of reactions that unfold from cyclic ether radicals depends intrinsically on the size of the ring and the structure of any substituents retained in the formation step. The present work examines unimolecular reactions of peroxy radicals from 2-ethyloxetane, a four-membered cyclic ether formed during n-pentane oxidation, and reveals stereoisomer-specific reaction pathways. Automated quantum chemical computations were conducted on constitutional and stereoisomers of ROȮ derived from O2-addition to 2-ethyloxetanyl radicals. Pressure-dependent rate calculations were conducted by solving the master equation from 300 – 1000 K and from 0.01 – 100 atm. Branching fractions were then calculated at 650 K and 825 K, the peak temperatures at which cyclic ethers form in alkane oxidation. Isomer-specific reaction pathways of anti-ROO and syn-ROO and resulting impact on radical production were evident. Q̇OOH ring-opening reactions were significant as were rates of bi-cyclic ether formation common in alkyl radical oxidation. Detailed prescription of rates and reaction mechanisms describing cyclic ether consumption mechanisms are important to enable accurate modeling of reactions of ephemeral Q̇OOH radicals because of the direct, isomer-specific formation pathways. In addition, detailed cyclic ether mechanisms are required to reduce mechanism truncation error. The results herein provide insight on connections between cyclic ethers and chain-reaction pathways yielding ȮH, HOȮ, and other radicals, in addition to pathways leading to performic acid (HOOC(=O)H), the decomposition of which via O–O scission results in an exothermic, chain-branching step. 

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