Revealing the Monooxygenase Mechanism for Selective Ring Cleavage of Anthraquinone by BTG13 through Multiscale Simulations.

BTG13, a non-heme iron-dependent enzyme with a distinctive coordination environment of four histidines and a carboxylated lysine, has been found to catalyze the cleavage of the C4a-C10 bond in anthraquinone. Contrary to typical dioxygenase mechanisms, our quantum mechanical/molecular mechanical (QM/MM) calculations reveal that BTG13 functions more like a monooxygenase. It selectively inserts an oxygen atom into the C10-C4a bond, creating a lactone species that subsequently hydrolyzes, leading to the formation of a ring-opened product.

Unraveling the Mechanism of the Oxidative C-C Bond Coupling Reaction Catalyzed by Deoxypodophyllotoxin Synthase.

Deoxypodophyllotoxin synthase (DPS), a nonheme Fe(II)/2-oxoglutarate (2OG)-dependent oxygenase, is a key enzyme that is involved in the construction of the fused-ring system in (-)-podophyllotoxin biosynthesis by catalyzing the C-C coupling reaction. However, the mechanistic details of DPS-catalyzed ring formation remain unclear. Herein, our quantum mechanics/molecular mechanics (QM/MM) calculations reveal a novel mechanism that involves the recycling of CO (a product of decarboxylation of 2OG) to prevent the formation of hydroxylated byproducts.

Hyperspectral Compressive Snapshot Reconstruction via Coupled Low-Rank Subspace Representation and Self-Supervised Deep Network.

Coded aperture snapshot spectral imaging (CASSI) is an important technique for capturing three-dimensional (3D) hyperspectral images (HSIs), and involves an inverse problem of reconstructing the 3D HSI from its corresponding coded 2D measurements. Existing model-based and learning-based methods either could not explore the implicit feature of different HSIs or require a large amount of paired data for training, resulting in low reconstruction accuracy or poor generalization performance as well as interpretability. To remedy these deficiencies, this paper proposes a novel HSI reconstruction method, which exploits the global spectral correlation from the HSI itself through a formulation of model-driven low-rank subspace representation and learns the deep prior by a data-driven self-supervised deep learning scheme.

Host- and virus-induced gene silencing of HOG1-MAPK cascade genes in Rhizophagus irregularis inhibit arbuscule development and reduce resistance of plants to drought stress.

Arbuscular mycorrhizal (AM) fungi can form beneficial associations with the most terrestrial vascular plant species. AM fungi not only facilitate plant nutrient acquisition but also enhance plant tolerance to various environmental stresses such as drought stress. However, the molecular mechanisms by which AM fungal mitogen-activated protein kinase (MAPK) cascades mediate the host adaptation to drought stimulus remains to be investigated.

Mechanistic Insight into Peptidyl-Cysteine Oxidation by the Copper-Dependent Formylglycine-Generating Enzyme.

The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a very likely mechanism for this transformation. The reaction starts with dioxygen binding to the tris-thiolate Cu center to form a triplet Cu -superoxide complex.

C(sp )-H Hydroxylation in Diiron β-Hydroxylase CmlA Transpires by Amine-Assisted O Activation Avoiding Fe O Species.

Through QM/MM modeling, we discovered that C(sp )-H β-hydroxylation in the diiron hydroxylase CmlA transpires by traceless amine-assisted O activation. Different from the canonical diiron hydroxylase sMMO, this aliphatic-amine-assisted O activation avoids generating the high-valent diferryl Fe O species, but alternatively renders a diferric Fe O species as the reactive oxidant. From this unprecedented O activation mode, the derived C(sp )-H hydroxylation mechanism in CmlA also differs drastically from the toluene aromatic C(sp )-H hydroxylation in the diiron hydroxylase T4MO.

Mechanistic insights into dioxygen activation by a manganese corrole complex: a broken-symmetry DFT study.

The Mn-oxygen species have been implicated as key intermediates in various Mn-mediated oxidation reactions. However, artificial oxidants were often used for the synthesis of the Mn-oxygen intermediates. Remarkably, the Mn(v)-oxo and Mn(iv)-peroxo species have been observed in the activation of O by Mn(iii) corroles in the presence of base (OH) and hydrogen donors.

Ligand-Promoted Rh -Catalyzed C2-Selective C-H Alkenylation and Polyenylation of Imidazoles with Alkenyl Carboxylic Acids.

The first Rh -catalyzed, directed decarbonylative C2-H alkenylation of imidazoles with readily available alkenyl carboxylic acids is reported. The reaction proceeds in a highly regio- and stereoselective manner, providing efficient access to C2-alkenylated imidazoles that are generally inaccessible by known C-H alkenylation methods. This transformation accommodates a wide range of alkenyl carboxylic acids, including challenging conjugated polyene carboxylic acids, and diversely decorated imidazoles with high functional group compatibility.

A SPX domain-containing phosphate transporter from Rhizophagus irregularis handles phosphate homeostasis at symbiotic interface of arbuscular mycorrhizas.

Reciprocal symbiosis of > 70% of terrestrial vascular plants with arbuscular mycorrhizal (AM) fungi provides the fungi with fatty acids and sugars. In return, AM fungi facilitate plant phosphate (Pi) uptake from soil. However, how AM fungi handle Pi transport and homeostasis at the symbiotic interface of AM symbiosis is poorly understood.

Monophenolase and catecholase activity of Aspergillus oryzae catechol oxidase: insights from hybrid QM/MM calculations.

Catechol oxidase from Aspergillus oryzae (AoCO4) can not only catalyze oxidation of o-diphenols to o-quinones, but can also catalyze monooxygenation of small phenolics. To gain insight into the catecholase and monophenolase activities of AoCO4, the reaction mechanism of catechol oxidation was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The oxy-form of AoCO4 was found to be a μ-η2:η2 side-on peroxo dicopper(ii) complex, which can undergo a proton coupled electron transfer from the substrate rather than a proton transfer from the nearby Ser302 residue to generate a hydroperoxide.

The auxin-inducible phosphate transporter AsPT5 mediates phosphate transport and is indispensable for arbuscule formation in Chinese milk vetch at moderately high phosphate supply.

Phosphorus is a macronutrient that is essential for plant survival. Most land plants have evolved the ability to form a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, which enhances phosphate (Pi) acquisition. Modulation of Pi transporter systems is the master strategy used by mycorrhizal plants to adapt to ambient Pi concentrations.

Mechanistic insights into ring cleavage of hydroquinone by PnpCD from quantum mechanical/molecular mechanical calculations.

PnpCD is a mononuclear non-heme iron(ii) dioxygenase containing an unusual 2His-1Glu-1Asn metal-binding motif. To gain insights into the catalytic mechanism of the ring opening of hydroquinone by PnpCD, hybrid quantum mechanics/molecular mechanics calculations have been performed by using two models with different protonation states of the substrate (nonionized and ionized forms of the Fe-bound hydroxyl group of hydroquinone). In both cases, the structure of the reactive Fe-O species reveals a trigonal bipyramidal complex, in which Asn258 is no longer coordinated to the iron center.

Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation.

The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out.

Low overpotential water oxidation at neutral pH catalyzed by a copper(ii) porphyrin.

Low overpotential water oxidation under mild conditions is required for new energy conversion technologies with potential application prospects. Extensive studies on molecular catalysis have been performed to gain fundamental knowledge for the rational designing of cheap, efficient and robust catalysts. We herein report a water-soluble Cu complex of tetrakis(4--methylpyridyl)porphyrin (), which catalyzes the oxygen evolution reaction (OER) in neutral aqueous solutions with small overpotentials: the onset potential of the catalytic water oxidation wave measured at current density = 0.

Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations.

NOV1, a stilbene cleavage oxygenase, catalyzes the cleavage of the central double bond of stilbenes to two phenolic aldehydes, using a 4-His Fe(II) center and dioxygen. Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the reaction mechanism of the central double bond cleavage of phytoalexin resveratrol by NOV1. Our results showed that the oxygen molecule prefers to bind to the iron center in a side-on fashion, as suggested from the experiment.

Origin of Nitric Oxide Reduction Activity in Flavo-Diiron NO Reductase: Key Roles of the Second Coordination Sphere.

The second coordination sphere constitutes a distinguishing factor in the active site to modulate enzymatic reactivity. To unravel the origin of NO-to-N O reduction activity of non-heme diiron enzymes, herein we report a strong second-coordination-sphere interaction between a conserved Tyr and the key iron-nitrosyl intermediate of Tm FDP (flavo-diiron protein), which leads to decreased reaction barriers towards N-N formation and N-O cleavage in NO reduction. This finding supports the direct coupling of diiron dinitrosyl as the N-N formation mode in our QM/MM modeling, and reconciles the mechanistic controversy of external reduction between FDPs and synthetic biomimetics of the iron-nitrosyls.

Electrocatalytic Water Oxidation by a Water-Soluble Copper(II) Complex with a Copper-Bound Carbonate Group Acting as a Potential Proton Shuttle.

Water-soluble copper(II) complexes of the dianionic tridentate pincer ligand N,N'-2,6-dimethylphenyl-2,6-pyridinedicarboxamidate (L) are catalysts for water oxidation. In [L-Cu-DMF] (1, DMF = dimethylformamide) and [L-Cu-OAc] (2, OAc = acetate), ligand L binds Cu through three N atoms, which define an equatorial plane. The fourth coordination site of the equatorial plane is occupied by DMF in 1 and by OAc in 2.

Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations.

Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an Fe/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated Fe-oxo species, which has a square pyramidal geometry with the oxo group trans to His134.

Hydrolytic cleavage of both CS carbon-sulfur bonds by multinuclear Pd(II) complexes at room temperature.

Developing homogeneous catalysts that convert CS and COS pollutants into environmentally benign products is important for both fundamental catalytic research and applied environmental science. Here we report a series of air-stable dimeric Pd complexes that mediate the facile hydrolytic cleavage of both CS carbon-sulfur bonds at 25 °C to produce CO and trimeric Pd complexes. Oxidation of the trimeric complexes with HNO regenerates the dimeric starting complexes with the release of SO and NO.

Energy-Related Small Molecule Activation Reactions: Oxygen Reduction and Hydrogen and Oxygen Evolution Reactions Catalyzed by Porphyrin- and Corrole-Based Systems.

Globally increasing energy demands and environmental concerns related to the use of fossil fuels have stimulated extensive research to identify new energy systems and economies that are sustainable, clean, low cost, and environmentally benign. Hydrogen generation from solar-driven water splitting is a promising strategy to store solar energy in chemical bonds. The subsequent combustion of hydrogen in fuel cells produces electric energy, and the only exhaust is water.

How do Enzymes Utilize Reactive OH Radicals? Lessons from Nonheme HppE and Fenton Systems.

The iron(IV)-oxo (ferryl) intermediate has been amply established as the principal oxidant in nonheme enzymes and the key player in C-H bond activations and functionalizations. In contrast to this status, our present QM/MM calculations of the mechanism of fosfomycin biosynthesis (a broad range antibiotic) by the nonheme HppE enzyme rule out the iron(IV)-oxo as the reactive species in the hydrogen abstraction (H-abstraction) step of the pro-R hydrogen from the (S)-2-hydroxypropylphosphonic substrate. Moreover, the study reveals that the ferryl species is bypassed in HppE, while the actual oxidant is an HO(•) radical hydrogen-bonded to a ferric-hydroxo complex, resulting via the homolytic dissociation of the hydrogen peroxide complex, Fe(II)-H2O2.

Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study.

To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol.

Electrocatalytic Water Oxidation by a Water-Soluble Nickel Porphyrin Complex at Neutral pH with Low Overpotential.

The water-soluble cationic nickel(II) complex of meso-tetrakis(4-N-methylpyridyl)porphyrin (1) can electrocatalyze water oxidation to O2 in neutral aqueous solution (pH 7.0) with the onset of the catalytic wave appearing at ∼1.0 V (vs NHE).