Dioxygen Molecule Research Articles

Photolysis of Dissolved Organic Matter over Hematite Nanoplatelets.

Solar photoexcitation of chromophoric groups in dissolved organic matter (DOM), when coupled to photoreduction of ubiquitous Fe(III)-oxide nanoparticles, can significantly accelerate DOM degradation in near-surface terrestrial systems, but the mechanisms of these reactions remain elusive. We examined the photolysis of chromophoric soil DOM coated onto hematite nanoplatelets featuring (001) exposed facets using a combination of molecular spectroscopies and density functional theory (DFT) computations. Reactive oxygen species (ROS) probed by electron paramagnetic resonance (EPR) spectroscopy revealed that both singlet oxygen and superoxide are the predominant ROS responsible for DOM degradation. DFT calculations confirmed that Fe(II) on the hematite (001) surface, created by interfacial electron transfer from photoexcited chromophores in DOM, can reduce dioxygen molecules to superoxide radicals (•O2-) through a one-electron transfer process. 1H nuclear magnetic resonance (NMR) and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) spectroscopies show that the association of DOM with hematite enhances the cleavage of aromatic groups during photodegradation. The findings point to a pivotal role for organic matter at the interface that guides specific ROS generation and the subsequent photodegradation process, as well as the prospect of using ROS signatures as a forensic tool to help interpret more complicated field-relevant systems.

Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement.

Metal-dependent formate dehydrogenases are very promising targets for enzyme optimization and design of bio-inspired catalysts for CO2 reduction, towards innovative strategies for climate change mitigation. For effective application of these enzymes, the catalytic mechanism must be better understood, and the molecular determinants clarified. Despite numerous studies, several doubts persist, namely regarding the role played by the possible dissociation of the SeCys ligand from the Mo/W active site. Additionally, the oxygen sensitivity of these enzymes must also be understood as it poses an important obstacle for biotechnological applications. This work presents a combined biochemical, spectroscopic, and structural characterization of Desulfovibrio vulgaris FdhAB (DvFdhAB) when exposed to oxygen in the presence of a substrate (formate or CO2). This study reveals that O2 inactivation is promoted by the presence of either substrate and involves forming a different species in the active site, captured in the crystal structures, where the SeCys ligand is displaced from tungsten coordination and replaced by a dioxygen or peroxide molecule. This form was reproducibly obtained and supports the conclusion that, although W-DvFdhAB can catalyse the oxidation of formate in the presence of oxygen for some minutes, it gets irreversibly inactivated after prolonged O2 exposure in the presence of either substrate.

TEMPO-conjugated tobacco mosaic virus as a magnetic resonance imaging contrast agent for detection of superoxide production in the inflamed liver.

Superoxide, an anionic dioxygen molecule, plays a crucial role in redox regulation within the body but is implicated in various pathological conditions when produced excessively. Efforts to develop superoxide detection strategies have led to the exploration of organic-based contrast agents for magnetic resonance imaging (MRI). This study compares the effectiveness of two such agents, nTMV-TEMPO and kTMV-TEMPO, for detecting superoxide in a mouse liver model with lipopolysaccharide (LPS)-induced inflammation. The study demonstrates that kTMV-TEMPO, with a strategically positioned lysine residue for TEMPO attachment, outperforms nTMV-TEMPO as an MRI contrast agent. The enhanced sensitivity of kTMV-TEMPO is attributed to its more exposed TEMPO attachment site, facilitating stronger interactions with water protons and superoxide radicals. EPR kinetics experiments confirm kTMV-TEMPO's faster oxidation and reduction rates, making it a promising sensor for superoxide in inflamed liver tissue. In vivo experiments using healthy and LPS-induced inflamed mice reveal that reduced kTMV-TEMPO remains MRI-inactive in healthy mice but becomes MRI-active in inflamed livers. The contrast enhancement in inflamed livers is substantial, validating the potential of kTMV-TEMPO for detecting superoxide in vivo. This research underscores the importance of optimizing contrast agents for in vivo imaging applications. The enhanced sensitivity and biocompatibility of kTMV-TEMPO make it a promising candidate for further studies in the realm of medical imaging, particularly in the context of monitoring oxidative stress-related diseases.

Synthetic Advances for Mechanistic Insights: Metal-Oxygen Intermediates with a Macrocyclic Pyridinophane System.

ConspectusMetalloenzymes, which are proteins containing earth-abundant transition-metal ions as cofactors in the active site, generate various metal-oxygen intermediates via activating a dioxygen molecule (O2) to mediate vital metabolic functions, such as the oxidative metabolism of xenobiotics and the biotransformation of naturally occurring molecules. By replicating the active sites of metalloenzymes, many bioinorganic chemists have studied the geometric and electronic properties and reactivities of model complexes to understand the nature of enzymatic intermediates and develop bioinspired metal catalysts. Among the reported model complexes, nonporphyrinic macrocyclic ligands are the predominant coordination system widely used in stabilizing and isolating diverse metal-oxygen intermediates, which allows us to extensively investigate the physicochemical characteristics of the analogs of reactive intermediates of metalloenzymes. In particular, it has been reported that the ring size of the macrocyclic ligands, defined by the number of atoms in the macrocyclic ring, drastically affects the identity of the metal-oxygen intermediate. Thus, systematic modification of the macrocyclic ligands has been a great subject being examined in various inorganic fields.In this Account, we describe synthetic advances of a macrocyclic ligand system by introducing pyridine donors into a 12-membered tetraazamacrocyclic ligand (12-TMC) that initially has 4 amine donors. Interestingly, the backbone of the pyridinophane ligand with 2 pyridine and 2 amine donors in a 12-membered ring is shown to be much more folded than in other macrocyclic ligands, thereby allowing the axial and equatorial donors to separately control the electronic structure of metal complexes. Then, we looked over independent electronic and steric effects on metal-oxygen species with thorough physicochemical analysis. The NiIII-peroxo complexes exhibit nucleophilic reactivity dependent on the steric hindrance of the second coordination sphere. Furthermore, the C-H bond strength of the second coordination sphere has also been an important factor in determining the stability of MnIV-bis(hydroxo) intermediates. Electronic tuning on CoIII-hydroperoxo intermediates results in a trend between the electron-donating abilities of para-substituents on pyridine in the pyridinophane ligand and electrophilic reactivities, from which mechanistic insights into the metal-hydroperoxo species have been gained. Importantly, the metal-oxygen intermediates supported by the pyridinophane ligand system have revealed quite challenging chemical reactions, including dioxygenase-like nitrile activation by CoIII-peroxo intermediates and the oxidation of aldehyde and aromatic compounds by manganese-oxygen intermediates. Based on the fine substitution of donors, we have addressed that those novel reactions originated from the unique framework of the pyridinophane system incorporating spin-crossover behavior and high redox potentials of the metal-oxygen intermediates. These results will be valuable for the structure-activity relationship of metal-oxygen intermediates, giving a better understanding on the enzymatic coordination system where amino acid ligands vary for specific chemical reactions.

Investigation of the Reaction Mechanisms in La1-XSrxCo1-YFeyO3 Electrode by DFT Calculations

Solid Oxide Cells (SOCs) are electrochemical devices working at high temperatures for a clean hydrogen and electricity production in electrolysis and fuel cell modes, respectively. This technology has attracted a growing attention thanks to its high efficiency without the use of expensive catalysts. Although SOCs could play a key role in the energy transition, its commercialization at large scale is still limited due to performance and degradation issues. The state of the art oxygen electrode, La1-xSrxCo1-yFeyO3 (LSCF) exhibits a high electrochemical activity combined with a good mixed ionic and electronic conductivity. However, LSCF is prone to decompose under operation with a Strontium segregation at the surface reducing the cell performance over time [1].To date, the driving force of Sr segregation in LSCF and its impact on the cell performance is not precisely understood. However, to be able to discern these phenomena, it is still needed to better understand at atomic scale the mechanisms occurring at the electrode in the absence of Sr segregation. Therefore, we carried out a first study on the bulk properties of the parent material LSF [3] and LSCF using Density Functional Theory (DFT) calculations. Now we turn our attention to the surface properties of LSCF. In particular, the oxygen reduction reaction is decomposed in fuel cell mode into a sequence of elementary reactions. Thereby, a special focus lies on the identification of the rate determining steps limiting the overall reaction.To shade light into this, we modeled the A-site terminated (100) surface of LSCF using a symmetric slab. Our calculations revealed the existence of peroxide species at the surface arising from the reductive adsorption of a dioxygen molecule into a surface oxygen vacancy. Incorporation and dissociation of the peroxide requires a surface oxygen vacancy or sub-surface oxygen vacancy. To make this reaction happen, the peroxide and the vacancy have to encounter each other. Thereby it is still unclear weather the oxygen vacancy diffuses towards the peroxide, or vice-versa. Due to the particular orientation of the peroxide, which does not stand perpendicularly out of the (100) plane, but leans towards the direction between two A-site surface ions (cf. Fig. 1), four possible orientations of the peroxide exist. Thus, on-site rotations of the peroxide and its hopping to nearest neighbor sites are considered, as well as the diffusion of oxygen vacancies on surface and sub-surface. The Nudged Elastic Band (NEB) method is used to calculate the activation barriers. Diffusion coefficients are then determined using Transition State Theory (TST) combined with Kinetic Monte Carlo (KMC) calculations. These diffusion coefficients will be used as inputs to improve the existing elementary kinetic models [3] in order to investigate more precisely the performance and durability of SOCs under working conditions.[1] Chen, K., Jiang, S.P. Surface Segregation in Solid Oxide Cell Oxygen Electrodes: Phenomena, Mitigation Strategies and Electrochemical Properties. Electrochem. Energ. Rev. 3, 730–765 (2020). https://doi.org/10.1007/s41918-020-00078-z[2] Hartmann, C., Geneste, G., Laurencin, J., Hole polarons in LaFeO3 and La1 − x Sr x FeO3 − δ : Stability, trapping, mobility, effect of Sr concentration, and oxygen vacancies. Accepted in Phys. Rev. B. [3] E. Effori, J. Laurencin, E. D. R. Silva, M. Hubert, T. David, M. Petitjean, G. Geneste, L. Dessemond, and E. Siebert, J.Electrochem. Soc. 168, 044520 (2021). Figure 1

Modeling the Enzyme Specificity by Molecular Cages through Regulating Reactive Oxygen Species Evolution.

Mimicking the active site and the substrate binding cavity of the enzyme to achieve specificity in catalytic reactions is an essential challenge. Herein, porous coordination cages (PCCs) with intrinsic cavities and tunable metal centers have proved the regulation of reactive oxygen species (ROS) generating pathways as evidenced by multiple photo-induced oxidations. Remarkably, in the presence of the Zn4 -μ4 -O center, PCC converted dioxygen molecules from triplet to singlet excitons, whereas the Ni4 -μ4 -O center promoted the efficient dissociation of electrons and holes to conduct electron transfer towards substrates. Accordingly, the distinct ROS generation behavior of PCC-6-Zn and PCC-6-Ni enables the conversion of O2 to 1 O2 and O2 ⋅- , respectively. In contrast, the Co4 -μ4 -O center combined the 1 O2 and O2 ⋅- together to generate carbonyl radicals, which in turn reacted with the oxygen molecules. Harnessing the three oxygen activation pathways, PCC-6-M (M=Zn/Ni/Co) display specific catalytic activities in thioanisole oxidation (PCC-6-Zn), benzylamine coupling (PCC-6-Ni), and aldehyde autoxidation (PCC-6-Co). This work not only provides fundamental insights into the regulation of ROS generation by a supramolecular catalyst but also demonstrates a rare example of achieving reaction specificity through mimicking natural enzymes by PCCs.

Modeling the Enzyme Specificity by Molecular Cages through Regulating Reactive Oxygen Species Evolution

AbstractMimicking the active site and the substrate binding cavity of the enzyme to achieve specificity in catalytic reactions is an essential challenge. Herein, porous coordination cages (PCCs) with intrinsic cavities and tunable metal centers have proved the regulation of reactive oxygen species (ROS) generating pathways as evidenced by multiple photo‐induced oxidations. Remarkably, in the presence of the Zn4‐μ4‐O center, PCC converted dioxygen molecules from triplet to singlet excitons, whereas the Ni4‐μ4‐O center promoted the efficient dissociation of electrons and holes to conduct electron transfer towards substrates. Accordingly, the distinct ROS generation behavior of PCC‐6‐Zn and PCC‐6‐Ni enables the conversion of O2 to 1O2 and O2⋅−, respectively. In contrast, the Co4‐μ4‐O center combined the 1O2 and O2⋅− together to generate carbonyl radicals, which in turn reacted with the oxygen molecules. Harnessing the three oxygen activation pathways, PCC‐6‐M (M=Zn/Ni/Co) display specific catalytic activities in thioanisole oxidation (PCC‐6‐Zn), benzylamine coupling (PCC‐6‐Ni), and aldehyde autoxidation (PCC‐6‐Co). This work not only provides fundamental insights into the regulation of ROS generation by a supramolecular catalyst but also demonstrates a rare example of achieving reaction specificity through mimicking natural enzymes by PCCs.

Investigation of the Reaction Mechanisms in La1-XSrxCo1-YFeyO3 Electrode by DFT Calculations

La1-xSrxCoy-1FeyO3-δ (LSCF) is a widely used oxygen electrode in Solid Oxide Cells (SOCs). Despite its high electrochemical activity combined with a good mixed ionic and electronic conductivity, it is prone to a phase decomposition upon operation decreasing the global cell performance. However, the underlying mechanisms for the reaction mechanism and the degradation are still not precisely understood and require investigations at atomic scale. Therefore, Density Functional Theory (DFT) calculations are used to better unravel the mechanisms occurring in the electrode. In particular, the interaction of the dioxygen gas with the AO-terminated (100) surface is studied. In this context, the oxygen reduction reaction is decomposed in a series of elementary steps including oxygen vacancy formation, adsorption of the dioxygen molecule on the bare surface and into a surface vacancy accompanied with the formation of intermediate oxygen species, followed by the dissociation and incorporation into the bulk. The calculations have been carried out at two different Cobalt contents (y=0.125 and y=0.25).

Calcium silicate hydrate decorated by Fe, Ti co-modified birnessite direct multi-component photocatalyst: Design, preparation and photocatalytic performance under visible light irradiation

Constructing a multi-component structure is an effective strategy to promote the formation of oxygen vacancies (OVs), which can enhance electron transition to improve the photocatalytic activity of materials. In this work, it was designed a series of novel photocatalysts supported on calcium silicate hydrates (C-S-H) via density functional theory calculation. These designed photocatalysts were then synthesized and marked as Bir@C-S-H, TiO2/Bir@C-S-H, and α-Fe2O3/TiO2/Bir@C-S-H, respectively. In comparison to other catalysts, α-Fe2O3/TiO2/Bir@C-S-H photocatalyst has a higher specific surface area, a lower band gap, more OVs, which can activate more dioxygen molecules, and more reactive radicals. The photocatalytic activity of as-synthesized photocatalysts was verified by using HCHO as the target pollutant. To the treatment of 80 ppm HCHO, the α-Fe2O3/TiO2/Bir@C-S-H exhibits 100% HCHO conversion corresponding gas hourly space velocity of 60 L/(g•h) with a relative humidity of 60% under visible light irradiation, while Bir@C-S-H and TiO2/Bir@C-S-H present 89.92% and 94.17% HCHO conversion, respectively at same conditions. This work demonstrates a more effective calcium silicate hydrate decorated by Fe, Ti co-modified birnessite heterostructures for HCHO oxidation, which can be directly used as decorative materials, providing a novel guidance for practical application.

Mechanistic insights into aerobic oxidative cleavage of glycol catalyzed by an Anderson-type polyoxometalate [IMo6O24]5.

A computational investigation of the aerobic oxidative C-C bond cleavage reaction of glycol catalyzed by an Anderson-type heteropolyanion HPA [IMo6O24]5- in the presence of acetonitrile as solvent has been performed at the WB97XD/6-31G(d,p)/lanl2dz level. Two reaction pathways have been identified. The catalytic cycle of each pathway consists of three steps: oxidation cleavage of a glycol molecule by the HPA, oxidation of the HPA by one dioxygen molecule, and, finally, oxidation of a second glycol and regeneration of the catalyst. These reaction pathways have been thoroughly investigated in terms of energetic, natural bond orbital (NBO), natural charges, and geometrical parameters. It is found that (i) even though the top oxygen atoms of the Anderson heteropolyanion are not the most negatively charged ones, they are more likely to react with the diol hydroxyl groups, (ii) a direct relationship between the presence of the iodine ion I(VII) and the studied oxidation reaction could not be identified, and (iii) in terms of energy, the transfer of the two hydrogen atoms is the most energetic step.

Regulating the Pt-MnO2 Interaction and Interface for Room Temperature Formaldehyde Oxidation.

Formaldehyde (HCHO) is a hazardous pollutant in indoor space for humans because of its carcinogenicity. Removing the pollutant by MnO2-based catalysts is of great interest because of their high oxidation performance at room temperature. In this work, we regulate the Pt-MnO2 (MnO2 = manganese oxide) interaction and interface by embedding Pt in MnO2 (Pt-in-MnO2) and by dispersing Pt on MnO2 (Pt-on-MnO2) for HCHO oxidation over Pt-MnO2 catalysts with trace Pt loading of 0.01 wt %. In comparison to the Pt-in-MnO2 catalyst, the Pt-on-MnO2 catalyst has a higher Brunauer-Emmett-Teller surface area, a more active lattice oxygen, more oxygen vacancy activating more dioxygen molecules, more exposed Pt atoms, and noninternal diffusion of mass transfer, which contribute to the higher HCHO oxidation performance. The HCHO oxidation performance is stable over the Pt-MnO2 catalysts under high space velocity and high moisture humidity conditions, showing great potential for practical applications. This work demonstrates a more effective Pt-dispersed MnO2 catalyst than Pt-embedded MnO2 catalyst for HCHO oxidation, providing universally important guidance for metal-support interaction and interface regulation for oxidation reactions.

Competitive sensitization effect towards Luminescence-tuned Lanthanide-doped TiO2/SiO2 Core-shell nanoparticles for enhanced responsivity oxygen detection

The luminescence of TiO2 doped with Sm3+ can be excited through TiO2 band-to-band absorption, which exhibits oxygen sensitivity. However, its carrier behaviors and oxygen sensing mechanism have not yet been clarified, which inhibits the further improvement of sensitivity. In this study, using Eu3+ ions as an “energy level probe,” we demonstrated a novel strategy using a C@SiO2:2%Sm3+@TiO2 hollow double-shell nanostructure containing surface oxygen vacancies, designated a competitive sensitization effect for the first time. Density-functional theory combined with the experimental results revealed the carrier behaviors and oxygen sensing mechanism. Further, we demonstrated that the charge state of oxygen vacancies is controlled by the adsorption and desorption of dioxygen molecules, which affects electron relaxation and indirectly affects the luminescent behaviors. The effective exploitation of the competitive sensitization effect and revelation of the oxygen sensing mechanism ensured that the excitation of Sm3+ in C@SiO2:2%Sm3+@TiO2 can be controlled by the ambient oxygen concentration. Therefore, compared to the widely reported Sm3+-doped TiO2, C@SiO2:2%Sm3+@TiO2 demonstrated increased oxygen sensitivity (by over three folds) with a detection minimum of sub-100 ppm. Moreover, as ambient oxygen concentration changes, the luminescence color of the films prepared by using C@SiO2:2%Sm3+@TiO2 and commercial blue phosphors changes significantly (from pink to blue).

Development of a novel ReaxFF reactive potential for organochloride molecules.

This article presents a new reactive potential in the ReaxFF formalism. It aims to include the chlorine element and opens up the fields of use of ReaxFF to the whole class of organochloride compounds including conjugated or aromatic groups. Numerous compounds in this family raise global awareness due to their environmental impact, and such a reactive potential will help investigate their degradation pathways. The new force field, named CHONCl-2022_weak, belongs to the aqueous branch. The force field parameters were fitted against high-level quantum chemistry calculations, including complete active space self-consistent field/NEVPT2 calculations and density functional theory calculations, and their accuracy was evaluated using a validation set. The root means square deviation against quantum mechanics energies is 0.38eV (8.91kcal mol-1). From a structural point of view, the root means square deviation is about 0.06 Å for the bond lengths, 11.86° for the angles, and 4.12° for the dihedral angles. With CHONCl-2022_weak new force field, we successfully investigated the regioselectivity for nucleophilic or electrophilic attacks on polychlorinated biphenyls, which are toxic and permanent pollutants. The rotation barriers along the bond linking the two benzene rings, which is crucial in the toxicity of these compounds, are well reproduced by CHONCl-2022_weak. Then, our new reactive potential is used to investigate the chlorobenzene reactivity in the presence of hydroxyl radicals in atmospheric condition or in aqueous solution. The reaction pathways computed with ReaxFF agree with the quantum mechanics results. We showed that, in the presence of dioxygen molecules, in atmospheric condition, the oxidation of chlorobenzene likely leads to the formation of highly oxygenated compounds after the abstraction of hydrogen radicals. In water, the addition of a hydroxyl radical leads to the formation of chlorophenol or phenol molecules, as already predicted from plasma-induced degradation experiments.

Evidence of Gas-Phase Attachment of Molecular Oxygen to Deprotonated Hydroquinone During Ion-Mobility Mass Spectrometry.

Gas-phase addition of dioxygen to certain ions is a well-known phenomenon in mass spectrometry. For this reaction to occur, the presence of a distonic radical site on the precursor ion is thought to be a prerequisite. Herein, we report that oxygen adduct formation can take place also with deprotonated hydroquinone, which in fact is an even-electron species without a radical site. When the product-ion spectrum of the m/z 109 ion, generated by electrospray ionization from a solution of hydroquinone in acetonitrile, was recorded under ion-mobility conditions, a new peak was observed at m/z 141. However, an analogous peak was not visible in the spectrum acquired under nonmobility conditions (i.e., without any gas introduced to the mobility cell). Presumably, traces of oxygen present in the collision gas instigate an ion-molecule reaction to produce an adduct of m/z 141, which upon activation results in CO and H2O loss to form a product ion of m/z 95. Isotope-labeling studies confirmed that one of the hydrogen atoms from the hydroxy group and another from the aromatic ring contribute to the water loss instigated from the m/z 141 adduct. Furthermore, computational methods indicated the three-dimensional structure of the ground-state deprotonated hydroquinone to be distinctly different from those of its 1,2- and 1,3-isomers. Calculations predicted that all atoms in the two m/z 109 ions generated from catechol and resorcinol lie on one plane. In contrast, the structure of the m/z 109 ion from hydroquinone was significantly different. Computations predicted that the hydrogen atom on the intact hydroxyl group of deprotonated hydroquinone protrudes out of plane from rest of the atoms. Consequently, the exposed OH group can interact with an incoming dioxygen molecule. Computations conducted at the CAM-B3LYP/6-311++g(2d,2p) level of theory detected a minimum energy crossing point (MECP) at -4.3 kJ mol-1 below the separated O2 + deprotonated hydroquinone triplet threshold. In contrast, similar calculations conducted for catechol and resorcinol yielded MECPs of +116.9 and +69.1 kJ mol-1, respectively, above the associated triplet thresholds. These results indicated that the curve crossing required to form singlet products upon reaction with triplet O2 is favorable in the case of hydroquinone and unfavorable in the cases of catechol and resorcinol. In practical terms, the selective oxygen addition appears to be a diagnostically useful reaction to differentiate hydroquinone from its ring isomers.

The role of Heisenberg spin exchange and the quantum Zeno effect in the spin-selective reaction between spin-1/2 and spin-1 particles.

The kinetics of spin-selective reactions involving triplet molecules, such as triplet-triplet annihilation or electron transfer to dioxygen molecules in the ground triplet spin state, are strongly dependent on the dipole-dipole interaction (DDI) of electron spins in spin-1 particles. The effect of this interaction on the intersystem crossing in the reaction encounter complex of the paramagnetic particles was previously considered for some particular cases using oversimplified approaches. In this study, we consider a rigorous kinetic model of the irreversible reaction between the spin-1/2 and spin-1 particles in an encounter complex with the reactive doublet state. This model explicitly includes both isotropic exchange coupling of the reactants and spin dependence of the reaction rate in the form of the Haberkorn reaction term. For the time-independent DDI, an analytical expression for the reaction kinetics was derived. The effect of DDI fluctuations was analyzed using numerical simulations. It was found that increasing both the exchange coupling and the reaction rate constants can significantly slow down the quartet-doublet spin transitions and, as a consequence, the observed spin-selective reaction rate. Additionally, the presence of the irreversible reaction in the doublet states affects a coherent evolution in the non-reactive quartet subsystem.

The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid.

Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.

Trinuclear Nickel Catalyst for Water Oxidation: Intramolecular Proton-Coupled Electron Transfer Triggered Trimetallic Cooperative O–O Bond Formation

Trinuclear Nickel Catalyst for Water Oxidation: Intramolecular Proton-Coupled Electron Transfer Triggered Trimetallic Cooperative O–O Bond Formation

Non-heme oxoiron complexes as active intermediates in the water oxidation process with hydrogen/oxygen atom transfer reactions.

In this study, we explore the water oxidation process with the help of density functional theory. The formation of an oxygen-oxygen bond is crucial in the water oxidation process. Here, we report the formation of the oxygen-oxygen bond by the N5-coordinate oxoiron species with a higher oxidation state of FeIV and FeV. This bond formation is studied through the nucleophilic addition of water molecules and the transfer of the oxygen atom from meta-chloroperbenzoic acid (mCPBA). Our study reveals that the oxygen-oxygen bond formation by reacting mCPBA with FeVO requires less activation barrier (13.7 kcal mol-1) than the other three pathways. This bond formation by the oxygen atom transfer (OAT) pathway is more favorable than that achieved by the hydrogen atom transfer (HAT) pathway. In both cases, the oxygen-oxygen bond formation occurs by interacting the σ*dz2-2pz molecular orbital of the iron-oxo intermediate with the 2px orbital of the oxygen atom. From this study, we understand that the oxygen-oxygen bond formation by FeIVO with the OAT process is also feasible (16 kcal mol-1), suggesting that FeVO may not always be required for the water oxidation process by non-heme N5-oxoiron. After the oxygen-oxygen bond formation, the release of the dioxygen molecule occurs with the addition of the water molecule. The release of dioxygen requires a barrier of 7.0 kcal mol-1. The oxygen-oxygen bond formation is found to be the rate-determining step.

Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase

Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme’s catalytic cycle may have to be turned by 180 degrees.

Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis.

PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1II-Fe2III-superoxo and Fe1II-Fe2IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1II-Fe2III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1II-Fe2IV═O complex. In the second-round reaction, the Fe1II-Fe2IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1II-Fe2IV═O compared to Fe1II-Fe2III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.