Peroxo State Research Articles

Copper monooxygenase reactivity: Do consensus mechanisms accurately reflect experimental observations?

An important question is whether consensus mechanisms for copper monooxygenase enzymes such as peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase (DBM) generated via computational and spectroscopic approaches account for important experimental observations. We examine this question in the light of recent crystallographic and QMMM reports which suggest that alternative mechanisms involving an open to closed conformational cycle may be more representative of a number of experimental findings that remain unaccounted for in the canonical mononuclear mechanisms. These include (i) the almost negligible reactivity of the catalytic copper site (CuM) with oxygen in the absence of substrate, (ii) the carbonyl chemistry and in particular the substrate-induced activation exemplified by the lowered CO stretching frequency, (iii) the peroxide shunt chemistry which demands an intermediate that facilitates equilibrium between a Cu(II)-peroxo state and a Cu(I)-dioxygen state, and (iv) clear evidence for both closed and open conformational states in both PHM and DBM. An alternative mechanism involving a dinuclear copper intermediate formed via an open to closed conformational transition appears better able to accommodate these experimental observations, as well as being shown by QMMM methodologies to be energetically feasible. This suggests that future experiments should be designed to distinguish between these competing mechanisms and the factors that govern the oxygen reactivity of the copper centers. In particular, determining how oxygen reactivity is activated by binding of substrate, should be considered an important new challenge.

End-On Copper(I) Superoxo and Cu(II) Peroxo and Hydroperoxo Complexes Generated by Cryoreduction/Annealing and Characterized by EPR/ENDOR Spectroscopy.

In this report, we investigate the physical and chemical properties of monocopper Cu(I) superoxo and Cu(II) peroxo and hydroperoxo complexes. These are prepared by cryoreduction/annealing of the parent [LCuI(O2)]+ Cu(I) dioxygen adducts with the tripodal, N4-coordinating, tetradentate ligands L = PVtmpa, DMMtmpa, TMG3tren and are best described as [LCuII(O2•-)]+ Cu(II) complexes that possess end-on (η1-O2•-) superoxo coordination. Cryogenic γ-irradiation (77 K) of the EPR-silent parent complexes generates mobile electrons from the solvent that reduce the [LCuII(O2•-)]+ within the frozen matrix, trapping the reduced form fixed in the structure of the parent complex. Cryoannealing, namely progressively raising the temperature of a frozen sample in stages and then cooling back to low temperature at each stage for examination, tracks the reduced product as it relaxes its structure and undergoes chemical transformations. We employ EPR and ENDOR (electron-nuclear double resonance) as powerful spectroscopic tools for examining the properties of the states that form. Surprisingly, the primary products of reduction of the Cu(II) superoxo species are metastable cuprous superoxo [LCuI(O2•-)]+ complexes. During annealing to higher temperatures this state first undergoes internal electron transfer (IET) to form the end-on Cu(II) peroxo state, which is then protonated to form Cu(II)-OOH species. This is the first time these methods, which have been used to determine key details of metalloenzyme catalytic cycles and are a powerful tools for tracking PCET reactions, have been applied to copper coordination compounds.

Resolving the adsorption of molecular O2 on the rutile TiO2(110) surface by noncontact atomic force microscopy

Interaction of molecular oxygen with semiconducting oxide surfaces plays a key role in many technologies. The topic is difficult to approach both by experiment and in theory, mainly due to multiple stable charge states, adsorption configurations, and reaction channels of adsorbed oxygen species. Here we use a combination of noncontact atomic force microscopy (AFM) and density functional theory (DFT) to resolve [Formula: see text] adsorption on the rutile [Formula: see text](110) surface, which presents a longstanding challenge in the surface chemistry of metal oxides. We show that chemically inert AFM tips terminated by an oxygen adatom provide excellent resolution of both the adsorbed species and the oxygen sublattice of the substrate. Adsorbed [Formula: see text] molecules can accept either one or two electron polarons from the surface, forming superoxo or peroxo species. The peroxo state is energetically preferred under any conditions relevant for applications. The possibility of nonintrusive imaging allows us to explain behavior related to electron/hole injection from the tip, interaction with UV light, and the effect of thermal annealing.

Unraveling Oxygen Evolution in Li-Rich Oxides: A Unified Modeling of the Intermediate Peroxo/Superoxo-like Dimers.

Peroxo/superoxo is a key intermediate in oxygen evolution/reduction reactions in (electro)catalysis. However, peroxo/superoxo analogues have aroused controversies relevant to the origin of oxygen-anion redox. Specifically, some characteristics such as the magnitude of the O-O bond length in bulk materials have been puzzling during oxygen oxidation, as has the relationship between the peroxo/superoxo intermediate and the release of oxygen. The latter is a major safety concern to the application of oxygen-anion redox in lithium ion batteries. Herein, we present a unified modeling of the full delithiation process for model system Li2MnO3 by using first-principles calculations. We find that the cationic antisite defects and the electron deficiency are two major limiting factors in the anionic oxidation whose state can evolve, as the degree of delithiation increases, from the electron/hole, through peroxo-like O2δ- dimer formation, to the eventual release of gas-phase oxygen molecule. During the delithiation process, the dangling oxygen (i.e., singly coordinated with Mn) pairs play a critical role in intermediate dimer formation. Meanwhile, we identify five generic binding patterns of O2δ- dimers with Mn ions for which the O-O bond length varies from 1.45 Å in the peroxo state to 1.22 Å in the gas-phase oxygen molecule. Moreover, the dominant features of the three molecular orbitals, σc, πa, and πb, are distinguished, with the corresponding energy levels being highly delocalized and mixed as a result of the interplay with the host lattice. This work provides a deep understanding of the intermediate states of the anionic redox and suggests new strategies that mitigate oxygen release for the design of highly efficient and safe Li-rich cathode materials.

Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations.

Enzymatic methane hydroxylation is proposed to efficiently occur at the dinuclear copper site of particulate methane monooxygenase (pMMO), which is an integral membrane metalloenzyme in methanotrophic bacteria. The resting state and a possible peroxo state of the dicopper active site of pMMO are discussed by using combined quantum mechanics and molecular mechanics calculations on the basis of reported X-ray crystal structures of the resting state of pMMO by Rosenzweig and co-workers. The dicopper site has a unique structure, in which one copper is coordinated by two histidine imidazoles and another is chelated by a histidine imidazole and primary amine of an N-terminal histidine. The resting state of the dicopper site is assignable to the mixed-valent Cu(I)Cu(II) state from a computed Cu-Cu distance of 2.62 Å from calculations at the B3LYP-D/TZVP level of theory. A μ-η(2):η(2)-peroxo-Cu(II)2 structure similar to those of hemocyanin and tyrosinase is reasonably obtained by using the resting state structure and dioxygen. Computed Cu-Cu and O-O distances are 3.63 and 1.46 Å, respectively, in the open-shell singlet state. Structural features of the dicopper peroxo species of pMMO are compared with those of hemocyanin and tyrosinase and synthetic dicopper model compounds. Optical features of the μ-η(2):η(2)-peroxo-Cu(II)2 state are calculated and analyzed with TD-DFT calculations.

An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway.

Streptomyces venezuelae CmlI catalyzes the six-electron oxygenation of the arylamine precursor of chloramphenicol in a nonribosomal peptide synthetase (NRPS)-based pathway to yield the nitroaryl group of the antibiotic. Optical, EPR, and Mössbauer studies show that the enzyme contains a nonheme dinuclear iron cluster. Addition of O(2) to the diferrous state of the cluster results in an exceptionally long-lived intermediate (t(1/2) = 3 h at 4 °C) that is assigned as a peroxodiferric species (CmlI-peroxo) based upon the observation of an (18)O(2)-sensitive resonance Raman (rR) vibration. CmlI-peroxo is spectroscopically distinct from the well characterized and commonly observed cis-μ-1,2-peroxo (μ-η(1):η(1)) intermediates of nonheme diiron enzymes. Specifically, it exhibits a blue-shifted broad absorption band around 500 nm and a rR spectrum with a ν(O-O) that is at least 60 cm(-1) lower in energy. Mössbauer studies of the peroxo state reveal a diferric cluster having iron sites with small quadrupole splittings and distinct isomer shifts (0.54 and 0.62 mm/s). Taken together, the spectroscopic comparisons clearly indicate that CmlI-peroxo does not have a μ-η(1):η(1)-peroxo ligand; we propose that a μ-η(1):η(2)-peroxo ligand accounts for its distinct spectroscopic properties. CmlI-peroxo reacts with a range of arylamine substrates by an apparent second-order process, indicating that CmlI-peroxo is the reactive species of the catalytic cycle. Efficient production of chloramphenicol from the free arylamine precursor suggests that CmlI catalyzes the ultimate step in the biosynthetic pathway and that the precursor is not bound to the NRPS during this step.

Hiking on the potential energy surface of a functional tyrosinase model – implications of singlet, broken-symmetry and triplet description

The singlet, open-shell singlet and triplet potential energy surfaces (PES) for the peroxo state of a catalytic functional tyrosinase model have been investigated by density functional theory calculations. The broken-symmetry solution exhibits considerable stabilisation over the whole PES but the importance of the triplet state is unravelled as well.

Roles of carboxylate donors in O–O bond scission of peroxodi-iron(iii) to high-spin oxodi-iron(iv) with a new carboxylate-containing dinucleating ligand

Carboxylate donor stabilizes the peroxo state in dioxygen activation via reversible O–O bond scission of peroxodi-iron(iii) to high spin oxodi-iron(iv).

Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase

BackgroundDihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs), often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os) is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO), a RO member consists of catalytic terminal oxygenase (CARDO-O), ferredoxin (CARDO-F), and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex.ResultsIn the present study, we determined the crystal structures of the reduced carbazole (CAR)-bound, dioxygen-bound, and both CAR- and dioxygen-bound CARDO-O: CARDO-F binary complex structures at 1.95, 1.85, and 2.00 Å resolution. These structures revealed the conformational changes that occur in the catalytic cycle. Structural comparison between complex structures in each step of the catalytic mechanism provides several implications, such as the order of substrate and dioxygen bindings, the iron-dioxygen species likely being Fe(III)-(hydro)peroxo, and the creation of room for dioxygen binding and the promotion of dioxygen binding in desirable fashion by preceding substrate binding.ConclusionsThe RO catalytic mechanism is proposed as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes (e.g., movements of the nonheme iron and the ligand residue) that create room for oxygen binding. Dioxygen bound in a side-on fashion onto nonheme iron is activated by reduction to the peroxo state [Fe(III)-(hydro)peroxo]. This state may react directly with the bound substrate, or O–O bond cleavage may occur to generate Fe(V)-oxo-hydroxo species prior to the reaction. After producing a cis-dihydrodiol, the product is released by reducing the nonheme iron. This proposed scheme describes the catalytic cycle of ROs and provides important information for a better understanding of the mechanism.

Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes

We present a systematic study using density functional theory (DFT) and coupled cluster (CCSD(T)) computations with an aim of characterizing a non-heme ferric-superoxo complex [(TMC)Fe(O2)](2+) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) that was proposed to perform allylic C-H activation of cyclohexene (Lee, Y.-M. et al. J. Am. Chem. Soc.2010, 132, 10668). As such, we investigated a series of iron-O2 species without and with a sixth ligand bound to the iron ion in different O2 coordination modes (end-on and side-on) and different spin states. Most of the iron-O2 complexes were found to be iron(III)-superoxo species, Fe(III)(O2(-)), with high-spin (S = 5/2) or intermediate-spin (S = 3/2) ferric centers coupled ferromagnetically or antiferromagnetically to the superoxide anion radical. One iron(IV)-peroxo state, Fe(IV)(O2(2-)), was also examined. The preference for ferromagnetic or antiferromagnetic coupling modes between the superoxo and ferric radicals was found to depend on the FeOO angle, where a side-on tilt favors ferromagnetic coupling whereas the end-on tilt favors antiferromagnetic states. Experimental findings, e.g., the effects of solvent, spin state, and redox potential of non-heme Fe(II) complexes on O2 activation, were corroborated in this work. Solvent effects were found to disfavor O2 binding, relative to the unbound ferrous ion and O2. The potential H-abstraction reactivity of the iron(III)-superoxo species was considered in light of the recently proposed exchange-enhanced reactivity principle (Shaik, S.; Chen, H.; Janardanan, D. Nat. Chem.2011, 3, 19). It is concluded that localization and/or decoupling of an unpaired electron in the d-block of high-spin Fe(III) center in the S = 2 and 3 ferric-superoxo complexes during H abstractions enhances exchange stabilization and may be the root cause of the observed reactivity of [(TMC)Fe(O2)](2+).

Transient Oxygen States in Catalysis: Ammonia Oxidation at Ag(111)

Although the reactive sticking probability of oxygen at Ag(111) is of the order of 10(-6) at 295 K, ammonia oxidation is a facile process at low temperatures. A combination of quantitative analysis of photoelectron spectra together with high resolution electron energy loss spectroscopy provides kinetic and spectroscopic evidence for an ammonia-dioxygen complex, stable at 100 K, as the key intermediate. The reactive oxygen O(2)(s) is a transient dioxygen precursor of the unreactive peroxo state O(2)(δ-)(a). It is present as a complex when ammonia and dioxygen are coadsorbed at low temperature (100 K) with evidence from both O(1s) and energy loss spectra. Hydroxyl and amide/imide species are formed, followed by dehydroxylation and "oxide" formation at 260 K. This is a further example (zinc was the first) of how an sp-metal, where dioxygen bond cleavage is slow, provides an alternative pathway via a transient dioxygen state to catalytic oxidation through precursor assisted dioxygen bond cleavage. Whether it is a general characteristic of sp-metals remains to be established. Comparisons are made with the homogeneously catalyzed Gif reaction, the selective oxidation of hydrocarbons by dioxygen.

Hydrogen Peroxide Dependent cis-Dihydroxylation of Benzoate by Fully Oxidized Benzoate 1,2-Dioxygenase

Rieske dioxygenases catalyze the reductive activation of O2 for the formation of cis-dihydrodiols from unactivated aromatic compounds. It is known that O2 is activated at a mononuclear non-heme iron site utilizing electrons supplied by a nearby Rieske iron sulfur cluster. However, it is controversial whether the reactive species is an Fe(III)-(hydro)peroxo or an Fe(II)-(hydro)peroxo (or electronically equivalent species formed by breaking the O-O bond). Here it is shown that benzoate 1,2 dioxygenase oxygenase component (BZDO) prepared in a form with the Rieske cluster oxidized and the mononuclear iron in the Fe(III) state can utilize H2O2 as a source of reduced oxygen to form the correct cis-dihydrodiol product from benzoate. The reaction approaches stoichiometric yield relative to the mononuclear Fe(III) concentration, being limited to a single turnover by inefficient product release from the Fe(III)-product complex. EPR and Mössbauer studies show that the iron remains ferric throughout this single turnover "peroxide shunt" reaction. These results strongly support Fe(III)-(hydro)peroxo (or Fe(V)-oxo-hydroxo) as the reactive species because there is no source of additional reducing equivalents to form the Fe(II)-(hydro)peroxo state. This conclusion could be further tested in the case of BZDO because the peroxide shunt occurs very slowly compared with normal turnover, allowing the reactive intermediate to be trapped for spectroscopic analysis. We attribute the slow reaction rate to a forced change in the normally strict order of the substrate binding and enzyme reduction steps that regulate the catalytic cycle. The reactive intermediate is a high-spin ferric species exhibiting an unusual negative zero field splitting and other EPR and Mössbauer spectroscopic properties reminiscent of previously characterized side-on-bound peroxide adducts of Fe(III) model complexes. If the species in BZDO is a similar adduct, its isomer shift is most consistent with an Fe(III)-hydroperoxo reactive state.

Adsorption-state-dependent subpicosecond photoinduced desorption dynamics

Femtosecond laser excitation has been used to initiate desorption of molecular oxygen from the (111) surface of Pd and to study the adsorption-state dependence of the substrate-adsorbate coupling. The relative populations of the two chemical states, peroxo (O2(2-)) and superoxo (O2-), were varied by changing the total coverage. Two-pulse correlation measurements exhibit a dominant 400 fs response and a slower 10 ps decay that are relatively independent of the initial O2 coverage. In contrast, the photodesorption yield and the nonlinearity of the fluence dependence show a systematic coverage dependence. The coverage-independent subpicosecond response indicates that the photoinduced desorption from the two states is driven primarily by the same electron-mediated mechanism, while the coverage dependence of the yield indicates that the desorption efficiency from the superoxo state is greater than that from the peroxo state. These results are discussed in the context of the electron-phonon two-temperature model with an empirical adsorbate-electron frictional coupling that depends on both the electronic temperature and the activation energy for desorption. With a coupling strength that decreases as the activation energy decreases, the trends with varying coverage, absorbed fluence, and time delay can all be reproduced. The model is consistent with a transition from a resonantly enhanced (diabatic) regime to an adiabatic regime as the system relaxes, accounting for the biexponential correlation behavior.

Infrared spectroscopy of physisorbed and chemisorbed O2 on Pt(111).

The adsorption of O2 on the Pt(111) surface, with particular emphasis on the influence of substrate temperature, has been studied by infrared reflection absorption spectroscopy (IRAS). In the temperature range 30-90 K the IRAS spectra reveal three different molecular adsorption states. A physisorbed state appears below 40 K while chemisorbed peroxo- and superoxo-like states are observed in the whole temperature range, the characteristic vibrational frequencies are at full coverages of 16O2, 1543 cm(-1) and around 700 cm(-1) and 870 cm(-1), respectively. Flash heating from 30 K to 45 K reveal that the physisorbed state acts as a precursor to the superoxo chemisorption. Theoretical calculations suggest that peroxo molecules may occupy both fcc and hcp threefold sites on the Pt(111) surface. However, within the high resolution of the IRAS measurements we only observe one peroxo state in the temperature range 45-90 K, assigned to occupy the fcc site. The peroxo adsorption probability is significantly lower at 45 K than at 90 K, presumably due to reduced thermal activation from the physisorbed precursor state. A longer lifetime in this precursor state at the low temperature results in formation of larger superoxo islands already at low oxygen coverage.

Reactivity toward Dioxygen of Dicobalt Face-to-Face Diporphyrins in Aprotic Media. Experimental and Theoretical Aspects. Possible Mechanistic Implication in the Reduction of Dioxygen

The reactivity toward dioxygen of two series of dicobalt cofacial diporphyrins in solution in an aprotic solvent is described. Some of these compounds are efficient electrocatalysts for the four-electron reduction of dioxygen when adsorbed on a graphite electrode immersed in aqueous acid. Their electrochemical and spectroscopic (UV−vis, EPR) behavior in solution shows that, contrary to what is observed with cobalt monomers, the neutral [PCoII CoIIP] (1) (P stands for a porphyrin ring) form does not react with dioxygen. Uniquely the one- and two-electron-oxidized forms of the dimer, [PCoII·CoIIP]+ (1+) and [PCoII---CoIIP]2+ (12+), respectively, reversibly bind dioxygen, giving two complexes, 2 and 3, at room temperature and in the absence of a good axial ligand. The stability constants of the two O2 complexes have been measured spectrophotometrically and/or electrochemically, and prove to be remarkably high. As a whole, the present O2 binding processes appear unprecedented as basically different in many respects from the process classically described in the case of cobalt monomers. Extended Hückel molecular orbital (EHMO) calculations, based on the crystal structure of the Co2FTF4 dimer in its uncomplexed form (Co−Co distance 3.42 Å), show that, in the absence of very important deformations of its structure, the only possible geometry for the O2 complex of the two-electron-oxidized derivative [PCo−O2−CoP]2+ (3) is the μ-η2:η2-peroxo structure. The calculated corresponding electronic diagram affords a rationale for most of the experimentally observed properties. Specifically, the O2 complex of the one-electron-oxidized form [PCo−O2•−CoP]+ (2), the reduced form of complex 3, should be considered as a species in which the O2 moiety is further reduced, at least partially, as compared to its peroxo state in 3, i.e., consequently in an oxidation state intermediate between peroxo (−1) and oxo (−2). Preliminary results indicate that this species reacts with one proton, while the two-electron-oxidized O2 complex 3 is resistant to protonation. The possible implications of these specific properties of the dicobalt dimers in the four-electron reduction mechanism of O2 are discussed, and structural and mechanistic similarities with bioinorganic dinuclear sites appear significant.