Geometric and electronic structure/function correlations in non-heme iron enzymes

High-valent metal-oxo species transformation and regulation by co-existing chloride: Reaction pathways and impacts on the generation of chlorinated by-products

High-valent metal-oxo species (HMOS) have been extensively recognized in advanced oxidation processes (AOPs) owing to their high selectivity and high chemical utilization efficiency. However, the interactions between HMOS and halide ions in sewage wastewater are complicated, leading to ongoing debates on the intrinsic reactive species and impacts on remediation. Herein, we prepared three typical HMOS, including Fe(IV), Mn(V)-nitrilotriacetic acid complex (Mn(V)NTA) and Co(IV) through peroxymonosulfate (PMS) activation and comparatively studied their interactions with Cl- to reveal different reactive chlorine species (RCS) and the effects of HMOS types on RCS generation pathways. Our results show that the presence of Cl- alters the cleavage behavior of the peroxide OO bond in PMS and prohibits the generation of Fe(IV), spontaneously promoting SO4•- production and its subsequent transformation to secondary radicals like Cl• and Cl2•-. The generation and oxidation capacity of Mn(V)NTA was scarcely influenced by Cl-, while Cl- would substantially consume Co(IV) and promote HOCl generation through an oxygen-transfer reaction, evidenced by density functional theory (DFT) and deuterium oxide solvent exchange experiment. The two-electron-transfer standard redox potentials of Fe(IV), Mn(V)NTA and Co(IV) were calculated as 2.43, 2.55 and 2.85 V, respectively. Due to the different reactive species and pathways in the presence of Cl-, the amounts of chlorinated by-products followed the order of Co(II)/PMS > Fe(II)/PMS > Mn(II)NTA/PMS. Thus, this work renovates the knowledge of halide chemistry in HMOS-based systems and sheds light on the impact on the treatment of salinity-containing wastewater.

Initial Steps in Methanobactin Biosynthesis: Substrate Binding by the Mixed-Valent Diiron Enzyme MbnBC

The MbnBC enzyme complex converts cysteine residues in a peptide substrate, MbnA, to oxazolone/thioamide groups during the biosynthesis of copper chelator methanobactin (Mbn). MbnBC belongs to the mixed-valent diiron oxygenase (MVDO) family, of which members use an Fe(II)Fe(III) cofactor to react with dioxygen for substrate modification. Several crystal structures of the inactive Fe(III)Fe(III) form of MbnBC alone and in complex with MbnA have been reported, but a mechanistic understanding requires determination of the oxidation states of the crystallographically observed Fe ions in the catalytically active Fe(II)Fe(III) state, along with the site of MbnA binding. Here, we have used electron nuclear double resonance (ENDOR) spectroscopy to determine such structural and electronic properties of the active site, in particular, the mode of substrate binding to the MV state, information not accessible by X-ray crystallography alone. The oxidation states of the two Fe ions were determined by 15N ENDOR analysis. The presence and locations of both bridging and terminal exogenous solvent ligands were determined using 1H and 2H ENDOR. In addition, 2H ENDOR using an isotopically labeled MbnA substrate indicates that MbnA binds to the Fe(III) ion of the cluster via the sulfur atom of its N-terminal modifiable cysteine residue, with displacement of a coordinated solvent ligand as shown by complementary 1H ENDOR. These results, which underscore the utility of ENDOR in studying MVDOs, provide a molecular picture of the initial steps in Mbn biosynthesis.

An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer

Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C4-H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C4-H hydroxylation selectivity. Furthermore, an active site Tyr233 residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233 phenol loses a proton to the nearby Asp179 residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4-H bond of the substrate and guides the selectivity to the C4-hydroxylation of the substrate.

Efficient Inhibition of Deep Conversion of Partial Oxidation Products in C-H Bonds' Functionalization Utilizing O2 via Relay Catalysis of Dual Metalloporphyrins on Surface of Hybrid Silica Possessing Capacity for Product Exclusion

To inhibit the deep conversion of partial oxidation products (POX-products) in C-H bonds' functionalization utilizing O2, 5-(4-(chloromethyl)phenyl)-10,15,20-tris(perfluorophenyl)porphyrin cobalt(II) and 5-(4-(chloromethyl)phenyl)-10,15,20-tris(perfluorophenyl)porphyrin copper(II) were immobilized on the surface of hybrid silica to conduct relay catalysis on the surface. Fluorocarbons with low polarity and heterogeneous catalysis were devised to decrease the convenient accessibility of polar POX-products to catalytic centers on the lower polar surface. Relay catalysis between Co and Cu was designed to utilize the oxidation intermediates alkyl hydroperoxides to transform more C-H bonds. Systematic characterizations were conducted to investigate the structure of catalytic materials and confirm their successful syntheses. Applied to C-H bond oxidation, not only deep conversion of POX-products was inhibited but also substrate conversion and POX-product selectivity were improved simultaneously. For cyclohexane oxidation, conversion was improved from 3.87% to 5.27% with selectivity from 84.8% to 92.3%, which was mainly attributed to the relay catalysis on the surface excluding products. The effects of the catalytic materials, product exclusion, relay catalysis, kinetic study, substrate scope, and reaction mechanism were also investigated. To our knowledge, a practical and novel strategy was presented to inhibit the deep conversion of POX-products and to achieve efficient and accurate oxidative functionalization of hydrocarbons. Also, a valuable protocol was provided to avoid over-reaction in other chemical transformations requiring high selectivity.

Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin

The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.

Computational Insights into the Catalysis of the pH Dependence of Bromite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica (DaCld)

The heme-containing chlorite dismutases catalyze the rapid and efficient decomposition of chlorite (ClO2-) to yield Cl- and O2, and the catalytic efficiency of chlorite dismutase from Dechloromonas aromatica (DaCld) in catalyzing the decomposition of bromite (BrO2-) was dependent on pH, which was supposed to be caused by the conversion of active Cpd I to the inactive Cpd II by proton-coupled electron transfer (PCET) from the pocket Tyr118 to the propionate side chain of heme at high pH. However, the direct evidence of PCET and how the pH affects the efficiency of DaCld, as well as whether Cpd II is really inactive, are still poorly understood. Here, on the basis of the high-resolution crystal structures, the computational models in both acidic (pH 5.0) and alkaline (pH 9.0) environments were constructed, and a series of quantum mechanical/molecular mechanical calculations were performed. On the basis of our calculation results, the O-Br bond cleavage of BrO2- always follows the homolytic mode to generate Cpd II rather than Cpd I. It is different from the O-O cleavage of O2/H2O2 or peracetic acid catalyzed by the other heme-containing enzymes. Thus, in the subsequent O-O rebound reaction, it is the Fe(IV)═O in Cpd II that combines with the O-Br radical. Because the porphyrin ring in Cpd II does not bear an unpaired electron, the previously suggested PCET from Tyr118 to the propionate side chain of heme was not theoretically recognized in an alkaline environment. In addition, the O-O rebound step in an alkaline solution corresponds to an energy barrier that is larger than that in an acidic environment, which can well explain the pH dependence of the activity of DaCld. In addition, the protonation state of the propionic acid side chains of heme and the surrounding hydrogen bond networks were calculated to have a significant impact on the barriers of the O-O rebound step, which is mainly achieved by affecting the reactivity of the Fe(IV)═O group in Cpd II. In an acidic environment, the relatively weaker coordination of the O2 atom to Fe leads to its higher reactivity toward the O-O rebound reaction. These observations may provide useful information for understanding the catalysis of chlorite dismutases.

Enhanced Reactivity through Equatorial Sulfur Coordination in Nonheme Iron(IV)-Oxo Complexes: Insights from Experiment and Theory

Sulfur ligation in metalloenzymes often gives the active site unique properties, whether it is the axial cysteinate ligand in the cytochrome P450s or the equatorial sulfur/thiol ligation in nonheme iron enzymes. To understand sulfur ligation to iron complexes and how it affects the structural, spectroscopic, and intrinsic properties of the active species and the catalysis of substrates, we pursued a systematic study and compared sulfur with amine-ligated iron(IV)-oxo complexes. We synthesized and characterized a biomimetic N4S-ligated iron(IV)-oxo complex and compared the obtained results with an analogous N5-ligated iron(IV)-oxo complex. Our work shows that the amine for sulfur replacement in the equatorial ligand framework leads to a rate enhancement for oxygen atom and hydrogen atom transfer reactions. Moreover, the sulfur-ligated iron(IV)-oxo complex reacts through a different reaction mechanism as compared to the N5-ligated iron(IV)-oxo complex, where the former reacts through hydride transfer with the latter reacting via radical pathways. We show that the reactivity differences are caused by a dramatic change in redox potential between the two complexes. Our studies highlight the importance of implementing a sulfur ligand into the equatorial ligand framework of nonheme iron(IV)-oxo complexes and how it affects the physicochemical properties of the oxidant and its reactivity.

Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II

Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.

Characterization of the active site in the thiocyanate-forming protein from Thlaspi arvense (TaTFP) using EPR spectroscopy

Glucosinolates are plant thioglucosides, which act as chemical defenses. Upon tissue damage, their myrosinase-catalyzed hydrolysis yields aglucones that rearrange to toxic isothiocyanates. Specifier proteins such as thiocyanate-forming protein from Thlaspi arvense (TaTFP) are non-heme iron proteins, which capture the aglucone to form alternative products, e.g. nitriles or thiocyanates. To resolve the electronic state of the bound iron cofactor in TaTFP, we applied continuous wave electron paramagnetic resonance (CW EPR) spectroscopy at X-and Q-band frequencies (∼9.4 and ∼34 GHz). We found characteristic features of high spin and low spin states of a d 5 electronic configuration and local rhombic symmetry during catalysis. We monitored the oxidation states of bound iron during conversion of allylglucosinolate by myrosinase and TaTFP in presence and absence of supplemented Fe2+. Without added Fe2+, most high spin features of bound Fe3+ were preserved, while different g'-values of the low spin part indicated slight rearrangements in the coordination sphere and/or structural geometry. We also examined involvement of the redox pair Fe3+/Fe2 in samples with supplemented Fe2+. The absence of any EPR signal related to Fe3+ or Fe2+ using an iron-binding deficient TaTFP variant allowed us to conclude that recorded EPR signals originated from the bound iron cofactor.

Spectroscopic and Theoretical Investigation of High-Spin Square-Planar and Trigonal Fe(II) Complexes Supported by Fluorinated Alkoxides

The electronic structures and spectroscopic behavior of three high-spin FeII complexes of fluorinated alkoxides were studied: square-planar {K(DME)2}2[Fe(pinF)2] (S) and quasi square-planar {K(C222)}2[Fe(pinF)2] (S') and trigonal-planar {K(18C6)}[Fe(OC4F9)3] (T) where pinF = perfluoropinacolate and OC4F9 = tris-perfluoro-t-butoxide. The zero-field splitting (ZFS) and hyperfine structure parameters of the S = 2 ground states were determined using field-dependent 57Fe Mössbauer and high-field and -frequency electron paramagnetic resonance (HFEPR) spectroscopies. The spin Hamiltonian parameters were analyzed with crystal field theory and corroborated by density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) calculations. Whereas the ZFS tensor of S has a small rhombicity, E/D = 0.082, and a positive D = 15.17 cm-1, T exhibits a negative D = -9.16 cm-1 and a large rhombicity, E/D = 0.246. Computational investigation of the structural factors suggests that the ground-state electronic configuration and geometry of T's Fe site are determined by the interaction of [Fe(OC4F9)3]- with {K(18C6)}+. In contrast, two distinct countercations of S/S' have a negligible influence on their [Fe(pinF)2]2- moieties. Instead, the distortions in S' are likely induced by the chelate ring conformation change from δλ, observed for S, to the δδ conformation, determined for S'.

Preparations of trans- and cis-μ-1,2-Peroxodiiron(III) Complexes

The iron(II) complex with cis,cis-1,3,5-tris(benzylamino)cyclohexane (Bn3CY) (1) has been synthesized and characterized, which reacted with dioxygen to form the peroxo complex 2 in acetone at -60 °C. On the basis of spectroscopic measurements for 2, it was confirmed that the peroxo complex 2 has a trans-μ-1,2 fashion. Additionally, the peroxo complex 2 was reacted with benzoate anion as a bridging agent to give a peroxo complex 3. The results of resonance Raman and 1H-NMR studies supported that the peroxo complex 3 is a cis-μ-1,2-peroxodiiron(III) complex. These spectral features were interpreted by using DFT calculations.

Direct and remote control of electronic structures and redox potentials in μ-oxo diferric complexes

Non-heme diiron enzymes activate O2 for the oxidation of substrates in the form of peroxo FeIII2 or high-valent FeIV2 intermediates. We have developed a dinucleating bis(tetradentate) ligand system that stabilizes peroxo and hydroperoxo FeIII2 complexes with terminal 6-methylpyridine donors, while the peroxo FeIII2 intermediate is reactive with terminal pyridine donors presumably via conversion to a fluent high-valent FeIV2 intermediate. We present here a derivative with electron-donating methoxy substituents at the pyridine donors and its diferric complexes with an {FeIIIX(μ-O)FeIIIX} (X- = Cl-, OAc-, and OH-) or an {FeIII(μ-O)(μ-OAc)FeIII} core. The complex-induced oxidation of EtOH with H2O2 provides μ-OAc-, and in acetone, the complex with mixed OH-/OAc- exogenous donors is obtained. Both reactivities indicate a reactive fluent peroxo FeIII2 intermediate. The coupling constant J and the LMCT transitions are insensitive to the nature of the directly bound ligands X- and reflect mainly the electronic structure of the central {FeIII(μ-O)FeIII} core, while Mössbauer spectroscopy and d-d transitions probe the local FeIII sites. The remote methoxy substituents decrease the potential for the oxidation to FeIV by ∼100 mV, while directly bound OH- in {FeIII(OH)(μ-O)FeIII(OH)} with a short 1.91 Å FeIII-OOH bond decreases the potential by 590 mV compared to {FeIII(OAc)(μ-O)FeIII(OAc)} with a 2.01 Å FeIII-OOAc bond. Interestingly, this FeIII-OH bond is even shorter (1.87 Å) in the mixed OH-/OAc- complex but the potential is the mean value of the potentials of the OH-/OH- and OAc-/OAc- complexes, thus reflecting the electron density of the central {FeIII(μ-O)FeIII} core and not of the local FeIII-OH unit.

Enhancement of Reactivity of a RuIV-Oxo Complex in Oxygen-Atom-Transfer Catalysis by Hydrogen-Bonding with Amide Moieties in the Second Coordination Sphere

We have synthesized and characterized a RuII-OH2 complex (2), which has a pentadentate ligand with two pivalamide groups as bulky hydrogen-bonding (HB) moieties in the second coordination sphere (SCS). Complex 2 exhibits a coordination equilibrium through the coordination of one of the pivalamide oxygens to the Ru center in water, affording a η6-coordinated complex, 3. A detailed thermodynamic analysis of the coordination equilibrium revealed that the formation of 3 from 2 is entropy-driven owing to the dissociation of the axial aqua ligand in 2. Complex 2 was oxidized by a CeIV salt to produce the corresponding RuIII(OH) complex (5), which was characterized crystallographically. In the crystal structure of 5, hydrogen bonds are formed among the NH groups of the pivalamide moieties and the oxygen atom of the hydroxo ligand. Further 1e--oxidation of 5 yields the corresponding RuIV(O) complex, 6, which has intramolecular HB of the oxo ligand with two amide N-H protons. Additionally, the RuIII(OH) complex, 5, exhibits disproportionation to the corresponding RuIV(O) complex, 6, and a mixture of the RuII complexes, 2 and 3, in an acidic aqueous solution. We investigated the oxidation of a phenol derivative using complex 6 as the active species and clarified the switch of the reaction mechanism from hydrogen-atom transfer at pH 2.5 to electron transfer, followed by proton transfer at pH 1.0. Additionally, the intramolecular HB in 6 exerts enhancing effects on oxygen-atom transfer reactions from 6 to alkenes such as cyclohexene and its water-soluble derivative to afford the corresponding epoxides, relative to the corresponding RuIV(O) complex (6') lacking the HB moieties in the SCS.

The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations

This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).

Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes

Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.

Homoprotocatechuate dioxygenase active site: Imitating the secondary sphere base via computational design

Oxidative ring cleavage reactions have attracted great interest and various studies on the catechol ring-cleaving enzyme homoprotocatechuate dioxygenase (HPCD) have been reported in the literature. The available data on how the proton transfer takes place led us to design a potential HPCD model structure. A secondary sphere effect of utmost importance, the assistance of His200, which is critical for the catechol proton to migrate to dioxygen, was cautiously included on the first coordination shell. This was done mainly by modifying the axial ligands in the first coordination shell of HPCD such that the dual basic/acidic role in the proton transfer pathway of His200 was reproduced. Model systems with mono-, bi-, and tridentate ligands are reported. Energetically feasible reaction channels on synthetically promising ligand structures are identified. Key structural and electronic principles for obtaining viable proton transfer paths are outlined.

Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

Homoleptic Fe(III) and Fe(IV) Complexes of a Dianionic C3-Symmetric Scorpionate

High-valent iron species have been implicated as key intermediates in catalytic oxidation reactions, both in biological and synthetic systems. Many heteroleptic Fe(IV) complexes have now been prepared and characterized, especially using strongly π-donating oxo, imido, or nitrido ligands. On the other hand, homoleptic examples are scarce. Herein, we investigate the redox chemistry of iron complexes of the dianonic tris-skatylmethylphosphonium (TSMP^2-) scorpionate ligand. One-electron oxidation of the tetrahedral, bis-ligated [(TSMP)₂Fe^II]^2- leads to the octahedral [(TSMP)₂Fe^III]^-. The latter undergoes thermal spin-cross-over both in the solid state and solution, which we characterize using superconducting quantum inference device (SQUID), Evans method, and paramagnetic nuclear magnetic resonance spectroscopy. Furthermore, [(TSMP)₂Fe^III]^- can be reversibly oxidized to the stable high-valent [(TSMP)₂Fe^IV]⁰ complex. We use a variety of electrochemical, spectroscopic, and computational techniques as well as SQUID magnetometry to establish a triplet (S = 1) ground state with a metal-centered oxidation and little spin delocalization on the ligand. The complex also has a fairly isotropic g-tensor (g_iso = 1.97) combined with a positive zero-field splitting (ZFS) parameter D (+19.1 cm^-1) and very low rhombicity, in agreement with quantum chemical calculations. This thorough spectroscopic characterization contributes to a general understanding of octahedral Fe(IV) complexes.

Isostructural bridging diferrous chalcogenide cores [FeII(μ-E)FeII] (E = O, S, Se, Te) with decreasing antiferromagnetic coupling down the chalcogenide series

Iron compounds containing a bridging oxo or sulfido moiety are ubiquitous in biological systems, but substitution with the heavier chalcogenides selenium and tellurium, however, is much rarer, with only a few examples reported to date. Here we show that treatment of the ferrous starting material [(^tBupyrpyrr₂)Fe(OEt₂)] (1-OEt₂) (^tBupyrpyrr₂ = 3,5-^tBu₂-bis(pyrrolyl)pyridine) with phosphine chalcogenide reagents E = PR₃ results in the neutral phosphine chalcogenide adduct series [(^tBupyrpyrr₂)Fe(EPR₃)] (E = O, S, Se; R = Ph; E = Te; R = ^tBu) (1-E) without any electron transfer, whereas treatment of the anionic starting material [K]₂[(^tBupyrpyrr₂)Fe₂(μ-N₂)] (2-N₂) with the appropriate chalcogenide transfer source yields cleanly the isostructural ferrous bridging mono-chalcogenide ate complexes [K]₂[(^tBupyrpyrr₂)Fe₂(μ-E)] (2-E) (E = O, S, Se, and Te) having significant deviation in the Fe-E-Fe bridge from linear in the case of E = O to more acute for the heaviest chalcogenide. All bridging chalcogenide complexes were analyzed using a variety of spectroscopic techniques, including ¹H NMR, UV-Vis electronic absorbtion, and ⁵⁷Fe Mössbauer. The spin-state and degree of communication between the two ferrous ions were probed via SQUID magnetometry, where it was found that all iron centers were high-spin (S = 2) Fe^II, with magnetic exchange coupling between the Fe^II ions. Magnetic studies established that antiferromagnetic coupling between the ferrous ions decreases as the identity of the chalcogen is tuned from O to the heaviest congener Te.

Computational Discovery of Stable Metal-Organic Frameworks for Methane-to-Methanol Catalysis

The challenge of direct partial oxidation of methane to methanol has motivated the targeted search of metal-organic frameworks (MOFs) as a promising class of materials for this transformation because of their site-isolated metals with tunable ligand environments. Thousands of MOFs have been synthesized, yet relatively few have been screened for their promise in methane conversion. We developed a high-throughput virtual screening workflow that identifies MOFs from a diverse space of experimental MOFs that have not been studied for catalysis, yet are thermally stable, synthesizable, and have promising unsaturated metal sites for C-H activation via a terminal metal-oxo species. We carried out density functional theory calculations of the radical rebound mechanism for methane-to-methanol conversion on models of the secondary building units (SBUs) from 87 selected MOFs. While we showed that oxo formation favorability decreases with increasing 3d filling, consistent with prior work, previously observed scaling relations between oxo formation and hydrogen atom transfer (HAT) are disrupted by the greater diversity in our MOF set. Accordingly, we focused on Mn MOFs, which favor oxo intermediates without disfavoring HAT or leading to high methanol release energies─a key feature for methane hydroxylation activity. We identified three Mn MOFs comprising unsaturated Mn centers bound to weak-field carboxylate ligands in planar or bent geometries with promising methane-to-methanol kinetics and thermodynamics. The energetic spans of these MOFs are indicative of promising turnover frequencies for methane to methanol that warrant further experimental catalytic studies.

Influence of Cysteine 440 on the Active Site Properties of 3-Deoxy-d-Arabino-Heptulosonate 7-Phosphate Synthase in Mycobacterium tuberculosis (MtDAHPS)

The shikimate pathway, which produces aromatic amino acids and key intermediates, is critical to the viability of the tuberculosis-causing pathogen Mycobacterium tuberculosis. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) catalyzes the first committed step of this pathway and possesses regulatory functions. Its active site contains two cysteinyls: one (Cys₈₇) bound to a metal ion, while the other (Cys₄₄₀) is in proximity to the first but is located on a connecting loop. This arrangement seemingly appeared as a disulfide linkage. However, Cys₄₄₀ is not metal binding, and its positioning indicates that it could collapse the disulfide linkage. Hence, its potential role may be more than simply structural support of the active site fold. Using a multiscale computational approach, molecular dynamics (MD) simulations, and DFT-based calculations, the influence of Cys₄₄₀ on the active site properties has been investigated. MD simulations reveal an unusually long disulfide bond, more than 3.0 Å, whereas DFT calculations identified two stable active site conformers in the triplet and quintet spin states. Analysis of group spin density distribution identified antiferromagnetic coupling in each conformer, which suggests their relatively low potential energy and stable conformations. The conformer in the triplet spin state could favor enzyme reactivity due to its low HOMO-LUMO energy gap. In addition, reduction of the Cys₄₄₀ thiolate group results in collapse of the active site metal-ligand configuration with large exothermicity. Hence, Cys₄₄₀ could activate and inactivate the enzyme. For the first time, the study revealed the role of Cys₄₄₀ as being vital for the catalytic activity of the enzyme rather than solely for the structural stabilization of its active site. Thus, the findings may lead to a novel basis for antituberculosis drug design and development that would disrupt the contributions of the Cys₄₄₀.

Reactivities of iron(IV)-oxido compounds with pentadentate bispidine ligands

The Fe^IVO complexes of bispidines (3,7-diazabicyclo[3.3.1]nonane derivatives) are known to be highly reactive oxidants - with the tetradentate bispidine, the so far most reactive ferryl complex has been reported and two isomeric pentadentate ligands also lead to very reactive high-valent oxidants. With a series of 4 new bispidine derivatives we now try to address the question why the bispidine scaffold in general leads to very reactive oxidants and how this can be tuned by ligand modifications. The study is based on a full structural, spectroscopic and electrochemical analysis of the iron(II) precursors, spectroscopic data of the iron(IV)-oxido complexes, a kinetic analysis of the stoichiometric oxidation of thioanisole by five different bispidine‑iron(IV)-oxido complexes and on product analyses of reactions by the five ferryl oxidants with thioanisole, β-methylstyrene and cis-stilbene as substrates.

Evidence for a High-Valent Iron-Fluoride That Mediates Oxidative C(sp3)-H Fluorination

[Fe^II(NCCH₃)(NTB)](OTf)₂ (NTB = tris(2-benzimidazoylmethyl)amine, OTf = trifluoromethanesulfonate) was reacted with difluoro(phenyl)-λ³-iodane (PhIF₂) in the presence of a variety of saturated hydrocarbons, resulting in the oxidative fluorination of the hydrocarbons in moderate-to-good yields. Kinetic and product analysis point towards a hydrogen atom transfer oxidation prior to fluorine radical rebound to form the fluorinated product. The combined evidence supports the formation of a formally Fe^IV(F)₂ oxidant that performs hydrogen atom transfer followed by the formation of a dimeric μ-F-(Fe^III)₂ product that is a plausible fluorine atom transfer rebound reagent. This approach mimics the heme paradigm for hydrocarbon hydroxylation, opening up avenues for oxidative hydrocarbon halogenation.

Room-Temperature Conversion of Methane to Methanediol by [FeO2]. J Phys Chem Lett 2023;14:1633-1640. [PMID: 36752636 DOI: 10.1021/acs.jpclett.2c03786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Inspired by the activities of P-450 enzyme and Rieske oxygenases in nature, in which the high-valent Fe-oxo complexes play a key role for oxidation of alkanes, the oxidation process of methane by the high-valent iron oxide cation [FeO₂]⁺ has been explored by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry complemented by high-level quantum chemical calculations. In contrast to the previously reported [FeO]⁺/CH₄ and [Fe(O)OH]⁺/CH₄ systems, which afford [FeOH]⁺ as the main product, the generation of Fe⁺ dominates the reaction of [FeO₂]⁺ with CH₄. Theoretical calculations suggest a novel "oxygen rebound" pathway for the liberation of methanediol. In particular, the inevitable valence increase of Fe prior to C-H activation is similar to the cytochrome P-450 mediated processes. To our best knowledge, this study provides the first example of methane activation by the high-valent Fe(V)-oxo species in the gas phase, which may thus bridge the gas-phase model and the condensed-phase biosystems.

Magnetic anisotropy and structural flexibility in the field-induced single ion magnets [Co{(OPPh2)(EPPh2)N}2], E = S, Se, explored by experimental and computational methods

During the last few years, a large number of mononuclear Co(II) complexes of various coordination geometries have been explored as potential single ion magnets (SIMs). In the work presented herein, the Co(II) S = 3/2 tetrahedral [Co{(OPPh2)(EPPh2)N}2], E = S, Se, complexes (abbreviated as CoO2E2), bearing chalcogenated mixed donor-atom imidodiphosphinato ligands, were studied by both experimental and computational techniques. Specifically, direct current (DC) magnetometry provided estimations of their zero-field splitting (zfs) axial (D) and rhombic (E) parameter values, which were more accurately determined by a combination of far-infrared magnetic spectroscopy and high-frequency and -field EPR spectroscopy studies. The latter combination of techniques was also implemented for the S = 3/2 tetrahedral [Co{(EPiPr2)2N}2], E = S, Se, complexes, confirming the previously determined magnitude of their zfs parameters. For both pairs of complexes (E = S, Se), it is concluded that the identity of the E donor atom does not significantly affect their zfs parameters. High-resolution multifrequency EPR studies of CoO2E2 provided evidence of multiple conformations, which are more clearly observed for CoO2Se2, in agreement with the structural disorder previously established for this complex by X-ray crystallography. The CoO2E2 complexes were shown to be field-induced SIMs, i.e., they exhibit slow relaxation of magnetization in the presence of an external DC magnetic field. Advanced quantum-chemical calculations on CoO2E2 provided additional insight into their electronic and structural properties.

DFT insights into the mechanism of O2 activation catalyzed by a structural and functional model of cysteine dioxygenase with tris(2-pyridyl)methane-based ligand architecture

Cysteine dioxygenation is an important step in the metabolism of toxic L-cysteine (Cys) in the human body, carried out by cysteine dioxygenase enzyme (CDO). The disruption of this process is found to elicit neurological health issues. This work reports a computational investigation of mechanistic aspects of this reaction, using a recently reported tris(2-pyridyl)methane-based biomimetic model complex of CDO. The computed results indicate that, the initial SO2 bond formation process is the slowest step in the S-dioxygenation process, possessing an activation barrier of 12.7 kcal/mol. The remaining steps were found to be downhill requiring very small activation energies. The transition states were found to undergo spin crossover between triplet and quintet states, while the singlet surface remained unstable throughout the entire reaction. In essence, the mechanistic scheme and multistate reactivity pattern together with the relatively small computed rate-limiting activation barrier as well as the exothermic formation energy demonstrate that the model complex is an efficient biomimetic CDO model. In addition, the study also substantiates the involvement of Fe(IV)oxido intermediates in the mechanism of S-dioxygenation by the chosen model complex. The insights derived from the O₂ activation process might pave way for development of more accurate CDO model catalysts that might be capable of even more efficiently mimicking the geometric, spectroscopic and functional features of the CDO enzyme.

Elucidating the Role of O2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases

Oxygenations of aromatic soil and water contaminants with molecular O₂ catalyzed by Rieske dioxygenases are frequent initial steps of biodegradation in natural and engineered environments. Many of these non-heme ferrous iron enzymes are known to be involved in contaminant metabolism, but the understanding of enzyme–substrate interactions that lead to successful biodegradation is still elusive. Here, we studied the mechanisms of O₂ activation and substrate hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and substrate-specific factors that determine the efficiency of oxygenated product formation. Experiments in enzyme assays of 2-nitrotoluene dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-, fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates reveal that typically 20–100% of the enzyme’s activity involves unproductive paths of O₂ activation with generation of reactive oxygen species through so-called O₂ uncoupling. The ¹⁸O and ¹³C kinetic isotope effects of O₂ activation and nitroaromatic substrate hydroxylation, respectively, suggest that O₂ uncoupling occurs after generation of Fe^III-(hydro)peroxo species in the catalytic cycle. While 2NTDO hydroxylates ortho-substituted nitroaromatic substrates more efficiently, NBDO favors meta-substituted, presumably due to distinct active site residues of the two enzymes. Our data implies, however, that the O₂ uncoupling and hydroxylation activity cannot be assessed from simple structure–reactivity relationships. By quantifying O₂ uncoupling by Rieske dioxygenases, our work provides a mechanistic link between contaminant biodegradation, the generation of reactive oxygen species, and possible adaptation strategies of microorganisms to the exposure of new contaminants.

Metal-Metal Bond Umpolung in Heterometallic Extended Metal Atom Chains

Understanding the fundamental properties governing metal–metal interactions is crucial to understanding the electronic structure and thereby applications of multimetallic systems in catalysis, material science, and magnetism. One such property that is relatively underexplored within multimetallic systems is metal–metal bond polarity, parameterized by the electronegativities (χ) of the metal atoms involved in the bond. In heterobimetallic systems, metal–metal bond polarity is a function of the donor–acceptor (Δχ) interactions of the two bonded metal atoms, with electropositive early transition metals acting as electron acceptors and electronegative late transition metals acting as electron donors. We show in this work, through the preparation and systematic study of a series of Mo₂M(dpa)₄(OTf)₂ (M = Cr, Mn, Fe, Co, and Ni; dpa = 2,2′-dipyridylamide; OTf = trifluoromethanesulfonate) heterometallic extended metal atom chain (HEMAC) complexes that this expected trend in χ can be reversed. Physical characterization via single-crystal X-ray diffraction, magnetometry, and spectroscopic methods as well as electronic structure calculations supports the presence of a σ symmetry 3c/3e^– bond that is delocalized across the entire metal-atom chain and forms the basis of the heterometallic Mo₂–M interaction. The delocalized 3c/3e^– interaction is discussed within the context of the analogous 3c/3e^– π bonding in the vinoxy radical, CH₂CHO. The vinoxy comparison establishes three predictions for the σ symmetry 3c/3e^– bond in HEMACS: (1) an umpolung effect that causes the Mo–M interactions to become more covalent as Δχ increases, (2) distortion of the σ bonding and non-bonding orbitals to emphasize Mo–M bonding and de-emphasize Mo–Mo bonding, and (3) an increase in Mo spin population with increasing Mo–M covalency. In agreement with these predictions, we find that the Mo₂···M covalency increases with increasing Δχ of the Mo and M atoms (Δχ_Mo–M increases as M = Cr < Mn < Fe < Co < Ni), an umpolung of the trend predicted in the absence of σ delocalization. We attribute the observed trend in covalency to the decreased energic differential (ΔE) between the heterometal orbital and the σ bonding molecular orbital of the Mo₂ quadruple bond, which serves as an energetically stable, “ligand”-like electron-pair donor to the heterometal ion acceptor. As M is changed from Cr to Ni, the σ bonding and nonbonding orbitals do indeed distort as anticipated, and the spin population of the outer Mo group is increased by at least a factor of 2. These findings provide a predictive framework for multimetallic compounds and advance the current understanding of the electronic structures of molecular heteromultimetallic systems, which can be extrapolated to applications in the context of mixed-metal surface catalysis and multimetallic proteins.

This work describes how use of a metal−metal quadruply bonded metalloligand can reverse expected trends in metal−metal bond polarity through the preparation and systematic study of a novel series of Mo₂M(dpa)₄(OTf)₂ (M = Cr, Mn, Fe, Co, and Ni) heterotrimetallic extended metal atom chain (HEMAC) complexes. These complexes feature a 3c/3e⁻ metal−metal bond that is delocalized across the entire metal atom chain and is compared to the 3c/3e⁻ π bonding in the vinoxyl radical.

Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA

Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.

Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N2

Nitrogen (N₂) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N₂. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of ¹⁵N-labeled hydroxylamine to ¹⁵N₂. This conversion did not happen under oxygen (O₂)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a K_m of 92.9 ± 3.0 μM for hydroxylamine and a k_cat of 0.028 ± 0.001 s⁻¹. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N₂.

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.

Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues

FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•Co^II•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•Fe^II•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.

Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins

Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A Mn^III(μ-O)(μ-OH)Fe^III species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the Mn^III(μ-O)(μ-OH)Fe^III state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded Mn^III(μ-OH)Fe^III species. This final intermediate precedes formation of the Mn^III/Fe^III resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.

Oriented External Electric Fields Regurating the Reaction Mechanism of CH4 Oxidation Catalyzed by Fe(IV)-Oxo-Corrolazine: Insight from Density Functional Calculations

Methane is the simplest alkane and can be used as an alternative energy source for oil and coal, but the greenhouse effect caused by its leakage into the air is not negligible, and its conversion into liquid methanol not only facilitates transportation, but also contributes to carbon neutrality. In order to find an efficient method for converting methane to methanol, CH₄ oxidation catalyzed by Fe(IV)-Oxo-corrolazine (Fe(IV)-Oxo-Cz) and its reaction mechanism regulation by oriented external electric fields (OEEFs) are systematically studied by density functional calculations. The calculations show that Fe(IV)-Oxo-Cz can abstract one H atom from CH₄ to form the intermediate with OH group connecting on the corrolazine ring, with the energy barrier of 25.44 kcal mol⁻¹. And then the product methanol is formed through the following rebound reaction. Moreover, the energy barrier can be reduced to 20.72 kcal mol⁻¹ through a two-state reaction pathway. Furthermore, the effect of OEEFs on the reaction is investigated. We found that OEEFs can effectively regulate the reaction by adjusting the stability of the reactant and the transition state through the interaction of electric field-molecular dipole moment. When the electric field is negative, the energy barrier of the reaction decreases with the increase of electric intensity. Moreover, the OEEF aligned along the intrinsic Fe‒O reaction axis can effectively regulate the ability of forming the OH on the corrolazine ring by adjusting the charges of O and H atoms. When the electric field intensity is −0.010 a.u., the OH can be directly rebounded to the CH₃· before it is connecting on the corrolazine ring, thus forming the product directly from the transition state without passing through the intermediate with only an energy barrier of 17.34 kcal mol⁻¹, which greatly improves the selectivity of the reaction.

Substrate-Specific Coupling of O2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases

Rieske dioxygenases catalyze the initial steps in the hydroxylation of aromatic compounds and are critical for the metabolism of xenobiotic substances. Because substrates do not bind to the mononuclear non-heme Fe^II center, elementary steps leading to O₂ activation and substrate hydroxylation are difficult to delineate, thus making it challenging to rationalize divergent observations on enzyme mechanisms, reactivity, and substrate specificity. Here, we show for nitrobenzene dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes to nitrite and substituted catechols, that unproductive O₂ activation with the release of the unreacted substrate and reactive oxygen species represents an important path in the catalytic cycle. Through correlation of O₂ uncoupling for a series of substituted nitroaromatic compounds with ¹⁸O and ¹³C kinetic isotope effects of dissolved O₂ and aromatic substrates, respectively, we show that O₂ uncoupling occurs after the rate-limiting formation of Fe^III-(hydro)peroxo species from which substrates are hydroxylated. Substituent effects on the extent of O₂ uncoupling suggest that the positioning of the substrate in the active site rather than the susceptibility of the substrate for attack by electrophilic oxygen species is responsible for unproductive O₂ uncoupling. The proposed catalytic cycle provides a mechanistic basis for assessing the very different efficiencies of substrate hydroxylation vs unproductive O₂ activation and generation of reactive oxygen species in reactions catalyzed by Rieske dioxygenases.

Charge Maintenance during Catalysis in Nonheme Iron Oxygenases

Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O₂-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.

Electronic Structure and Reactivity of Dioxygen-Derived Aliphatic Thiolate-Ligated Fe-Peroxo and Fe(IV) Oxo Compounds

Herein, we examine the electronic and geometric structural properties of O₂-derived aliphatic thiolate-ligated Fe-peroxo, Fe-hydroxo, and Fe(IV) oxo compounds. The latter cleaves strong C-H bonds (96 kcal mol^-1) on par with the valine C-H bond cleaved by isopencillin N synthase (IPNS). Stopped-flow kinetics studies indicate that the barrier to O₂ binding to [Fe^II(S^Me2N₄(tren))]⁺ (3) is extremely low (E_a = 36(2) kJ mol^-1), as theoretically predicted for IPNS. Dioxygen binding to 3 is shown to be reversible, and a superoxo intermediate, [Fe^III(S^Me2N₄(tren))(O₂)]⁺ (6), forms in the first 25 ms of the reaction at -40 °C prior to the rate-determining (E_a = 46(2) kJ mol^-1) formation of peroxo-bridged [(S^Me2N₄(tren))Fe(III)]₂(μ-O₂)²⁺ (7). A log(k_obs) vs log([Fe]) plot for the formation of 7 is consistent with the second-order dependence on iron, and H₂O₂ assays are consistent with a 2:1 ratio of Fe/H₂O₂. Peroxo 7 is shown to convert to ferric-hydroxo [Fe^III(S^Me2N(tren))(OH)]⁺ (9, g_⊥ = 2.24, g_∥ = 1.96), the identity of which was determined via its independent synthesis. Rates of the conversion 7 → 9 are shown to be dependent on the X-H bond strength of the H-atom donor, with a k_H/k_D = 4 when CD₃OD is used in place of CH₃OH as a solvent. A crystallographically characterized cis thiolate-ligated high-valent iron oxo, [Fe^IV(O)(S^Me2N₄(tren))]⁺ (11), is shown to form en route to hydroxo 9. Electronic structure calculations were shown to be consistent with 11 being an S = 1 Fe(IV)═O with an unusually high ν_Fe-O stretching frequency at 918 cm^-1 in line with the extremely short Fe-O bond (1.603(7) Å).