Dioxygen Activation by Enzymes with Mononuclear Non-Heme Iron Active Sites

Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH

Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.

Redox Processes Involving Oxygen: The Surprising Influence of Redox-Inactive Lewis Acids

Metalloenzymes with heteromultimetallic active sites perform chemical reactions that control several biogeochemical cycles. Transformations catalyzed by such enzymes include dioxygen generation and reduction, dinitrogen reduction, and carbon dioxide reduction-instrumental transformations for progress in the context of artificial photosynthesis and sustainable fertilizer production. While the roles of the respective metals are of interest in all these enzymatic transformations, they share a common factor in the transfer of one or multiple redox equivalents. In light of this feature, it is surprising to find that incorporation of redox-inactive metals into the active site of such an enzyme is critical to its function. To illustrate, the presence of a redox-inactive Ca2+ center is crucial in the Oxygen Evolving Complex, and yet particularly intriguing given that the transformation catalyzed by this cluster is a redox process involving four electrons. Therefore, the effects of redox inactive metals on redox processes-electron transfer, oxygen- and hydrogen-atom transfer, and O-O bond cleavage and formation reactions-mediated by transition metals have been studied extensively. Significant effects of redox inactive metals have been observed on these redox transformations; linear free energy correlations between Lewis acidity and the redox properties of synthetic model complexes are observed for several reactions. In this Perspective, these effects and their relevance to multielectron processes will be discussed.

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.

A high-spin alkylperoxo-iron(iii) complex with cis-anionic ligands: implications for the superoxide reductase mechanism

The N3O macrocycle of the 12-TMCO ligand stabilizes a high spin (S = 5/2) [FeIII(12-TMCO)(OOtBu)Cl]+ (3-Cl) species in the reaction of [FeII(12-TMCO)(OTf)2] (1-(OTf)2) with tert-butylhydroperoxide (tBuOOH) in the presence of tetraethylammonium chloride (NEt4Cl) in acetonitrile at -20 °C. In the absence of NEt4Cl the oxo-iron(iv) complex 2 [FeIV(12-TMCO)(O)(CH3CN)]2+ is formed, which can be further converted to 3-Cl by adding NEt4Cl and tBuOOH. The role of the cis-chloride ligand in the stabilization of the FeIII-OOtBu moiety can be extended to other anions including the thiolate ligand relevant to the enzyme superoxide reductase (SOR). The present study underlines the importance of subtle electronic changes and secondary interactions in the stability of the biologically relevant metal-dioxygen intermediates. It also provides some rationale for the dramatically different outcomes of the chemistry of iron(iii)peroxy intermediates formed in the catalytic cycles of SOR (Fe-O cleavage) and cytochrome P450 (O-O bond lysis) in similar N4S coordination environments.

Influence of Equatorial Co-Ligands on the Reactivity of LFeIIIOIPh

Previous biomimetic studies clearly proved that equatorial ligands significantly influence the redox potential and thus the stability/reactivity of biologically important oxoiron intermediates; however, no such studies were performed on FeIIIOIPh species. In this study, the influence of substituted pyridine co-ligands on the reactivity of iron(III)-iodosylbenzene adduct has been investigated in sulfoxidation and epoxidation reactions. Selective oxidation of thioanisole, cis-cyclooctene, and cis- and trans-stilbene in the presence of a catalytic amount of [FeII(PBI)3](OTf)2 with PhI(OAc)2 provide products in good to excellent yields through an FeIIIOIPh intermediate depending on the co-ligand (4R-Py) used. Several mechanistic studies were performed to gain more insight into the mechanism of oxygen atom transfer (OAT) reactions to support the reactive intermediate and investigate the effect of the equatorial co-ligands. Based on competitive experiments, including a linear free-energy relationship between the relative reaction rates (logkrel) and the σp (4R-Py) parameters, strong evidence has been observed for the electrophilic character of the reactive species. The presence of the [(PBI)2(4R-Py)FeIIIOIPh]3+ intermediates and the effect of the co-ligands was also supported by UV-visible measurements, including the color change from red to green and the hypsochromic shifts in the presence of co-ligands. This is another indication that the title iron(III)-iodosylbenzene adduct is able to oxygenate sulfides and alkenes before it is transformed into the oxoiron form by cleavage of the O-I bond.

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).

Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor

The aerobic oxidation of carbon-hydrogen (C-H) bonds in biology is currently known to be accomplished by a limited set of cofactors that typically include heme, nonheme iron, and copper. While manganese cofactors perform difficult oxidation reactions, including water oxidation within Photosystem II, they are generally not known to be used for C-H bond activation, and those that do catalyze this important reaction display limited intrinsic reactivity. Here we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis, AibH1H2, requires manganese to functionalize a strong, aliphatic C-H bond (BDE = 100 kcal/mol). Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site at the locus of O2 activation and substrate coordination. This result expands the known reactivity of biological manganese-iron cofactors, which was previously restricted to single-electron transfer or stoichiometric protein oxidation. Furthermore, the AibH1H2 cofactor is supported by a protein fold distinct from typical bimetallic oxygenases, and bioinformatic analyses identify related proteins abundant in microorganisms. This suggests that many uncharacterized monooxygenases may similarly require manganese to perform oxidative biochemical tasks.

Electric field effect of positive and negative charges of substituents on electronic structure and reactivity of oxoiron(IV) porphyrin π-cation radical complex

Electric field effect by the positive and negative changes near the active site is an important factor for controlling the reactivity of metalloenzymes. Previously, we reported that the positive charge of the N-methyl-2-pyridinium cation increases the reactivity of oxoiron(IV) porphyrin π-cation radical complex (Compound I), due to the attractive Coulomb interaction with electrons in Compound I. To further investigate the electric field effect, we study here the effect of the negative charge of the sulfonate group on the electronic structure and reactivity using Compound I of meso-tetrakis(2,4,6-trimethyl-3-sulfonatophenyl)porphyrin (TMPS-I). Although Compound I has been known as a very unstable complex, TMPS-I is very stable in 0.1 M acetate buffer at pH = 6. The half-life of TMPS-I is estimated to be 6.9 × 10³ s, which is the longest in Compound I previously reported. The redox potential of TMPS-I is estimated to be 0.76 V vs SCE in phosphate buffer, pH = 10. Kinetic analysis with stopped-flow technique indicates TMPS-I is less reactive than Compounds I reported previously. However, ¹H NMR and EPR spectra of TMPS-I are very close to those of Compounds I reported previously. The DFT calculations show that the orbital energy of Compound I is drastically altered by the positive and negative charges on the meso-phenyl group, suggesting the electric field effect. The difference of the reactivity of Compound I can be rationalized with the change of the orbital energy caused by the intramolecular electric field effect of the positive and negative charges.

The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986T is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity

The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986^T (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

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.

Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling

One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH⁺/ne^-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH⁺/ne^- reactions. Such control can allow functional modeling of hydrogenases (H⁺ + e^- → 1/2 H₂), cytochrome c oxidase (O₂ + 4 e^- + 4 H⁺ → 2 H₂O), monooxygenases (RR'CH₂ + O₂ + 2 e^- + 2 H⁺ → RR'CHOH + H₂O) and dioxygenases (S + O₂ → SO₂; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.

The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases

Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2 activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2 activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme Fe^II upon abstraction of a water ligand, (ii) binding of O2 , and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII center through thermoneutral H₂O reorientation and exothermic O2 binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII in agreement with a strategy that avoids unproductive O2 activation.

Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1

The 2-oxoglutarate (2OG)-dependent non-heme enzyme FtmOx1 catalyzes the endoperoxide biosynthesis of verruculogen. Although several mechanistic studies have been carried out, the catalytic mechanism of FtmOx1 is not well determined owing to the lack of a reliable complex structure of FtmOx1 with fumitremorgin B. Herein we provide the X-ray crystal structure of the ternary complex FtmOx1⋅2OG⋅fumitremorgin B at a resolution of 1.22 Å. Our structures show that the binding of fumitremorgin B induces significant compression of the active pocket and that Y68 is in close proximity to C26 of the substrate. Further MD simulation and QM/MM calculations support a CarC-like mechanism, in which Y68 acts as the H atom donor for quenching the C26-centered substrate radical. Our results are consistent with all available experimental data and highlight the importance of accurate complex structures in the mechanistic study of enzymatic catalysis.

Synthesis and Structural Characterization of Pyridine-2,6-dicarboxamide and Furan-2,5-dicarboxamide Derivatives

Derivatives based on pyridine-2-6- and furan-2,5-dicarboxamide scaffolds reveal numerous chemical properties and biological activities. This fact makes them an exciting research topic in supramolecular and coordination chemistry and in discovering new pharmacologically-active compounds. This work aimed to obtain a series of symmetrical pyridine-2-6- and furan-2,5-dicarboxamides through a condensation reaction of the appropriate acyl chlorides and aromatic amides. Successful syntheses were confirmed with NMR spectroscopy. We solved their crystal structures for seven compounds; two pyridine and five furan derivatives. Based on our crystallographic studies, we were able to indicate supramolecular features of the crystals under investigation. Additionally, Hirshfeld surface analysis allowed us to calculate a distribution of intermolecular contacts in the dicarboxamide crystals.

Activation of O2 across a C(sp3)-C(sp3) bond

The activation of atmospheric molecular dioxygen (O₂) is reported, which occurred across a C(sp³)-C(sp³) bond of a piperazine derivative without any catalyst at ambient conditions under the formation of 1,2,4,7-dioxadiazoctane, an 8-membered (larger-ring) cyclic organic peroxide.

Rate-Limiting Step of Epoxidation Reaction of the Oxoiron(IV) Porphyrin π-Cation Radical Complex: Electron Transfer Coupled Bond Formation Mechanism

Epoxidation reactions catalyzed by high-valent metal-oxo species are key reactions in various biological and chemical processes. Because the redox potentials of alkenes are higher than those of most high-valent metal-oxo species, the electron transfer (ET) from the alkene to the high-valent metal-oxo species in the epoxidation reaction is endergonic and must be coupled with another exergonic process. To reveal the mechanism of the ET, we performed a Marcus plot analysis for the epoxidation reaction of the oxoiron(IV) porphyrin π-cation radical complex (compound I) with alkene. The Marcus plots can be simulated with a linear line with the gradient of 0.50 when the redox potential of compound I varies and 0.07 when the redox potential of alkene varies. These results indicate that the ET process is involved in the rate-limiting step and coupled with the following O-C bond formation process: ET coupled bond formation mechanism. The DFT calculations support this conclusion and disclose the details of the mechanism. As the alkene comes close to the oxo ligand, the energy of the highest occupied molecular orbital (HOMO) of the alkene increases and the energy for the ET becomes small enough to allow the ET. Finally, the ET occurs from the HOMO of the alkene to the porphyrin π-radical orbital. The shift of one electron from the HOMO of the alkene by the ET simultaneously results in the O-C half bond formation between the oxo ligand and the alkene. The ET process itself is still endergonic and reversible, but the bond formation coupled with the ET changes the overall process to exergonic and irreversible. We also discuss the similarity with the aromatic hydroxylation reaction and the relevance to the epoxidation reactions of other metal-oxo complexes and peracid.

Bioinspired mononuclear Mn complexes for O2 activation and biologically relevant reactions

A general interest in harnessing the oxidizing power of dioxygen (O₂) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O₂ reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O₂-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O₂ activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.

The influence of secondary interactions on the [Ni(O2)]+ mediated aldehyde oxidation reactions

A rate enhancement of one to two orders of magnitude can be obtained in the aldehyde deformylation reactions by replacing the -N(CH₃) groups of [Ni^III(O₂)(Me₄[12]aneN₄)]⁺ (Me₄[12]aneN₄ = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane) and [Ni^III(O₂)(Me₄[13]aneN₄)]⁺ (Me₄[13]aneN₄ = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclotridecane) complexes by -NH in [Ni^III(O₂)([12]aneN₄)]⁺ (2; [12]aneN₄ = 1,4,7,10-tetraazacyclododecane) and [Ni^III(O₂)([13]aneN₄)]⁺ (4; [13]aneN₄ = 1,4,7,10-tetraazacyclotridecane). Based on detailed spectroscopic, reaction-kinetics and theoretical investigations, the higher reactivities of 2 and 4 are attributed to the changes in the secondary-sphere interactions between the [Ni^III(O₂)]⁺ and [12]aneN₄ or [13]aneN₄ moieties, which open up an alternative electrophilic pathway for the aldehyde oxidation reaction. Identification of primary kinetic isotope effects on the reactivity and stability of 2 when the -NH groups of the [12]aneN₄ ligand are deuterated may also suggest the presence of secondary interaction between the -NH groups of [12]aneN₄ and [Ni^III(O₂)]⁺ moieties, although, such interactions are not obvious in the DFT calculated optimized structure at the employed level of theory.

Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed β-propeller hydrolase family

Xylonolactonase Cc XylC from Caulobacter crescentus catalyzes the hydrolysis of the intramolecular ester bond of d‐xylonolactone. We have determined crystal structures of Cc XylC in complex with d‐xylonolactone isomer analogues d‐xylopyranose and (r)‐(+)‐4‐hydroxy‐2‐pyrrolidinone at high resolution. Cc XylC has a 6‐bladed β‐propeller architecture, which contains a central open channel having the active site at one end. According to our previous native mass spectrometry studies, Cc XylC is able to specifically bind Fe²⁺. The crystal structures, presented here, revealed an active site bound metal ion with an octahedral binding geometry. The side chains of three amino acid residues, Glu18, Asn146, and Asp196, which participate in binding of metal ion are located in the same plane. The solved complex structures allowed suggesting a reaction mechanism for intramolecular ester bond hydrolysis in which the major contribution for catalysis arises from the carbonyl oxygen coordination of the xylonolactone substrate to the Fe²⁺. The structure of Cc XylC was compared with eight other ester hydrolases of the β‐propeller hydrolase family. The previously published crystal structures of other β‐propeller hydrolases contain either Ca²⁺, Mg²⁺, or Zn²⁺ and show clear similarities in ligand and metal ion binding geometries to that of Cc XylC. It would be interesting to reinvestigate the metal binding specificity of these enzymes and clarify whether they are also able to use Fe²⁺ as a catalytic metal. This could further expand our understanding of utilization of Fe²⁺ not only in oxidative enzymes but also in hydrolases.

PDB Code(s): 7PLB, 7PLC and 7PLD;

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His₂₁₇-His₂₂₂-Asp₃₇₂ for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C₇-C₈ positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C₇-O and C₈-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.

Xylonolactonase from Caulobacter crescentus Is a Mononuclear Nonheme Iron Hydrolase

Caulobacter crescentus xylonolactonase (Cc XylC, EC 3.1.1.68) catalyzes an intramolecular ester bond hydrolysis over a nonenzymatic acid/base catalysis. Cc XylC is a member of the SMP30 protein family, whose members have previously been reported to be active in the presence of bivalent metal ions, such as Ca²⁺, Zn²⁺, and Mg²⁺. By native mass spectrometry, we studied the binding of several bivalent metal ions to Cc XylC and observed that it binds only one of them, namely, the Fe²⁺ cation, specifically and with a high affinity (K_d = 0.5 μM), pointing out that Cc XylC is a mononuclear iron protein. We propose that bivalent metal cations also promote the reaction nonenzymatically by stabilizing a short-lived bicyclic intermediate on the lactone isomerization reaction. An analysis of the reaction kinetics showed that Cc XylC complexed with Fe²⁺ can speed up the hydrolysis of d-xylono-1,4-lactone by 100-fold and that of d-glucono-1,5-lactone by 10-fold as compared to the nonenzymatic reaction. To our knowledge, this is the first discovery of a nonheme mononuclear iron-binding enzyme that catalyzes an ester bond hydrolysis reaction.

Catalytic Reduction of Dioxygen to Water by a Bioinspired Non-Heme Iron Complex via a 2+2 Mechanism

We report a bioinspired non-heme Fe complex with a tripodal [N₃O]^- ligand framework (Fe(PMG)(Cl)₂) that is electrocatalytically active toward dioxygen reduction with acetic acid as a proton source in acetonitrile solution. Under electrochemical and chemical conditions, Fe(PMG)(Cl)₂ selectively produces water via a 2+2 mechanism, where H₂O₂ is generated as a discrete intermediate species before further reduction to two equivalents of H₂O. Mechanistic studies support a catalytic cycle for dioxygen reduction where an off-cycle peroxo dimer species is the resting state of the catalyst. Spectroscopic analysis of the reduced complex Fe^II(PMG)Cl shows the stoichiometric formation of an Fe(III)-hydroxide species following exposure to H₂O₂; no catalytic activity for H₂O₂ disproportionation is observed, although the complex is electrochemically active for H₂O₂ reduction to H₂O. Electrochemical studies, spectrochemical experiments, and DFT calculations suggest that the carboxylate moiety of the ligand is sensitive to hydrogen-bonding interactions with the acetic acid proton donor upon reduction from Fe(III)/(II), favoring chloride loss trans to the tris-alkyl amine moiety of the ligand framework. These results offer insight into how mononuclear non-heme Fe active sites in metalloproteins distribute added charge and poise proton donors during reactions with dioxygen.

Revisiting Alkane Hydroxylation with m-CPBA (mChloroperbenzoic Acid) Catalyzed by Nickel(II) Complexes

Mechanistic studies are performed on the alkane hydroxylation with m -CPBA ( m -chloroperbenzoic acid) catalyzed by nickel(II) complexes, Ni II (L). In the oxidation of cycloalkanes, Ni II (TPA) acts as an efficient catalyst with a high yield and a high alcohol selectivity. In the oxidation of adamantane, the tertiary carbon is predominantly oxidized. The reaction rate shows first-order dependence on [substrate] and [Ni II (L)] but is independent on [ m CPBA]; v obs = k 2 [substrate][ Ni II (L)]. The reaction exhibited a relatively large kinetic deuterium isotope effect ( KIE ) of 6.7, demonstrating that the hydrogen atom abstraction is involved in the rate-limiting step of the catalytic cycle. Furthermore, Ni II (L) supported by related tetradentate ligands exhibit apparently different catalytic activity, suggesting contribution of the Ni II (L) in the catalytic cycle. Based on the kinetic analysis and the significant effects of O 2 and CCl 4 on the product distribution pattern, possible contributions of (L)Ni II -O• and the acyloxyl radical as the reactive oxidants are discussed.

Human Aspartyl (Asparaginyl) Hydroxylase. A Multifaceted Enzyme with Broad Intra- and Extracellular Activity

Human aspartyl (asparaginyl) β-hydroxylase (HAAH), a unique iron and 2-oxoglutarate dependent oxygenase, has shown increased importance as a suspected oncogenic protein. HAAH and its associated mRNA are upregulated in a wide variety of cancer types, however, the current role of HAAH in the malignant transformation of cells is unknown. HAAH is suspected to play an important role in NOTCH signaling via selective hydroxylation of aspartic acid and asparagine residues of epidermal growth factor (EGF)-like domains. HAAH hydroxylation also potentially mediates calcium signaling and oxygen sensing. In this review we summarize the current state of understanding of the biochemistry and chemical biology of this enzyme, identify key differences from other family members, outline its broader intra- and extracellular roles, and identify the most promising areas for future research efforts.

Synthesis, characterization, and reactivity of oxoiron(IV) porphyrin π-cation radical complexes bearing cationic N-methyl-2-pyridinium group

Electronic charge near the active site is an important factor for controlling the reactivity of metalloenzymes. Here, to investigate the effect of the cationic charge near the heme in heme proteins, we synthesized new iron porphyrin complexes (1 and 2) having cationic 3-methyl-N-methyl-2-pyrdinium group and N-methyl-2-pyridinium group at one of the four meso-positions, respectively. The N-methyl-2-pyridinium groups could be introduced by Stille coupling used palladium catalysts. Oxoiron(IV) porphyrin π-cation radical complexes (Compound I) of 1 (1-CompI) and 2 (2-CompI) are soluble in most organic solvents, allowing direct comparison of their electronic structure and reactivity with Compound I of tetramesitylporphyrin (3-CompI) and tetrakis-(2,6-dichlorophenyl)porphyrin (4-CompI) under the same conditions. Spectroscopic data for 1-CompI are close to those for 3-CompI, but the redox potential for 1-CompI is close to that of 4-CompI. Kinetic analysis of the epoxidation reactions shows that 1-CompI and 2-CompI are (~250-fold) more reactive than 3-CompI, and comparable to 4-CompI. DFT calculations allow to propose that the positive shift of the redox potential and the enhanced reactivity of 1-CompI and 2-CompI is induced by the intramolecular electric field effect of N-methyl-2-pyridinium cation, not by the electron-withdrawing effect.

Significant Solvent Effect on Reactivity of Oxoiron(IV) Porphyrin π-Cation Radical Complex: Activation in n-Alkane Solvent

The solvent effect on the reactivity of high-valent metal oxo complexes has not been studied well, because of their solubility and stability. We synthesize oxoiron(IV) porphyrin π-cation radical complexes (1-CompI and 2-CompI) having the n-hexyl side chains. 1-CompI and 2-CompI are soluble in various solvents, even in hexane, at -80 °C, allowing for the study of their reactivity in various organic solvents. We show that pentane, hexane, heptane, and tert-butyl methyl ether significantly increase the reactivity of 1-CompI and 2-CompI, but dichloromethane, the most frequently used solvent in previous studies, is the worst for increasing the reactivity among the solvents. ¹H NMR and EPR spectroscopies show no significant change in hexane, but the Eyring plots for the epoxidation reactions indicate that the entropies of activation in n-alkane solvents are larger than those in dichloromethane. The observed solvent effect can be rationalized with reorganization energy of the solvent in the reaction.

The most reactive iron and manganese complexes with N-pentadentate ligands for dioxygen activation—synthesis, characteristics, applications

The iron and manganese complexes that activate oxygen atom play multiple role in technologically relevant reactions as well as in biological transformations, in which exist in different redox states. Among them, high-valent oxo intermediate seems to be the most important one. Iron, and/or manganese-based processes have found application in many areas, starting from catalysis and sustainable technologies, through DNA oxidative cleavage, to new substances useful in chemotherapeutic drugs. This review is not only the latest detailed list of uses of homogeneous N-pentadentate iron and manganese catalysts for syntheses of valuable molecules with huge applications in green technologies, but also a kind of "a cookbook", collecting "recipes" for the discussed complexes, in which the sources necessary to obtain a full characterization of the compounds are presented. Following the catalytic activity of metalloenzymes, and taking into account the ubiquity of iron and manganese salts, which in combination with properly designed ligands may show similarity to natural systems, the discussed complexes can find application as new anti-cancer drugs. Also, owing to ability of oxygen atom to exchange in reaction with H₂O, they can be successfully applied in photodriven reactions of water oxidation, as well as in chemically regenerated fuel cells as a redox catalyst.

Iron(III) Complex-Functionalized Gold Nanocomposite as a Strategic Tool for Targeted Photochemotherapy in Red Light

Iron(III)-phenolate/carboxylate complexes exhibiting photoredox chemistry and photoactivated reactive oxygen species (ROS) generation at their ligand-to-metal charge-transfer (LMCT) bands have emerged as potential strategic tools for photoactivated chemotherapy. Herein, the synthesis, in-depth characterization, photochemical assays, and remarkable red light-induced photocytotoxicities in adenocarcinomic human immortalized human keratinocytes (HaCaT) and alveolar basal epithelial (A549) cells of iron(III)-phenolate/carboxylate complex of molecular formula, [Fe(L¹)(L²)] (1), where L¹ is bis(3,5 di-tert-butyl-2-hydroxybenzyl)glycine and L² is 5-(1,2-dithiolan-3-yl)-N-(1,10-phenanthroline-5-yl)pentanamide, and the gold nanocomposite functionalized with complex 1 (1-AuNPs) are reported. There was a significant red shift in the UV-visible absorption band on functionalization of complex 1 to the gold nanoparticles (λ_max: 573 nm, 1; λ_max: 660 nm, 1-AuNPs), rendering the nanocomposite an ideal candidate for photochemotherapeutic applications. The notable findings in our present studies are (i) the remarkable cytotoxicity of the nanocomposite (1-AuNPs) to A549 (IC₅₀: 0.006 μM) and HaCaT (IC₅₀: 0.0075 μM) cells in red light (600-720 nm, 30 J/cm²) while almost nontoxic (IC₅₀ > 500 μg/mL, 0.053 μM) in the dark, (ii) the nontoxicity of 1-AuNPs to normal human diploid fibroblasts (WI-38) or human peripheral lung epithelial (HPL1D) cells (IC₅₀ > 500 μg/mL, 0.053 μM) both in the dark and red light signifying the target-specific anticancer activity of the nanocomposite, (iii) localization of 1-AuNPs in mitochondria and partly nucleus, (iv) remarkable red light-induced generation of reactive oxygen species (ROS: ¹O₂, ^•OH) in vitro, (v) disruption of the mitochondrial membrane due to enhanced oxidative stress, and (vi) caspase 3/7-dependent apoptosis. A similar cytotoxic profile of complex 1 was another key finding of our studies. Overall, our current investigations show a new red light-absorbing iron(III)-phenolate/carboxylate complex-functionalized gold nanocomposite (1-AuNPs) as the emerging next-generation iron-based photochemotherapeutic agent for targeted cancer treatment modality.

Mechanistic Insight into Concerted Proton-Electron Transfer of a Ru(IV)-Oxo Complex: A Possible Oxidative Asynchronicity

We have thoroughly investigated the oxidation of benzyl alcohol (BA) derivatives by a Ru^IV(O) complex (Ru^IV(O)) in the absence or presence of Brønsted acids in order to elucidate the proton-coupled electron-transfer (PCET) mechanisms in C-H oxidation on the basis of a kinetic analysis. Oxidation of BA derivatives by Ru^IV(O) without acids proceeded through concerted proton-electron transfer (CPET) with a large kinetic isotope effect (KIE). In contrast, the oxidation of 3,4,5-trimethoxy-BA ((MeO)₃-BA) by Ru^IV(O) was accelerated by the addition of acids, in which the KIE value reached 1.1 with TFA (550 mM), indicating an alteration of the PCET mechanism from CPET to stepwise electron transfer (ET) followed by proton transfer (PT). Although the oxidized products of BA derivatives were confirmed to be the corresponding benzaldehydes in the range of acid concentrations (0-550 mM), a one-electron-reduction potential of Ru^IV(O) was positively shifted with increases in the concentrations of acids. The elevated reduction potential of Ru^IV(O) strongly influenced the PCET mechanisms in the oxidation of (MeO)₃-BA, changing the mechanism from CPET to ET/PT, as evidenced by the driving-force dependence of logarithms of reaction rate constants in light of the Marcus theory of ET. In addition, dependence of activation parameters on acid concentrations suggested that an oxidative asynchronous CPET, which is not an admixture of the CPET and ET/PT mechanisms, is probably operative in the boundary region (0 mM < [TFA] < 50 mM) involving a one-proton-interacted Ru^IV(O)···H⁺ as a dominant reactive species.

Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase

The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of Cupriavidus metallidurans TDO (cmTDO) to improve our understanding of oxygen activation and initial oxidation of l-Trp. On the basis of the stopped-flow results, rapid freeze-quench (RFQ) experiments were performed to capture and characterize this intermediate by Mössbauer spectroscopy. By incorporating the chlorite dismutase-chlorite system to produce high concentrations of solubilized O₂, we were able to capture the Michaelis complex of cmTDO in a nearly quantitative yield. The RFQ-Mössbauer results confirmed the identity of the Michaelis complex as an O₂-bound ferrous species. They revealed remarkable similarities between the electronic properties of the Michaelis complex and those of the O₂ adduct of myoglobin. We also found that the decay of this reactive intermediate is the rate-limiting step of the catalytic reaction. An inverse α-secondary substrate kinetic isotope effect was observed with a k_H/k_D of 0.87 ± 0.03 when (indole-d₅)-l-Trp was employed as the substrate. This work provides an important piece of spectroscopic evidence of the chemical identity of the Michaelis complex of bacterial TDO.

Fe(III) bipyridyl or phenanthroline complexes with oxidase-like activity for sensitive colorimetric detection of glutathione

In this study, three types of Fe(III) bipyridyl or phenanthroline (Fe(III)-L₃ ) complex could directly catalyze 3,3',5,5'-tetramethylbenzidine (TMB) to induce blue chromogenic changes without H₂ O₂ . Fe(III)-L₃ complex could induce a colour change in TMB directly after a short incubation time. Due to the high oxidase-like activity of the Fe(III)-L₃ complexes, superoxide anion radicals (O₂ ^•- ) were formed in solution. Intermediates radical involving oxo-iron species were then produced that oxidized TMB to its oxidation products (oxTMB), which had an absorbance maximum at 652 nm. Glutathione (GSH) could inhibit the oxidation reaction of the Fe(III)-L₃ complex-TMB system, a rapidly colorimetric method was established for the specific detection of GSH that had a detection limit of 0.1 μM. Furthermore, Fe(III)-L₃ complexes could catalyze TMB to oxTMB directly without H₂ O₂ . This fast and simple colorimetric method may open a new avenue for application in the point-of-care diagnosis field using the TMB chromogenic system.

Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view

This study aims to clarify the interaction mechanism of substrate with catechol 2,3-dioxygenase (C23O) through multi-technique combination. A novel C23O (named C23O-2G) was cloned, heterogeneously expressed, and identified as a new member in subfamily I.2 of extradiol dioxygenases. Based on the simulations of molecular docking and dynamics, the exact binding sites of catechol on C23O-2G were identified, and the catalytic mechanism mediated by key residues was proposed. The roles of the predicted residues during catalysis were confirmed by site-directed mutagenesis, and the mutation of Thr254 could significantly increase catalytic efficiency and substrate specificity of C23O-2G. The binding and thermodynamic parameters obtained from fluorescence spectra suggested that catechol could effectively quench the intrinsic fluorescence of C23O-2G via static and dynamic quenching mechanisms and spontaneously formed C23O-2G/catechol complex by the binding forces of hydrogen bond and van der Waals force. The results of UV-vis spectra, synchronous fluorescence, and CD spectra revealed obvious changes in the microenvironment and conformation of C23O-2G, especially for the secondary structure. The atomic force microscope images further demonstrated the changes from an appearance point of view. This study could improve our mechanistic understanding of representative dioxygenases involved in aromatic compound degradation.

C-H Amination via Nitrene Transfer Catalyzed by Mononuclear Non-Heme Iron-Dependent Enzymes

Expanding the reaction scope of natural metalloenzymes can provide new opportunities for biocatalysis. Mononuclear non-heme iron-dependent enzymes represent a large class of biological catalysts involved in the biosynthesis of natural products and catabolism of xenobiotics, among other processes. Here, we report that several members of this enzyme family, including Rieske dioxygenases as well as α-ketoglutarate-dependent dioxygenases and halogenases, are able to catalyze the intramolecular C-H amination of a sulfonyl azide substrate, thereby exhibiting a promiscuous nitrene transfer reactivity. One of these enzymes, naphthalene dioxygenase (NDO), was further engineered resulting in several active site variants that function as C-H aminases. Furthermore, this enzyme could be applied to execute this non-native transformation on a gram scale in a bioreactor, thus demonstrating its potential for synthetic applications. These studies highlight the functional versatility of non-heme iron-dependent enzymes and pave the way to their further investigation and development as promising biocatalysts for non-native metal-catalyzed transformations.

Ligand Taxonomy for Bioinorganic Modeling of Dioxygen-Activating Non-Heme Iron Enzymes

Novel functions emerge from novel structures. To develop efficient catalytic systems for challenging chemical transformations, chemists often seek inspirations from enzymatic catalysis. A large number of iron complexes supported by nitrogen-rich multidentate ligands have thus been developed to mimic oxo-transfer reactivity of dioxygen-activating metalloenzymes. Such efforts have significantly advanced our understanding of the reaction mechanisms by trapping key intermediates and elucidating their geometric and electronic properties. Critical to the success of this biomimetic approach is the design and synthesis of elaborate ligand systems to balance the thermodynamic stability, structural adaptability, and chemical reactivity. In this Concept article, representative design strategies for biomimetic atom-transfer chemistry are discussed from the perspectives of "ligand builders". Emphasis is placed on how the primary coordination sphere is constructed, and how it can be elaborated further by rational design for desired functions.