Non-heme Fe(IV)-oxo intermediates

Redox-Active Ligands Permit Multielectron O2 Homolysis and O-Atom Transfer at Exceptionally High-Valent Vanadyl Complexes

A five-coordinate chlorovanadium species supported by two redox-active N-phenyl aminophenol ligands was prepared. Experimental and computational data support formulation of this complex as [(Phap)(Phisq)VIVCl], containing one dianionic [Phap]2- amidophenolate and one monoanionic [Phisq]•- iminosemiquinonate radical. Exposure of [(Phap)(Phisq)VIVCl] to O2 readily cleaves the O═O bond to generate [(Phisq)(Phibq)VIV(O)Cl], containing an [Phibq] iminobenzoquinone, so the 2e- oxidation is entirely ligand centered. [(Phisq)(Phibq)VIV(O)Cl] is reduced by net H2 abstraction from 9,10-dihydroanthracene, or in reactions with main-group nucleophiles, such as PPh3 and Me2S, which form a new bond to oxygen and regenerate [(Phap)(Phisq)VIVCl]. Accordingly, the dioxygenase-type O2 activation and O-atom transfer cycling are a direct consequence of ligand redox noninnocence and covalency in the vanadium─aminophenol bonding. The reactions with O-atom donor and acceptor substrates establish a V≡O BDE of 73 ± 14 kcal mol-1 in [(Phisq)(Phibq)VIV(O)Cl]. Reported V≡O BDEs in redox-innocent vanadyl complexes typically fall in the range of 120-170 kcal mol-1. Unlike later 3d metals, where M═O species are typically high energy and activated by, for instance, occupancy of M-O π* antibonding MOs, the exceptionally weak V≡O bond in [(Phisq)(Phibq)VIV-(O)Cl] reflects stabilization of the reduced product. Thus, this research highlights an alternative pathway to generating strong oxidants that are not strong outer-sphere electron acceptors, with implications for the design of early metal catalysts for aerobic oxidations of weak O-atom acceptors or strong X-H bonds.

Nonheme Manganese-Catalyzed Oxidative N-Dealkylation of Tertiary Amides: Manganese(IV)-Oxo Aminopyridine Cation Radical Species and Hydride Transfer Mechanism

The development of efficient and practical N-dealkylation reactions stands as a longstanding objective in synthetic chemistry. Inspired by the oxidative N-dealkylation reactions mediated by heme and nonheme metalloenzymes, we disclose a biomimetic oxidative N-dealkylation catalysis that utilizes a nonheme manganese complex bearing anthryl-appended aminopyridine ligand and hydrogen peroxide (H2O2) as the terminal oxidant. A variety of Weinreb amides and cyclic aliphatic amines are efficiently transformed into valuable methyl hydroxamates and ω-amino acids through oxidative C-N bond cleavage. Mechanistic studies, including density functional theory (DFT) calculations, reveal that a manganese(IV)-oxo aminopyridine cation radical species, which is formed via the bromoacetic acid-assisted heterolytic O-O bond cleavage of a presumed manganese(III)-hydroperoxo aminopyridine species and the subsequent intramolecular electron transfer (ET) from the anthryl group of the aminopyridine ligand to the manganese center, is the active intermediate that initiates the oxidative N-dealkylation reactions; this process is reminiscent to the heterolytic O-O bond cleavage of iron(III)-hydroperoxo porphyrin intermediates (Cpd 0) to form iron(IV)-oxo porphyrin π-cation radicals (Cpd I) that are responsible for diverse selective oxidation reactions. Moreover, it is revealed that the oxidative activation of the C-H bond adjacent to the nitrogen atom proceeds via a hydride transfer (HT) mechanism, which involves a concerted asynchronous proton-coupled electron transfer (PCET), followed by an ET process. Thus, this study reports the first instance of catalytic oxidative N-dealkylation of a variety of tertiary amides, such as Weinreb amides and cyclic aliphatic amines, mediated by a Cpd I-like nonheme manganese(IV)-oxo aminopyridine cation radical species via an initial HT pathway.

What Factors Determine the Brevione B Desaturation Mechanism in the Nonheme Iron Dioxygenase BrvJ?

The natural product synthesis of brevione J undergoes a cascade of reactions including an oxidative desaturation and a ring-expansion. The C1-C2 desaturation of brevione B is catalyzed by the nonheme iron dioxygenase BrvJ using one molecule of O2 and α-ketoglutarate (αKG). However, whether the subsequent oxidative ring expansion reaction is also catalyzed by the same enzyme is unknown and remains controversial. To gain insight into the mechanism of brevione J biosynthesis a computational study is reported here using molecular dynamics and density functional theory approaches. The work predicts that both cycles can proceed in the same protein structure on an iron center with O2 and αKG for each cycle. The rate-determining step is a hydrogen atom abstraction step in both reaction cycles. Interestingly, the OH rebound barriers are high in energy in cycle 1 due to stereochemical interactions and substrate positioning that enable an efficient desaturation reaction.

Bispidine coordination chemistry

Bispidines are extremely rigid ligands, easy to prepare in a large variety, with denticities of four to ten, various donor sets and charges, for mono- and oligonuclear transition metal, main group and rare earth complexes. In the last approx. 20 years significantly more than 50 new bispidine based ligands were prepared and their coordination chemistry studied. Biological probes and medicinal applications is one main area in bispidine coordination chemistry, where fast complex formation, high stability, metal ion selectivity and inertness are of utmost importance. Oxygen activation and oxidation catalysis is another main focus in bispidine coordination chemistry, with catalyst efficiency and stability as well as product selectivity as important requirements. Particularly successful applications in these areas are presented and discussed in detail, in addition to fundamental principles that show the importance of ligand rigidity, cavity size and shape as overarching fundamental properties.

Biosynthesis of unique natural product scaffolds by Fe(II)/αKG-dependent oxygenases

Fe(II)/αKG-dependent oxygenases are multifunctional oxidases responsible for the formation of unique natural product skeletons. Studies of these enzymes are important because the knowledge of their catalytic functions, enzyme structures, and reaction mechanisms can be used to create non-natural enzymes through mutation and synthesize non-natural compounds. In this review, I will introduce the research we have conducted on two fungal Fe(II)/αKG-dependent oxygenases, TlxI-J and TqaL. TlxI-J is the first Fe(II)/αKG-dependent oxygenase type enzyme heterodimer that catalyzes consecutive oxidation reactions, hydroxylation followed by retro-aldol or ketal formation, to form the complex skeletons of meroterpenoids. TqaL is the first naturally occurring aziridine synthase, and I will discuss the mechanism of its unique C-N bond formation in nonproteinogenic amino acid biosynthesis. This review will advance research on the discovery of new enzymes and the analysis of their functions by reviewing the structures and functions of these extraordinary Fe(II)/αKG-dependent oxygenases, and promote their use in the synthesis of new natural medicines.

Exploring the Ascorbate Requirement of the 2-Oxoglutarate-Dependent Dioxygenases

In humans, the 2-oxoglutarate-dependent dioxygenases (2-OGDDs) catalyze hydroxylation reactions involved in cell metabolism, the biosynthesis of small molecules, DNA and RNA demethylation, the hypoxic response and the formation of collagen. The reaction is catalyzed by a highly oxidizing ferryl-oxo species produced when the active site non-heme iron engages molecular oxygen. Enzyme activity is specifically stimulated by l-ascorbic acid (ascorbate, vitamin C), an effect not well mimicked by other reducing agents. In this perspective article we discuss the reliance of the 2-OGDDs on ascorbate availability. We draw upon findings from studies with different 2-OGDDs to piece together a comprehensive theory for the specific role of ascorbate in supporting enzyme activity. Our discussion centers on the capacity for ascorbate to act as an efficient radical scavenger and its propensity to reduce and chelate transition metals. In addition, we consider the evidence supporting stereospecific binding of ascorbate in the enzyme active site.

A 5,000-fold increase in the HAT reactivity of a nonheme FeIV=O complex simply by replacing two pyridines of the pentadentate N4Py ligand with pyrazoles

A pentadentate [N5] ligand (N2Py2Pz) based on the classic N4Py (N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) framework has been synthesized by replacing the two pyridylmethyl arms with corresponding (N-methyl)pyrazolylmethyl units to form [N-bis(1-methyl-2-pyrazolyl)methyl-N-(bis-2-pyridylmethyl)amine] (L1). The oxidation of the iron(II) precursor (N2Py2Pz)FeII(OTf)2 (1) with (tBuSO2)C6H4IO at 298 K leads to the formation of the [FeIV(O)(N2Py2Pz)]2+ intermediate (2) with a near-IR band at 750 nm (εM = 250 M-1cm-1) and a t1/2 ~ 2 min at 298 K. The introduction of the less basic pyrazolylmethyl ligands in place of two pyridylmethyl units generates FeIV=O intermediate 2 that exhibits a cyclohexane oxidation rate of 0.29 s-1 at 298 K, which is 5,000-fold faster than that observed for the classic FeIV(O)N4Py parent complex and 40,000-fold more reactive than the least reactive FeIV(O)N2Py2Q' complex in this series (Py = pyridine, Q' = isoquinoline) recently reported by Nordlander.

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

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

Insights into C-H Activation Reactivity of Fe (IV)O Porphyrinoid Complexes: A Computational Investigation

This work presents a detailed comparative analysis of C-H activations catalyzed by three different Fe(IV)O porphyrinoid complexes. The study considers the usual heme porphyrin (complex I) as the base compound, porphyrazine (complex II), which is obtained by replacing carbon with nitrogen at the meso position, and phthalocyanine (complex III), which is obtained through the peripheral benzoannulation of porphyrazine. The main focus here is to explore the impact of bridging groups and peripheral functionalization in heme systems on reactivity. Chloride is used as the axial ligand for all complexes and dihydroanthracene (DHA) is used as the substrate. Factors such as distortion energy and different electron acceptor orbitals significantly affect the overall reactivity. The effect of substitution on quantum mechanical tunneling, using H/D kinetic isotope effect studies, is also included. The results reveal a fascinating reactivity order: meso nitrogen substitution enhances reactivity, while additional benzo-annulation hinders reactivity, leading to the order complex II >complex I >complex III. In comparison to the usual model compound I, which is Fe(IV)O-porphyrin π cation radical with an -SH axial ligand, complex II was found to be more reactive. The electron affinity of the Fe(IV)O complexes and the dissociation energy of the forming Fe(IV)O-H bond aligns with observed reactivity trend. These findings support the use of accessible iron frameworks derived from porphyrin in C-H activation processes.

Recent Insights into the Reaction Mechanisms of Non-Heme Diiron Enzymes Containing Oxoiron(IV) Complexes

Oxoiron(IV) complexes are key intermediates in the catalytic reactions of some non-heme diiron enzymes. These enzymes, across various subfamilies, activate dioxygen to generate high-valent diiron-oxo species, which, in turn, drive the activation of substrates and mediate a variety of challenging oxidative transformations. In this review, we summarize the structures, formation mechanisms, and functions of high-valent diiron-oxo intermediates in eight representative diiron enzymes (sMMO, RNR, ToMO, MIOX, PhnZ, SCD1, AlkB, and SznF) spanning five subfamilies. We also categorize and analyze the structural and mechanistic differences among these enzymes.

Copper-dependent halogenase catalyses unactivated C-H bond functionalization

Carbon-hydrogen (C-H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp3)-H bond1-3. In recent years, metalloenzymes have been found to perform C(sp3)-H bond functionalization4,5. Despite substantial progresses in the past two decades6,7, enzymatic halogenation and pseudohalogenation of unactivated C(sp3)-H-providing a functional handle for further modification-have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes8. Here we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp3)-H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp3)-H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs-one interchain and two intrachain-of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp3)-H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

Biosynthesis of the α-D-Mannosidase Inhibitor (-)-Swainsonine

(-)-Swainsonine is a polyhydroxylated indolizidine alkaloid with potent inhibitory activity against α-D-mannosidases. In this work, we successfully reconstituted swainsonine biosynthetic pathway both in vivo and in vitro. Our study unveiled an unexpected epimerization mechanism involving two α-ketoglutarate-dependent non-heme iron dioxygenases (SwnH2 and SwnH1), and an unusual imine reductase (SwnN), which displays substrate-dependent stereospecificity. The stereochemical outcome of SwnN-catalyzed iminium reduction is ultimately dictated by SwnH1-catalyzed C8-hydroxylation. We also serendipitously discovered that an O -acetyl group can serve as a detachable protecting/directing group, altering the site-selectivity of SwnH2-catalyzed hydroxylation while maintaining the stereoselectivity. Insights gained from the biochemical characterization of these tailoring enzymes enabled biocatalytic synthesis of a new polyhydroxylated indolizidine alkaloid, opening doors to the biosynthesis of diverse natural product-based glycosidase inhibitors.

Amphoteric reactivity of iron(III)-hydroperoxo complex generated from proton- and salicylate-assisted dioxygen activation

We report the synthesis and characterization of an iron(III)-hydroperoxo complex generated from salicylate-assisted dioxygen activation by a cation-liganded iron(II) complex. Spectroscopic and theoretical data revealed stabilization of the end-on hydroperoxo ligand, and mechanistic insights, including a "V-shaped" Hammett plot, were confirmed by conducting oxygen atom transfer and proton-coupled electron transfer reactions.

Origins of Catalysis in Non-Heme Fe(II)/2-Oxoglutarate-Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides

Histone lysine demethylase 4 A (KDM4A), a non-heme Fe(II)/2-oxoglutarate (2OG) dependent oxygenase that catalyzes the demethylation of tri-methylated lysine residues at the 9, 27, and 36 positions of histone H3 (H3 K9me3, H3 K27me3, and H3 K36me3). These methylated residues show contrasting transcriptional roles; therefore, understanding KDM4A's catalytic mechanisms with these substrates is essential to explain the factors that control the different sequence-dependent demethylations. In this study, we use molecular dynamics (MD)-based combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate determinants of KDM4A catalysis with H3 K9me3, H3 K27me3 and H3 K36me3 substrates. In KDM4A-H3(5-14)K9me3 and KDM4A-H3(23-32)K27me3 ferryl complexes, the O-H distance positively correlates with the activation barrier of the rate-limiting step, however in the KDM4A-H3(32-41)K36me3, no direct one-to-one relationship was found implying that the synergistic effects between the geometric parameters, second sphere interactions and the intrinsic electric field contribute for the effective catalysis for this substrate. The intrinsic electric field along the Fe-O bond changes between the three complexes and shows a positive correlation with the HAT activation barrier, suggesting that modulating electric field can be used for fine engineering KDM catalysis with a specific substrate. The results reveal how KDM4A uses a combination of strategies to enable near equally efficient demethylation of different H3Kme3 residues.

Overcoming Selectivity Trade-Offs in Alkene Azidodifluoroalkylation: An Enlightening Synergistic Catalytic Approach

Recent advances in dual catalysis involving biomimetic conversion strategies that utilize radical ligand transfer (RLT) often rely on large doses of precious metal additives. The role of these additives within the mechanism remains ambiguous, leading to complex reaction conditions, uncertain pathways, and increased costs. These challenges complicate the study of the reaction process and are accompanied by potential safety risks. To address these issues, azide salt was used as an alternative to TMSN3. This replacement not only avoids the drawbacks associated with almost parallel research on alkene azidodifluoroalkylation but also eliminates the need for ligands. Comparative analysis indicates that existing biomimetic synergistic catalysis strategies require Ag2CO3 additives to enhance selectivity in alkene difunctionalization reactions, highlighting the superior simplicity, environmental friendliness, and operational ease of our developed synergistic catalysis strategy. Furthermore, under the guidance of our proposed mechanism, an alkene azidosulfonation was designed, validating the innovative and practical applicability of our synergistic catalysis approach.

Computational Insights into Hydrogen Atom Transfer Mediators in C-H Activation Catalysis of Nonheme Fe(IV)O Complexes

This study presents a detailed density functional theory (DFT) investigation into the mechanism and energetics of C-H activations catalyzed by bioinspired Fe(IV)O complexes, particularly in the presence of N-hydroxy mediators. The findings show that these mediators significantly enhance the reactivity of the iron-oxo complex. The study examines three substrates with varying bond dissociation energies─ethylbenzene, cyclohexane, and cyclohexadiene─alongside the [Fe(IV)O(N4Py)]2+ complex. Mediators N-hydroxyphthalimide (NHPI) and N-hydroxyquinolinimide (NHQI) were chosen for their strong oxidative abilities. The results reveal that NO-H bond cleavage in N-hydroxy compounds occurs more readily than C-H bond cleavage in hydrocarbons, as supported by the Marcus cross-relation applied to H-abstraction. This leads to the rapid formation of aminoxyl radicals, which are more reactive than Fe(IV)O species, lowering the activation energy and enhancing the reaction rate. The C-H bond activation aligns with the Bell-Evans-Polanyi principle, correlating the activation energy with the substrate bond dissociation energy. The investigation reveals that the mediator pathway is favored both thermodynamically and kinetically. Additionally, distortion energy provides a compelling explanation for the observed reactivity trends, further highlighting NHQI's superior efficiency compared to NHPI. Additionally, quantum mechanical tunneling plays a significant role, as evidenced by the computed kinetic isotope effect, which matches experimental data.

10-Fold Increase in Hydrogen Atom Transfer Reactivity for a Series of S = 1 FeIV═O Complexes Over the S = 2 [(TQA)FeIV═O]2+ Complex via Entropic Lowering of Reaction Barriers by Secondary Sphere Cycloalkyl Substitution

Nonheme iron enzymes utilize S = 2 iron(IV)-oxo intermediates as oxidants in biological oxygenations. In contrast, corresponding synthetic nonheme FeIV═O complexes characterized to date favor the S = 1 ground state that generally shows much poorer oxidative reactivity than their S = 2 counterparts. However, one intriguing exception found by Nam a decade ago is the S = 1 [FeIV(O)(Me3NTB)]2+ complex (Me3NTB = [tris((N-methyl-benzimidazol-2-yl)methyl)amine], 1O) with a hydrogen atom transfer (HAT) reactivity that is 70% that of the S = 2 [FeIV(O)(TQA)]2+ complex (TQA = tris(2-quinolylmethyl)amine, 3O). In our efforts to further explore this direction, we have unexpectedly uncovered a family of new S = 1 complexes with HAT reaction rates beyond the currently reported limits in the tripodal ligand family, surpassing oxidation rates found for the S = 2 [FeIV(O)(TQA)]2+ complex by as much as an order of magnitude. This is achieved simply by replacing the secondary sphere methyl groups of the Me3NTB ligand with larger cycloalkyl-CH2 (R groups in 2OR) moieties ranging from c-propylmethyl to c-hexylmethyl. These 2OR complexes show Mössbauer data at 4 K and 1H NMR spectra at 193 and 233 K that reveal S = 1 ground states, in line with DFT calculations. Nevertheless, they give rise to the most reactive synthetic nonheme oxoiron(IV) complexes found to date within the tripodal ligand family. Our DFT study indicates transition state stabilization through entropy effects, similar to enzymatic catalysis.

Deciphering the Role of Crown-ether Receptor Orientation in C-H Oxidation Catalyzed by Supramolecular Nonheme FeIV(O) Complexes

The outstanding efficiency and selectivity of enzymatic reactions, such as C-H oxidation by nonheme iron oxygenases, stems from a precise control of substrate positioning inside the active site. The resulting proximity between a specific moiety (a certain C-H bond) and the reactant (a FeIV(O) active species) translates into higher rates and selectivity, that can be in part replicated also with artificial supramolecular catalysts. However, structural modification of the position and orientation of the binding site both in enzymes and in artificial catalysts often leads to significant variations in reactivity that can be difficult to rationalize due to the system's complexity. Herein, we quantitatively analyzed the impact of such a structural modification (namely receptor orientation) on the C-H oxidation reactivity (kinetics, Effective Molarity) and selectivity by comparing simple supramolecular FeIV(O) models. Overall, we did not observe significant differences in reaction rates, but we noticed slight changes in the selectivity profile. These results indicate that, when a crown-ether is employed as a recognition site, the key ingredient for enhanced reactivity is the presence of the supramolecular receptor itself rather than its exact orientation, providing a guide for the rational design of supramolecular catalysts.

How Do Variants of Residues in the First Coordination Sphere, Second Coordination Sphere, and Remote Areas Influence the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate Dependent Ethylene-Forming Enzyme?

The ethylene-forming enzyme (EFE) is a Fe(II)/2-oxoglutarate (2OG) and l-arginine (l-Arg)-dependent oxygenase that primarily decomposes 2OG into ethylene while also catalyzing l-Arg hydroxylation. While the hydroxylation mechanism in EFE is similar to other Fe(II)/2OG-dependent oxygenases, the formation of ethylene is unique. Various redesign strategies have aimed to increase ethylene production in EFE, but success has been limited, highlighting the need for alternate approaches. It is crucial to incorporate an accurate and comprehensive description of the integrative and multidimensional effects of the protein environment to enhance the redesign strategy in metalloenzymes, particularly in EFE. This involves understanding the role of the second coordination sphere (SCS) and long-range (LR) interacting residues, correlated motions, electronic structure, intrinsic electric field (IntEF), as well as the stabilization of transition states and reaction intermediates. In this study, we employ a molecular dynamics-based quantum mechanics/molecular mechanics approach to examine the integrative effects of the protein environment on reactions catalyzed by EFE variants from the first coordination sphere (FCS, D191E), SCS (A198V and R171A) and LR (E215A). The study uncovers how substitutions at different positions in EFE similarly impact the ethylene-forming reaction while posing distinct effects on the hydroxylation reaction. Results predict the effect of the variants in controlling the 2OG coordination mode in the Fe(II) center. Specifically, the study suggests that D191E uniquely prefers transitioning from an off-line to an in-line 2OG coordination mode before dioxygen binding. However, studies on the 2OG flip in the presence of off-line approaching dioxygen and dioxygen binding in the D191E variant indicate that the 2OG flip might not be feasible in the 5C Fe(II) state. Calculations show the possibility of a hydrogen atom transfer (HAT)-assisted oxygen flip in EFE and its variants (other than D191E). MD simulations elucidate the characteristic dynamic change in the α7 region in the D191E variant that might contribute to its increased hydroxylation reaction. Results indicate the possibility of forming an in-line ferryl from the IM2 (Fe(III)-partial bond intermediate) in the D191E variant. This alternative pathway from IM2 may also exist in WT EFE and other variants, which are yet to be explored. The study also delineates the impact of substitutions on the electronic structure and IntEF. Overall, the calculations support the idea that understanding the integrative and multidimensional effects of the protein environment on the reactions catalyzed by EFE variants provides the basics for improved enzyme redesign protocols of EFE to increase ethylene production. The results of this study will also contribute to the development of alternate redesign strategies for other metalloenzymes.

Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction

Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.

Photocatalytic Substrate Oxidation Catalyzed by a Ruthenium(II) Complex with a Phenazine Moiety as the Active Site Using Dioxygen as a Terminal Oxidant

We have developed photocatalytic oxidation of aromatic substrates using O2 as a terminal oxidant to afford only 2e--oxidized products without the reductive activation of O2 in acidic water under visible-light irradiation. A RuII complex (1) bearing a pyrazine moiety as the active site in tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine (tpphz) as a ligand was employed as a photocatalyst. The active species for the photocatalysis was revealed to be not complex 1 itself but the protonated form, 1-H+, protonated at the vacant diimine site of tpphz. Upon photoexcitation in the presence of an organic substrate, 1-H+ was converted to the corresponding dihydro-intermediate (2-H+), where the pyrazine moiety of the ligand received 2e- and 2H+ from the substrate. 2-H+ was facilely oxidized by O2 to recover 1-H+. Consequently, an oxidation product of the substrate and H2O2 derived from dioxygen reduction were obtained; however, the H2O2 formed was also used for oxidation of 2-H+. In the oxidation of benzyl alcohol to benzaldehyde, the turnover number reached 240 for 10 h, and the quantum yield was determined to be 4.0%. The absence of ring-opening products in the oxidation of cyclobutanol suggests that the catalytic reaction proceeds through a mechanism involving formal hydride transfer. Mechanistic studies revealed that the photocatalytic substrate oxidation by 1-H+ was achieved in neither the lowest singlet excited state nor triplet excited state (S1 or T1) but in the second lowest singlet excited state (S2), i.e., 1(π-π*)* of the tpphz ligand. Thus, the photocatalytic substrate oxidation by 1-H+ can be categorized into unusual anti-Kasha photocatalysis.

Electron transfer in biological systems

Examples of how metalloproteins feature in electron transfer processes in biological systems are reviewed. Attention is focused on the electron transport chains of cellular respiration and photosynthesis, and on metalloproteins that directly couple electron transfer to a chemical reaction. Brief mention is also made of extracellular electron transport. While covering highlights of the recent and the current literature, this review is aimed primarily at introducing the senior undergraduate and the novice postgraduate student to this important aspect of bioinorganic chemistry.

Quantum effects in CH activation with [Cu2O2]2+ complexes

We investigate the mechanism of primary alkane CH bond activation with dioxo-dicopper ([Cu2O2]2+) complexes, which serve as model catalysts for enzymes capable of activating CH bonds under mild conditions. As large H/D kinetic isotope effects (KIEs) are observed in enzymes and their synthetic mimics, we employ density functional theory along with variational transition-state theory with multidimensional tunneling to estimate reaction rate coefficients. By systematically varying ligand electrophilicity and substrate chain length, we examine trends in rate coefficients and kinetic isotope effects for the two proposed CH activation pathways - one-step oxo-insertion and two-step radical recombination. Although larger tunneling transmission coefficients are obtained for the radical pathway, the oxo-insertion mechanism yields higher rate coefficients on account of lower activation barriers. The question of the preferred CH activation mechanism, however, remains open: excellent agreement is observed between the predicted and known experimental KIE results for the radical pathway, while calculated Hammett slopes for the oxo-insertion pathway closely mirror experiments.

What is the Origin of the Regioselective C3-Hydroxylation of L-Arg by the Nonheme Iron Enzyme Capreomycin C?

The nonheme iron dioxygenase capreomycin C (CmnC) hydroxylates a free L-arginine amino acid regio- and stereospecifically at the C3-position as part of the capreomycin antibiotics biosynthesis. Little is known on its structure, catalytic cycle and substrate specificity and, therefore, a comprehensive computational study was performed. A large QM cluster model of CmnC was created of 297 atoms and the mechanisms for C3-H, C4-H and C5-H hydroxylation and C3-C4 desaturation were investigated. All low-energy pathways correspond to radical reaction mechanisms with an initial hydrogen atom abstraction followed by OH rebound to form alcohol product complexes. The work is compared to alternative L-Arg hydroxylating nonheme iron dioxygenases and the differences in active site polarity are compared. We show that a tight hydrogen bonding network in the substrate binding pocket positions the substrate in an ideal orientation for C3-H activation, whereby the polar groups in the substrate binding pocket induce an electric field effect that guides the selectivity.

New Frontiers in Nonheme Enzymatic Oxyferryl Species

Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.

Stereoelectronic Tuning of Bioinspired Nonheme Iron(IV)-Oxo Species by Amide Groups in Primary and Secondary Coordination Spheres for Selective Oxygenation Reactions

Two mononuclear iron(II) complexes, [(6-amide2-BPMEN)FeII](OTf)2 (1) and [(6-amide-Me-BPMEN)FeII(OTf)](OTf) (2), supported by two BPMEN-derived (BPMEN = N1,N2-dimethyl-N1,N2-bis(pyridine-2-yl-methyl)ethane-1,2-diamine) ligands bearing one or two amide functionalities have been isolated to study their reactivity in the oxygenation of C-H and C═C bonds using isopropyl 2-iodoxybenzoate (iPr-IBX ester) as the oxidant. Both 1 and 2 contain six-coordinate high-spin iron(II) centers in the solid state and in solution. The 6-amide2-BPMEN ligand stabilizes an S = 1 iron(IV)-oxo intermediate, [(6-amide2-BPMEN)FeIV(O)]2+ (1A). The oxidant (1A) oxygenates the C-H and C═C bonds with a high selectivity. Oxidant 1A, upon treatment with 2,6-lutidine, is transformed into another oxidant [{(6-amide2-BPMEN)-(H)}FeIV(O)]+ (1B) through deprotonation of an amide group, resulting in a stronger equatorial ligand field and subsequent stabilization of the triplet ground state. In contrast, no iron-oxo species could be observed from complex 2 and [(6-Me2-BPMEN)FeII(OTf)2] (3) under similar experimental conditions. The iron(IV)-oxo oxidant 1A shows the highest A/K selectivity in cyclohexane oxidation and 3°/2° selectivity in adamantane oxidation reported for any synthetic nonheme iron(IV)-oxo complexes. Theoretical investigation reveals that the hydrogen bonding interaction between the -NH group of the noncoordinating amide group and Fe═O core smears out the equatorial charge density, reducing the triplet-quintet splitting, and thus helping complex 1A to achieve better reactivity.

Cu-Promoted ipso-Hydroxylation of sp2 Bonds with Concomitant Aromatic 1,2-Rearrangement Involving a Cu-oxyl-hydroxo Species

Herein, we report the first example of Cu-promoted β ipso-hydroxylation of substituted benzophenones using a bidentate directing group (DG) and H2O2 as an oxidant. In addition to the new C-O bond formed, the ipso-oxidation induces a very unusual 1,2-rearrangement of the iminyl group to the vicinal γ position. This transformation is highly dependent on the substrate utilized (favored for 4-methoxy-substituted benzophenones) and on the DG used (2-picolylamine leads to selective γ-C-H functionalization, while β ipso-oxidation requires 2-(2-aminoethyl)pyridine). An analysis of the oxidation of substrate-ligands derived from 2-(2-aminoethyl)pyridine and unsymmetrical 4-MeO-substituted benzophenones indicates high regioselectivity (up to 89:11 for the MeO-substituted arene ring and up to 92:8 for β ipso- vs γ-C-H hydroxylation). Mechanistic studies (which include spectroscopic characterization of reaction intermediates, kinetics, and calculations) suggest the formation of a mononuclear CuIIOOH species before the rate-determining step (rds) of the reaction. DFT calculations suggest that the γ-C-H hydroxylation pathway involves a one-step concerted O-O cleavage and electrophilic aromatic attack. Conversely, β ipso-hydroxylation occurs in a stepwise fashion, in which O-O bond cleavage produces a CuIII(O·)(OH) before electrophilic aromatic attack. Calculations also shed light on the mechanism of the 1,2-rearrangement step, which involves strain release from a spiro 5-membered to a 6-membered Cu chelate.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

A bis-Phenolate Carbene-Supported bis-μ-Oxo Iron(IV/IV) Complex with a [FeIV(μ-O)2FeIV] Diamond Core Derived from Dioxygen Activation

The diiron(II) complex, [(OCO)Fe(MeCN)]2 (1, MeCN = acetonitrile), supported by the bis-phenolate carbene pincer ligand, 1,3-bis(3,5-di-tert-butyl-2-hydroxyphenyl)benzimidazolin-2-ylidene (OCO), was synthesized and characterized by single-crystal X-ray diffraction, 1H nuclear magnetic resonance, infrared (IR) vibrational, ultraviolet/visible/near-infrared (UV/vis/NIR) electronic absorption, 57Fe Mössbauer, X-band electron paramagnetic resonance (EPR) and SQUID magnetization measurements. Complex 1 activates dioxygen to yield the diferric, μ-oxo-bridged complex [(OCO)Fe(py)(μ-O)Fe(O(C═O)O)(py)] (2) that was isolated and fully characterized. In 2, one of the iron-carbene bonds was oxidized to give a urea motif, resulting in an O(CNHC═O)O binding site, while the other Fe(OCO) unit remained unchanged. When the reaction is performed at -80 °C, an intensively colored, purple intermediate is observed (INT, λmax = 570 nm; ε = 5600 mol L-1 cm-1). INT acts as a sluggish oxidant, reacting only with easily oxidizable substrates, such as PPh3 or 2-phenylpropionic aldehyde (2-PPA). The identity of INT can be best described as a dinuclear complex containing a closed diamond core motif [(OCO)FeIV(μ-O)2FeIV(OCO)]. This proposal is based on extensive spectroscopic [UV/vis/NIR electronic absorption, 57Fe Mössbauer, X-band EPR, resonance Raman (rRaman), X-ray absorption, and nuclear resonance vibrational (NRVS)] and computational studies. The conversion of the diiron(II) complex 1 to the oxo diiron(IV) intermediate INT is reminiscent of the O2 activation process in soluble methane monooxygenases (sMMO). Most importantly, the low reactivity of INT supports the consensus that the [FeIV(μ-O)2FeIV] diamond core in sMMO is kinetically inert and needs to open up to terminal FeIV═O cores to react with the strong C-H bonds of methane.

Experimentally Assessing the Electronic Structure and Spin-State Energetics in MnFe Dimers Using 1s3p Resonant Inelastic X-ray Scattering

The synergistic interaction between Mn and Fe centers is investigated via a comprehensive analysis of full 1s3p resonant inelastic X-ray scattering (RIXS) planes at both the Fe and Mn K-edges in a series of homo- and heterometallic molecular systems. Deconvolution of the experimental two-dimensional 1s3p RIXS maps provides insights into the modulation of metal-ligand covalency and variations in the metal multiplet structure induced by subtle electronic structural differences imposed by the presence of the second metal. These modulations in the electronic structure are key toward understanding the reactivity of biological systems with active sites that require heterometallic centers, including MnFe purple acid phosphatases and MnFe ribonucleotide reductases. Herein, we demonstrate the capabilities of 1s3p RIXS to provide information on the excited state energetics in both element- and spin-selective fashion. The contributing excited states are identified and isolated by their multiplicity and π- and σ-contributions, building a conceptual bridge between the electronic structures of metal centers and their reactivity. The ability of the presented 1s3p RIXS methodology to address fundamental questions in transition metal catalysis reactivity is highlighted.

Intramolecular C-H Oxidation in Iron(V)-oxo-carboxylato Species Relevant in the γ-Lactonization of Alkyl Carboxylic Acids

High-valent oxoiron species have been invoked as oxidizing agents in a variety of iron-dependent oxygenases. Taking inspiration from nature, selected nonheme iron complexes have been developed as catalysts to elicit C-H oxidation through the mediation of putative oxoiron(V) species, akin to those proposed for Rieske oxygenases. The addition of carboxylic acids in these iron-catalyzed C-H oxidations has proved highly beneficial in terms of product yields and selectivities, suggesting the direct involvement of iron(V)-oxo-carboxylato species. When the carboxylic acid functionality is present in the alkane substrate, it acts as a directing group, enabling the selective intramolecular γ-C-H hydroxylation that eventually affords γ-lactones. While this mechanistic frame is solidly supported by previous mechanistic studies, direct spectroscopic detection of the key iron(V)-oxo-carboxylato intermediate and its competence for engaging in the selective γ-C-H oxidation leading to lactonization have not been accomplished. In this work, we generate a series of well-defined iron(V)-oxo-carboxylato species (2c-2f) differing in the nature of the bound carboxylate ligand. Species 2c-2f are characterized by a set of spectroscopic techniques, including UV-vis spectroscopy, cold-spray ionization mass spectrometry (CSI-MS), and, in selected cases, EPR and Mössbauer spectroscopies. We demonstrate that 2c-2f undergo site-selective γ-lactonization of the carboxylate ligand in a stereoretentive manner, thus unequivocally identifying metal-oxo-carboxylato species as the powerful yet selective C-H cleaving species in catalytic γ-lactonization reactions of carboxylic acids. Reactivity experiments confirm that the intramolecular formation of γ-lactones is in competition with the intermolecular oxidation of external alkanes and olefins. Finally, mechanistic studies, together with DFT calculations, support a mechanism involving a site-selective C-H cleavage in the γ-position of the carboxylate ligand by the oxo moiety, followed by a fast carboxylate rebound, eventually leading to the selective formation of γ-lactones.

Impact of carboxylate ligation on the C-H activation reactivity of a non-heme Fe(IV)O complex: a computational investigation

A comprehensive DFT investigation has been presented to predict how a carboxylate-rich macrocycle would affect the reactivity of a non-heme Fe(IV)O complex towards C-H activation. The popular non-heme iron oxo complex [FeIV(O)(N4Py)]2+, (N4Py = N,N-(bis(2-pyridyl)methyl)N-bis(2-pyridylmethyl)amine) (1), has been selected here as the primary compound. It is transformed to the compound [FeIV(O)(nBu-P2DA)], where nBu-P2DA = N-(1',1'-bis(2-pyridyl)pentyl)iminodiacetate (2) after the replacement of two pyridine donors of N4Py with carboxylate groups. Two other complexes, namely 3 and 4, have been predicted sequentially substituting nitrogen with the carboxylate groups. Ethylbenzene and dihydrotoluene were chosen as substrates. In terms of C-H activation reactivity, an interesting pattern emerges: as the carboxylate group becomes more equatorially enriched, the reactivity increases, following the trend 1 < 2 < 3 < 4. This also aligns with available experimental reports related to complexes 1 and 2. Fe(IV)O complexes exhibit two-state reactivity (triplet and quintet), whereas the quintet state is more favourable due to the stabilization of the transition states through exchange interactions involving a greater number of unpaired electrons. A detailed analysis of the factors influencing reactivity has been performed, including distortion energy (which decreases for the transition state with the addition of carboxylate groups), the triplet-quintet oxidant energy gap (which consistently decreases as carboxylate group enrichment increases), steric factors, and quantum mechanical tunneling. This investigation provides a detailed explanation of the observed outcomes and predicts the higher reactivity of carboxylate-enriched Fe(IV)O complexes. After potential experimental verification, this could lead to the development of new, optimal catalysts for C-H activation.

Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH

Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post-translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single-point mutations in the Second Coordination Sphere (SCS) and long-range (LR) residues of AspH have been linked to pathological conditions such as the ophthalmologic condition Traboulsi syndrome and chronic kidney disease (CKD). Although the clinical impacts of these mutations are established, there is a critical knowledge gap regarding their specific atomistic effects on the catalytic mechanism of AspH. In this study, we report integrated computational investigations on the potential mechanistic implications of four mutant forms of human AspH with clinical importance: R735W, R735Q, R688Q, and G434V. All the mutant forms exhibited altered binding interactions with the co-substrate 2-oxoglutarate (2OG) and the main substrate in the ferric-superoxo and ferryl complexes, which are critical for catalysis, compared to the wild-type (WT). Importantly, the mutations strongly influence the energetics of the frontier molecular orbitals (FMOs) and, thereby, the activation energies for the hydrogen atom transfer (HAT) step compared to the WT AspH. Insights from our study can contribute to enzyme engineering and the development of selective modulators for WT and mutants of AspH, ultimately aiding in treating cancers, Traboulsi syndrome and, CKD.

Unveiling the importance of catalyst framework and non covalent interactions in an asymmetric Fe-catalyzed O-H insertion: insights from computational tools

Fe-based catalysts as well as enzymes typically yield low stereoselectivity for carbene insertion into X-H bonds. Here, we have utilized DFT methods to understand the mechanism and unusually high enantioselectivity in an Fe-spiroBox catalyzed carbene insertion reaction into the O-H bond of aliphatic alcohols. Our transition state model shows a unique binding of the reaction intermediates to the chiral catalyst enabled by weak non covalent interactions that is absent in other X-H insertion reactions.

An efficient pyrrolysyl-tRNA synthetase for economical production of MeHis-containing enzymes

Genetic code expansion has emerged as a powerful tool in enzyme design and engineering, providing new insights into sophisticated catalytic mechanisms and enabling the development of enzymes with new catalytic functions. In this regard, the non-canonical histidine analogue Nδ-methylhistidine (MeHis) has proven especially versatile due to its ability to serve as a metal coordinating ligand or a catalytic nucleophile with a similar mode of reactivity to small molecule catalysts such as 4-dimethylaminopyridine (DMAP). Here we report the development of a highly efficient aminoacyl tRNA synthetase (G1PylRSMIFAF) for encoding MeHis into proteins, by transplanting five known active site mutations from Methanomethylophilus alvus (MaPylRS) into the single domain PylRS from Methanogenic archaeon ISO4-G1. In contrast to the high concentrations of MeHis (5-10 mM) needed with the Ma system, G1PylRSMIFAF can operate efficiently using MeHis concentrations of ∼0.1 mM, allowing more economical production of a range of MeHis-containing enzymes in high titres. Interestingly G1PylRSMIFAF is also a 'polyspecific' aminoacyl tRNA synthetase (aaRS), enabling incorporation of five different non-canonical amino acids (ncAAs) including 3-pyridylalanine and 2-fluorophenylalanine. This study provides an important step towards scalable production of engineered enzymes that contain non-canonical amino acids such as MeHis as key catalytic elements.

Enhancing the high-spin reactivity in C-H bond activation by Iron (IV)-Oxo species: insights from paclitaxel hydroxylation by CYP2C8

Previous theoretical studies have revealed that high-spin states possess flatter potential energy surfaces than low-spin states in reactions involving iron(IV)-oxo species of cytochrome P450 enzymes (P450s), nonheme enzymes, or biomimetic complexes. Therefore, actively utilizing high-spin states to enhance challenging chemical transformations, such as C-H bond activation, represents an intriguing research avenue. However, the inherent instability of high-spin states relative to low-spin states in pre-reaction complexes often hinders their accessibility around the transition state, especially in heme systems with strong ligand fields. Counterintuitively, our investigation of the metabolic hydroxylation of paclitaxel by human CYP2C8 using a hybrid quantum mechanics and molecular mechanics (QM/MM) approach showed that the high-spin sextet state exhibits unusually high stability, when the reaction follows a secondary reaction pathway leading to 6β-hydroxypaclitaxel. We thoroughly analyzed the factors contributing to the enhanced stabilization of the high-spin state, and the knowledge obtained could be instrumental in designing competent biomimetic catalysts and biocatalysts for C-H bond activation.

Exploring the Bonding Nature of Iron(IV)-Oxo Species through Valence Bond Calculations and Electron Density Analysis

Compound I (Cpd I) plays a pivotal role in substrate transformations within the catalytic cycle of cytochrome P450 enzymes (P450s). A key constituent of Cpd I is the iron(IV)-oxo unit, a structural motif also found in other heme enzymes and nonheme enzymes. In this study, we performed ab initio valence bond (VB) calculations, employing the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) methods, to unveil the bonding nature of this vital "Fe(IV)═O″ unit in bioinorganic chemistry. Comparisons were drawn with the triplet O2 molecule, which shares some electronic characteristics with iron(IV)-oxo. Additionally, Cpd I models of horseradish peroxidase (HRP) and catalase (CAT) were analyzed to assess the proximal ligand effect on the electronic structure of iron(IV)-oxo. Our VB analysis underscores the significant role of noncovalent resonance effects in shaping the iron(IV)-oxo bonding. The resonance stabilization within the π and σ frameworks occurs to comparable degrees, with additional stabilization resulting from resonance between VB structures from these frameworks. Furthermore, we elucidated the substantial influence of proximal and equatorial ligands in modulating the relative significance of different VB structures. Notably, in the presence of these ligands, iron(IV)-oxo is better described as iron(III)-oxyl or iron(II)-oxygen, displaying weak covalent character but enhanced by resonance effects. Although both species exhibit diradicaloid characters, resonance stabilization in iron(IV)-oxo is weaker than in O2. Further exploration using the Laplacian of electron density shows that, unlike O2, which exhibits a charge concentration region between its two oxygen atoms, iron(IV)-oxo species display a charge depletion region.

Trapping an Elusive Fe(IV)-Superoxo Intermediate Inside a Self-Assembled Nanocage in Water at Room Temperature

Molecular cavities that mimic natural metalloenzymes have shown the potential to trap elusive reaction intermediates. Here, we demonstrate the formation of a rare yet stable Fe(IV)-superoxo intermediate at room temperature subsequent to dioxygen binding at the Fe(III) site of a (Et4N)2[FeIII(Cl)(bTAML)] complex confined inside the hydrophobic interior of a water-soluble Pd6L412+ nanocage. Using a combination of electron paramagnetic resonance, Mössbauer, Raman/IR vibrational, X-ray absorption, and emission spectroscopies, we demonstrate that the cage-encapsulated complex has a Fe(IV) oxidation state characterized by a stable S = 1/2 spin state and a short Fe-O bond distance of ∼1.70 Å. We find that the O2 reaction in confinement is reversible, while the formed Fe(IV)-superoxo complex readily reacts when presented with substrates having weak C-H bonds, highlighting the lability of the O-O bond. We envision that such optimally trapped high-valent superoxos can show new classes of reactivities catalyzing both oxygen atom transfer and C-H bond activation reactions.

Unraveling the Geometry-Driven C═C Epoxidation and C-H Hydroxylation Reactivity of Tetra-Coordinated Nonheme Iron(IV)-Oxo Complexes

The electronic structure and reactivity of tetra-coordinated nonheme iron(IV)-oxo complexes have remained unexplored for years. The recent synthesis of a closed-shell iron(IV)-oxo complex [(quinisox)FeIV(O)]+ (1) has set up a platform to understand how such complexes compare with the celebrated open-shell iron-oxo chemistry. Herein, using density functional theory and ab initio calculations, we present an in-depth electronic structure investigation of the C═C epoxidation [oxygen atom transfer (OAT)] and C-H hydroxylation [hydrogen atom transfer (HAT)] reactivity of 1. Using a solvent-coordinated geometry of 1 (1') and other potential tetra-coordinated iron(IV)-oxo complexes bearing rigid ligands (2 and 3), we established the geometric origin of spin-state energetics and reactivity of 1. Complex 1 featuring a strong Fe-O bond exhibits OAT and HAT reactivity in its quintet state. The lowest quintet OAT pathway has a lower barrier by ∼4 kcal/mol than the quintet HAT pathway, corroborating the experimentally observed gas-phase OAT reactivity preference. A conventional HAT reactivity preference for 2 and a comparable OAT and HAT reactivity for 3 are observed. This further supports the geometry-driven reactivity preference for 1. Noncovalent interaction analyses reveal a pronounced π-π interaction between the substrate and ligand in the OAT transition state, rationalizing the origin of the observed reactivity preference for 1.

Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code

The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their FeIV=O ("ferryl") intermediates. Here, we show that a similar approach can be used to perturb the conserved Fe coordination environment of 2-oxoglutarate (2OG) dependent oxygenases, a versatile class of enzymes that employ highly-reactive ferryl intermediates to mediate challenging C-H functionalizations. Replacement of one of the cis-disposed histidine ligands in the oxygenase VioC with a less electron donating N δ-methyl-histidine (MeHis) preserves both catalytic function and reaction selectivity. Significantly, the key ferryl intermediate responsible for C-H activation can be accumulated in both the wildtype and the modified protein. In contrast to heme enzymes, where metal-oxo reactivity is extremely sensitive to the nature of the proximal ligand, the rates of C-H activation and the observed large kinetic isotope effects are only minimally affected by axial ligand replacement in VioC. This study showcases a powerful tool for modulating the coordination sphere of nonheme iron enzymes that will enhance our understanding of the factors governing their divergent activities.

Radical-relay C(sp3)-H azidation catalyzed by an engineered nonheme iron enzyme

Nonheme iron enzymes are versatile biocatalysts for a broad range of unique and powerful transformations, such as hydroxylation, chlorination, and epimerization as well as cyclization/ring-opening of organic molecules. Beyond their native biological functions, these enzymes are robust for engineering due to their structural diversity and high evolvability. Based on enzyme promiscuity and directed evolution as well as inspired by synthetic organic chemistry, nonheme iron enzymes can be repurposed to catalyze reactions previously only accessible with synthetic catalysts. To this end, our group has engineered a series of nonheme iron enzymes to employ non-natural radical-relay mechanisms for new-to-nature radical transformations. In particular, we have demonstrated that a nonheme iron enzyme, (4-hydroxyphenyl)pyruvate dioxygenase from streptomyces avermitilis (SavHppD), can be repurposed to enable abiological radical-relay process to access C(sp3)-H azidation products. This represents the first known instance of enzymatic radical relay azidation reactions. In this chapter, we describe the detailed experimental protocol to convert promiscuous nonheme iron enzymes into efficient and selective biocatalyst for radical relay azidation reactions. One round of directed evolution is described in detail, which includes the generation and handling of site-saturation mutagenesis, protein expression and whole-cell reactions screening in a 96-well plate. These protocol details might be useful to engineer various nonheme iron enzymes for other applications.

Controlling Reactivity through Spin Manipulation: Steric Bulkiness of Peroxocobalt(III) Complexes

The intrinsic relationship between spin states and reactivity in peroxocobalt(III) complexes was investigated, specifically focusing on the influence of steric modulation on supporting ligands. Together with the previously reported [CoIII(TBDAP)(O2)]+ (2Tb), which exhibits spin crossover characteristics, two peroxocobalt(III) complexes, [CoIII(MDAP)(O2)]+ (2Me) and [CoIII(ADDAP)(O2)]+ (2Ad), bearing pyridinophane ligands with distinct N-substituents such as methyl and adamantyl groups, were synthesized and characterized. By manipulating the steric bulkiness of the N-substituents, control of spin states in peroxocobalt(III) complexes was demonstrated through various physicochemical analyses. Notably, 2Ad oxidized the nitriles to generate hydroximatocobalt(III) complexes, while 2Me displayed an inability for such oxidation reactions. Furthermore, both 2Ad and 2Tb exhibited similarities in spectroscopic and geometric features, demonstrating spin crossover behavior between S = 0 and S = 1. The steric bulkiness of the adamantyl and tert-butyl group on the axial amines was attributed to inducing a weak ligand field on the cobalt(III) center. Thus, 2Ad and 2Tb are an S = 1 state under the reaction conditions. In contrast, the less bulky methyl group on the amines of 2Me resulted in an S = 0 state. The redox potential of the peroxocobalt(III) complexes was also influenced by the ligand field arising from the steric bulkiness of the N-substituents in the order of 2Me (-0.01 V) < 2Tb (0.29 V) = 2Ad (0.29 V). Theoretical calculations using DFT supported the experimental observations, providing insights into the electronic structure and emphasizing the importance of the spin state of peroxocobalt(III) complexes in nitrile activation.

The interplay of covalency, cooperativity, and coupling strength in governing C-H bond activation in Ni2E2 (E = O, S, Se, Te) complexes

Dinickel dichalcogenide complexes hold vital multifaceted significance across catalysis, electron transfer, magnetism, materials science, and energy conversion. Understanding their structure, bonding, and reactivity is crucial for all aforementioned applications. These complexes are classified as dichalcogenide, subchalcogenide, or chalcogenide based on metal oxidation and coordinated chalcogen, and due to the associated complex electronic structure, ambiguity often lingers about their classification. In this work, using DFT, CASSCF/NEVPT2, and DLPNO-CCSD(T) methods, we have studied in detail [(NiL)2(E2)] (L = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane; E = O, S, Se and Te) complexes and explored their reactivity towards C-H bond activation for the first time. Through a comprehensive analysis of the structure, bonding, and reactivity of a series of [(NiL)2(E2)] complexes with E = O, S, Se, and Te, our computational findings suggest that {Ni2O2} and {Ni2S2} are best categorised as dichalcogenide-type complexes. In contrast, {Ni2Se2} and {Ni2Te2} display tendencies consistent with the subchalcogenide classification, and this aligns with the earlier structural correlation proposed (Berry and co-workers, J. Am. Chem. Soc. 2015, 137, 4993) reports on the importance of the E-E bond strength. Our study suggests the reactivity order of {Ni2O2} > {Ni2S2} > {Ni2Se2} > {Ni2Te2} for C-H bond activation, and the origin of the difference in reactivity was attributed to the difference in the Ni-E bond covalency, and electronic cooperativity between two Ni centres that switch among the classification during the reaction. Further non-adiabatic analysis at the C-H bond activation step demonstrates a decrease in coupling strength as we progress down the group, indicating a correlation with metal-ligand covalency. Notably, the reactivity trend is found to be correlated to the strength of the antiferromagnetic exchange coupling constant J via developing a magneto-structural-barrier map - offering a hitherto unknown route to fine-tune the reactivity of this important class of compound.

Synthesis, Characterization, and Reactivity of Bispidine-Iron(IV)-Tosylimido Species

Reported are the synthesis and detailed studies of the iron(IV)-tosylimido complexes of two isomeric pentadentate bispidine ligands (bispidines are 3,7-diazabicyclo[3.3.1]nonane derivatives). This completes a series of five tosylimido complexes with comparable pentadentate amine/pyridine ligands, where the corresponding [(L)FeIV═O]2+ oxidants have been studied in detail. The characterization of the two new complexes in solution (UV-vis-NIR, Mössbauer, HR-ESI-MS) shows that these oxidants have an intermediate spin (S = 1) electronic ground state. The reactivities have been studied as oxidants in C-H activation at 1,3-cyclohexadiene and nitrogen atom transfer to thioanisole. For the latter substrate, the entire set of data for the five ligands and for both nitrogen and oxygen atom transfer is now available and the interesting observation is that oxygen atom transfer is, as expected, generally faster than nitrogen atom transfer, with the exception of the two ligands that have four and three pyridine groups oriented parallel to the Fe-O and Fe-N axes. A thorough DFT analysis indicates that this is due to steric effects in the case of the [(L)FeIV═O]2+ species, which are less important in the [(L)FeIV═NTs]2+ compounds due to partial electron transfer from the thioanisole substrate to the iron(IV)-tosylimido oxidant.

Spectroscopic and computational studies of a bifunctional iron- and 2-oxoglutarate dependent enzyme, AsqJ

Iron and 2-oxoglutarate dependent (Fe/2OG) enzymes exhibit an exceedingly broad reaction repertoire. The most prevalent reactivity is hydroxylation, but many other reactivities have also been discovered in recent years, including halogenation, desaturation, epoxidation, endoperoxidation, epimerization, and cyclization. To fully explore the reaction mechanisms that support such a diverse reactivities in Fe/2OG enzyme, it is necessary to utilize a multi-faceted research methodology, consisting of molecular probe design and synthesis, in vitro enzyme assay development, enzyme kinetics, spectroscopy, protein crystallography, and theoretical calculations. By using such a multi-faceted research approach, we have explored reaction mechanisms of desaturation and epoxidation catalyzed by a bi-functional Fe/2OG enzyme, AsqJ. Herein, we describe the experimental protocols and computational workflows used in our studies.

Spectroscopic definition of ferrous active sites in non-heme iron enzymes

Non-heme iron enzymes play key roles in antibiotic, neurotransmitter, and natural product biosynthesis, DNA repair, hypoxia regulation, and disease states. These enzymes had been refractory to traditional bioinorganic spectroscopic methods. Thus, we developed variable-temperature variable-field magnetic circular dichroism (VTVH MCD) spectroscopy to experimentally define the excited and ground ligand field states of non-heme ferrous enzymes (Solomon et al., 1995). This method provides detailed geometric and electronic structure insight and thus enables a molecular level understanding of catalytic mechanisms. Application of this method across the five classes of non-heme ferrous enzymes has defined that a general mechanistic strategy is utilized where O2 activation is controlled to occur only in the presence of all cosubstrates.

Discovery and substrate specificity engineering of nucleotide halogenases

C2'-halogenation has been recognized as an essential modification to enhance the drug-like properties of nucleotide analogs. The direct C2'-halogenation of the nucleotide 2'-deoxyadenosine-5'-monophosphate (dAMP) has recently been achieved using the Fe(II)/α-ketoglutarate-dependent nucleotide halogenase AdaV. However, the limited substrate scope of this enzyme hampers its broader applications. In this study, we report two halogenases capable of halogenating 2'-deoxyguanosine monophosphate (dGMP), thereby expanding the family of nucleotide halogenases. Computational studies reveal that nucleotide specificity is regulated by the binding pose of the phosphate group. Based on these findings, we successfully engineered the substrate specificity of these halogenases by mutating second-sphere residues. This work expands the toolbox of nucleotide halogenases and provides insights into the regulation mechanism of nucleotide specificity.

The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A

Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.

Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase

Halogenation plays a unique role in the design of agrochemicals. Enzymatic halogenation reactions have attracted great attention due to their excellent specificity and mild reaction conditions. S-adenosyl-l-methionine (SAM)-dependent halogenases mediate the nucleophilic attack of halide ions (X-) to SAM to produce 5'-XDA. However, only 11 SAM-dependent fluorinases and 3 chlorinases have been reported, highlighting the desire for additional halogenases. SAM-dependent hydroxide adenosyltransferase (HATase) has a similar reaction mechanism as halogenases but uses water as a substrate instead of halide ions. Here, we explored a HATase from the thermophile Thermotoga maritima MSB8 and transformed it into a halogenase. We identified a key dyad W8L/V71T for the halogenation reaction. We also obtained the best performing mutants for each halogenation reaction: M1, M2 and M4 for Cl-, Br- and I-, respectively. The M4 mutant retained the thermostability of HATase in the iodination reaction at 80 °C, which surpasses the natural halogenase SalL. QM/MM revealed that these mutants bind halide ions with more suitable angles for nucleophilic attack of C5' of SAM, thus conferring halogenation capabilities. Our work achieved the halide ion specificity of halogenases and generated thermostable halogenases for the first time, which provides new opportunities to expand the halogenase repertoire from hydroxylase.

Origin of Unprecedented Formation and Reactivity of FeIV═O Species via Oxygen Activation: Role of Noncovalent Interactions and Magnetic Coupling

Emulating the capabilities of the soluble methane monooxygenase (sMMO) enzymes, which effortlessly activate oxygen at diiron(II) centers to form a reactive diiron(IV) intermediate Q, which then performs the challenging oxidation of methane to methanol, poses a significant challenge. Very recently, one of us reported the mononuclear complex [(cyclam)FeII(CH3CN)2]2+ (1), which performed a rare bimolecular activation of the molecule of O2 to generate two molecules of FeIV═O without the requirement of external proton or electron sources, similar to sMMO. In the present study, we employed the density functional theory (DFT) calculations to investigate this unique mechanism of O2 activation. We show that secondary hydrogen-bonding interactions between ligand N-H groups and O2 play a vital role in reducing the energy barrier associated with the initial O2 binding at 1 and O-O bond cleavage to form the FeIV═O complex. Further, the unique reactivity of FeIV═O species toward simultaneous C-H and O-H bond activation process has been demonstrated. Our study unveils that the nature of the magnetic coupling between the diiron centers is also crucial. Given that the influence of magnetic coupling and noncovalent interactions in catalysis remains largely unexplored, this unexplored realm presents numerous avenues for experimental chemists to develop novel structural and functional analogues of sMMO.