Rationalization of the Barrier Height for p-Z-styrene Epoxidation by Iron(IV)-Oxo Porphyrin Cation Radicals with Variable Axial Ligands

QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase

The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.

Can the isonitrile biosynthesis enzyme ScoE assist with the biosynthesis of isonitrile groups in drug molecules? A computational study

Computational studies show that the isonitrile synthesizing enzyme ScoE can catalyse the conversion of γ-Gly substituents in substrates to isonitrile. This enables efficient isonitrile substitution into target molecules such as axisonitrile-1.

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

The nonheme iron enzyme ScoE catalyzes the biosynthesis of an isonitrile substituent in a peptide chain. To understand details of the reaction mechanism we created a large active site cluster model of 212 atoms that contains substrate, the active oxidant and the first- and second-coordination sphere of the protein and solvent. Several possible reaction mechanisms were tested and it is shown that isonitrile can only be formed through two consecutive catalytic cycles that both use one molecule of dioxygen and α-ketoglutarate. In both cycles the active species is an iron(IV)-oxo species that in the first reaction cycle reacts through two consecutive hydrogen atom abstraction steps: first from the N–H group and thereafter from the C–H group to desaturate the NH-CH2 bond. The alternative ordering of hydrogen atom abstraction steps was also tested but found to be higher in energy. Moreover, the electronic configurations along that pathway implicate an initial hydride transfer followed by proton transfer. We highlight an active site Lys residue that is shown to donate charge in the transition states and influences the relative barrier heights and bifurcation pathways. A second catalytic cycle of the reaction of iron(IV)-oxo with desaturated substrate starts with hydrogen atom abstraction followed by decarboxylation to give isonitrile directly. The catalytic cycle is completed with a proton transfer to iron(II)-hydroxo to generate the iron(II)-water resting state. The work is compared with experimental observation and previous computational studies on this system and put in a larger perspective of nonheme iron chemistry.

Effect of the Ligand Backbone on the Reactivity and Mechanistic Paradigm of Non-Heme Iron(IV)-Oxo during Olefin Epoxidation

The oxygen atom transfer (OAT) reactivity of the non-heme [Fe^IV (2PyN2Q)(O)]²⁺ (2) containing the sterically bulky quinoline-pyridine pentadentate ligand (2PyN2Q) has been thoroughly studied with different olefins. The ferryl-oxo complex 2 shows excellent OAT reactivity during epoxidations. The steric encumbrance and electronic effect of the ligand influence the mechanistic shuttle between OAT pathway I and isomerization pathway II (during the reaction stereo pure olefins), resulting in a mixture of cis-trans epoxide products. In contrast, the sterically less hindered and electronically different [Fe^IV (N4Py)(O)]²⁺ (1) provides only cis-stilbene epoxide. A Hammett study suggests the role of dominant inductive electronic along with minor resonance effect during electron transfer from olefin to 2 in the rate-limiting step. Additionally, a computational study supports the involvement of stepwise pathways during olefin epoxidation. The ferryl bend due to the bulkier ligand incorporation leads to destabilization of both d z 2 and d x 2 - y 2 orbitals, leading to a very small quintet-triplet gap and enhanced reactivity for 2 compared to 1. Thus, the present study unveils the role of steric and electronic effects of the ligand towards mechanistic modification during olefin epoxidation.

Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights

Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.

A comprehensive insight into aldehyde deformylation: mechanistic implications from biology and chemistry

Aldehyde deformylation is an important reaction in biology, organic chemistry and inorganic chemistry and the process has been widely applied and utilized. For instance, in biology, the aldehyde deformylation reaction has wide differences in biological function, whereby cyanobacteria convert aldehydes into alkanes or alkenes, which are used as natural products for, e.g., defense mechanisms. By contrast, the cytochromes P450 catalyse the biosynthesis of hormones, such as estrogen, through an aldehyde deformylation reaction step. In organic chemistry, the aldehyde deformylation reaction is a common process for replacing functional groups on a molecule, and as such, many different synthetic methods and procedures have been reported that involve an aldehyde deformylation step. In bioinorganic chemistry, a variety of metal(iii)-peroxo complexes have been synthesized as biomimetic models and shown to react efficiently with aldehydes through deformylation reactions. This review paper provides an overview of the various aldehyde deformylation reactions in organic chemistry, biology and biomimetic model systems, and shows a broad range of different chemical reaction mechanisms for this process. Although a nucleophilic attack at the carbonyl centre is the consensus reaction mechanism, several examples of an alternative electrophilic reaction mechanism starting with hydrogen atom abstraction have been reported as well. There is still much to learn and to discover on aldehyde deformylation reactions, as deciphered in this review paper.

Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways

DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.

How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by Nδ-Methyl Histidine Affect Its Properties and Functions? A Computational Study

Heme peroxidases have important functions in nature related to the detoxification of H₂O₂. They generally undergo a catalytic cycle where, in the first stage, the iron(III)-heme-H₂O₂ complex is converted into an iron(IV)-oxo-heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered N_δ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially N_δ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the N_δ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the N_δ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by N_δ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on N_δ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.

Electronically Asynchronous Transition States for C–N Bond Formation by Electrophilic [CoIII(TAML)]-Nitrene Radical Complexes Involving Substrate-to-Ligand Single-Electron Transfer and a Cobalt-Centered Spin Shuttle

The oxidation state of the redox noninnocent tetra-amido macrocyclic ligand (TAML) scaffold was recently shown to affect the formation of nitrene radical species on cobalt(III) upon reaction with PhI=NNs [van LeestN. P.; J. Am. Chem. Soc.2020, 142, 552−56331846578]. For the neutral [Co^III(TAML^sq)] complex, this leads to the doublet (S = 1/2) mono-nitrene radical species [Co^III(TAML^q)(N^•Ns)(Y)] (bearing an unidentified sixth ligand Y in at least the frozen state), while a triplet (S = 1) bis-nitrene radical species [Co^III(TAML^q)(N^•Ns)₂]^– is generated from the anionic [Co^III(TAML^red)]^– complex. The one-electron-reduced Fischer-type nitrene radicals (N^•Ns^–) are formed through single (mono-nitrene) or double (bis-nitrene) ligand-to-substrate single-electron transfer (SET). In this work, we describe the reactivity and mechanisms of these nitrene radical complexes in catalytic aziridination. We report that [Co^III(TAML^sq)] and [Co^III(TAML^red)]^– are both effective catalysts for chemoselective (C=C versus C–H bonds) and diastereoselective aziridination of styrene derivatives, cyclohexane, and 1-hexene under mild and even aerobic (for [Co^III(TAML^red)]^–) conditions. Experimental (Hammett plots; [Co^III(TAML)]-nitrene radical formation and quantification under catalytic conditions; single-turnover experiments; and tests regarding catalyst decomposition, radical inhibition, and radical trapping) in combination with computational (density functional theory (DFT), N-electron valence state perturbation theory corrected complete active space self-consistent field (NEVPT2-CASSCF)) studies reveal that [Co^III(TAML^q)(N^•Ns)(Y)], [Co^III(TAML^q)(N^•Ns)₂]^–, and [Co^III(TAML^sq)(N^•Ns)]^– are key electrophilic intermediates in aziridination reactions. Surprisingly, the electrophilic one-electron-reduced Fischer-type nitrene radicals do not react as would be expected for nitrene radicals (i.e., via radical addition and radical rebound). Instead, nitrene transfer proceeds through unusual electronically asynchronous transition states, in which the (partial) styrene substrate to TAML ligand (single-) electron transfer precedes C–N coupling. The actual C–N bond formation processes are best described as involving a nucleophilic attack of the nitrene (radical) lone pair at the thus (partially) formed styrene radical cation. These processes are coupled to TAML-to-cobalt and cobalt-to-nitrene single-electron transfer, effectively leading to the formation of an amido-γ-benzyl radical (NsN^––CH₂–^•CH–Ph) bound to an intermediate spin (S = 1) cobalt(III) center. Hence, the TAML moiety can be regarded to act as a transient electron acceptor, the cobalt center behaves as a spin shuttle, and the nitrene radical acts as a nucleophile. Such a mechanism was hitherto unknown for cobalt-catalyzed hypovalent group transfer and the more general transition-metal-catalyzed nitrene transfer to alkenes but is now shown to complement the known concerted and stepwise mechanisms for N-group transfer.

Bioengineering of Cytochrome P450 OleTJE: How Does Substrate Positioning Affect the Product Distributions?

The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleT_JE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleT_JE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.

Inorganic reaction mechanisms. A personal journey

This review covers highlights of the work performed in the van Eldik group on inorganic reaction mechanisms over the past two decades in the form of a personal journey. Topics that are covered include, from NO to HNO chemistry, peroxide activation in model porphyrin and enzymatic systems, the wonder-world of Ru^III(edta) chemistry, redox chemistry of Ru(iii) complexes, Ru(ii) polypyridyl complexes and their application, relevant physicochemical properties and reaction mechanisms in ionic liquids, and mechanistic insight from computational chemistry. In each of these sections, typical examples of mechanistic studies are presented in reference to related work reported in the literature.

Epoxidation Catalyzed by the Nonheme Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate

Mechanisms of enzymatic epoxidation via oxygen atom transfer (OAT) to an olefin moiety is mainly derived from the studies on thiolate-heme containing epoxidases, such as cytochrome P450 epoxidases. The molecular basis of epoxidation catalyzed by nonheme-iron enzymes is much less explored. Herein, we present a detailed study on epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, AsqJ. The native substrate and analogues with different para substituents ranging from electron-donating groups (e.g., methoxy) to electron-withdrawing groups (e.g., trifluoromethyl) were used to probe the mechanism. The results derived from transient-state enzyme kinetics, Mössbauer spectroscopy, reaction product analysis, X-ray crystallography, density functional theory calculations, and molecular dynamic simulations collectively revealed the following mechanistic insights: (1) The rapid O₂ addition to the AsqJ Fe(II) center occurs with the iron-bound 2OG adopting an online-binding mode in which the C1 carboxylate group of 2OG is trans to the proximal histidine (His134) of the 2-His-1-carboxylate facial triad, instead of assuming the offline-binding mode with the C1 carboxylate group trans to the distal histidine (His211); (2) The decay rate constant of the ferryl intermediate is not strongly affected by the nature of the para substituents of the substrate during the OAT step, a reactivity behavior that is drastically different from nonheme Fe(IV)-oxo synthetic model complexes; (3) The OAT step most likely proceeds through a stepwise process with the initial formation of a C(benzylic)-O bond to generate an Fe-alkoxide species, which is observed in the AsqJ crystal structure. The subsequent C3-O bond formation completes the epoxide installation.

The oxidation of cyclo-olefin by the S = 2 ground-state complex [FeIV(O)(TQA)(NCMe)]2

Density functional theory calculation is used to investigate the oxidation of cyclo-olefin (cyclobutene, cyclopentene, cyclohexene, cycloheptene, and cyclo-octene) by the complex [Fe^IV(O)(TQA)(NCMe)]²⁺, which has S = 2 ground state, and the effect of electronic factors and steric hindrance on reaction barriers. Our results suggest that the oxo-iron(IV) complex can oxidise C-H and C = C bonds via a single-state mechanism, and two different ways of electron transport exist. The energy barriers initially decrease with increasing substrate size, and the trend then reverses. Comparison of the energy barrier in different systems reveals that except for the reaction between [Fe^IV(O)(TQA)(NCMe)]²⁺ and cycloheptene, oxo-iron(IV) complexes prefer epoxidation to hydroxylation. However, the hydroxylated product is more stable than the corresponding epoxidated product. This result indicates that the products of epoxidation tend to decompose first. The energy barrier of hydroxylation and epoxidation originates from the balance of orbital interaction and Pauli repulsion from the equatorial ligand and protons on the approaching substrate. In this regard, we calculate the weak interaction between two fragments (oxo-iron complex and substrates) using the independent gradient model and drawn the corresponding 3D isosurface representations of reactants.

Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study

Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.

Chemoselectivity in the Oxidation of Cycloalkenes with a Non-Heme Iron(IV)-Oxo-Chloride Complex: Epoxidation vs. Hydroxylation Selectivity

We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]⁺, which models the active species in iron-dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways: allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze effects of the substrate, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase.

Mechanism of Oxidative Activation of Fluorinated Aromatic Compounds by N-Bridged Diiron-Phthalocyanine: What Determines the Reactivity?

The biodegradation of compounds with C-F bonds is challenging due to the fact that these bonds are stronger than the C-H bond in methane. In this work, results on the unprecedented reactivity of a biomimetic model complex that contains an N-bridged diiron-phthalocyanine are presented; this model complex is shown to react with perfluorinated arenes under addition of H₂ O₂ effectively. To get mechanistic insight into this unusual reactivity, detailed density functional theory calculations on the mechanism of C₆ F₆ activation by an iron(IV)-oxo active species of the N-bridged diiron phthalocyanine system were performed. Our studies show that the reaction proceeds through a rate-determining electrophilic C-O addition reaction followed by a 1,2-fluoride shift to give the ketone product, which can further rearrange to the phenol. A thermochemical analysis shows that the weakest C-F bond is the aliphatic C-F bond in the ketone intermediate. The oxidative defluorination of perfluoroaromatics is demonstrated to proceed through a completely different mechanism compared to that of aromatic C-H hydroxylation by iron(IV)-oxo intermediates such as cytochrome P450 Compound I.

Interplay Between Steric and Electronic Effects: A Joint Spectroscopy and Computational Study of Nonheme Iron(IV)-Oxo Complexes

Iron is an essential element in nonheme enzymes that plays a crucial role in many vital oxidative transformations and metabolic reactions in the human body. Many of those reactions are regio- and stereospecific and it is believed that the selectivity is guided by second-coordination sphere effects in the protein. Here, results are shown of a few engineered biomimetic ligand frameworks based on the N4Py (N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) scaffold and the second-coordination sphere effects are studied. For the first time, selective substitutions in the ligand framework have been shown to tune the catalytic properties of the iron(IV)-oxo complexes by regulating the steric and electronic factors. In particular, a better positioning of the oxidant and substrate in the rate-determining transition state lowers the reaction barriers. Therefore, an optimum balance between steric and electronic factors mediates the ideal positioning of oxidant and substrate in the rate-determining transition state that affects the reactivity of high-valent reaction intermediates.

Mechanistic study of styrene aziridination by iron(iv) nitrides

A combined experimental and computational investigation reveals that styrene aziridination by an iron(iv) nitride occurs by a stepwise mechanism involving multistate character.

A combined experimental and computational investigation was undertaken to investigate the mechanism of aziridination of styrene by the tris(carbene)borate iron(iv) nitride complex, PhB(^tBuIm)₃Fe Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> N. While mechanistic investigations suggest that aziridination occurs via a reversible, stepwise pathway, it was not possible to confirm the mechanism using only experimental techniques. Density functional theory calculations support a stepwise radical addition mechanism, but suggest that a low-lying triplet (S = 1) state provides the lowest energy path for C–N bond formation (24.6 kcal mol^–1) and not the singlet ground (S = 0) state. A second spin flip may take place in order to facilitate ring closure and the formation of the quintet (S = 2) aziridino product. A Hammett analysis shows that electron-withdrawing groups increase the rate of reaction σ_p (ρ = 1.2 ± 0.2). This finding is supported by the computational results, which show that the rate-determining step drops from 24.6 kcal mol^–1 to 18.3 kcal mol^–1 when (p-NO₂C₆H₄)CH Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> CH₂ is used and slightly increases to 25.5 kcal mol^–1 using (p-NMe₂C₆H₄)CH Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> CH₂ as the substrate.

Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes

The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O⁻H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O⁻H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower.

Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases

Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO₂ . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.

Dramatic rate-enhancement of oxygen atom transfer by an iron(iv)-oxo species by equatorial ligand field perturbations

The reactivity and characterization of a novel iron(iv)-oxo species is reported that gives enhanced reactivity as a result of second-coordination sphere perturbations of the ligand system.

Biomimetic Reactivity of Oxygen-Derived Manganese and Iron Porphyrinoid Complexes

Heme proteins utilize the heme cofactor, an iron porphyrin, to perform a diverse range of reactions including dioxygen binding and transport, electron transfer, and oxidation/oxygenations. These reactions share several key metalloporphyrin intermediates, typically derived from dioxygen and its congeners such as hydrogen peroxide. These species are composed of metal-dioxygen, metal-superoxo, metal-peroxo, and metal-oxo adducts. A wide variety of synthetic metalloporphyrinoid complexes have been synthesized to generate and stabilize these intermediates. These complexes have been studied to determine the spectroscopic features, structures, and reactivities of such species in controlled and well-defined environments. In this Review, we summarize recent findings on the reactivity of these species with common porphyrinoid scaffolds employed for biomimetic studies. The proposed mechanisms of action are emphasized. This Review is organized by structural type of metal-oxygen intermediate and broken into subsections based on the metal (manganese and iron) and porphyrinoid ligand (porphyrin, corrole, and corrolazine).

Reactivity Patterns of (Protonated) Compound II and Compound I of Cytochrome P450: Which is the Better Oxidant?

The cytochromes P450 are versatile enzymes in human physiology that perform substrate hydroxylation reactions extremely efficiently. In this work, we present results of a computational study on the reactivity patterns of Compound I, Compound II, and protonated Compound II with model substrates, and we address the question of which of these compounds is the most effective oxidant? All calculations, regardless of the substrate, implicated that Compound I is the superior oxidant of the three. However, Compound II and protonated Compound II were found to react with free energies of activation that are only a few kcal mol^-1 higher in energy than those obtained with Compound I. Therefore, Compound II and protonated Compound II should be able to react with aliphatic groups with moderate C-H bond strengths. We have analysed all results in detail and have given electronic, thermochemical, valence bond, and molecular orbital rationalizations on the reactivity differences and explained experimental product distributions. Overall, the findings implied that alternative oxidants could operate alongside Compound I in complex reaction mechanisms of enzymatic and synthetic iron porphyrinoid complexes.

Oxygen Atom Transfer Using an Iron(IV)-Oxo Embedded in a Tetracyclic N-Heterocyclic Carbene System: How Does the Reactivity Compare to Cytochrome P450 Compound I?

N-Heterocyclic carbenes (NHC) are commonly featured as ligands in transition metal catalysis. Recently, a cyclic system containing four NHC groups with a central iron atom was synthesized and its iron(IV)-oxo species, [Fe^IV (O)(cNHC₄ )]²⁺ , was characterized. This tetracyclic NHC ligand system may give the iron(IV)-oxo species unique catalytic properties as compared to traditional non-heme and heme iron ligand systems. Therefore, we performed a computational study on the structure and reactivity of the [Fe^IV (O)(cNHC₄ )]²⁺ complex in substrate hydroxylation and epoxidation reactions. The reactivity patterns are compared with cytochrome P450 Compound I and non-heme iron(IV)-oxo models and it is shown that the [Fe^IV (O)(cNHC₄ )]²⁺ system is an effective oxidant with oxidative power analogous to P450 Compound I. Unfortunately, in polar solvents, a solvent molecule will bind to the sixth ligand position and decrease the catalytic activity of the oxidant. A molecular orbital and valence bond analysis provides insight into the origin of the reactivity differences and makes predictions of how to further exploit these systems in chemical catalysis.

Suicide Inhibition of Cytochrome P450 Enzymes by Cyclopropylamines via a Ring-Opening Mechanism: Proton-Coupled Electron Transfer Makes a Difference

N-benzyl-N-cyclopropylamine (BCA) has been attracting great interests for decades for its partial suicide inactivation role to cytochrome P450 (P450) via a ring-opening mechanism besides acting as a role of normal substrates. Understanding the mechanism of such partial inactivation is vital to the clinical drug design. Thus, density functional theoretical (DFT) calculations were carried out on such P450-catalyzed reactions, not only on the metabolic pathway, but on the ring-opening inactivation one. Our theoretical results demonstrated that, in the metabolic pathway, besides the normal carbinolamine, an unexpected enamine was formed via the dual hydrogen abstraction (DHA) process, in which the competition between rotation of the H-abstracted substrate radical and the rotation of hydroxyl group of the protonated Cpd II moiety plays a significant role in product branch; In the inactivation pathway, the well-noted single electron transfer (SET) mechanism-involved process was invalidated for its high energy barrier, a proton-coupled electron transfer [PCET(ET)] mechanism plays a role. Our results are consistent with other related theoretical works on heteroatom-hydrogen (X-H, X = O, N) activation and revealed new features. The revealed mechanisms will play a positive role in relative drug design.

A Systematic Account on Aromatic Hydroxylation by a Cytochrome P450 Model Compound I: A Low-Pressure Mass Spectrometry and Computational Study

Cytochrome P450 enzymes are heme-containing mono-oxygenases that mainly react through oxygen-atom transfer. Specific features of substrate and oxidant that determine the reaction rate constant for oxygen atom transfer are still poorly understood and therefore, we did a systematic gas-phase study on reactions by iron(IV)-oxo porphyrin cation radical structures with arenes. We present herein the first results obtained by using Fourier transform-ion cyclotron resonance mass spectrometry and provide rate constants and product distributions for the assayed reactions. Product distributions and kinetic isotope effect studies implicate a rate-determining aromatic hydroxylation reaction that correlates with the ionization energy of the substrate and no evidence of aliphatic hydroxylation products is observed. To further understand the details of the reaction mechanism, a computational study on a model complex was performed. These studies confirm the experimental hypothesis of dominant aromatic over aliphatic hydroxylation and show that the lack of an axial ligand affects the aliphatic pathways. Moreover, a two-parabola valence bond model is used to rationalize the rate constant and identify key properties of the oxidant and substrate that drive the reaction. In particular, the work shows that aromatic hydroxylation rates correlate with the ionization energy of the substrate as well as with the electron affinity of the oxidant.

Singlet versus Triplet Reactivity in an Mn(V)-Oxo Species: Testing Theoretical Predictions Against Experimental Evidence

Discerning the factors that control the reactivity of high-valent metal-oxo species is critical to both an understanding of metalloenzyme reactivity and related transition metal catalysts. Computational studies have suggested that an excited higher spin state in a number of metal-oxo species can provide a lower energy barrier for oxidation reactions, leading to the conclusion that this unobserved higher spin state complex should be considered as the active oxidant. However, testing these computational predictions by experiment is difficult and has rarely been accomplished. Herein, we describe a detailed computational study on the role of spin state in the reactivity of a high-valent manganese(V)-oxo complex with para-Z-substituted thioanisoles and utilize experimental evidence to distinguish between the theoretical results. The calculations show an unusual change in mechanism occurs for the dominant singlet spin state that correlates with the electron-donating property of the para-Z substituent, while this change is not observed on the triplet spin state. Minimum energy crossing point calculations predict small spin-orbit coupling constants making the spin state change from low spin to high spin unlikely. The trends in reactivity for the para-Z-substituted thioanisole derivatives provide an experimental measure for the spin state reactivity in manganese-oxo corrolazine complexes. Hence, the calculations show that the V-shaped Hammett plot is reproduced by the singlet surface but not by the triplet state trend. The substituent effect is explained with valence bond models, which confirm a change from an electrophilic to a nucleophilic mechanism through a change of substituent.

Challenging Density Functional Theory Calculations with Hemes and Porphyrins

In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol(-1)). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.

Alkyl Chain Growth on a Transition Metal Center: How Does Iron Compare to Ruthenium and Osmium?

Industrial Fischer-Tropsch processes involve the synthesis of hydrocarbons usually on metal surface catalysts. On the other hand, very few homogeneous catalysts are known to perform a Fischer-Tropsch style of reaction. In recent work, we established the catalytic properties of a diruthenium-platinum carbene complex, [(CpRu)₂(μ²-H)(μ²-NHCH₃)(μ³-C)PtCH₃(P(CH₃)₃)₂](CO)_n⁺ with n = 0, 2 and Cp = η⁵-C₅(CH₃)₅, and showed it to react efficiently by initial hydrogen atom transfer followed by methyl transfer to form an alkyl chain on the Ru-center. In particular, the catalytic efficiency was shown to increase after the addition of two CO molecules. As such, this system could be viewed as a potential homogeneous Fischer-Tropsch catalyst. Herein, we have engineered the catalytic center of the catalyst and investigated the reactivity of trimetal carbene complexes of the same type using iron, ruthenium and osmium at the central metal scaffold. The work shows that the reactivity should increase from diosmium to diruthenium to diiron; however, a non-linear trend is observed due to multiple factors contributing to the individual barrier heights. We identified all individual components of these reaction steps in detail and established the difference in reactivity of the various complexes.

Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function

Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.

Properties and reactivities of nonheme iron(IV)-oxo versus iron(V)-oxo: long-range electron transfer versus hydrogen atom abstraction

Recent work of Nam and co-workers [J. Yoon, S. A. Wilson, Y. K. Jang, M. S. Seo, K. Nehru, B. Hedman, K. O. Hodgson, E. Bill, E. I. Solomon and W. Nam, Angew. Chem., Int. Ed., 2009, 48, 1257] on a biomimetic iron complex implicated a mixture of iron(IV)-oxo and iron(V)-oxo intermediates but the latter could not be spectroscopically characterized, hence its involvement was postulated. To gain insight into the relative activity of these iron(IV)-oxo versus iron(V)-oxo intermediates, we have performed an extensive density functional theory (DFT) study on the chemical properties of the chemical system of Nam et al., namely [Fe(O)(BQEN)(NCCH3)](2+/3+) with BQEN = N,N'-dimethyl-N,N'-bis(8-quinolyl)ethane-1,2-diamine and their reactivity in hydrogen atom abstraction from ethylbenzene. We show that the perceived iron(V)-oxo species actually is an iron(IV)-oxo ligand cation radical, similar to cytochrome P450 compound I. Moreover, this intermediate has an extremely large electron affinity and therefore can abstract electrons from substrates readily. In our particular system, this means that prior to the hydrogen atom abstraction, an electron is abstracted to form an iron(IV)-oxo species, which subsequently abstracts a hydrogen atom from the substrate. Thus, our calculations show for the first time how some nonheme iron complexes react by long-range electron transfer and others directly via hydrogen atom abstraction. We have rationalized our results with detailed thermochemical cycles that explain the observed reactivity patterns.

Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes

A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.

Hydrogen-bonding interactions trigger a spin-flip in iron(III) porphyrin complexes

A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=⁵/₂) and intermediate spin (S=³/₂) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.

Transition metal complexes and the activation of dioxygen

In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.