The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: a QM/MM study

Optimization of Fe3O4 nanozyme activity via single amino acid modification mimicking an enzyme active site

Histidine modification effectively improved the affinity of Fe₃O₄ nanozyme to H₂O₂, enhancing its catalytic efficiency by mimicking peroxidase active site.

Alzheimer's Disease: A Heme-Aβ Perspective

Redox active iron is utilized in biology for various electron transfer and catalytic reactions essential for life, yet this same chemistry mediates the formation of partially reduced oxygen species (PROS). Oxidative stress derived from the iron accumulated in the amyloid plaques originating from amyloid β (Aβ) peptides and neurofibrillary tangles derived from hyperphosphorylated tau proteins has been implicated in the pathogenesis of Alzheimer's disease (AD). Altered heme homeostasis leading to dysregulation of expression of heme proteins and heme deposits in the amyloid plaques are characteristic of the AD brain. However, the pathogenic significance of heme in neurodegeneration in AD has been unappreciated due to the lack of detailed understanding of the chemistry of the interaction of heme and Aβ peptides. As a result, the biochemistry and biophysics of heme complexes of Aβ peptides (heme-Aβ) remained largely unexplored. In this Account, we discuss the active site environment of heme bound Aβ complexes, which involves three amino acid residues unique in mammalian Aβ (Arg5, Tyr10, and His13) and missing in Aβ from rodents, which do not get affected by AD. The histidine residue binds heme, while the arginine and the tyrosine act as key second sphere residues of the heme-Aβ active site that play a crucial role in its reactivity. Generation of PROS, enhanced peroxidase activity, and oxidation of neurotransmitters such as serotonin (5-HT) are all found to be catalyzed by heme-Aβ in in vitro assays, and these reactivities can potentially be linked to the observed neuropathologies in AD brain. Association of Cu with heme-Aβ leads to the formation of heme-Cu-Aβ. The heme-Cu-Aβ complex produces a greater amount of PROS than reduced heme-Aβ or Cu-Aβ alone. Nitric oxide (NO), a signaling molecule, is found to ameliorate the detrimental effects of heme-Aβ and Cu bound heme-Aβ complexes by detaching heme from the heme-Aβ complex and releasing it into the environment solution. Heme-Aβ complexes show fast electron transfer with oxidized cytochrome c and rapid heme transfer with apomyoglobin and aponeuroglobin. NO, cytochrome c, and apoglobins can all lead to reduction in PROS generated by reduced heme-Aβ. Synthetic analogues of heme, offering a hydrophobic distal environment, have been used to trap oxygen bound intermediates, which provides insight into the mechanism of PROS generation by reduced heme-Aβ. Artificial constructs of Aβ on nonbiological platforms are used not only to stabilize metastable and physiologically relevant large and small amyloid aggregates but also to monitor the interaction of various drug candidates with heme and Cu bound Aβ aggregates, representing a tractable avenue for testing therapeutic agents targeting metals and cofactors in AD.

Site-selective formation of an iron(iv)-oxo species at the more electron-rich iron atom of heteroleptic μ-nitrido diiron phthalocyanines

A combination of MS and computation on μ-nitrido bridged diiron complexes reveals H₂O₂ binding to the complex and generates an oxidant capable of oxidizing methane.

Iron(iv)–oxo species have been identified as the active intermediates in key enzymatic processes, and their catalytic properties are strongly affected by the equatorial and axial ligands bound to the metal, but details of these effects are still unresolved. In our aim to create better and more efficient oxidants of H-atom abstraction reactions, we have investigated a unique heteroleptic diiron phthalocyanine complex. We propose a novel intramolecular approach to determine the structural features that govern the catalytic activity of iron(iv)–oxo sites. Heteroleptic μ-nitrido diiron phthalocyanine complexes having an unsubstituted phthalocyanine (Pc1) and a phthalocyanine ligand substituted with electron-withdrawing alkylsulfonyl groups (PcSO₂R) were prepared and characterized. A reaction with terminal oxidants gives two isomeric iron(iv)–oxo and iron(iii)–hydroperoxo species with abundances dependent on the equatorial ligand. Cryospray ionization mass spectrometry (CSI-MS) characterized both hydroperoxo and diiron oxo species in the presence of H₂O₂. When m-CPBA was used as the oxidant, the formation of diiron oxo species (PcSO₂R)FeNFe(Pc1) Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O was also evidenced. Sufficient amounts of these transient species were trapped in the quadrupole region of the mass-spectrometer and underwent a CID-MS/MS fragmentation. Analyses of fragmentation patterns indicated a preferential formation of hydroperoxo and oxo moieties at more electron-rich iron sites of both heteroleptic μ-nitrido complexes. DFT calculations show that both isomers are close in energy. However, the analysis of the iron(iii)–hydroperoxo bond strength reveals major differences for the (Pc1)FeN(PcSO₂R)Fe^IIIOOH system as compared to (PcSO₂R)FeN(Pc1)Fe^IIIOOH system, and, hence binding of a terminal oxidant will be preferentially on more electron-rich sides. Subsequent kinetics studies showed that these oxidants are able to even oxidize methane to formic acid efficiently.

Effect of axial ligands on electronic structure and O2 reduction by iron porphyrin complexes: Towards a quantitative understanding of the "push effect"

Axial ligands play a dominating role in determining the electronic structure and reactivity of iron porphyrin active sites and synthetic models. Several properties unique to the cysteine bound heme enzyme, cytochrome P450, is attributed to the "push effect" of the thiolate axial ligand. In this mini-review the ground state electronic structure of iron porphyrins with imidazole, phenolate and thiolate complexes, derived using a combination of spectroscopy and DFT calculations, are discussed. The differences in kinetics and selectivity of oxygen reduction reaction (ORR), catalyzed by these iron porphyrin complexes with different axial ligands, help elucidate the varying push effects of the different axial ligands on oxygen activation by ferrous porphyrin. The spectroscopic and kinetic data help to develop a quantitative understanding of the "push effect" and, in particular, the electrostatic and covalent contributions to it.

An updated view on horseradish peroxidases: recombinant production and biotechnological applications

Horseradish peroxidase has been the subject of scientific research for centuries. It has been used exhaustively as reporter enzyme in diagnostics and histochemistry and still plays a major role in these applications. Numerous studies have been conducted on the role of horseradish peroxidase in the plant and its catalytic mechanism. However, little progress has been made in its recombinant production. Until now, commercial preparations of horseradish peroxidase are still isolated from plant roots. These preparations are commonly mixtures of various isoenzymes of which only a small fraction has been described so far. The composition of isoenzymes in these mixed isolates is subjected to uncontrollable environmental conditions. Nowadays, horseradish peroxidase regains interest due to its broad applicability in the fields of medicine, life sciences, and biotechnology in cancer therapy, biosensor systems, bioremediation, and biocatalysis. These medically and commercially relevant applications, the recent discovery of new natural isoenzymes with different biochemical properties, as well as the challenges in recombinant production render this enzyme particularly interesting for future biotechnological solutions. Therefore, we reviewed previous studies as well as current developments with biotechnological emphasis on new applications and the major remaining biotechnological challenge—the efficient recombinant production of horseradish peroxidase enzymes.

Heme enzymes. Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase

Heme enzymes activate oxygen through formation of transient iron-oxo (ferryl) intermediates of the heme iron. A long-standing question has been the nature of the iron-oxygen bond and, in particular, the protonation state. We present neutron structures of the ferric derivative of cytochrome c peroxidase and its ferryl intermediate; these allow direct visualization of protonation states. We demonstrate that the ferryl heme is an Fe(IV)=O species and is not protonated. Comparison of the structures shows that the distal histidine becomes protonated on formation of the ferryl intermediate, which has implications for the understanding of O-O bond cleavage in heme enzymes. The structures highlight the advantages of neutron cryo-crystallography in probing reaction mechanisms and visualizing protonation states in enzyme intermediates.

Molecular mechanism of a hotdog-fold acyl-CoA thioesterase

Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and metabolism, as well as polyketide biosynthesis. The reaction molecular mechanism of most hotdog-fold acyl-CoA thioesterases remains unknown, but several hypotheses have been put forward in structural and biochemical investigations. The reaction of a human thioesterase (hTHEM2), representing a thioesterase family with a hotdog fold where a coenzyme A moiety is cleaved, was simulated by quantum mechanics/molecular mechanics metadynamics techniques to elucidate atomic and electronic details of its mechanism, its transition-state conformation, and the free energy landscape of the process. A single-displacement acid-base-like mechanism, in which a nucleophilic water molecule is activated by an aspartate residue acting as a base, was found, confirming previous experimental proposals. The results provide unambiguous evidence of the formation of a tetrahedral-like transition state. They also explain the roles of other conserved active-site residues during the reaction, especially that of a nearby histidine/serine pair that protonates the thioester sulfur atom, the participation of which could not be elucidated from mutation analyses alone.

Applications of density functional theory to iron-containing molecules of bioinorganic interest

The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.

Single-site N-N bond cleavage by Mo(IV): possible mechanisms of hydrazido(1-) to nitrido conversion

Mo(NMe(2))(4) and the tridentate, dipyrrolyl ligand H(2)dpma(mes) were found to form 5-coordinate Mo(NMe(2))(2)(dpma(mes)) (1), which exhibits spin-crossover behaviour in solution. The complex is a ground state singlet with a barrier of 1150 cm(-1) for production of the triplet in d(8)-toluene. The complex reacts with 1,1-disubstituted hydrazines or O-benzylhydroxylamine to produce nitrido MoN(NMe(2))(dpma(mes)). The mechanism of the 1,1-dimethylhydrazine reaction with 1 was examined along with the mechanism of substitution of NMe(2) with H(2)NNMe(2) in a diamagnetic zirconium analogue. The proposed mechanism involves production of a hydrazido(1-) intermediate, Mo(NMe(2))(NHNMe(2))(dpma(mes)), which undergoes an α,β-proton shift and N-N bond cleavage with metal oxidation to form the nitrido. The rate law for the reaction was found to be -d[1]/dt = k(obs)[1][hydrazine] by initial rate experiments and examination of the full reaction profile. This conversion from hydrazido(1-) to nitrido is somewhat analogous to the proposed mechanism for O-O bond cleavage in some peroxidases.

The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics

Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide to water and oxygen (2H(2)O(2) → 2H(2)O+O(2)) with high efficiency. The enzyme is first oxidized to a high-valent iron intermediate, known as Compound I (Cpd I, Por(·+)-Fe(IV)=O) which, at difference from other hydroperoxidases, is reduced back to the resting state by further reacting with H(2)O(2). The normal catalase activity is reduced if Cpd I is consumed in a competing side reaction, forming a species named Cpd I*. In recent years, Density Functional Theory (DFT) methods have unraveled the electronic configuration of these high-valent iron species, helping to assign the intermediates trapped in the crystal structures of oxidized catalases. It has been demonstrated that the a priori assumption that the H(+)/H(-) type of mechanism for Cpd I reduction leads to the generation of singlet oxygen is not justified. Moreover, it has been shown by ab initio metadynamics simulations that two pathways are operative for Cpd I reduction: a His-mediated mechanism (described as H·/H(+) + e(-)) in which the distal His acts as an acid-base catalyst and a direct mechanism (described as H·/H·) in which the distal His does not play a direct role. Independently of the mechanism, the reaction proceeds by two one-electron transfers rather than one two-electron transfer, as previously assumed. Electron transfer to Cpd I, regardless of whether the electron is exogenous or endogenous, facilitates protonation of the oxoferryl group, to the point that formation of Cpd I* may be controlled by the easiness of protonation of reduced Cpd I.

Theoretical study of the mechanism of oxoiron(IV) formation from H2O2 and a nonheme iron(II) complex: O-O cleavage involving proton-coupled electron transfer

It has recently been shown that the nonheme oxoiron(IV) species supported by the 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane ligand (TMC) can be generated in near-quantitative yield by reacting [Fe(II)(TMC)(OTf)(2)] with a stoichiometric amount of H(2)O(2) in CH(3)CN in the presence of 2,6-lutidine (Li, F.; England, J.; Que, L., Jr. J. Am. Chem. Soc. 2010, 132, 2134-2135). This finding has major implications for O-O bond cleavage events in both Fenton chemistry and nonheme iron enzymes. To understand the mechanism of this process, especially the intimate details of the O-O bond cleavage step, a series of density functional theory (DFT) calculations and analyses have been carried out. Two distinct reaction paths (A and B) were identified. Path A consists of two principal steps: (1) coordination of H(2)O(2) to Fe(II) and (2) a combination of partial homolytic O-O bond cleavage and proton-coupled electron transfer (PCET). The latter combination renders the rate-limiting O-O cleavage effectively a heterolytic process. Path B proceeds via a simultaneous homolytic O-O bond cleavage of H(2)O(2) and Fe-O bond formation. This is followed by H abstraction from the resultant Fe(III)-OH species by an •OH radical. Calculations suggest that path B is plausible in the absence of base. However, once 2,6-lutidine is added to the reacting system, the reaction barrier is lowered and more importantly the mechanistic path switches to path A, where 2,6-lutidine plays an essential role as an acid-base catalyst in a manner similar to how the distal histidine or glutamate residue assists in compound I formation in heme peroxidases. The reaction was found to proceed predominantly on the quintet spin state surface, and a transition to the triplet state, the experimentally known ground state for the TMC-oxoiron(IV) species, occurs in the last stage of the oxoiron(IV) formation process.

Multireference and multiconfiguration ab initio methods in heme-related systems: what have we learned so far?

This work reviews the recent applications of ab initio multireference/multiconfiguration (MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and hexa-coordinate species, as well as the high-valent iron-oxo species. The current accuracy of these methods in the various systems is discussed, with special attention to potential sources of systematic errors. Thus, the review summarizes and tries to rationalize the key elements of MR/MC calculations, namely, the choice of the employed active space, especially the so-called double-shell effect that has already been recognized to be important in transition-metal-containing systems, and the impact of these elements on the spin-state energetics of heme species, as well as on the bonding mechanism of small molecules to the heme. It is shown that expansion of the MC wave function into one based on localized orbitals provides a compact and insightful view on some otherwise complex electronic structures. The effects of protein environment on the MR/MC results are summarized for the few available quantum mechanical/molecular mechanical (QM/MM) studies. Comparisons with corresponding DFT results are also made wherever available. Potential future directions are proposed.

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation

We have investigated the dynamics of water molecules in the distal pocket of horseradish peroxidase to elucidate the role that they may play in the formation of the principal active species of the enzymatic cycle (compound I, Por(o+)-Fe(IV)=O) upon reaction of the resting Fe(III) state with hydrogen peroxide. The equilibrium molecular dynamics simulations show that, in accord with experimental evidence, the active site access channel is hydrated with an average of two to three water molecules within 5 A from the bound hydrogen peroxide. Although the channel is always hydrated, the specific conformations in which a water molecule bridges H(2)O(2) and the distal histidine, which were found (Derat; et al. J. Am. Chem. Soc. 2007, 129, 6346.) to display a low-energy barrier for the initial acid-base step of the reaction, occur with low probability but are relevant within the time scale of catalysis. Metadynamics simulations, which were used to reconstruct the free-energy landscape of water motion in the access channel, revealed that preferred interaction sites within the channel are separated by small energy barriers (<1.5 kcal/mol). Most importantly, water-bridged conformations lie on a shoulder just 1 kcal/mol above one local minimum and thus are easily accessible. Such an energy landscape appears as a requisite for the effectiveness of compound I formation, whereby the H-bonding pattern involving reactants and catalytic residues (including the intervening water molecule) has to rearrange to deliver the proton to the distal OH moiety of the hydrogen peroxide and thereby lead to heterolytic O-O cleavage. Our study provides an example of a system for which the "reactive configurations" (i.e., structures characterized by a low barrier for the chemical transformation) correspond to a minor population of the system and show how equilibrium molecular dynamics and free-energy calculations may conveniently be used to ascertain that such reactive conformations are indeed accessible to the system. Once again, the MD and QM/MM combination shows that a single water molecule acts as a biocatalyst in the cycle of HRP.

Coupling and uncoupling mechanisms in the methoxythreonine mutant of cytochrome P450cam: a quantum mechanical/molecular mechanical study

The Thr252 residue plays a vital role in the catalytic cycle of cytochrome P450cam during the formation of the active species (Compound I) from its precursor (Compound 0). We investigate the effect of replacing Thr252 by methoxythreonine (MeO-Thr) on this protonation reaction (coupling) and on the competing formation of the ferric resting state and H₂O₂ (uncoupling) by combined quantum mechanical/molecular mechanical (QM/MM) methods. For each reaction, two possible mechanisms are studied, and for each of these the residues Asp251 and Glu366 are considered as proton sources. The computed QM/MM barriers indicate that uncoupling is unfavorable in the case of the Thr252MeO-Thr mutant, whereas there are two energetically feasible proton transfer pathways for coupling. The corresponding rate-limiting barriers for the formation of Compound I are higher in the mutant than in the wild-type enzyme. These findings are consistent with the experimental observations that the Thr252MeO-Thr mutant forms the alcohol product exclusively (via Compound I), but at lower reaction rates compared with the wild-type enzyme.

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.

Effects of substrate, protein environment, and proximal ligand mutation on compound I and compound 0 of chloroperoxidase

This paper investigates the enzyme chloroperoxidase (CPO) by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The effects of anionic substrate, protein environment, and proximal ligand mutation on the high-valent iron-oxo species, compound I (Cpd I), and the ferric hydroperoxide complex, compound 0 (Cpd 0), are studied. The results indicate that the presence of an anionic substrate (acetate) and the protonation state of one critical residue (Glu104) have a considerable impact on the relative stabilities of Cpd I and Cpd 0. In the absence of the substrate or when the substrate is protonated, Cpd I is considerably more stable, and its formation barrier is smaller than in the case where the substrate is in its anionic state and when Glu104 is deprotonated. This trend, which is shown to be a simple manifestation of the Hammond principle, reproduces the experimental observation that the working pH of the enzyme is acidic. Furthermore, in the absence of substrate (or when it is protonated), the relative Cpd 0/Cpd I energies are found to be a good index of Cpd I stability in heme enzymes and to follow the experimental order: horseradish peroxidase (HRP) > CPO > P450. In silico mutation of the proximal ligand from cysteine to selenocysteine was found to have no effect at all on the properties of Cpd I (e.g., spin density on the chalcogen, Mössbauer parameters, etc.) and its relative stability to Cpd 0 or on the corresponding barrier for formation. This surprising finding shows that the polar CPO pocket applies a leveling effect that stabilizes the anionic forms of the proximal ligands (CysS(-) and CysSe(-)). This in turn means that the Se-Cpd I of the mutant CPO is observable.

QM/MM methods for biomolecular systems

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity

Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.

Ligand-Field Dependence of the Excited State Dynamics of Hangman Bisporphyrin Dyad Complexes

A new Hangman porphyrin architecture has been developed to interrogate the ligand-field dependence of photoinduced PCET versus excitation energy transfer and intersystem crossing in PZn(II)-PFe(III)-OH dyads (P = porphyrin). In this design, a hanging carboxylic acid group establishes a hydrogen-bonding network to anchor the weak-field OH- ligand in the distal site of the PFe(III)-OH acceptor, whereas the proximal site is left available to accept strong-field imidazole ligands. Thus, controlling the tertiary coordination environment gives access to the first synthetic example of a porphyrin dyad with a biologically relevant weak-field/strong-field configuration of axial ligands at the heme. Transient absorption spectroscopy has been employed to probe the fate of the initial PZn(II)-based S1 excited state, revealing rapid S1 quenching for all dyads in the presence and absence of strong-field imidazole ligands (tau = 6-50 ps). The absence of a (P*+)Zn(II) signal that would complement photoinduced PCET at the PFe(III)-OH subunit (i.e., PFe(III)-OH --> PFe(II)-OH2) shows that excitation energy transfer and intersystem crossing channels dominate the quenching, regardless of whether proximal strong field ligands are present. Moreover, this photophysical assignment is independent of the solvent dielectric constant and whether a phenylene or biphenylene spacer is used to span the two porphyrin subunits. Electronic structure calculations suggest that the structural reorganization attendant to reductive PCET at the high-spin Fe(III)-OH center imposes a severe kinetic cost that can only be alleviated by inducing a low-spin electronic configuration with two strong-field axial ligands.

Hydrogen Peroxide Decomposition by a Non-Heme Iron(III) Catalase Mimic: A DFT Study

Non-heme iron(III) complexes of 14-membered tetraaza macrocycles have previously been found to catalytically decompose hydrogen peroxide to water and molecular oxygen, like the native enzyme catalase. Here the mechanism of this reaction is theoretically investigated by DFT calculations at the (U)B3LYP/6-31G* level, with focus on the reactivity of the possible spin states of the FeIII complexes. The computations suggest that H2O2 decomposition follows a homolytic route with intermediate formation of an iron(IV) oxo radical cation species (L.+FeIV==O) that resembles Compound I of natural iron porphyrin systems. Along the whole catalytic cycle, no significant energetic differences were found for the reaction proceeding on the doublet (S=1/2) or on the quartet (S=3/2) hypersurface, with the single exception of the rate-determining O--O bond cleavage of the first associated hydrogen peroxide molecule, for which reaction via the doublet state is preferred. The sextet (S=5/2) state of the FeIII complexes appears to be unreactive in catalase-like reactions.

Proton-Directed Redox Control of O−O Bond Activation by Heme Hydroperoxidase Models

Hangman metalloporphyrin complexes poise an acid-base group over a redox-active metal center and in doing so allow the "pull" effect of the secondary coordination environment of the heme cofactor of hydroperoxidase enzymes to be modeled. Stopped-flow investigations have been performed to decipher the influence of a proton-donor group on O-O bond activation. Low-temperature reactions of tetramesitylporphyrin (TMP) and Hangman iron complexes containing acid (HPX-CO2H) and methyl ester (HPX-CO2Me) functional groups with peroxyacids generate high-valent Fe=O active sites. Reactions of peroxyacids with (TMP)FeIII(OH) and methyl ester Hangman (HPX-CO2Me)FeIII(OH) give both O-O heterolysis and homolysis products, Compound I (Cpd I) and Compound II (Cpd II), respectively. However, only the former is observed when the hanging group is the acid, (HPX-CO2H)FeIII(OH), because odd-electron homolytic O-O bond cleavage is inhibited. This proton-controlled, 2e- (heterolysis) vs 1e- (homolysis) redox specificity sheds light on the exceptional catalytic performance of the Hangman metalloporphyrin complexes and provides tangible benchmarks for using proton-coupled multielectron reactions to catalyze O-O bond-breaking and bond-making reactions.

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.

Proton-shuffle mechanism of O-O activation for formation of a high-valent oxo-iron species of bleomycin

Bleomycins (BLMs) can utilize H2O2 to cleave DNA in the presence of ferric ions. DFT calculations were used to study the mechanism of O-O bond cleavage in the low-spin FeIII-hydroperoxo complex of BLM. The following alternative hypotheses were investigated using realistic structural models: (a) heterolytic cleavage of the O-O bond, generating a Compound I (Cpd I) like intermediate, formally BLM-FeV=O; (b) homolytic O-O cleavage, leading to a BLM-FeIV=O species and an OH* radical; and (c) a direct O-O cleavage/H-abstraction mechanism by ABLM. The calculations showed that (a) is a facile and viable mechanism; it involves acid-base proton reshuffle mediated by the side-chain linkers of BLM, causing thereby heterolytic cleavage of the O-O bond and generation of Cpd I. Formation of Cpd I is found to involve a barrier of 13.3 kcal/mol, which is lower than the barriers in the alternative mechanisms (b and c) that possess respective barriers of 31 and 17 kcal/mol. The so-formed Cpd I species with a radical on the side-chain linker, methylvalerate (V), adjacent to the BLM-FeIV=O complex, resembles the formation of the active species of cytochrome c peroxidase in the Poulos-Kraut proton-shuffle mechanism in heme peroxidases (Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199-8205). Experimental data are discussed and shown to be in accord with this proposal. It suggests that the high-valence Cpd I species of BLM participates in the DNA cleavage. This is an alternative mechanistic hypothesis to the exclusive reactivity scenario based on ABLM (FeIII-OOH).

Structure and quantum chemical characterization of chloroperoxidase compound 0, a common reaction intermediate of diverse heme enzymes

We have determined the crystal structure of the chloroperoxidase (CPO) hydroperoxo reaction intermediate (CPO compound 0) at 1.75-A resolution. The intermediate was generated through controlled photoreduction of the CPO oxygen complex during x-ray data collection, which was monitored by recording of the crystal absorption spectra. Initially, the peroxo-anion species was formed and then protonated to yield compound 0. Quantum chemical calculations indicate that the peroxo-anion species is not stable and collapses instantaneously to compound 0. Compound 0 is present in the ferric low-spin doublet ground state and is characterized by a long O O bond length of 1.5 A and a Fe O bond distance of 1.8 A, which is also observed in the crystal structure.

An Efficient Proton-Coupled Electron-Transfer Process during Oxidation of Ferulic Acid by Horseradish Peroxidase: Coming Full Cycle

Quantum mechanics/molecular mechanics calculations were utilized to study the process of oxidation of a native substrate (ferulic acid) by the active species of horseradish peroxidase (Dunford, H. B. Heme Peroxidases; Wiley-VCH: New York, 1999), Compound I and Compound II, and the manner by which the enzyme returns to its resting state. The results match experimental findings and reveal additional novel features. The calculations demonstrate that both oxidation processes are initiated by a proton-coupled electron-transfer (PCET) step, in which the active species of the enzyme participate only as electron-transfer partners, while the entire proton-transfer event is being relayed from the substrate to and from the His42 residue by a water molecule (W402). The reason for the observed (Henriksen, A; Smith, A. T.; Gajhede, M. J. Biol. Chem. 1999, 274, 35005-35011) similar reactivities of Compound I and Compound II toward ferulic acid is that the reactive isomer of Compound II is the, hitherto unobserved, Por(*)(+)Fe(III)OH isomer that resembles Compound I. The PCET mechanism reveals that His42 and W402 are crucial moieties and they determine the function of the HRP enzyme and account for its ability to perform substrate oxidation (Poulos, T. L. Peroxidases and Cytochrome P450. In The Porphyrin Handbook; Kadish, K. M., Smith, K. M., Guilard, R., Eds.; Academic Press: New York, 2000; Vol. 4, pp 189). In view of the results, the possibility of manipulating substrate oxidation by magnetic fields is an intriguing possibility.