What Factors Affect the Regioselectivity of Oxidation by Cytochrome P450? A DFT Study of Allylic Hydroxylation and Double Bond Epoxidation in a Model Reaction

Quantitative Prediction of Regioselectivity Toward Cytochrome P450/3A4 Using Machine Learning Approaches

In the drug discovery process, it is important to know the properties of both drug candidates and their metabolites. Fast and precise prediction of metabolites is essential. However, it has been difficult to predict metabolites because of the complexity of the mechanism of cytochrome P450/3A4 (CYP 3A4), which is the main metabolite enzyme of drugs. In this study, we focus on the regioselectivity of CYP 3A4, i.e., the selectivity of metabolic sites. We have developed a model to predict the regioselectivity of drug candidates by using machine learning (ML) approaches.

How do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.

The effect and influence of cis-ligands on the electronic and oxidizing properties of nonheme oxoiron biomimetics. A density functional study

Density functional theory studies on the nature of the cis effect and cis influence of ligands on oxoiron nonheme complexes have been performed. A detailed analysis of the electronic and oxidizing properties of [Fe(IV)O(TPA)L](+) with L = F(-), Cl(-), and Br(-) and TPA = tris-(2-pyridylmethyl)amine are presented and compared with [Fe(IV)O(TPA)NCCH(3)](2+). The calculations show that the electronic cis effect is determined by favorable orbital overlap between first-row elements with the metal, which are missing between the metal and second- and third-row elements. As a consequence, the metal 3d block is split into a one-below-two set of orbitals with L = Cl(-) and Br(-), and the HOMO/LUMO energy gap is widened with respect to the system with L = F(-). However, this larger HOMO/LUMO gap does not lead to large differences in electron affinities of the complexes. Moreover, a quantum mechanical analysis of the binding of the ligand shows that it is built up from a large electric field effect of the ligand on the oxoiron species and a much smaller quantum mechanical effect due to orbital overlap. These contributions are of similar strength for the three tested halogen cis ligands and result in similar reactivity patterns with substrates. The calculations show that [Fe(IV)O(TPA)L](+) with L = F(-), Cl(-), and Br(-) have closely lying triplet and quintet spin states, but only the quintet spin state is reactive with substrates. Therefore, the efficiency of the oxidant will be determined by the triplet-quintet spin state crossing of the reaction. The reaction of styrene with a doubly charged reactant, that is, [Fe(V)O(TPA)L](2+) with L = F(-), Cl(-), and Br(-) or [Fe(V)O(TPA)NCCH(3)](3+), leads to an initial electron transfer from the substrate to the metal followed by a highly exothermic epoxidation mechanism. These reactivity differences are mainly determined by the overall charge of the system rather than the nature of the cis ligand.

Origin of the correlation of the rate constant of substrate hydroxylation by nonheme iron(IV)-oxo complexes with the bond-dissociation energy of the C-H bond of the substrate

Mononuclear nonheme iron containing systems are versatile and vital oxidants of substrate hydroxylation reactions in many biosystems, whereby the rate constant of hydroxylation correlates with the strength of the C-H bond that is broken in the process. The thermodynamic reason behind these correlations, however, has never been established. In this work results of a series of density functional theory calculations of substrate hydroxylation by a mononuclear nonheme iron(IV)-oxo oxidant with a 2 His/1 Asp structural motif analogous to alpha-ketoglutarate dependent dioxygenases are presented. The calculations show that these oxidants are very efficient and able to hydroxylate strong C-H bonds, whereby the hydrogen abstraction barriers correlate linearly with the strength of the C-H bond of the substrate that is broken. These trends have been rationalized using a valence bond (VB) curve-crossing diagram, which explains the correlation using electron transfer mechanisms in the hydrogen abstraction processes. We also rationalized the subsequent reaction step for radical rebound and show that the barrier is proportional to the electron affinity of the iron(III)-hydroxo intermediate complex. It is shown that nonheme iron(IV)-hydroxo complexes have a larger electron affinity than heme iron(IV)-hydroxo complexes and therefore also experience larger radical rebound barriers, which may have implications for product distributions and rearrangement reactions. Thus, detailed comparisons between heme and nonheme iron(IV)-oxo oxidants reveal the fundamental differences in monoxygenation capabilities of these important classes of oxidants in biosystems and synthetic analogues for the first time and enable us to make predictions of experimental processes.

QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism

Using a structure generated by induced fit modeling of the protein-ligand complex, the reaction path for hydrogen atom abstraction in P450 BM3 is studied by means of mixed QM/MM methods to determine the structures and energetics along the reaction path. The IFD structure is suitable for hydrogen atom abstraction at the ω-1 position. The electronic structures obtained are similar to those observed in P450 cam. We show that the barrier for the hydrogen abstraction step from QM/MM modeling is 13.3 kcal/mol in quartet and 15.6 kcal/mol in doublet. Although there is some strain energy present in the ligand, the activation barrier is not dramatically affected. A crystal water molecule, HOH502, plays a role as catalyst and decreases the activation barrier by about 2 kcal/mol and reaction energy by about 3-4 kcal/mol. In order to achieve reactive chemistry at the remaining experimentally observed positions in the hydrocarbon tail of the ligand, other structures would have to be utilized as a starting point for the reaction. Finally, the present results still leave open the question of whether DFT methods provide an accurate computation of the barrier height in the P450 hydrogen atom abstraction reaction.

Density functional studies on thromboxane biosynthesis: mechanism and role of the heme-thiolate system

Reaction mechanisms for the isomerization of prostaglandin H(2) to thromboxane A(2), and degradation to 12-L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) and malondialdehyde (MDA), catalyzed by thromboxane synthase, were investigated using the unrestricted Becke-three-parameter plus Lee-Yang-Parr (UB3LYP) density functional level theory. In addition to the reaction pathway through Fe(IV)-porphyrin intermediates, a new reaction pathway through Fe(III)-porphyrin pi-cation radical intermediates was found. Both reactions proceed with the homolytic cleavage of endoperoxide O-O to give an alkoxy radical. This intermediate converts into an allyl radical intermediate by a C-C homolytic cleavage, followed by the formation of thromboxane A(2) having a 6-membered ring through a one electron transfer, or the degradation into HHT and MDA. The proposed mechanism shows that an iron(III)-containing system having electron acceptor ability is essential for the 6-membered ring formation leading to thromboxane A(2). Our results suggest that the step of the endoperoxide O-O homolytic bond cleavage has the highest activation energy following the binding of prostaglandin H(2) to thromboxane synthase.

Is the bound substrate in nitric oxide synthase protonated or neutral and what is the active oxidant that performs substrate hydroxylation?

We present here results of a series of density functional theory (DFT) studies on enzyme active site models of nitric oxide synthase (NOS) and address the key steps in the catalytic cycle whereby the substrate (L-arginine) is hydroxylated to N(omega)-hydroxo-arginine. It has been proposed that the mechanism follows a cytochrome P450-type catalytic cycle; however, our calculations find an alternative low energy pathway whereby the bound L-arginine substrate has two important functions in the catalytic cycle, namely first as a proton donor and later as the substrate in the reaction mechanism. Thus, the DFT studies show that the oxo-iron active species (compound I) cannot abstract a proton and neither a hydrogen atom from protonated L-arginine due to the strength of the N-H bonds of the substrate. However, the hydroxylation of neutral arginine by compound I and its one electron reduced form (compound II) requires much lower barriers and is highly exothermic. Detailed analysis of proton transfer mechanisms shows that the basicity of the dioxo dianion and the hydroperoxo-iron (compound 0) intermediates in the catalytic cycle are larger than that of arginine, which makes it likely that protonated arginine donates one of the two protons needed during the first catalytic cycle of NOS. Therefore, DFT predicts that in NOS enzymes arginine binds to the active site in its protonated form, but is deprotonated during the oxygen activation process in the catalytic cycle by either the dioxo dianion species or compound 0. As a result of the low ionization potential of neutral arginine, the actual hydroxylation reaction starts with an initial electron transfer from the substrate to compound I to create compound II followed by a concerted hydrogen abstraction/radical rebound from the substrate. These studies indicate that compound II is the actual oxidant in NOS enzymes that performs the hydroxylation reaction of arginine, which is in sharp contrast with the cytochromes P450 where compound II was shown to be a sluggish oxidant. This is the first example of an enzyme where compound II is able to participate in the reaction mechanism. Moreover, arginine hydroxylation by NOS enzymes is catalyzed in a significantly different way from the cytochromes P450 although the active sites of the two enzyme classes are very similar in structure. Detailed studies of environmental effects on the reaction mechanism show that environmental perturbations as appear in the protein have little effect and do not change the energies of the reaction. Finally, a valence bond curve crossing model has been set up to explain the obtained reaction mechanisms for the hydrogen abstraction processes in P450 and NOS enzymes.

Preferential Hydroxylation over Epoxidation Catalysis by a Horseradish Peroxidase Mutant: A Cytochrome P450 Mimic

Density functional theory calculations are presented on the catalytic properties of a horseradish peroxidase mutant whereby the axial nitrogen atom is replaced by phosphorus. This mutant has never been studied experimentally and only one theoretical report on this system is known (de Visser, S. P. J. Phys. Chem. B 2006, 110, 20759-20761). Thus, a one-atom substitution in horseradish peroxidase changes the properties of the catalytic center of the enzyme to more cytochrome P450-type qualities. In particular, the phosphorus-substituted horseradish peroxidase mutant reacts with substrates via a unique reactivity pattern, whereby alkanes are regioselectively hydroxylated even in the presence of a double bond. Reaction barriers of propene epoxidation and hydroxylation are almost identical to ones observed for a cytochrome P450 catalyst and significantly higher than those obtained for a horseradish peroxidase catalyst. It is shown that the regioselectivity difference is entropy and thermally driven and that the electron-transfer processes that occur during the reaction mechanism follow cytochrome P450-type patterns in the hydroxylation reaction.

NR Transfer Reactivity of Azo-Compound I of P450. How Does the Nitrogen Substituent Tune the Reactivity of the Species toward CH and CC Activation?

We studied electronic structures and reactivity patterns of azo-compound I species (RN-Cpd I) by comparison to O-Cpd I of, e.g., cytochrome P450. The study shows that the RN-Cpd I species are capable of C=C aziridination and C-H amidation, in a two-state mechanism similar to that of O-Cpd I. However, unlike O-Cpd I, here the nitrogen substituent (R) exerts a major impact on structure and reactivity. Thus, it is demonstrated that Fe=NR bonds of RN-Cpd I will generally be substantially longer than Fe=O bonds; electron-withdrawing R groups will generate a very long Fe=N bond, whereas electron-releasing R groups should have the opposite effect and hence a shorter Fe=N bond. The R substituent controls also the reactivity of RN-Cpd I toward C=C and C-H bonds by exerting steric and electronic effects. Our analysis shows that an electron-releasing substituent will lower the barriers for both bond activation reactions, since the electronic factor makes the reactions highly exothermic, while an electron-withdrawing one should raise both barriers. The steric bulk of the substituent is predicted to inhibit more strongly the aziridination reactions. It is predicted that electron-releasing substituents with small bulk will create powerful aziridination reagents, whereas electron-withdrawing substituents like MeSO(2) will prefer C-H bond activation with preference that increases with steric bulk. Finally, the study predicts (i) that the reactions of RN-Cpd I will be less stereospecific than those of O-Cpd I and (ii) that aziridination will be more stereoselective than amidation.

Systematic study on the mechanism of aldehyde oxidation to carboxylic acid by cytochrome P450

The mechanism of aldehyde to carboxylic acid conversion catalyzed by P450 enzymes via a series of reactions was studied systematically for the first time with density functional theory calculations. A two-state reactivity mechanism has been proposed, which can be adopted for many aldehyde oxidation reactions catalyzed by P450 enzymes. The mechanism involves initial hydrogen abstraction as the rate-limiting step and this is followed by steps of oxygen rebound without barriers owing to the quick recombination of the resultant radical species. Meanwhile, in an attempt to explore whether there exist some rules for the hydroxylation of aldehyde substrates by P450, the transition state barriers of the rate-limiting step for a series of aldehyde hydroxylation reactions have been compared. A predictive pattern of extended barrier/bond energy correlation for different hydroxylations of aldehyde substrates by P450 has been established, which was further confirmed to be a reliable reactivity scale by experimental results.

Mechanistic Insight into the Aromatic Hydroxylation by High-Valent Iron(IV)-oxo Porphyrin π-Cation Radical Complexes

Mechanistic studies of the aromatic hydroxylation by high-valent iron(IV)-oxo porphyrin pi-cation radicals revealed that the aromatic oxidation involves an initial electrophilic attack on the pi-system of the aromatic ring to produce a tetrahedral radical or cationic sigma-complex. The mechanism was proposed on the basis of experimental results such as a large negative Hammett rho value and an inverse kinetic isotope effect. By carrying out isotope labeling studies, the oxygen in oxygenated products was found to derive from the iron-oxo porphyrin intermediates.

Activation Parameters for Cyclohexene Oxygenation by an Oxoiron(IV) Porphyrin π-Cation Radical Complex: Entropy Control of an Allylic Hydroxylation Reaction

Activation parameters for epoxidation and allylic hydroxylation reactions of cyclohexene with FeIVO(TMP)*+Cl (1) were determined. Within the experimental temperature range, the epoxidation reaction was enthalpy-controlled (i.e., DeltaH > -TDeltaS), while the allylic hydroxylation reaction was entropy-controlled (i.e., -TDeltaS > DeltaH). An unexpectedly large contribution of the entropy term for the allylic hydroxylation reaction indicated that the free energy of activation, DeltaG, rather than the activation energy, Ea, should be used to discuss the reaction mechanism and chemoselectivity. The results of this study bring caution to previous density functional theory studies, in which the reaction mechanism and chemoselectivity are evaluated from calculated Ea.

Theoretical study of N-demethylation of substituted N,N-dimethylanilines by cytochrome P450: the mechanistic significance of kinetic isotope effect profiles

The mechanism of N-demethylation of N,N-dimethylanilines (DMAs) by cytochrome P450, a highly debated topic in mechanistic bioinorganic chemistry (Karki, S. B.; Dinnocenczo, J. P.; Jones, J. P.; Korzekwa, K. R. J. Am. Chem. Soc. 1995, 117, 3657), is studied here using DFT calculations of the reactions of the active species of the enzyme, Compound I (Cpd I), with four para-(H, Cl, CN, NO2) substituted DMAs. The calculations resolve mechanistic controversies, offer a consistent mechanistic view, and reveal the following features: (a) the reaction pathways involve C-H hydroxylation by Cpd I followed by a nonenzymatic carbinolamine decomposition. (b) C-H hydroxylation is initiated by a hydrogen atom transfer (HAT) step that possesses a "polar" character. As such, the HAT energy barriers correlate with the energy level of the HOMO of the DMAs. (c) The series exhibits a switch from spin-selective reactivity for DMA and p-Cl-DMA to two-state reactivity, with low- and high-spin states, for p-CN-DMA and p-NO2-DMA. (d) The computed kinetic isotope effect profiles (KIEPs) for these scenarios match the experimentally determined KIEPs. Theory further shows that the KIEs and TS structures vary in a manner predicted by the Melander-Westheimer postulate: as the substituent becomes more electron withdrawing, the TS is shifted to a later position along the H-transfer coordinate and the corresponding KIEs increases. (e) The generated carbinolaniline can readily dissociate from the heme and decomposes in a nonenzymatic environment, which involves water assisted proton shift.

Oxidative dehalogenation of perhalogenated benzenes by cytochrome P450 compound I

Resolution of the identity PBE (RI-PBE) and B3LYP density functional theory calculations are used to understand the cytochrome P450-catalyzed, Compound I-mediated oxidation of perchlorobenzenes, perfluorobenzenes, their phenols, and mixed chlorofluorobenzenes to form benzoquinones. Addition of Compound I to the chlorine-bearing carbon of perchlorobenzenes and perchlorophenols results in an apparently barrierless 1,2-shift of the chlorine atom to form hexachlorocyclohexadienones and hydroxypentachlorocyclohexadienones, respectively. Hexachlorocyclohexadienone has a significant electron affinity, and its radical anion expels chloride in a facile manner to give the pentachlorophenoxyl radical. Deprotonation of hydroxypentachlorocyclohexadienones results in the expulsion of chloride and provides a direct route to the production of tetrachloroquinones. Barrier heights for Compound I addition to fluorine-bearing carbons of hexafluorobenzene and pentafluorophenol are comparable to those computed for oxidation of benzene via an analogous reaction path. In contrast to the chlorinated cases, fluorine migration to cyclohexadienones occurs with a moderate barrier. Additionally, gas-phase elimination of fluoride from the hexafluorocyclohexadienone radical anion and deprotonated hydroxypentafluorocyclohexadienone are not facile. Rather, consideration of implicit and explicit solvent is required to achieve favorable thermochemistry for fluoride elimination and generation of the experimentally observed products. Finally, the theoretical approach described herein is predictive of the experimentally observed preferential elimination of fluorine from chloropentafluorobenzene and 1,3,5-trichloro-2,4,6-trifluorobenzene. These studies illustrate the effectiveness of P450 Compound I as an oxidant of halogenated aromatic hydrocarbons, which are persistent environmental contaminants, and the potential utility of such computational methods for predicting P450 metabolism.

Combined experimental and theoretical study on aromatic hydroxylation by mononuclear nonheme iron(IV)-oxo complexes

The hydroxylation of aromatic compounds by mononuclear nonheme iron(IV)-oxo complexes, [FeIV(Bn-tpen)(O)]2+ (Bn-tpen=N-benzyl-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine) and [FeIV(N4Py)(O)]2+ (N4Py=N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), has been investigated by a combined experimental and theoretical approach. In the experimental work, we have performed kinetic studies of the oxidation of anthracene with nonheme iron(IV)-oxo complexes generated in situ, thereby determining kinetic and thermodynamic parameters, a Hammett rho value, and a kinetic isotope effect (KIE) value. A large negative Hammett rho value of -3.9 and an inverse KIE value of 0.9 indicate that the iron-oxo group attacks the aromatic ring via an electrophilic pathway. By carrying out isotope labeling experiments, the oxygen in oxygenated products was found to derive from the nonheme iron(IV)-oxo species. In the theoretical work, we have conducted density functional theory (DFT) calculations on the hydroxylation of benzene by [FeIV(N4Py)(O)]2+. The calculations show that the reaction proceeds via two-state reactivity patterns on competing triplet and quintet spin states via an initial rate determining electrophilic substitution step. In analogy to heme iron(IV)-oxo catalysts, the ligand is noninnocent and actively participates in the reaction mechanism by reshuttling a proton from the ipso position to the oxo group. Calculated kinetic isotope effects of C6H6 versus C6D6 confirm an inverse isotope effect for the electrophilic substitution pathway. Based on the experimental and theoretical results, we have concluded that the aromatic ring oxidation by mononuclear nonheme iron(IV)-oxo complexes does not occur via a hydrogen atom abstraction mechanism but involves an initial electrophilic attack on the pi-system of the aromatic ring to produce a tetrahedral radical or cationic sigma-complex.

Characterization of manganese(V)-oxo polyoxometalate intermediates and their properties in oxygen-transfer reactions

A manganese(III)-substituted polyoxometalate, [alpha2-P2MnIII(L)W17O61]7- (P2W17MnIII), was studied as an oxidation catalyst using iodopentafluorobenzene bis(tifluoroacetate) (F5PhI(TFAc)2) as a monooxygen donor. Pink P2W17MnIII turns green upon addition of F5PhI(TFAc)2. The 19F NMR spectrum of F5PhI(TFAc)2 with excess P2W17MnIII at -50 degrees C showed the formation of an intermediate attributed to P2W17MnIII-F5PhI(TFAc)2 that disappeared upon warming. The 31P NMR spectra of P2W17MnIII with excess F5PhI(TFAc)2 at -50 and -20 degrees C showed a pair of narrow peaks attributed to a diamagnetic, singlet manganese(V)-oxo species, P2W17MnV=O. An additional broad peak at -10.6 ppm was attributed to both the P2W17MnIII-F5PhI(TFAc)2 complex and a paramagnetic, triplet manganese(V)-oxo species. The electronic structure and reactivity of P2W17MnV=O were modeled by DFT calculations using the analogous Keggin compound, [PMnV=OW11O39]4-. Calculations with a pure functional, UBLYP, showed singlet and triplet ground states of similar energy. Further calculations using both the UBLYP and UB3LYP functionals for epoxidation and hydroxylation of propene showed lowest lying triplet transition states for both transformations, while singlet and quintet transition states were of higher energy. The calculations especially after corrections for the solvent effect indicate that [PMnV=OW11O39]4- should be highly reactive, even more reactive than analogous MnV=O porphyrin species. Kinetic measurements of the reaction of P2W17MnV=O with 1-octene indicated, however, that P2W17MnV=O was less reactive than a MnV=O porphyrin. The experimental enthalpy of activation confirmed that the energy barrier for epoxidation is low, but the highly negative entropy of activation leads to a high free energy of activation. This result originates in our view from the strong solvation of the highly charged polyoxometalate by the polar solvent used and adventitious water. The higher negative charge of the polyoxometalate in the transition versus ground state leads to electrostriction of the solvent molecules and to a loss of degrees of freedom, resulting in a highly negative entropy of activation and slower reactions.

Can the peroxosuccinate complex in the catalytic cycle of taurine/α-ketoglutarate dioxygenase (TauD) act as an alternative oxidant?

Density functional theoretical studies on the catalytic properties of the peroxosuccinate intermediate in the catalytic cycle of taurine/alpha-ketoglutarate dioxygenase suggest that it cannot act as a second oxidant.

Prediction of activation energies for hydrogen abstraction by cytochrome p450

We have estimated the activation energy for hydrogen abstraction by compound I in cytochrome P450 for a diverse set of 24 small organic substrates using state-of-the-art density functional theory (B3LYP). We then show that these results can be reproduced by computationally less demanding methods, for example, by using small organic mimics of compound I with both B3LYP and the semiempirical AM1 method (mean absolute error of 3-4 kJ/mol) or by calculating the bond dissociation energy, without relaxation of the radical (B3LYP) or estimated from three-point fit to a Morse potential (AM1; errors of 4 and 5 kJ/mol, respectively). We can assign activation energies of 74, 61, 53, 47, and 30 kJ/mol to primary carbons, secondary/tertiary carbons, carbons with adjacent sp(2) or aromatic groups, ethers/thioethers, and amines, respectively, which gives a very simple and predictive model. Finally, some of the less demanding methods are applied to study the CYP3A4 metabolism of progesterone and dextromethorphan.

On the identity and reactivity patterns of the “second oxidant” of the T252A mutant of cytochrome P450cam in the oxidation of 5-methylenenylcamphor

Density functional calculations show that in the absence of Compound I, the primary oxidant species of P450, the precursor species, Compound 0 (FeOOH), can effect double bond activation of 5-methylenylcamphor (1). The mechanism is initiated by homolytic cleavage of the O-O bond and formation of an OH radical bound to the Compound II species by hydrogen bonding interactions. Subsequently, the so-formed OH radical can either activate the double bond of 1 or attack the meso position of the heme en route to heme degradation. The calculations show that double bond activation is preferred over attack on the heme. Past the double bond activation, the intermediate can either lead to epoxidation or to a glycol formation. The glycol formation is predicted to be preferred, although in the P450(cam) pocket the competition may be closer. Therefore, in the absence of Compound I, Compound 0 will be capable of epoxidizing double bonds. Previous studies [E. Derat, D. Kumar, H. Hirao, S. Shaik, J. Am. Chem. Soc. 128 (2006) 473-484] showed that in the case of a substrate that can undergo only C-H activation, the bound OH prefers heme degradation over hydrogen abstraction. Since the epoxidation barrier for Compound I is much smaller than that of Compound 0 (12.8 vs. 18.9kcal/mol), when Compound I is present in the cycle, Compound 0 will be silent. As such, our mechanism explains lucidly why T252A P450(cam) can epoxidize olefins like 5-methylenylcamphor but is ineffective in camphor hydroxylation [S. Jin, T.M. Makris, T. A. Bryson, S.G. Sligar, J.H. Dawson, J. Am. Chem. Soc. 125 (2003) 3406-3407]. Our calculations show that the glycol formation is a marker reaction of Compound 0 with 5-methylenylcamphor. If this product can be found in T252A P450(cam) or in similar mutants of other P450 isozymes, this will constitute a more definitive proof for the action of Cpd 0 in P450 enzymes.

What Factors Influence the Ratio of CH Hydroxylation versus CC Epoxidation by a Nonheme Cytochrome P450 Biomimetic?

Density functional calculations on a nonheme biomimetic (Fe=O(TMCS+) have been performed and its catalytic properties versus propene investigated. Our studies show that this catalyst is able to chemoselectively hydroxylate C=H bonds even in the presence of C=C double bonds. This phenomenon has been analyzed and found to occur due to Pauli repusions between protons on the TMCS ligand with protons attached to the approaching substrate. The geometries of the rate determining transition states indicate that the steric hindrance is larger in the epoxidation transition states than in the hydroxylation ones with much shorter distances; hence the hydroxylation pathway is favored over the epoxidation. Although, the reactant experiences close lying triplet and quintet spin states, the dominant reaction mechanism takes place on the quintet spin state surface; i.e., Fe=O(TMCS)+ reacts via single-state reactivity. Our calculations show that this spin state selectivity is the result of geometric orientation of the transition state structures, whereby the triplet ones are destabilized by electrostatic repulsions between the substrate and the ligand while the quintet spin transition states are aligned along the ideal axis. The reactivity patterns and geometries are compared with oxoiron species of dioxygenase and monoxygenase enzymes. Thus, Fe=O(TMCS)+ shows some similarities with P450 enzyme reactivity: it chemoselectively hydroxylates C=H bonds even in the presence of a C=C double bond and therefore is an acceptable P450 biomimetic. However, the absolute barriers of substrate oxidation by Fe=O(TMCS)+ are higher than the ones obtained with heme enzymes, but the chemoselectivity is lesser affected by external perturbations such as hydrogen bonding of a methanol molecule toward the thiolate sulfur or a dielectric constant. This is the first oxoiron complex whereby we calculated a chemoselective hydroxylation over epoxidation in the gas phase.

Substitution of Hydrogen by Deuterium Changes the Regioselectivity of Ethylbenzene Hydroxylation by an Oxo–Iron–Porphyrin Catalyst

Heme oxo-iron complexes are powerful oxygenation catalysts of environmentally benign hydroxylation processes. We have performed density functional theoretic calculations on a model system, that is, an oxo-iron-porphyrin (Por) complex [(Fe=O)Cl(Por)], and studied its reactivity toward a realistic substrate, namely, ethylbenzene. The calculations showed that the dominant reaction process in the gas phase is benzyl hydroxylation leading to 1-phenylethanol, with an energetic barrier of 9.1 kcal mol(-1), while the competing para-phenyl hydroxylation has a barrier 3.0 kcal mol(-1) higher in energy. This benzyl hydroxylation barrier is the lowest C-H hydroxylation barrier we have obtained so far for oxo-iron-porphyrin complexes. Due to electronic differences between the intermediates in the phenyl and benzyl hydroxylation processes, the phenyl hydroxylation process is considerably stabilised over the benzyl hydroxylation mechanism in environments with a large dielectric constant. In addition, we calculated kinetic isotope effects of the substitution of one or more hydrogen atoms of ethylbenzene by deuterium atoms and studied its effect on the reaction barriers. Thus, in a medium with a large dielectric constant, a regioselectivity change occurs between [H(10)]ethylbenzene and [D(10)]ethylbenzene whereby the deuterated species gives phenol products whereas the hydrogenated species gives mainly 1-phenylethanol products. This remarkable metabolic switching was analysed and found to occur due to 1) differences in strength between a C-H versus a C-D bond and 2) stabilisation of cationic intermediates in a medium with a large dielectric constant. We have compared our calculations with experimental work on synthetic oxo-iron-porphyrin catalysts as well as with enzyme-reactivity studies.

What External Perturbations Influence the Electronic Properties of Catalase Compound I?

We have performed density functional theory calculations on an active-site model of catalase compound I and studied the responses of the catalytic center to external perturbations. Thus, in the gas phase, compound I has close-lying doublet and quartet spin states with three unpaired electrons: two residing in pi(FeO) orbitals and the third on the heme. The addition of a dielectric constant to the model changes the doublet-quartet energy ordering but keeps the same electronic configuration. By contrast, the addition of an external electric field along one of the principal axes of the system can change the doublet-quartet energy splitting by as much as 6 kcal mol(-1) in favor of either the quartet or the doublet spin state. This sensitivity is much stronger than the effect obtained for iron heme models with thiolate or imidazole axial ligands. Moreover, an external electric field is able to change the electronic system from a heme-based radical [Fe=O(Por*+)OTyr-] to a tyrosinate radical [Fe=O(Por)OTyr*]. This again shows that oxo-iron heme systems are chameleonic species that are influenced by external perturbations and change their character and catalytic properties depending on the local environment.

Catalysts for Monooxygenations Made from Polyoxometalate: An Iron(V)−Oxo Derivative of the Lindqvist Anion

This work uses density functional calculations to design a new high-valent Fe(V)=O catalyst [Mo5O18Fe=O]3-, which is based on the Lindqvist polyoxometalate (Mo6O19(2-)). Because the parent species is stable to oxidative conditions, one may assume that the newly proposed iron-oxo species will be stable, too. The calculated Mössbauer spectroscopic data may be helpful toward an eventual identification of the species. The calculations of C-H hydroxylation and C=C epoxidation of propene show that, if made, [Mo5O18Fe=O]3- should be a potent oxidant that will be subject to strong solvent effect. Moreover, the Lindqvist catalyst leads to an intriguing result; the reaction that starts along an epoxidation pathway with C=C activation ends with a C-H hydroxylation product ((4)6) due to rearrangement on the catalyst. The origins of this result are analyzed in terms of the structure of the catalyst and the electronic requirements for conversion of an epoxidation intermediate to a hydroxylation product. Thus, if made, the [Mo5O18Fe=O]3 will be a selective C-H hydroxylation reagent.

Does Substrate Oxidation Determine the Regioselectivity of Cyclohexene and Propene Oxidation by Cytochrome P450?

DFT and QM/MM computations of allylic C-H hydroxylation versus C=C epoxidation in cyclohexene and propene by Compound I of P450cam demonstrate that the relative barriers for the oxidative processes themselves are not good predictors of the observed selectivity. However, a kinetic expression previously developed (Kozuch, S.; Shaik, S. J. Am. Chem. Soc. 2006, 128, 3355) for catalytic cycles under steady-state conditions, predicts, in accord with experiment, that propene will undergo exclusive C=C epoxidation, while cyclohexene will undergo both reactions with a small preference for epoxidation. The model expression for the effective barrier of the cycle forms a general basis for understanding and predicting the selectivity of P450 isozymes.

Propene Activation by the Oxo-Iron Active Species of Taurine/α-Ketoglutarate Dioxygenase (TauD) Enzyme. How Does the Catalysis Compare to Heme-Enzymes?

Density functional calculations on the oxygenation reaction of propene by a model for taurine/alpha-ketoglutarate dioxygenase (TauD) enzyme are presented. The oxo-iron active species of TauD is shown to be a powerful and aggressive oxidant, which is able to hydroxylate C-H bonds and epoxidize C=C bonds with low barriers. In the case of propene oxygenation, the hydroxylation and epoxidation mechanisms are competitive on a dominant quintet spin state surface. We have compared the mechanism and thermodynamics of TauD with oxo-iron heme catalysts, such as the cytochromes P450, and found some critical differences. The TauD model is found to be much more reactive toward oxygenation of substrates than oxo-iron complexes in a heme environment with much lower reaction barriers. We have analyzed this and assigned this to the strength of the O-H bond formed after hydrogen abstraction from a substrate, which is at least 10 kcal mol(-)(1) stronger in five-coordinated oxo-iron nonheme complexes than in six-coordinated oxo-iron heme complexes. Since, the metal in TauD enzymes is five-coordinated, whereas in heme-enzymes it is six-coordinated there are some critical differences in the valence molecular orbitals. Thus, in oxo-iron heme catalysts one of the antibonding pi orbitals is replaced by a low-lying nonbonding delta orbital resulting in a lower overall spin state. Moreover, heme-enzymes have an extra oxidation equivalent located on the heme, which is missing in non-heme oxo-iron catalysts. As a result, the oxo-iron species of TauD reacts via single-state reactivity on a dominant quintet spin state surface, whereas oxo-iron heme catalysts react via two-state reactivity on competing doublet and quartet spin states.

The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae

The pikromycin (Pik)/methymycin biosynthetic pathway of Streptomyces venezuelae represents a valuable system for dissecting the fundamental mechanisms of modular polyketide biosynthesis, aminodeoxysugar assembly, glycosyltransfer, and hydroxylation leading to the production of a series of macrolide antibiotics, including the natural ketolides narbomycin and pikromycin. In this study, we describe four x-ray crystal structures and allied functional studies for PikC, the remarkable P450 monooxygenase responsible for production of a number of related macrolide products from the Pik pathway. The results provide important new insights into the structural basis for the C10/C12 and C12/C14 hydroxylation patterns for the 12-(YC-17) and 14-membered ring (narbomycin) macrolides, respectively. This includes two different ligand-free structures in an asymmetric unit (resolution 2.1 A) and two co-crystal structures with bound endogenous substrates YC-17 (resolution 2.35 A)or narbomycin (resolution 1.7 A). A central feature of the enzyme-substrate interaction involves anchoring of the desosamine residue in two alternative binding pockets based on a series of distinct amino acid residues that form a salt bridge and a hydrogen-bonding network with the deoxysugar C3' dimethylamino group. Functional significance of the salt bridge was corroborated by site-directed mutagenesis that revealed a key role for Glu-94 in YC-17 binding and Glu-85 for narbomycin binding. Taken together, the x-ray structure analysis, site-directed mutagenesis, and corresponding product distribution studies reveal that PikC substrate tolerance and product diversity result from a combination of alternative anchoring modes rather than an induced fit mechanism.