Insight into the catalytic mechanism of vanadium haloperoxidases. DFT investigation of vanadium cofactor reactivity

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.     

Structure and function of vanadium haloperoxidases

A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.     

Theoretical study of oxidation of molecular nitrogen with vanadium peroxo complexes

The structure and reactivity toward molecular nitrogen of vanadium diperoxo complexes, as well as the influence of the protonation and coordination of trifluoroacetate on the reactivity, were studied using the density functional method. The most stable form of the starting complex is the ozonide [V(O₃)O₂]^–. The triplet state of the complex is formed with small energy expenses for electron transfer from the peroxo ligand to the vanadium atom to form V^IV. The transfer of the O atom to the N₂ molecule to form N₂O is possible for several transition states. The nature of possible complexes and transition states retains upon protonation but the number of different structures increases depending on the ligand and the site of proton addition. Upon protonation the reactivity increases and the lowest activation barrier decreases from 27 to 20 kcal mol^–1. The coordination of trifluoracetate anion also decreases the activation barrier for the intermolecular transfer of oxygen to the nitrogen molecule.     

Mechanistic aspects of vanadium catalysed oxidations with peroxides

The enhancement of the reactivity of peroxides, particularly hydrogen peroxide and alkylhydroperoxides, in the presence of vanadium catalysis is a very well known process. The catalytic effect is determined by the formation of an intermediate whose nature depends on the peroxides used and on its interaction with the metal precursor, high-valent peroxo vanadium species being usually the reactive oxidants. During the last decades the mechanistic details for several types of oxidation reactions have been elucidated. Interestingly, in a number of cases theoretical calculations offered support to the proposed reaction pathways.In general, V(V) peroxo species behave as electrophilic oxygen transfer reagents thus reacting preferentially with the more nucleophilic functional group present in the molecule. In several instances the chemoselectivity observed in such processes is very high when not absolute. As far as vanadium peroxides are concerned, a radical oxidative reactivity toward alkanes and aromatics has been also observed; also for this latter chemistry, diverse research groups studied in detail the mechanism. On the other hand, no clear-cut evidence of nucleophilic reactivity of vanadium peroxo complexes has been obtained.Here we collect a selection of recent achievements concerning the reaction mechanisms in the vanadium catalysed oxidation and bromination reactions with peroxides.     

Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.     

The chemistry of peroxovanadium species in aqueous solutions. Structure and reactivity of a neutral diperoxovanadium complex as provided by V-NMR data, ab initio calculations and kinetic results

The addition of hydrogen peroxide to vanadium (V) precursors in aqueous acidic solutions leads to the formation of a cationic monoperoxospecies [VO(O₂)]⁺ and an anionic diperoxocomplex [VO(O₂)₂]⁻, depending on the pH and on the excess of H₂O₂. The latter may undergo protonation to form the neutral complex [HVO(O₂)₂]. ⁵¹V-NMR data and ab initio calculations suggest that the neutral complex is formed via protonation of a peroxide oxygen and that in such a species, as well as in the other two peroxovanadium derivatives, the usual η² arrangement of the peroxo groups is maintained. The comparison of reactivity data of the three complexes in the self-decomposition reaction and in the oxidation of uracil, indicates that the neutral diperoxocomplex exhibits an oxidizing power considerably larger than that of the other two peroxovanadium species.     

The reaction of dimethyltin(IV) dichloride with thiamine diphosphate (H2TDP): synthesis and structure of [SnMe2(HTDP)(H2O)]Cl.H2O, and possibility of a hitherto unsuspected role of the metal cofactor in the mechanism of vitamin-B1-dependent enzymes

The complex [SnMe(2)(HTDP)(H(2)O)]Cl.H(2)O, synthesized by reaction between dimethyltin(IV) dichloride and thiamine diphosphate hydrochloride (H(3)TDPCl) in water, was characterized by X-ray diffractometry and IR and Raman spectroscopy in the solid state, and by electrospray mass spectrometry (ESMS) and NMR spectroscopy ((1)H, (13)C, (31)P, (119)Sn and inverse-detection (1)H,(15)N HMBC) in aqueous solution. In the solid state the HTDP(-) anion chelates the metal via one oxygen atom of each phosphate group [Sn-O = 2.062(3), 2.292(3) A], and another oxygen atom belonging to the terminal phosphate links the SnMe(2)(2+) cations into chains. The tin atom has distorted octahedral coordination involving the trans methyl groups, the above-mentioned diphosphate oxygen atoms, and the oxygen atom of the coordinated water molecule. The thiamine moiety has F conformation. NMR studies suggest that the interaction between the organometallic cation and the HTDP(-) ligand persists in D(2)O solution, which is in keeping with the ESMS spectrum showing a peak corresponding to [SnMe(2)(HTDP)]. Both in the solid state and in solution, the acidic HTDP(-) proton in the complex is located on the N(1') atom of the pyrimidine ring. The enzymatic behavior of native pyruvate decarboxylase (EC 4.1.1.1, PDC), obtained from baker's yeast, was compared in a coupled assay with that shown by the "SnMe(2)-holoenzyme" created by incubation of apoPDC with [SnMe(2)(HTDP)(H(2)O)]Cl.H(2)O. The SnMe(2)-holoenzyme exhibited about 34% of the activity of the native enzyme (with a Michaelis-Menten constant of 2.7 microM, as against 6.4 microM for native PDC), so confirming the very low specificity of PDC regarding the identity of its metal ion cofactor. In view of the observed protonation of N(1'), it is suggested that the role of divalent cations in the mechanism of thiamine-diphosphate-dependent enzymes may be not only to anchor the cofactor in its binding site but also to shift the acidic proton of HTDP(-) from the diphosphate group to N(1'); protonation of N(1') is widely believed to be important for enzyme function, but the origin of the proton has never been clarified.     

A density functional theory investigation of the bromide oxidation mechanism by a vanadium bromoperoxidase model complex

Abstract  

Density functional theory has been used to study the mechanism of bromide oxidation by the oxo-peroxo complex K[VO(O₂)Hheida] (heida = N-(2-hydroxyethyl)iminodiacetic acid), which has the highest reported rate constant for bromide oxidation of any vanadium complex. Two possible mechanisms were explored, involving bromide attack on a protonated or unprotonated peroxo atom. The direct nucleophilic attack of bromide on a protonated peroxo begins the reaction, i.e. the protonated peroxo ligand is the active site of reaction. We examined five different transition states in the mechanism. Two transition states were found to have lower activation barriers. A reduction in the potential energy barriers, when calculated using the polarisable continuum model, indicates that with the involvement of acetonitrile as a solvent the transition states become more stable.     

Protonation of phosphovanadomolybdates H(3+x)PV(x)Mo(12-x)O40: computational insight into reactivity

Protonated phosphovanadomolybdates of the Keggin structure, H(3+x)PV(x)Mo(12-x)O(40) where x = 0, 1, 2, and derivatives with surface defects formed by loss of constitutional water were studied using high-level DFT calculations toward determination of the most stable species and possible active forms in oxidation catalysis in both the gas phase and in polar solutions. The calculations demonstrate that protonation at bridging positions is energetically much more favorable than protonation of terminal oxygen atoms. The preferential protonation site is determined by the stability of the metal-oxygen bond rather than the negative charge on the oxygen atom. In H(3)PMo(12)O(40), maximum distances between protons at bridging oxygen atoms are energetically favored. In contrast, for H(4)PVMo(11)O(40) and H(5)PV(2)Mo(10)O(40) protons prefer nucleophilic sites adjacent to vanadium atoms. Up to three protons are bound to the nucleophilic sites around the same vanadium atom in the stable isomeric forms of H(5)PV(2)Mo(10)O(40) that result in strong destabilization of oxo-vanadium(V) bonding to the Keggin unit. Such behavior arises from the different nature of the Mo-O and V-O bonds that can be traced to the different sizes of the valence d orbitals of the metals. Coordination of two protons at the same site yields water and an oxygen defect as a result of its dissociation. The energetic cost for the formation of surface defects decreases in the order: O(t) ? O(c) ? O(e) and is lower for the sites adjacent to vanadium atoms. Vanadium atoms near defects also have a significant contribution to the LUMO. Thus, vanadium-substituted polyoxometalates with defects near and, especially, between vanadium atoms present a plausible active form of polyoxometalates in oxidation reactions.     

Oxygen‐Promoted CH Bond Activation at Palladium

[Pd(P(Ar)(tBu)₂)₂] ( 1 , Ar=naphthyl) reacts with molecular oxygen to form Pd^II hydroxide dimers in which the naphthyl ring is cyclometalated and one equivalent of phosphine per palladium atom is released. This reaction involves the cleavage of both C? H and O? O bonds, two transformations central to catalytic aerobic oxidizations of hydrocarbons. Observations at low temperature suggest the initial formation of a superoxo complex, which then generates a peroxo complex prior to the C? H activation step. A transition state for energetically viable C? H activation across a Pd? peroxo bond was located computationally.     

Oxygen‐Promoted C?H Bond Activation at Palladium

[Pd(P(Ar)(tBu)₂)₂] ( 1 , Ar=naphthyl) reacts with molecular oxygen to form Pd^II hydroxide dimers in which the naphthyl ring is cyclometalated and one equivalent of phosphine per palladium atom is released. This reaction involves the cleavage of both C H and O O bonds, two transformations central to catalytic aerobic oxidizations of hydrocarbons. Observations at low temperature suggest the initial formation of a superoxo complex, which then generates a peroxo complex prior to the C H activation step. A transition state for energetically viable C H activation across a Pd peroxo bond was located computationally.     

Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.     

Hydrogen by Deuterium Substitution in an Aldehyde Tunes the Regioselectivity by a Nonheme Manganese(III)–Peroxo Complex

Mononuclear nonheme Mn^III‐peroxo complexes are important intermediates in biology, and take part in oxygen activation by photosystem II. Herein, we present work on two isomeric biomimetic side‐on Mn^III‐peroxo intermediates with bispidine ligand system and reactivity patterns with aldehydes. The complexes are characterized with UV/Vis and mass spectrometric techniques and reaction rates with cyclohexane carboxaldehyde (CCA) are measured. The reaction gives an unusual regioselectivity switch from aliphatic to aldehyde hydrogen atom abstraction upon deuteration of the substrate, leading to the corresponding carboxylic acid product for the latter, while the former gives a deformylation reaction. Mechanistic details are established from kinetic isotope effect studies and density functional theory calculations. Thus, replacement of C?H by C?D raises the hydrogen atom abstraction barriers and enables a regioselectivity switch to a competitive pathway that is slightly higher in energy.     

Active-site stereochemical control of oxygen atom transfer reactivity in sulfite oxidase

A number of both experimental and computational studies have recently been reported for symmetric, six-coordinate dioxomolybdenum(VI) complexes as models of the fully oxidized form of the molybdopterin enzyme sulfite oxidase (SO). Such studies have suggested that the two terminal oxo donors in SO are electronically equivalent. However, the consensus structure of the catalytically competent Mo(VI) active site in SO is five-coordinate square pyramidal, possessing two terminal oxo donors, an ene-1,2-dithiolate chelate and a cysteine sulfur donor ligand. Computational studies at the density functional level of theory have been performed on a minimal model of the SO active site, [Mo(VI)O2(S2C2Me2)(SCH3)]-, in C1 symmetry to evaluate the composition of the LUMO, which is the putative electron acceptor orbital in the oxygen atom transfer (OAT) reaction with the sulfite substrate. The LUMO in this model is principally composed of a Mo dxy - ppi* interaction between the Mo and the equatorial oxygen (Oeq), while the axial oxygen (Oax) possesses no contribution to this orbital. In fact, the LUMO+1 orbital which possesses a substantial amount of Oax character lies nearly 1 eV higher in energy than the LUMO. It has also been suggested that changes in the Oax-Mo-Sthiolate-C torsion angle during the course of enzyme catalysis may aid in selection of Oeq for OAT. Calculations were performed in which this torsion angle was varied by 20 degrees through 360 degrees . These calculations demonstrate that the Mo dxy -Oeq ppi* interaction, and therefore the Oeq atom character, always dominates the LUMO. The results presented here suggest that oxygen atom selection and activation are a direct function of the low-symmetry structure of the oxidized SO active site and provide a role for the ene-1,2-dithiolate in promoting OAT reactivity through its kinetic trans effect on the equatorial oxo donor.     

Pd-catalyzed homocoupling reaction of arylboronic acid: insights from density functional theory

The key step in the mechanism of the Palladium-catalyzed homocoupling of arylboronic acids ArB(OH)(2)(Ar = 4-Z-C(6)H(4) with Z = MeO, H, CN) in the presence of dioxygen, leading to symmetrical biaryls, has been elucidated by using density functional theory. In particular, by starting from the peroxo complex O(2)PdL(2)(L = PPh(3)), generated in the reaction of dioxygen with the Pd(0) catalyst, the fundamental role played by an intermediate formed by coordination of one oxygen atom of the peroxo complex to the oxophilic boron atom of the arylboronic acid has been pointed out. This adduct reacts with a second molecule of arylboronic acid to generate a cis-Ar-Pd(OOB(OH)(2))L(2) complex that can form the stable intermediate trans-Ar-Pd(OH)L(2) (experimentally characterized) through a sequence of hydrolysis and isomerization reactions. All theoretical insights are in agreement and do substantiate the experimentally postulated mechanism. Furthermore, direct comparison of experimental and computed spectroscopic parameters (here, (31)P chemical shifts) allows us to confirm the formation of the intermediate.     

Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy

We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.     

Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases

The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, H(peroxo), Q, and Q* in MMOH and ToMOH(peroxo) in a subclass of TMOH, ToMOH, are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss which changes could give rise to the different behavior of H(peroxo) and Q. In particular, analysis of multiple crystal structures reveals that T213 in MMOH and the analogous T201 in TMOH, located in the immediate vicinity of the active site, have different rotatory configurations. We study the rotational energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to which T213 and T201 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by the QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed Mo?ssbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the ToMOD regulatory protein, which is essential for intermediate formation and protein functioning in the ToMO system, is advanced. We find that the low quadrupole splitting parameter in the Mo?ssbauer spectrum observed for a ToMOH(peroxo) intermediate can be explained by protonation of the peroxo moiety, possibly stabilized by the T201 residue. Finally, similarities between the oxygen activation mechanisms of the monooxygenases and cytochrome P450 are discussed.     

Superelectrophilic activation of 4-heterocyclohexanones. Implications for polymer synthesis. A theoretical study

The stability and the reactivity of mono- and diprotonated 4-heterocyclohexanones as well as cyclohexanone in triflic acid have been studied at the PBE0/aug-cc-pvtz//PBE0/6-31+G** level of theory. In all cases the first protonation is an exergonic process occurring at a carbonyl oxygen except for 4-piperidone where a nitrogen atom is protonated fist. Second protonation is only slightly endergonic for all studied molecules except for cyclohexanone where the second protonation is very unfavorable thermodynamically. According to calculations, diprotonated 4-heterocyclohexanones are much more active in the reactions of triflic acid mediated polyalkoxyalkylation with aromatic hydrocarbons compared to monoprotonated ones. The increase of the reactivity of diprotonated 4-heterocyclohexanones is due to inductive effect rather than through space electrostatic influence as follows from the electronic structure analysis of dications. Moreover, the second protonation reduces the possibility of an aldol condensation side reaction, reducing the enol electrophilicity rendering heterocyclohexanones as promising monomers for superacid mediated polyhydroxyalkylation.     

Fe(II) mononuclear complexes with a new aminopyridyl ligand bearing a pivaloylamido arm. Preparation and spectroscopic characterizations of a Fe(III)-hydroperoxo complex with oxygen and nitrogen donors

Two new mononuclear FeII complexes, [(L52aH)FeII](PF6)2 (1-(PF6)2) and [(L52a)FeII]BPh4 (2-(BPh4)) have been synthesized with the new aminopyridyl ligand bearing a pivaloylamido arm L52aH (2,2-dimethyl-N-[6-({[2-(methyl-pyridin-2-ylmethyl-amino)-ethyl]-pyridin-2-ylmethyl-amino}-methyl)-pyridin-2-yl]-propionamide), or its deprotonated form L52a-. The structures of the ferrous complexes have been determined by X-ray analysis. The mononuclear FeII is in a pseudo-octahedral environment in both complexes, the six positions around the metal center being occupied by five nitrogen atoms and one oxygen atom from the ligand. Whatever the protonation state of the amide function, the structures are very similar, the FeII being 6-fold coordinated by the two amines, three pyridines, and the oxygen atom from the ligand. These two complexes exhibit an acid/base equilibrium in solution that has been studied by UV-vis spectroscopy and cyclic voltammetry in acetonitrile. The reactivity of 1-(PF6)2 with H2O2 in methanol affords the formation of a new low-spin FeIII(OOH) intermediate in which the oxygen atom is retained in the coordination sphere of the metal.