Is the bis-mu-oxo Cu2(III,III) state an intermediate in tyrosinase?

Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu2O2 Active Site of oxy-Tyrosinase

Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O2 toward the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady-state, stopped-flow kinetics approach that allows for the direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The obtained biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu2O2 core of oxy-tyrosinase. The correlation of these experimental results to quantum mechanics/molecular mechanics calculations provides a detailed mechanistic description of this H-transfer step. These new mechanistic insights revise and expand our fundamental understanding of Cu2O2 active sites in biology.

New mechanistic insights into coupled binuclear copper monooxygenases from the recent elucidation of the ternary intermediate of tyrosinase

Tyrosinase is the most predominant member of the coupled binuclear copper (CBC) protein family. The recent trapping and spectroscopic definition of the elusive catalytic ternary intermediate (enzyme/O2 /monophenol) of tyrosinase dictates a monooxygenation mechanism that revises previous proposals and involves cleavage of the μ-η2 :η2 -peroxide dicopper(II) O-O bond to accept the phenolic proton, followed by monophenolate coordination to copper concomitant with aromatic hydroxylation by the non-protonated μ-oxo. Here, we compare and contrast previously proposed and current mechanistic models for monophenol monooxygenation of tyrosinase. Next, we discuss how these recent insights provide new opportunities towards uncovering structure-function relationships in CBC enzymes, as well as understanding fundamental principles for O2 activation and reactivity by bioinorganic active sites.

Mechanistic Insights into the ortho-Defluorination-Hydroxylation of 2-Halophenolates Promoted by a Bis(μ-oxo)dicopper(III) Complex

C-F bonds are one of the most inert functionalities. Nevertheless, some [Cu₂O₂]²⁺ species are able to defluorinate-hydroxylate ortho-fluorophenolates in a chemoselective manner over other ortho-halophenolates. Albeit it is known that such reactivity is promoted by an electrophilic attack of a [Cu₂O₂]²⁺ core over the arene ring, the crucial details of the mechanism that explain the chemo- and regioselectivity of the reaction remain unknown, and it has not being determined either if Cu^II₂(η²:η²-O₂) or Cu^III₂(μ-O)₂ species are responsible for the initial attack on the arene. Herein, we present a combined theoretical and experimental mechanistic study to unravel the origin of the chemoselectivity of the ortho-defluorination-hydroxylation of 2-halophenolates by the [Cu₂(O)₂(DBED)₂]²⁺ complex (DBED = N,N'-di-tert-butylethylenediamine). Our results show that the equilibria between (side-on)peroxo (P) and bis(μ-oxo) (O) isomers plays a key role in the mechanism, with the latter being the reactive species. Furthermore, on the basis of quantum-mechanical calculations, we were able to rationalize the chemoselective preference of the [Cu₂(O)₂(DBED)₂]²⁺ catalyst for the C-F activation over C-Cl and C-H activations.

Monophenolase and catecholase activity of Aspergillus oryzae catechol oxidase: insights from hybrid QM/MM calculations

Catechol oxidase from Aspergillus oryzae (AoCO4) can not only catalyze oxidation of o-diphenols to o-quinones, but can also catalyze monooxygenation of small phenolics. To gain insight into the catecholase and monophenolase activities of AoCO4, the reaction mechanism of catechol oxidation was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The oxy-form of AoCO4 was found to be a μ-η2:η2 side-on peroxo dicopper(ii) complex, which can undergo a proton coupled electron transfer from the substrate rather than a proton transfer from the nearby Ser302 residue to generate a hydroperoxide. The μ-1,1-OOH Cu2(i,ii) complex is thermodynamically more stable than the μ-η1:η2 hydroperoxide. Moreover, the cleavage of the O-O bond in the μ-1,1-OOH Cu2(i,ii) intermediate has a much lower barrier than that in the μ-η1:η2 hydroperoxide species. In both cases, the O-O bond cleavage is the rate-limiting step, generating the reactive (μ-O˙)(μ-OH) dicopper(ii) complex. In addition, our results demonstrated that the oxidation of catechol to quinone is much more preferred than the hydroxylation reaction. These findings may provide useful information for understanding the reactivity of the Cu2O2 active site of coupled binuclear copper enzymes.

Theoretical rationalization for the equilibrium between (μ-η2:η2-peroxido)CuIICuII and bis(μ-oxido)CuIIICuIII complexes: perturbational effects from ligand frameworks

DFT calculations are carried out to investigate the geometric effects of the supporting ligands in the relative energies of the (μ-η2:η2-peroxido)CuIICuII complex 1 and the bis(μ-oxido)CuIIICuIII complex 2. The N3-tridentate ligand bearing acyclic propane diamine framework La preferentially provided 1, whereas the N3-tridentate ligand with cyclic diamine framework such as 1,4-diazacycloheptane Lb gave 2 after the oxygenation of the corresponding CuI complexes as reported previously [S. Itoh, et al., Inorg. Chem., 2014, 53, 8786-8794]. Calculations at the B3LYP*-D3 level of theory can reasonably explain the experimental results in relative energies, structures and harmonic frequencies of 1 and 2. Perturbational effects of the diamine chelates of La and Lb especially on the equilibrium of 1 and 2 are investigated in detail. In the range from 2.30 Å to 3.40 Å of the N-N distance in the diamine moiety, 1 is more stable than 2 by 8.4 kcal mol-1 at the distance of 3.40 Å. Calculated potential energies indicate that the decrease in the N-N distance is associated with a decrease in energy of 2, leading that 2 can be most stabilized at the N-N distance of 2.60 Å. Furthermore, molecular orbitals analyses are performed to explain that the energy gaps between the σ* orbital of the O-O bond and the dx2-y2 orbitals of the CuII ions of 1 get small as the diamine moiety is shrunk, leading to facilitate the O-O bond cleavage from 1 to 2.

A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective

Hydrogen Atom Transfer (HAT) promoted by a triplet state of the bis-oxoCu₂(iii) core generates a new radical rebound mechanism for the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme.

DFT/TDDFT insights into the chemistry, biochemistry and photophysics of copper coordination compounds

Highlighting the recent progress in DFT/TDDFT application to coordination chemistry of copper.

DFT studies of structural and some spectral parameters of copper(II) complexes with N,N,N',N″-tetrakis (2-hydroxyethyl/propyl) ethylenediamine and tris(2-hydroxyethyl)amine

The structures and some spectral parameters of three copper(II) complexes; [Cu(THEEN)(H2O)](PIC)2 (1), [Cu(THPEN)] (PIC)2 C3H8O (2) and [Cu(TEAH3)(PIC)] (PIC)⋅(H2O) (3), previously synthesized and characterized by X-ray diffraction, are here computationally studied by using density functional theory (DFT) in its hybrid form B3LYP. In these complexes, THEEN is N,N,N',N″-tetrakis(2-hydroxyethyl) ethylenediamine and THPEN is N,N,N',N″-tetrakis(2-hydroxypropyl) ethylenediamine, tetrapodal ligands and TEAH3 is tris(2-hydroxyethyl)amine, a tripodal ligand. The primary coordination sphere of copper(II) ion in complexes (1), (2) and (3) are optimized, structural parameters are calculated, vibrational bands are assigned and energy gaps of frontier orbital (HOMO-LUMO) have been calculated with B3LYP/6-31G/LANL2DZ level of theory using DMSO as solvent. The calculated geometric and spectral results reproduced the experimental data with well agreement. Theoretical calculated molecular orbitals (HOMO-LUMO) and their energies have been calculated that suggest charge transfer occurs within the complexes.

Dioxygen reactivity of new bispidine-copper complexes

The reactivity of copper complexes of three different second-generation bispidine-based ligands (bispidine = 3,7-diazabicyclo[3.3.1]nonane; mono- and bis-tetradentate; exclusively tertiary amine donors) with dioxygen [(reversible) binding of dioxygen by copper(I)] is reported. The UV-vis, electrospray ionization mass spectrometry, electron paramagnetic resonance, and vibrational spectra (resonance Raman) of the dioxygen adducts indicate that, depending on the ligand and reaction conditions, several different species (mono- and dinuclear, superoxo, peroxo, and hydroperoxo), partially in equilibrium with each other, are formed. Minor changes in the ligand structure and/or experimental conditions (solvent, temperature, relative concentrations) allow switching between the different forms. With one of the ligands, an end-on peroxodicopper(II) complex and a mononuclear hydroperoxocopper(II) complex could be characterized. With another ligand, reversible dioxygen binding was observed, leading to a metastable superoxocopper(II) complex. The amount of dioxygen involved in the reversible binding to Cu(I) was determined quantitatively. The mechanism of dioxygen binding as well as the preference of each of the three ligands for a particular dioxygen adduct is discussed on the basis of a computational (density functional theory) analysis.

Correlated wavefunction methods in bioinorganic chemistry

In this commentary the challenges faced in the application of wavefunction-based ab initio methods to (open-shell) transition metal complexes of (bio)inorganic interest are briefly touched on. Both single-reference and multireference methods are covered. It is stressed that the generation and nature of the reference wavefunction is a subject of major importance. How erroneous results can be easily obtained even with coupled-cluster theory is illustrated through the example of the septet-quintet separation in iron(IV)-oxo complexes. Second, the interplay between relativistic and correlation effects is important. This is demonstrated with coupled-cluster calculations on models for dinuclear copper active sites, where relativity has a major influence on the relative stabilities of the bis(μ-oxo) and side-on peroxo species.

How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design

Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate-determining transition state plus the catalytic groups modeled by side-chain mimics was optimized using B3LYP/6-31G(d) or, in one case, HF/3-21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X-ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate-active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 A from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 A. The implications for computational enzyme design are discussed.

Monooxygenase activity of type 3 copper proteins

The molecular mechanism of the monooxygenase (phenolase) activity of type 3 copper proteins has been examined in detail both in the model systems and in the enzymatic systems. The reaction of a side-on peroxo dicopper(II) model compound ( A) and neutral phenols proceeds via a proton-coupled electron-transfer (PCET) mechanism to generate phenoxyl radical species, which collapse each other to give the corresponding C-C coupling dimer products. In this reaction, a bis(mu-oxo)dicopper(III) complex ( B) generated by O-O bond homolysis of A is suggested to be a real active species. On the other hand, the reaction of lithium phenolates (deprotonated form of phenols) with the same side-on peroxo dicopper(II) complex proceeds via an electrophilic aromatic substitution mechanism to give the oxygenated products (catechols). The mechanistic difference between these two systems has been discussed on the basis of the Marcus theory of electron transfer and Hammett analysis. Mechanistic details of the monooxygenase activity of tyrosinase have also been examined using a simplified enzymatic reaction system to demonstrate that the enzymatic reaction mechanism is virtually the same as that of the model reaction, that is, an electrophilic aromatic substitution mechanism. In addition, the monooxygenase activity of the oxygen carrier protein hemocyanin has been explored for the first time by employing urea as an additive in the reaction system. In this case as well, the ortho-hydroxylation of phenols to catechols has been demonstrated to involve the same ionic mechanism.

Theoretical Characterization of End-On and Side-On Peroxide Coordination in Ligated Cu2O2 Models

The relative energetics of mu-eta1:eta1 (trans end-on) and mu-eta2:eta2 (side-on) peroxo isomers of Cu2O2 fragments supported by 0, 2, 4, and 6 ammonia ligands have been computed with various density functional, coupled-cluster, and multiconfigurational protocols. There is substantial disagreement between the different levels for most cases, although completely renormalized coupled-cluster methods appear to offer the most reliable predictions. The significant biradical character of the end-on peroxo isomer proves problematic for the density functionals, while the demands on active space size and the need to account for interactions between different states in second-order perturbation theory prove challenging for the multireference treatments. In the latter case, it proved impossible to achieve any convincing convergence.

Copper Cation Interactions with Biologically Essential Types of Ligands: A Computational DFT Study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.

A Combined Experimental and Theoretical Study of Carboxylate Coordination Modes: A Structural Probe

The variations of the frequency differences of symmetric and asymmetric stretching vibrations in a series of carboxylato Fe(II) complexes have been theoretically studied. It is shown that structural information can be obtained from a direct comparison between the difference (Delta = nu(as) - nu(s)) in the asymmetric (nu(as)) and symmetric (nu(s)) carboxylate vibrations of the free anion and that of the coordinated species. The coordination mode approaches C(2v) symmetry as Delta decreases with respect to its value for the noncoordinated carboxylate. The use of IR spectroscopy in the resolution of speculated crystallographic structures is suggested.

Theoretical Models on the Cu2O2 Torture Track: Mechanistic Implications for Oxytyrosinase and Small-Molecule Analogues

Accurately describing the relative energetics of alternative bis(mu-oxo) and mu-eta2:eta2 peroxo isomers of Cu2O2 cores supported by 0, 2, 4, and 6 ammonia ligands is remarkably challenging for a wide variety of theoretical models, primarily owing to the difficulty of maintaining a balanced description of rapidly changing dynamical and nondynamical electron correlation effects and a varying degree of biradical character along the isomerization coordinate. The completely renormalized coupled-cluster level of theory including triple excitations and extremely efficient pure density functional levels of theory quantitatively agree with one another and also agree qualitatively with experimental results for Cu2O2 cores supported by analogous but larger ligands. Standard coupled-cluster methods, such as CCSD(T), are in most cases considerably less accurate and exhibit poor convergence in predicted relative energies. Hybrid density functionals significantly underestimate the stability of the bis(mu-oxo) form, with the magnitude of the error being directly proportional to the percentage Hartree-Fock exchange in the functional. Single-root CASPT2 multireference second-order perturbation theory, by contrast, significantly overestimates the stability of bis(mu-oxo) isomers. Implications of these results for modeling the mechanism of C-H bond activation by supported Cu2O2 cores, like that found in the active site of oxytyrosinase, are discussed.

Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine

Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers' stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu-O(aqua) interactions were estimated to be about 60 kcal mol(-1) and for Cu-N7 bonding in the range of 75-83 kcal mol(-1). The broad range in Cu-N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.

AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS

We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples--methane monooxygenase, cytochrome P450, and triose phosphate isomerase--are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.

The catalytic cycle of catechol oxidase

Hybrid density functional theory with the B3LYP functional has been used to investigate the catalytic mechanism of catechol oxidase. Catechol oxidase belongs to a class of enzymes that has a copper dimer with histidine ligands at the active site. Another member of this class is tyrosinase, which has been studied by similar methods previously. An important advantage for the present study compared to the one for tyrosinase is that X-ray crystal structures exist for catechol oxidase. The most critical step in the mechanism for catechol oxidase is where the peroxide O-O bond is cleaved. In the suggested mechanism this cleavage occurs in concert with a proton transfer from the substrate. Shortly after the transition state is passed there is another proton transfer from the substrate, which completes the formation of a water molecule. An important feature of the mechanism, like the one for tyrosinase, is that no proton transfers to or from residues outside the metal complex are needed. The calculated energetics is in reasonable agreement with experiments. Comparisons are made to other similar enzymes studied previously.

The catalytic cycle of tyrosinase: peroxide attack on the phenolate ring followed by O[bond]O cleavage

The oxidation of phenols to ortho-quinones, catalyzed by tyrosinase, has been studied using the hybrid DFT method B3LYP. Since no X-ray structure exists for tyrosinase, information from the related enzymes hemocyanin and catechol oxidase were used to set up a chemical model for the calculations. Previous studies have indicated that the direct cleavage of O(2) forming a Cu(2)(III,III) state is energetically very unlikely. The present study therefore followed another mechanism previously suggested. In this mechanism, dioxygen attacks the phenolate ring which is then followed by O[bond]O cleavage. The calculations give a reasonable barrier for the O(2) attack of only 12.3 kcal/mol, provided one of the copper ligands is able to move substantially away from its direct copper coordination. This can be achieved with six histidine ligands even if these ligands are held in their positions by the enzyme, but can also be achieved if one of the coppers only has two histidine ligands and the third ligand is water. The next step of O[bond]O cleavage has a computed barrier of 14.4 kcal/mol, in reasonable agreement with the experimental overall rate for the catalytic cycle. For the other steps of the mechanism, only a preliminary investigation was made, indicating a few problems which require future QM/MM studies.

A comparison of the thermodynamics of O[bond]O cleavage for dicopper complexes in enzymes and synthetic systems

The preferred state, the peroxide Cu(2)(II,II) or the bis-mu-oxo Cu(2)(III,III) states, for oxygen-bridged copper dimers with nitrogen donors is reinvestigated. Experiments have indicated that for the enzymatic complexes with histidine ligands the peroxide state should be favored, at least for hemocyanin, while for the synthetic complexes with strained ligands the bis-mu-xo state should be intrinsically favored. The present B3LYP study essentially agrees with these results. The quite different results obtained in CASPT2 and some previous B3LYP studies for these systems are investigated and discussed. The conclusion, drawn in an earlier study, that the Cu(2)(III,III) state is an unlikely intermediate in the enzyme mechanisms of tyrosinase and catechol oxidase, still remains.

3-hydroxykynurenine as a substrate/activator for mushroom tyrosinase

3-Hydroxykynurenine is a tryptophan metabolite with an o-aminophenol structure. It is both a tyrosinase activator and a substrate, reducing the lag phase, stimulating the monophenolase activity, and being oxidized to xanthommatin. In the early stage of monophenol hydroxylation, catechol accumulation takes place, whereas 3-hydroxykynurenine is substantially unchanged and no significant amounts of the o-quinone are produced. These results suggest an activating action of 3-hydroxykynurenine toward o-hydroxylation of monophenols. 3-Hydroxykynurenine could therefore well act as a physiological device to control phenolics metabolism to catechols and quinonoids.

Synthesis, structure and catecholase activity of dinuclear copper and zinc complexes with an N(3)-ligand

The preparation and characterization of dinuclear [M(II)(dbcat)(idpa)](2) (M[double bond]Zn (1), Cu (3); dbcat[double bond]3,5-di-tert-butylcatecholate; idpa[double bond]3,3'-iminobis(N,N-dimethylpropylamine)) complexes are described. Crystallographic characterization of the complex [Cu(II)(dbcat)(idpa)](2) has shown that the co-ordination geometry around copper(II) ions is distorted square pyramidal (triclinic, P-1, a=10.576(1) A, b=11.927(1) A, c=12.621(1) A, alpha=77.89(1) degrees, beta=88.65(1) degrees, gamma=70.21(1) degrees, V=1462.7(2) A(3), Z=2, R=0.0387). Both 1 and 3 were suitable catalysts for the catalytic oxidation of dbcatH(2) to dtbq (dtbq=3,5-di-tert-butyl-1,2-benzoquinone) with dioxygen at ambient conditions in good yields. However, on the basis of kinetic studies the copper- and zinc-catalyzed reactions showed different mechanisms. In the first case valence tautomerism [Cu(II)(dbcat)(idpa)]<==>[Cu(I)(dbsq)(idpa)] precedes the reaction with O(2), while with the zinc complex metal-bound catecholate reacts directly with O(2) with the formation of free superoxide anion.

Bis(mu-oxo)dimetal "diamond" cores in copper and iron complexes relevant to biocatalysis

Although quite a familiar feature in high-valent manganese chemistry, the M(2)(mu-O)(2) diamond core motif has only recently been found in synthetic complexes for M=Cu or Fe. Structural and spectroscopic characterization of these more reactive Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) compounds has been possible through use of appropriately designed supporting ligands, low-temperature handling methods, and techniques such as electrospray ionization mass spectrometry and X-ray crystallography with area detector instrumentation for rapid data collection. Despite differences in electronic structures that have been revealed through experimental and theoretical studies, Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) cores exhibit analogously covalent metal-oxo bonding, remarkably congruent Raman and extended X-ray absorption fine structure (EXAFS) signatures, and similar tendencies to abstract hydrogen atoms from substrates. Core isomerization is another common reaction attribute, although different pathways are traversed; for Fe, bridge-to-terminal oxo migration has been discovered, while for Cu, reversible formation of an O-O bond to yield a peroxo isomer has been identified. Our understanding of biocatalysis has been enhanced significantly through the isolation and comprehensive characterization of the Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) complexes. In particular, it has led to the development of new mechanistic notions about how non-heme multimetal enzymes, such as methane monooxygenases, fatty acid desaturase, and tyrosinase, may function in the activation of dioxygen to catalyze a diverse array of organic transformations.