Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations

Cu(I) complexes obtained via spontaneous reduction of Cu(II) complexes supported by designed bidentate ligands: bioinspired Cu(I) based catalysts for aromatic hydroxylation

Copper(i) complexes [Cu(L1-7)2](ClO4) (1-7) of bidentate ligands (L1-L7) have been synthesized via spontaneous reduction and characterized as catalysts for aromatic C-H activation using H2O2 as the oxidant. The single crystal X-ray structure of 1 exhibited a distorted tetrahedral geometry. All the copper(i) complexes catalyzed direct hydroxylation of benzene to form phenol with good selectivity up to 98%. The determined kinetic isotope effect (KIE) values, 1.69-1.71, support the involvement of a radical type mechanism. The isotope-labeling experiments using H218O2 showed 92% incorporation of 18O into phenol and confirm that H2O2 is the key oxygen supplier. Overall, the catalytic efficiencies of the complexes are strongly influenced by the electronic and steric factor of the ligand, which is fine-tuned by the ligand architecture. The benzene hydroxylation reaction possibly proceeded via a radical mechanism, which was confirmed by the addition of radical scavengers (TEMPO) to the catalytic reaction that showed a reduction in phenol formation.

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

The lytic polysaccharide monooxygenase (LPMO) enzymes boost polysaccharide depolymerization through oxidative chemistry, which has fueled the hope for more energy-efficient production of biofuel. We have recently proposed a mechanism for the oxidation of the polysaccharide substrate (E. D. Hedegård and U. Ryde, Chem. Sci., 2018, 9, 3866-3880). In this mechanism, intermediates with superoxide, oxyl, as well as hydroxyl (i.e. [CuO2]+, [CuO]+ and [CuOH]2+) cores were involved. These complexes can have both singlet and triplet spin states, and both spin-states may be important for how LPMOs function during catalytic turnover. Previous calculations on LPMOs have exclusively been based on density functional theory (DFT). However, different DFT functionals are known to display large differences for spin-state splittings in transition-metal complexes, and this has also been an issue for LPMOs. In this paper, we study the accuracy of DFT for spin-state splittings in superoxide, oxyl, and hydroxyl intermediates involved in LPMO turnover. As reference we employ multiconfigurational perturbation theory (CASPT2).

Theory Demonstrated a "Coupled" Mechanism for O2 Activation and Substrate Hydroxylation by Binuclear Copper Monooxygenases

Multiscale simulations have been performed to address the longstanding issue of "dioxygen activation" by the binuclear copper monooxygenases (PHM and DβM), which have been traditionally classified as "noncoupled" binuclear copper enzymes. Our QM/MM calculations rule out that Cu_M(II)-O₂^• is an active species for H-abstraction from the substrate. In contrast, Cu_M(II)-O₂^• would abstract an H atom from the cosubstrate ascorbate to form a Cu_M(II)-OOH intermediate in PHM and DβM. Consistent with the recently reported structural features of DβM, the umbrella sampling shows that the "open" conformation of the Cu_M(II)-OOH intermediate could readily transform into the "closed" conformation in PHM, in which we located a mixed-valent μ-hydroperoxodicopper(I,II) intermediate, (μ-OOH)Cu(I)Cu(II). The subsequent O-O cleavage and OH moiety migration to Cu_H generate the unexpected species (μ-O^•)(μ-OH)Cu(II)Cu(II), which is revealed to be the reactive intermediate responsible for substrate hydroxylation. We also demonstrate that the flexible Met ligand is favorable for O-O cleavage reactions, while the replacement of Met with the strongly bound His ligand would inhibit the O-O cleavage reactivity. As such, the study not only demonstrates a "coupled" mechanism for O₂ activation by binuclear copper monooxygenases but also deciphers the full catalytic cycle of PHM and DβM in accord with the available experimental data. These findings of O₂ activation and substrate hydroxylation by binuclear copper monooxygenases could expand our understanding of the reactivities of the synthetic monocopper complexes.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

"Two-Story" Calix[6]arene-Based Zinc and Copper Complexes: Structure, Properties, and O2 Binding

A new "two-story" calix[6]arene-based ligand was synthesized, and its coordination chemistry was explored. It presents a tren cap connected to the calixarene small rim through three amido spacers. X-ray diffraction studies of its metal complexes revealed a six-coordinate Zn^II complex with all of the carbonyl groups of the amido arms bound and a five-coordinate Cu^II complex with only one amido arm bound. These dicationic complexes were poorly responsive toward exogenous neutral donors, but the amido arms were readily displaced by small anions or deprotonated with a base to give the corresponding monocationic complexes. Cyclic voltammetry in various solvents showed a reversible wave for the Cu^II/Cu^I couple at very negative potentials, denoting an electron-rich environment. The reversibility of the system was attributed to the amido arms, which can coordinate the metal center in both its +II and +I redox states. The reversibility was lost upon anion binding to Cu. Upon exposure of the Cu^I complex to O₂ at low temperature, a green species was obtained with a UV-vis signature typical of an end-on superoxide Cu^II complex. Such a species was proposed to be responsible for oxygen insertion reactions onto the ligand according to the unusual and selective four-electron oxidative pathway previously described with a "one-story" calix[6]tren ligand.

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin

The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Copper-Oxygen Complexes Revisited: Structures, Spectroscopy, and Reactivity

A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E. A.; Tolman, W. B. Chem. Rev. 2004, 104, 1047-1076), the field has seen significant expansion in the (1) range of cores synthesized and characterized, (2) amount of mechanistic work performed, particularly in the area of organic substrate oxidation, and (3) use of computational methods for both the corroboration and prediction of proposed intermediates. The scope of this review has been limited to well-characterized examples of copper-oxygen species but seeks to provide a thorough picture of the spectroscopic characteristics and reactivity trends of the copper-oxygen cores discussed.

Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions

Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex. Reactivity of a mononuclear copper(II)-alkylperoxide complex has also been examined to get insights into the intrinsic reactivity of copper(II)-peroxide species, which is usually considered as a sluggish oxidant or just a precursor of copper-oxyl radical type reactive species. However, our studies have unambiguously demonstrated that copper(II)-alkylperoxide complex can be a direct oxidant for C-H bond activation of organic substrates, when the C-H bond activation is coupled with O-O bond cleavage (concerted mechanism). The reactivity studies of these mononuclear copper(II) active-oxygen species (superoxide and alkylperoxide) will provide significantly important insights into the catalytic mechanism of copper monooxygenases as well as copper-catalyzed oxidation reactions in synthetic organic chemistry.

Supramolecular modeling of mono-copper enzyme active sites with calix[6]arene-based funnel complexes

Supramolecular bioinorganic chemistry is a natural evolution in biomimetic metallic systems since it constitutes a further degree of complexity in modeling. The traditional approach consisting of mimicking the first coordination sphere of metal sites proved to be very efficient, because valuable data are extracted from these examples to gain insight in natural systems mechanisms. But it does not reproduce several specific aspects of enzymes that can be mimicked by the implementation of a cavity embedding the labile active site and thus controlling the properties of the metal ion by noncovalent interactions. This Account reports on a strategy aimed at reproducing some supramolecular aspects encountered in the natural systems. The cavity complexes described herein display a coordination site constructed on a macrocycle. Thanks to a careful design of the cavity-based ligands, complexes orienting their labile site specifically toward the inside of the macrocycle were obtained. The supramolecular systems are based on the flexible calix[6]arene core that surrounds the metal ion labile site, thereby constraining exogenous molecules to pass through the conic funnel to reach the metal center. Such an architecture confers to the metal ion very unusual properties and behaviors, which in many aspects are biologically relevant. Three generations of calix[6]-based ligands are presented and discussed in the context of modeling the monocopper sites encountered in some enzymes. A wide range of phenomena are highlighted such as the impact that the size and shape of the access channel to the metal center have on the selectivity and rate of the binding process, the possible remote control of the electronics through small modifications operated on the cavity edges, induced-fit behavior associated with host-guest association (shoe-tree effect) that affects the redox properties of the metal ion and the electron exchange pathway, consequences of forbidden associative ligand exchange allowing a redox switch to drive an "antithermodynamic" ligand exchange, drastic effects of the full control of the second coordination sphere, and dioxygen activation in a confined chamber conducted to a selective and unusual four-electron redox process. All these findings bring new clues for better understanding the control exerted by the proteic environment on a metal center, allow the identification of new reaction pathways, and lead to new proposals for enzymatic catalytic cycle (such as the formation of an alkylhydroperoxide intermediate for mononuclear Cu-hydroxylases). The supramolecular systems may also be exploited for designing highly selective and sensitive probes for molecules of particular function and shape or to design new selective catalysts.

Solvent and Temperature Probes of the Long-Range Electron-Transfer Step in Tyramine β-Monooxygenase: Demonstration of a Long-Range Proton-Coupled Electron-Transfer Mechanism

Tyramine β-monooxygenase (TβM) belongs to a family of physiologically important dinuclear copper monooxygenases that function with a solvent-exposed active site. To accomplish each enzymatic turnover, an electron transfer (ET) must occur between two solvent-separated copper centers. In wild-type TβM, this event is too fast to be rate limiting. However, we have recently shown [Osborne, R. L.; et al. Biochemistry2013, 52, 1179] that the Tyr216Ala variant of TβM leads to rate-limiting ET. In this study, we present a pH–rate profile study of Tyr216Ala, together with deuterium oxide solvent kinetic isotope effects (KIEs). A solvent KIE of 2 on k_cat is found in a region where k_cat is pH/pD independent. As a control, the variant Tyr216Trp, for which ET is not rate determining, displays a solvent KIE of unity. We conclude, therefore, that the observed solvent KIE arises from the rate-limiting ET step in the Tyr216Ala variant, and show how small solvent KIEs (ca. 2) can be fully accommodated from equilibrium effects within the Marcus equation. To gain insight into the role of the enzyme in the long-range ET step, a temperature dependence study was also pursued. The small enthalpic barrier of ET (E_a = 3.6 kcal/mol) implicates a significant entropic barrier, which is attributed to the requirement for extensive rearrangement of the inter-copper environment during PCET catalyzed by the Tyr216Ala variant. The data lead to the proposal of a distinct inter-domain pathway for PCET in the dinuclear copper monooxygenases.

Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations

Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system to leave the crossing region. In the framework of open quantum systems, τFC is a short time approximation of the characteristic decoherence time of the electronic subsystem in interaction with its nuclear environment. The comparison of the respective values of τcoh and τFC allows us to probe the occurrence of non-Condon effects. We use ab initio MD simulations to analyze how decoherence appears in several biological cofactors. We conclude that we cannot account for its order of magnitude by considering only the atoms or bonds directly concerned with the transfer. Decoherence results from contributions from all atoms of the system appearing with a time delay that increases with the distance from the primarily concerned atoms or bonds. The delay and magnitude of the contributions depend on the chemical nature of the system. Finally, we present recent developments based on constrained DFT for efficient and accurate evaluations of the electronic coupling in ab initio MD simulations. These are promising methods to study the subtle fluctuations of the electronic coupling and the mechanisms of electronic decoherence in biological systems.

QM/MM calculations with deMon2k

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.

Reaction mechanism of the bicopper enzyme peptidylglycine α-hydroxylating monooxygenase

Peptidylglycine α-hydroxylating monooxygenase is a noninteracting bicopper enzyme that stereospecifically hydroxylates the terminal glycine of small peptides for its later amidation. Neuroendocrine messengers, such as oxytocin, rely on the biological activity of this enzyme. Each catalytic turnover requires one oxygen molecule, two protons from the solvent, and two electrons. Despite this enzyme having been widely studied, a consensus on the reaction mechanism has not yet been found. Experiments and theoretical studies favor a pro-S abstraction of a hydrogen atom followed by the rebinding of an OH group. However, several hydrogen-abstracting species have been postulated; because two protons are consumed during the reaction, several protonation states are available. An electron transfer between the copper atoms could play a crucial role for the catalysis as well. This leads to six possible abstracting species. In this study, we compare them on equal footing. We perform quantum mechanics/molecular mechanics calculations, considering the glycine hydrogen abstraction. Our results suggest that the most likely mechanism is a protonation of the abstracting species before the hydrogen abstraction and another protonation as well as a reduction before OH rebinding.