Conversion of Methane to Methanol at the Mononuclear and Dinuclear Copper Sites of Particulate Methane Monooxygenase (pMMO): A DFT and QM/MM Study

Modelling on a Biomimetic [Cu-O-Cu]2+-mediated Methane-to-Methanol Conversion Unveils the Site for Methane Activation

The Cu-O-Cu core exhibits methane-to-methanol conversion, mirroring the reactivity of the copper-containing enzyme pMMO. Herein, we computationally examined the reactivity of a biomimetic Cu-O-Cu core towards methane-to-methanol conversion. The oxygen atom of the Cu-O-Cu core abstracts hydrogen present in the C-H bond of methane. The spin density at the bridging oxygen helps to abstract hydrogen from the C-H bond. We modulated the spin density of the bridging oxygen by substituting only a single copper atom of the Cu-O-Cu core by metals (M) such as Fe, Co, and Ag. These substitutions result in bimetallic [Cu-O-M]2+ models. We observed that the energy barriers for the C-H activation step and the subsequent rebound step vary with the metal M. [Cu-O-Ag]2+ exhibits the highest reactivity for M2M conversion, while [Cu-O-Fe]2+ displays the lowest reactivity. To understand the different reactivity of these models towards M2M conversion, we employed distortion-interaction analysis, orbital analysis, spin density analysis, and quantum theory of atoms in molecules analysis. Orbital analysis reveals that all four adducts follow a hydrogen atom transfer mechanism for C-H activation. Further, spin density analysis reveals that a higher spin density on the bridging oxygen leads to a lower C-H activation barrier.

Mechanisms for Methane and Ammonia Oxidation by Particulate Methane Monooxygenase

Particulate MMO (pMMO) catalyzes the oxidation of methane to methanol and also ammonia to hydroxylamine. Experimental characterization of the active site has been very difficult partly because the enzyme is membrane-bound. However, recently, there has been major progress mainly through the use of cryogenic electron microscopy (cryoEM). Electron paramagnetic resonance (EPR) and X-ray spectroscopy have also been employed. Surprisingly, the active site has only one copper. There are two histidine ligands and one asparagine ligand, and the active site is surrounded by phenyl alanines but no charged amino acids in the close surrounding. The present study is the first quantum chemical study using a model of that active site (CuD). Low barrier mechanisms have been found, where an important part is that there are two initial proton-coupled electron transfer steps to a bound O2 ligand before the substrate enters. Surprisingly, this leads to large radical character for the oxygens even though they are protonated. That result is very important for the ability to accept a proton from the substrates. Methods have been used which have been thoroughly tested for redox enzyme mechanisms.

Orbital Analysis Captures the Existence of a Mixed-Valent CuIII -O-CuII Active-Site and its Role in Water-Assisted Aliphatic Hydroxylation

The Cu-O-Cu core has been proposed as a potential site for methane oxidation in particulate methane monooxygenase. In this work, we used density functional theory (DFT) to design a mixed-valent CuIII -O-CuII species from an experimentally known peroxo-dicopper complex supported by N-donor ligands containing phenolic groups. We found that the transfer of two-protons and two-electrons from phenolic groups to peroxo-dicopper core takes place, which results to the formation of a bis-μ-hydroxo-dicopper core. The bis-μ-hydroxo-dicopper core converts to a mixed-valent CuIII -O-CuII core with the removal of a water molecule. The orbital and spin density analyses unravel the mixed-valent nature of CuIII -O-CuII . We further investigated the reactivity of this mixed-valent core for aliphatic C-H hydroxylation. Our study unveiled that mixed-valent CuIII -O-CuII core follows a hydrogen atom transfer mechanism for C-H activation. An in-situ generated water molecule plays an important role in C-H hydroxylation by acting as a proton transfer bridge between carbon and oxygen. Furthermore, to assess the relevance of a mixed-valent CuIII -O-CuII core, we investigated aliphatic C-H activation by a symmetrical CuII -O-CuII core. DFT results show that the mixed-valent CuIII -O-CuII core is more reactive toward the C-H bond than the symmetrical CuII -O-CuII core.

Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases

Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.

From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering

Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.

Insight into the direct conversion of methane to methanol on modified ZIF-204 from the perspective of DFT-based calculations

Direct oxidation of methane over oxo-doped ZIF-204, a bio-mimetic metal-organic framework, is investigated under first-principles calculations based on density functional theory. In the pristine ZIF-204, the tetrahedral methane molecule anchors to an open monocopper site via the so-called η² configuration with a physisorption energy of 0.24 eV. This weak binding arises from an electrostatic interaction between the negative charge of carbon in the methane molecule and the positive Cu²⁺ cation in the framework. In the modified ZIF-204, the doped oxo species is stabilized at the axial position of a CuN₄-base square pyramid at a distance of 2.06 Å. The dative covalent bond between Cu and oxo is responsible for the formation energy of 1.06 eV. With the presence of the oxo group, the presenting of electrons in the O_p_z orbital accounts for the adsorption of methane via hydrogen bonding with an adsorption energy of 0.30 eV. The methane oxidation can occur via either a concerted direct oxo insertion mechanism or a hydrogen-atom abstraction radical rebound mechanism. Calculations on transition-state barriers show that reactions via the concerted direct oxo insertion mechanism can happen without energy barriers. Concerning the hydrogen-atom abstraction radical rebound mechanism, the C-H bond dissociation of the CH₄ molecule is barrierless, but the C-O bond recombination to form the CH₃OH molecule occurs through a low barrier of 0.16 eV. These predictions suggest the modified ZIF-204 is a promising catalyst for methane oxidization.

Single Atom Catalysts for Selective Methane Oxidation to Oxygenates

Direct conversion of methane (CH₄) to C_1-2 liquid oxygenates is a captivating approach to lock carbons in transportable value-added chemicals, while reducing global warming. Existing approaches utilizing the transformation of CH₄ to liquid fuel via tandemized steam methane reforming and the Fischer-Tropsch synthesis are energy and capital intensive. Chemocatalytic partial oxidation of methane remains challenging due to the negligible electron affinity, poor C-H bond polarizability, and high activation energy barrier. Transition-metal and stoichiometric catalysts utilizing harsh oxidants and reaction conditions perform poorly with randomized product distribution. Paradoxically, the catalysts which are active enough to break C-H also promote overoxidation, resulting in CO₂ generation and reduced carbon balance. Developing catalysts which can break C-H bonds of methane to selectively make useful chemicals at mild conditions is vital to commercialization. Single atom catalysts (SACs) with specifically coordinated metal centers on active support have displayed intrigued reactivity and selectivity for methane oxidation. SACs can significantly reduce the activation energy due to induced electrostatic polarization of the C-H bond to facilitate the accelerated reaction rate at the low reaction temperature. The distinct metal-support interaction can stabilize the intermediate and prevent the overoxidation of the reaction products. The present review accounts for recent progress in the field of SACs for the selective oxidation of CH₄ to C_1-2 oxygenates. The chemical nature of catalytic sites, effects of metal-support interaction, and stabilization of intermediate species on catalysts to minimize overoxidation are thoroughly discussed with a forward-looking perspective to improve the catalytic performance.

Refining details of the structural and electronic properties of the CuB site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations

This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the Cu_B catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His³³, His¹³⁷, and His¹³⁹ on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the Cu_B site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the Cu_B center is an essential factor that makes it less efficient than the Cu_C site in the methane oxidation. Therefore, according to the Cu_B site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O₂ molecule prior to its activation must be necessary. This scenario is less likely to occur in the Cu_C center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.

A computational mechanistic study of CH hydroxylation with mononuclear copper–oxygen complexes

A computational study of methane hydroxylation by oxygen-bound monocopper complexes.

Activation and catalytic transformation of methane under mild conditions

In the last few decades, worldwide scientists have been motivated by the promising production of chemicals from the widely existing methane (CH₄) under mild conditions for both chemical synthesis with low energy consumption and climate remediation. To achieve this goal, a whole library of catalytic chemistries of transforming CH₄ to various products under mild conditions is required to be developed. Worldwide scientists have made significant efforts to reach this goal. These significant efforts have demonstrated the feasibility of oxidation of CH₄ to value-added intermediate compounds including but not limited to CH₃OH, HCHO, HCOOH, and CH₃COOH under mild conditions. The fundamental understanding of these chemical and catalytic transformations of CH₄ under mild conditions have been achieved to some extent, although currently neither a catalyst nor a catalytic process can be used for chemical production under mild conditions at a large scale. In the academic community, over ten different reactions have been developed for converting CH₄ to different types of oxygenates under mild conditions in terms of a relatively low activation or catalysis temperature. However, there is still a lack of a molecular-level understanding of the activation and catalysis processes performed in extremely complex reaction environments under mild conditions. This article reviewed the fundamental understanding of these activation and catalysis achieved so far. Different oxidative activations of CH₄ or catalytic transformations toward chemical production under mild conditions were reviewed in parallel, by which the trend of developing catalysts for a specific reaction was identified and insights into the design of these catalysts were gained. As a whole, this review focused on discussing profound insights gained through endeavors of scientists in this field. It aimed to present a relatively complete picture for the activation and catalytic transformations of CH₄ to chemicals under mild conditions. Finally, suggestions of potential explorations for the production of chemicals from CH₄ under mild conditions were made. The facing challenges to achieve high yield of ideal products were highlighted and possible solutions to tackle them were briefly proposed.

A framework for constructing linear free energy relationships to design molecular transition metal catalysts

A computational framework for ligand-driven design of transition metal complexes is presented in this work. We propose a general procedure for the construction of active site-specific linear free energy relationships (LFERs), which are inspired from Hammett and Taft correlations in organic chemistry and grounded in the activation strain model (ASM). Ligand effects are isolated and quantified in terms of their contribution to interaction and strain energy components of ASM. Scalar descriptors that are easily obtainable are then employed to construct the complete LFER. We successfully demonstrate proof-of-concept by constructing and applying an LFER to CH activation with enzyme-inspired [Cu2O2]2+ complexes. The key benefit of using ASM is a built-in compensation or error cancellation between LFER prediction of interaction and strain terms, resulting in accurate barrier predictions for 37 of the 47 catalysts examined in this study. The LFER is also transferable with respect to level of theory and flexible towards the choice of reference system. The absence of interaction-strain compensation or poor model performance for the remaining systems is a consequence of the approximate nature of the chosen interaction energy descriptor and LFER construction of the strain term, which focuses largely on trends in substrate and not catalyst strain.

Biochemistry of aerobic biological methane oxidation

Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.

Methane activation by ZSM-5-supported transition metal centers

This review focuses on recent fundamental insights about methane dehydroaromatization (MDA) to benzene over ZSM-5-supported transition metal oxide-based catalysts (MO_x/ZSM-5, where M = V, Cr, Mo, W, Re, Fe). Benzene is an important organic intermediate, used for the synthesis of chemicals like ethylbenzene, cumene, cyclohexane, nitrobenzene and alkylbenzene. Current production of benzene is primarily from crude oil processing, but due to the abundant availability of natural gas, there is much recent interest in developing direct processes to convert CH₄ to liquid chemicals. Among the various gas-to-liquid methods, the thermodynamically-limited Methane DehydroAromatization (MDA) to benzene under non-oxidative conditions appears very promising as it circumvents deep oxidation of CH₄ to CO₂ and does not require the use of a co-reactant. The findings from the MDA catalysis literature is critically analyzed with emphasis on in situ and operando spectroscopic characterization to understand the molecular level details regarding the catalytic sites before and during the MDA reaction. Specifically, this review discusses the anchoring sites of the supported MO_x species on the ZSM-5 support, molecular structures of the initial dispersed surface MO_x sites, nature of the active sites during MDA, reaction mechanisms, rate-determining step, kinetics and catalyst activity of the MDA reaction. Finally, suggestions are given regarding future experimental investigations to fill the information gaps currently found in the literature.

Deciphering the origin of million-fold reactivity observed for the open core diiron [HO-FeIII-O-FeIV[double bond, length as m-dash]O]2+ species towards C-H bond activation: role of spin-states, spin-coupling, and spin-cooperation

High-valent metal-oxo species have been characterised as key intermediates in both heme and non-heme enzymes that are found to perform efficient aliphatic hydroxylation, epoxidation, halogenation, and dehydrogenation reactions. Several biomimetic model complexes have been synthesised over the years to mimic both the structure and function of metalloenzymes. The diamond-core [Fe2(μ-O)2] is one of the celebrated models in this context as this has been proposed as the catalytically active species in soluble methane monooxygenase enzymes (sMMO), which perform the challenging chemical conversion of methane to methanol at ease. In this context, a report of open core [HO(L)FeIII-O-FeIV(O)(L)]2+ (1) gains attention as this activates C-H bonds a million-fold faster compared to the diamond-core structure and has the dual catalytic ability to perform hydroxylation as well as desaturation with organic substrates. In this study, we have employed density functional methods to probe the origin of the very high reactivity observed for this complex and also to shed light on how this complex performs efficient hydroxylation and desaturation of alkanes. By modelling fifteen possible spin-states for 1 that could potentially participate in the reaction mechanism, our calculations reveal a doublet ground state for 1 arising from antiferromagnetic coupling between the quartet FeIV centre and the sextet FeIII centre, which regulates the reactivity of this species. The unusual stabilisation of the high-spin ground state for FeIV[double bond, length as m-dash]O is due to the strong overlap of with the orbital, reducing the antibonding interactions via spin-cooperation. The electronic structure features computed for 1 are consistent with experiments offering confidence in the methodology chosen. Further, we have probed various mechanistic pathways for the C-H bond activation as well as -OH rebound/desaturation of alkanes. An extremely small barrier height computed for the first hydrogen atom abstraction by the terminal FeIV[double bond, length as m-dash]O unit was found to be responsible for the million-fold activation observed in the experiments. The barrier height computed for -OH rebound by the FeIII-OH unit is also smaller suggesting a facile hydroxylation of organic substrates by 1. A strong spin-cooperation between the two iron centres also reduces the barrier for second hydrogen atom abstraction, thus making the desaturation pathway competitive. Both the spin-state as well as spin-coupling between the two metal centres play a crucial role in dictating the reactivity for species 1. By exploring various mechanistic pathways, our study unveils the fact that the bridged μ-oxo group is a poor electrophile for both C-H activation as well for -OH rebound. As more and more evidence is gathered in recent years for the open core geometry of sMMO enzymes, the idea of enhancing the reactivity via an open-core motif has far-reaching consequences.

Computational Study on the Light-Induced Oxidation of Iridium-Aqua Complex to Iridium-Oxo Complex over WO3(001) Surface

An iridium aqua complex [Ir^III(η⁵-C₅Me₅){bpy(COOH)₂}(H₂O)]²⁺ under visible light irradiation has been experimentally reported to form an iridium-oxo (Ir-oxo) complex [Ir^V(η⁵-C₅Me₅){bpy(COOH)₂}(O)]²⁺, which oxidizes H₂O to O₂. However, the mechanism for the formation of this Ir-oxo complex remains unclear, due to the difficulties in observing the unstable Ir-oxo complex and computing light-induced systems having different numbers of electrons. In this study, we perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to investigate more in detail our previously proposed deprotonation and light-induced oxidation reactions composing the formation of the Ir-oxo complex. In particular, we discuss effects of light irradiation and WO₃ support on the formation of the Ir-oxo complex. We suggest two distinct mechanisms, that is, direct and indirect for the light-induced oxidation. In the direct mechanism electrons are directly transferred from the occupied π* orbitals of Ir^III-OH or Ir^IV=O^• to the conduction band of the WO₃ surface, whereas in the indirect mechanism electrons are first excited from the valence band to the conduction band of the WO₃ surface due to the UV light, and then the resultant electron hole oxidizes the Ir complex. In the direct mechanism, in particular, we found that the lowest energy of the anode's conduction band determines the adsorption wavelength of the light irradiation, enabling us to predict alternative semiconductor anodes for more efficient formation of the Ir-oxo complex.

Theoretical study of aromatic hydroxylation of the [Cu2(H-XYL)O2]2+ complex mediated by a side-on peroxo dicopper core and Cu-ligand effects

In this work, the aromatic hydroxylation mechanism of the [Cu₂(H-XYL)O₂]²⁺ complex mediated by a peroxo dicopper core and Cu-ligand effects are investigated by using hybrid density functional theory (DFT) and the broken symmetry B3LYP method. Based on the calculated free-energy profiles, we proposed two available mechanisms. The first reaction steps of both mechanisms involve concerted O-O bond cleavage and C-O bond formation and the second step involves the Wagner-Meerwein rearrangement of the substrate by a [1,2] H shift (H_A shift from C_A to C_C) or (H_A shift from C_A to O_A) across the phenyl ring to form stable dienone intermediates, and this is followed by the protonation of bridging oxygen atoms to produce the final hydroxylated dicopper(ii) product. The H_A shift from C_A to C_C mechanism is the energetically most favorable, in which the first reaction step is the rate-limiting reaction, with a calculated free-energy barrier of 19.0 kcal mol^-1 and a deuterium kinetic isotope effect of 1.0, in agreement with experimental observations. The calculation also shows that the reaction started from the P-type species of [Cu₂(H-XYL)O₂]²⁺ which is capable of mediating the direct hydroxylation of aromatic substrates without the intermediacy of an O-type species. Finally, we designed some new complexes with different Cu-ligands and found the complex that computationally possesses a higher activity in mediating the hydroxylation of the ligand based aromatic substrate; here, Cu loses a pyridyl ligand donor by dissociation, compared to the [Cu₂(H-XYL)O₂]²⁺ complex.

Selective oxidation of methane to methanol with H2O2 over an Fe-MFI zeolite catalyst using sulfolane solvent

The effect of reaction conditions for direct oxidation of methane to methanol over Fe-MFI zeolite with H2O2 has been investigated. Sulfolane has been proved to be an efficient solvent for liquid-phase methane oxidation. A sulfolane/water mixture with an appropriate proportion led to an extremely high methanol production with a high selectivity.

Copper-Promoted Functionalization of Organic Molecules: from Biologically Relevant Cu/O2 Model Systems to Organometallic Transformations

Copper is one of the most abundant and less toxic transition metals. Nature takes advantage of the bioavailability and rich redox chemistry of Cu to carry out oxygenase and oxidase organic transformations using O₂ (or H₂O₂) as oxidant. Inspired by the reactivity of these Cu-dependent metalloenzymes, chemists have developed synthetic protocols to functionalize organic molecules under enviormentally benign conditions. Copper also promotes other transformations usually catalyzed by 4d and 5d transition metals (Pd, Pt, Rh, etc.) such as nitrene insertions or C-C and C-heteroatom coupling reactions. In this review, we summarized the most relevant research in which copper promotes or catalyzes the functionalization of organic molecules, including biological catalysis, bioinspired model systems, and organometallic reactivity. The reaction mechanisms by which these processes take place are discussed in detail.

Computational strategies to probe CH activation in dioxo-dicopper complexes

We employ density functional theory and energy decomposition analysis to probe the mechanism of CH activation in dioxo-dicopper complexes. The electrophilicity of monodentate N-donor ligands coordinated to Cu is systematically varied to examine the response of barriers to the two proposed pathways - one-step oxo-insertion and two-step radical recombination. Electron-withdrawing ligand stabilize the oxo-insertion transition state via charge transfer interactions, and therefore lead to lower barriers. On the other hand, barriers to the CH activation step in the radical recombination mechanism exhibit almost no dependence on N-donor electrophilicity. Based on the similarities between calculated and experimental Hammett relationships, the oxo-insertion pathway appears to be the preferred mechanism of CH activation in dioxo-dicopper catalysts.

Theoretical Overview of Methane Hydroxylation by Copper-Oxygen Species in Enzymatic and Zeolitic Catalysts

As fossil-based energy sources become more depleted and with renewable-energy technologies still in a very early stage of development, the utilization of highly abundant methane as a transitional solution for current energy demands is highly important despite difficulties in transport and storage. Technologies enabling the conversion of methane to liquid/condensable energy carriers that can be easily transported and integrated into the existing chemical infrastructures are therefore essential. Although there commercially exists a two-step gas-to-liquid process involving syngas production, a novel route of methane conversion that can circumvent the high-cost production of syngas should be developed. Among all of the conceptually possible methods for converting methane to methanol, methane hydroxylation (CH₄ + ¹/₂O₂ → CH₃OH) at low temperature seems to be the most viable since it provides a direct route of conversion and allows a much lower operational cost. However, it is hampered by the fact that the complete oxidation to CO₂ is thermodynamically more favored. To overcome this, an effective catalyst that is able to "mildly" oxidize methane and stabilize the resultant methyl radical toward methanol formation is required. Particulate methane monooxygenase (pMMO) and copper-exchanged zeolites are two catalysts known to hydroxylate methane into methanol at low temperature with high selectivity. Having been studied for more than 30 years, these copper-cored catalysts are still relevant topics of discussion since the actual structure of the active sites has not been agreed upon, and thus, the reaction mechanism and factors influencing their reactivity and productivity are yet to be understood. Density functional theory (DFT) has provided us with a powerful computational tool for accomplishing these tasks. This Account presents an overview of the recent progress in the computational elucidation of the catalytic mechanism of methane hydroxylation by mono-, di-, and trinuclear copper sites in pMMO and Cu-exchanged zeolites as well as its correlations to the influencing factors that must be controlled to achieve higher reactivity. First, we briefly introduce the catalytic mechanism of a bare CuO⁺ cation as the simplest copper-oxo system in methane hydroxylation. The system is then extended to the copper-oxo species in pMMO and zeolites, and the radical and nonradical mechanisms are examined. Investigations of the reactivities of mononuclear and dinuclear copper-oxo species in the pMMO active site suggest that the bis(μ-oxo)Cu^IICu^III, (μ-oxo)(μ-hydroxo)Cu^IICu^III, and Cu^IIIO species are important for the catalytic activity of pMMO. In the case of Cu-exchanged zeolites, as the mono(μ-oxo)Cu^IICu^II and tris(μ-oxo)Cu^IICu^IIICu^III active sites have been fully characterized in experiments, here we discuss the effects of zeolite structures on the geometry and reactivity of the active sites.

Metals and Methanotrophy

Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

Particulate methane monooxygenase (pMMO) is one of the few enzymes that can activate methane. The metal content of this enzyme has been highly controversial, with suggestions of a dinuclear Fe site or mono-, di-, or trinuclear Cu sites. Crystal structures have shown a mono- or dinuclear Cu site, but the resolution was low and the geometry of the dinuclear site unusual. We have employed quantum refinement (crystallographic refinement enhanced with quantum-mechanical calculations) to improve the structure of the active site. We compared a number of different mono- and dinuclear geometries, in some cases enhanced with more protein ligands or one or two water molecules, to determine which structure fits two sets of crystallographic raw data best. In all cases, the best results were obtained with mononuclear Cu sites, occasionally with an extra water molecule. Thus, we conclude that there is no crystallographic support for a dinuclear Cu site in pMMO.

Rationally designing mixed Cu–(μ-O)–M (M = Cu, Ag, Zn, Au) centers over zeolite materials with high catalytic activity towards methane activation

The direct conversion of methane to methanol on [Cu(μ-O)M]²⁺ (M = Cu, Ag, Zn, Au) bimetal centers in ZSM-5 zeolite is investigated using periodic DFT for the first time.

A Structurally Characterized CuIII Complex Supported by a Bis(anilido) Ligand and Its Oxidative Catalytic Activity

Three copper(II) complexes of the (R,R)-N,N'-bis(3,5-di-tert-butyl-2-aminobenzylidene)-1,2-diaminocyclohexane ligand, namely [Cu(^N L)], [Cu(^N LH)]⁺ and [Cu(^N LH₂ )]²⁺ , were prepared and structurally characterized. In [Cu(^N LH₂ )]²⁺ the copper ion lies in an octahedral geometry with the aniline groups coordinated in equatorial positions. In [Cu(^N L)] the anilines are deprotonated (anilido moieties) and coordinated to an almost square-planar metal ion. Complex [Cu(^N L)] displays two oxidation waves at E_1/2^ox, 1 =-0.14 V and E_1/2^ox, 2 =0.36 V vs. Fc⁺ /Fc in CH₂ Cl₂ . Complex [Cu(^N LH₂ )]²⁺ displays an irreversible oxidation wave at high potential (1.21 V), but shows a readily accessible and reversible metal-centered reduction at E_1/2^red =-0.67 V (Cu^II /Cu^I redox couple). Oxidation of [Cu(^N L)] by AgSbF₆ produces [Cu(^N L)](SbF₆ ), which was isolated as single crystals. X-ray structure analysis discloses a contraction of the coordination sphere by 0.05 Å upon oxidation, supporting a metal-centered process. Complex [Cu(^N L)](SbF₆ ) displays an intense NIR band at 1260 nm corresponding to an anilido-to-copper(III) charge transfer transition. This compound slowly evolves in CH₂ Cl₂ solution towards [Cu(^N LH)](SbF₆ ), which is a copper(II) complex comprised of both anilido and aniline groups coordinated to the metal center. The copper(III) complex [Cu(^N L)](SbF₆ ) is an efficient catalyst for benzyl alcohol oxidation, with 236 TON in 24 h at 298 K, without additives other than oxygen and a base.

A tale of two methane monooxygenases

Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.

Substrate and Lewis Acid Coordination Promote O-O Bond Cleavage of an Unreactive L2CuII2(O22-) Species to Form L2CuIII2(O)2 Cores with Enhanced Oxidative Reactivity

Copper-dependent metalloenzymes are widespread throughout metabolic pathways, coupling the reduction of O2 with the oxidation of organic substrates. Small-molecule synthetic analogs are useful platforms to generate L/Cu/O2 species that reproduce the structural, spectroscopic, and reactive properties of some copper-/O2-dependent enzymes. Landmark studies have shown that the conversion between dicopper(II)-peroxo species (L2CuII2(O22-) either side-on peroxo, SP, or end-on trans-peroxo, TP) and dicopper(III)-bis(μ-oxo) (L2CuIII2(O2-)2: O) can be controlled through ligand design, reaction conditions (temperature, solvent, and counteranion), or substrate coordination. We recently published ( J. Am. Chem. Soc. 2012 , 134 , 8513 , DOI: 10.1021/ja300674m ) the crystal structure of an unusual SP species [(MeAN)2CuII2(O22-)]2+ (SPMeAN, MeAN: N-methyl-N,N-bis[3-(dimethylamino)propyl]amine) that featured an elongated O-O bond but did not lead to O-O cleavage or reactivity toward external substrates. Herein, we report that SPMeAN can be activated to generate OMeAN and perform the oxidation of external substrates by two complementary strategies: (i) coordination of substituted sodium phenolates to form the substrate-bound OMeAN-RPhO- species that leads to ortho-hydroxylation in a tyrosinase-like fashion and (ii) addition of stoichiometric amounts (1 or 2 equiv) of Lewis acids (LA's) to form an unprecedented series of O-type species (OMeAN-LA) able to oxidize C-H and O-H bonds. Spectroscopic, computational, and mechanistic studies emphasize the unique plasticity of the SPMeAN core, which combines the assembly of exogenous reagents in the primary (phenolates) and secondary (Lewis acids association to the MeAN ligand) coordination spheres with O-O cleavage. These findings are reminiscent of the strategy followed by several metalloproteins and highlight the possible implication of O-type species in copper-/dioxygen-dependent enzymes such as tyrosinase (Ty) and particulate methane monooxygenase (pMMO).