Dicopper Site Research Articles

Rapid and Green Fabrication of Nanozyme with Geminal CuN3O Configuration for Efficient Catecholase-Mimicking.

Fabrication of nanozyme with catecholase-like catalytic activity faces the great challenge of merging outstanding activity with low cost as well as simple, rapid, and low-energy-consumed production, restricting its industrial applications. Herein, an inexpensive yet robust nanozyme (i.e., DT-Cu) via simple one-step coordination between diaminotriazole (DT) and CuSO4 within 1h in water at room temperature is constructed. The asymmetric dicopper site with CuN3O configuration for each copper as well as Cu─O bond length of ≈1.83 Å and Cu···Cu distance of ≈3.5 Å in DT-Cu resemble those in catechol oxidase (CO), which ensure its prominent intrinsic activity, outperforming most CO-mimicking nanozymes and artificial homogeneous catalysts. The use of inexpensive DT/CuSO4 in this one-pot strategy endows DT-Cu with only ≈20% cost of natural CO per activity unit. During catalysis, O2 experienced a 4e-dominated reduction process accompanied by the formation of 1O2 and H2O2 intermediates and the product of H2O. Benefiting from the low cost as well as the distinctive structure and superior intrinsic activity, DT-Cu presents potential applications ranging from biocatalysis to analytical detection of biomolecules such as epinephrine and beyond.

Dicopper(I) Sites Confined in a Single Metal-Organic Layer Boosting the Electroreduction of CO2 to CH4 in a Neutral Electrolyte.

It is challenging and important to achieve high performance for an electrochemical CO2 reduction reaction (eCO2RR) to yield CH4 under neutral conditions. So far, most of the reported active sites for eCO2RR to yield CH4 are single metal sites; the performances are far below the commercial requirements. Herein, we reported a nanosheet metal-organic layer in single-layer, namely, [Cu2(obpy)2] (Cuobpy-SL, Hobpy = 1H-[2,2']bipyridinyl-6-one), possessing dicopper(I) sites for eCO2RR to yield CH4 in a neutral aqueous solution. Detailed examination of Cuobpy-SL revealed high performance for CH4 production with a faradic efficiency of 82(1)% and a current density of ∼90 mA cm-2 at -1.4 V vs. reversible hydrogen electrode (RHE). No obvious degradation was observed over 100 h of continuous operation, representing a remarkable performance to date. Mechanism studies showed that compared with the conventional single-copper sites and completely exposed dicopper(I) sites, the dicopper(I) sites in the confined space formed by the molecular stacking have a strong affinity to key C1 intermediates such as *CO, *CHO, and *CH2O to facilitate the CH4 production, yet inhibiting C-C coupling.

Mechanistic insight into the effect of active site motif structures on direct oxidation of methane to methanol over Cu-ZSM-5.

Direct oxidation of methane to methanol (DMTM), a highly challenging reaction in C1 chemistry, has attracted lots of attention. Herein, we investigate the continuous H2O-mediated N2O-DMTM over a series of Cu-ZSM-5-n zeolites prepared by a solid-state ion-exchange method. Excellent CH3OH productivity (194.8 μmol gcat-1 h-1) and selectivity (67.1%) can be achieved over Cu-ZSM-5-0.3%, which surpasses most recently reported zeolite catalysts. The effect of the active site motif structure on the reaction was systematically investigated by the combined experimental and theoretical studies. It has been revealed that both the monomeric [Cu]+ and binuclear [Cu]+-[Cu]+ sites function to produce CH3OH, following the radical rebound mechanism, wherein the latter one plays a dominant role due to the synergistic effect of neighboring [Cu]+ that can efficiently reduce the N2O dissociation barrier to generate active oxygen for CH4 oxidation. Microkinetic modeling results further show that the dicopper site possesses a much higher net reaction rate (1.23 × 105 s-1) than the monomeric Cu site (0.962 s-1); moreover, H2O can shift the rate determining step from the CH3OH desorption step to the N2O dissociation step over the dicopper site, thereby efficiently favoring CH3OH production and resisting carbon deposition. Generally, the study in the present work would substantially favor other highly efficient catalyst designs.

Efficient electroreduction of CO to acetate using a metal-azolate framework with dicopper active sites.

Electrochemical reduction of CO to value-added products, especially C2 products, provides a potential approach to achieve carbon neutrality and overcome the energy crisis. Herein, we report a metal-azolate framework (CuBpz) with dicopper active sites as an electrocatalyst for the electrochemical CO reduction reaction (eCORR). As a result, CuBpz achieved an impressive faradaic efficiency (FE) of 47.8% for yielding acetate with a current density of -200 mA cm-2, while no obvious degradation was observed over 60 hours of continuous operation at a current density of -200 mA cm-2. Mechanism studies revealed that the dicopper site can promote C-C coupling between two C1 intermediates, thereby being conducive to the generation of the key *CH2COOH intermediate.

A nucleotide-copper(II) complex possessing a monooxygenase-like catalytic function.

The de novo design of artificial biocatalysts with enzyme-like active sites and catalytic functions has long been an attractive yet challenging goal. In this study, we present a nucleotide-Cu2+ complex, synthesized through a one-pot approach, capable of catalyzing ortho-hydroxylation reactions resembling those of minimalist monooxygenases. Both experimental and theoretical findings demonstrate that the catalyst, in which Cu2+ coordinates with both the nucleobase and phosphate moieties, forms a ternary-complex intermediate with H2O2 and tyramine substrates through multiple weak interactions. The subsequent electron transfer and hydrogen (or proton) transfer steps lead to the ortho-hydroxylation of tyramine, where the single copper center exhibits a similar function to natural dicopper sites. Moreover, Cu2+ bound to nucleotides or oligonucleotides exhibits thermophilic catalytic properties within the temperature range of 25 °C to 75 °C, while native enzymes are fully deactivated above 35 °C. This study may provide insights for the future design of oxidase-mimetic catalysts and serve as a guide for the design of primitive metallocentre-dependent enzymes.

Structure of Selective and Nonselective Dicopper (II) Sites in CuMFI for Methane Oxidation to Methanol

Structure of Selective and Nonselective Dicopper (II) Sites in CuMFI for Methane Oxidation to Methanol

A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity.

De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.

Cooperative Catalysis between Dual Copper Centers in a Metal-Organic Framework for Efficient Detoxification of Chemical Warfare Agent Simulants.

Chemical warfare agents (CWAs) are among the most lethal chemicals known to humans. Thus, developing multifunctional catalysts for highly efficient detoxification of various CWAs is of great importance. In this work, we developed a robust copper tetrazolate metal-organic framework (MOF) catalyst containing a dicopper unit similar to the coordination geometry of the active sites of natural phosphatase and tyrosinase enzymes. This catalyst aided in phosphate ester bond hydrolysis and hydrogen peroxide decomposition, ultimately achieving high detoxification efficiency against both a nerve agent simulant (diethoxy-phosphoryl cyanide (DECP)) with a half-life of 3.5 min and a sulfur mustard simulant (2-chloroethyl ethyl sulfide (CEES)) with a half-life of 4.5 min, making it competitive with other reported materials. The dicopper sites in ZZU-282 provide versatile binding modes with the substrates, thereby promoting the activation of substrates and enhancing the catalytic efficiency. A combination of postmodified metal exchange control experiments, density functional theory calculations, and catalytic evaluations confirmed that dual Cu sites are the active centers promoting the catalytic reaction. This study offers a new design perspective to achieve advanced catalysts for CWA detoxification.

Symmetry-Adapted Synthesis of Dicopper Oxidases with Divergent Dioxygen Reactivity.

Artificial metalloenzymes have fed our understanding of how inorganic reactivities emerge, evolve, and diversify in protein environments. Herein, we created dinuclear copper oxidases by genetically encoding a metal-ligating unnatural amino acid (bpy-Ala) per protomer in the vicinity of the innate C2 rotational axis of a homo-oligomeric protein. The inherent protein symmetry allows the precise multiplication and placement of two Cu(bpy) species. Depending on the location of bpy-Ala, the tailor-made metalloenzymes exhibited electronically uncoupled or coupled dicopper sites. Consequently, they displayed various reactivities with dioxygen associated with multiple protons and electrons, illustrating a diverse chemical repertoire of artificial copper-dependent enzymes.

A Porous π-π Stacking Framework with Dicopper(I) Sites and Adjacent Proton Relays for Electroreduction of CO2 to C2+ Products.

Crystalline porous materials sustained by supramolecular interactions (e.g., π-π stacking interactions) are a type of molecular crystals showing considerable stability, but their applications are rarely reported due to the high difficulty of their construction. Herein, a stable π-π stacking framework formed by a trinuclear copper(I) compound [Cu3(HBtz)3(Btz)Cl2] (CuBtz, HBtz = benzotriazole) with pyrazolate-bridged dicopper(I) sites is reported and employed for electrochemical CO2 reduction, showing an impressive performance of 73.7 ± 2.8% Faradaic efficiency for C2+ products [i.e., ethylene (44%), ethanol (21%), acetate (4.7%), and propanol (4%)] with a current density of 7.9 mA cm-2 at the potential of -1.3 V versus RHE in an H-type cell and a Faradic efficiency (61.6%) of C2+ products with a current density of ≈1 A cm-2 and a reaction rate of 5639 μmol m-2 s-1 at the potential of -1.6 V versus RHE in a flow cell device, representing an impressive performance reported to date. In-situ infrared spectroscopy, density functional theory calculations, and control experiments revealed that the uncoordinated nitrogen atoms of benzotriazolates in the immediate vicinity can act as proton relays and cooperate with the dicopper(I) site to promote the hydrogenation process of the *CO intermediate and the C-C coupling, resulting in the highly selective electroreduction of CO2 to C2+ products.

Antisymmetric Spin Exchange in a μ-1,2-Peroxodicopper(II) Complex with an Orthogonal Cu-O-O-Cu Arrangement and S = 1 Spin Ground State Characterized by THz-EPR.

A unique type of Cu2/O2 adduct with orthogonal (close to 90°) Cu–O–O–Cu arrangement has been proposed for initial stages of O2 binding at biological type III dicopper sites, and targeted ligand design has now allowed us to emulate such an adduct in a pyrazolate-based μ-η1:η1-peroxodicopper(II) complex (2) with Cu–O–O–Cu torsion φ of 87°, coined ⊥P intermediate. Full characterization of 2, including X-ray diffraction (dO–O = 1.452 Å) and Raman spectroscopy (ν̃O–O = 807 cm–1), completes a series of closely related Cu2/O2 intermediates featuring μ-η1:η1-peroxodicopper(II) cores with φ ranging from 55° (A, cis-peroxo CP; BrinkmeierA.et al., J. Am. Chem. Soc.2021, 143, 1036134191490) via 87° (2, ⊥P type) up to 104° (B, approaching trans-peroxo TP; KindermannN.et al., Angew. Chem., Int. Ed.2015, 54, 1738). SQUID magnetometry revealed ferromagnetic interaction of the CuII ions and a triplet (St = 1) ground state in 2. Frequency-domain THz-EPR has been employed to quantitatively investigate the spin systems of 2 and B. Magnetic transitions within the triplet ground states confirmed their substantial zero-field splittings (ZFS) suggested by magnetometry. Formally forbidden triplet-to-singlet transitions at 56 (2) and 157 cm–1 (B), which are in agreement with the exchange coupling strengths Jiso inferred from SQUID data, are reported for the first time for coupled dicopper(II) complexes. Rigorous analysis by spin-Hamiltonian-based simulations attributed the corresponding nonzero transition probabilities and the ZFS to substantial antisymmetric (Dzyaloshinskii–Moriya) exchange d and provided robust values and orientations for the d, J, and g tensors. These interactions can be correlated with the Cu–O–O–Cu geometries, revealing a linear increase of Jiso with the Cu–O–O–Cu torsion and a strong linear decrease with the Cu–O–O angle. Relevance of the ⊥P intermediate for O2 activation at type III dicopper sites and a potential role of antisymmetric exchange in the concomitant intersystem crossing are proposed.

Histamine derived dimer of µ-Chlorido-µ-Phenoxido Dicopper(II) complex as a potential enzyme mimic with catecholase activity

A new copper(II) complex, [Cu2(L1)(µ-Cl)2]2 (C1), of the binucleating 2,6-bis((2-(4′-imidazolyl)ethyl)aminomethylidene)-4-methylphenol (HL1) with N4O binding sites, has been synthesized to investigate as potential structural and functional model for catecholase activity of the dicopper(II) site. It has been characterized by spectroscopic techniques and X-ray crystallography. The complex C1 exists as chlorido bridged dimer of binuclear copper(II) units, each possessing one end-off compartmental ligand (L1) with endogenous µ-phenoxido and exogenous µ-chlorido groups leading to intermetallic distance Cu1···Cu2 of 3.129 Å and Cu1-O1(phenoxo)-Cu2 angle of 107.67(10)o. Each copper(II) center has distorted octahedral geometry with bridging by chlorides in the tetranuclear dimer. The crystal system is monoclinc with space group P21/c. Magnetic measurements reveal that C1 is strongly antiferromagnetically coupled with J = − 115.663 ± 0.82547 cm−1. The catecholase activity of the complex has been evaluated by oxidation of 3,5-di(tert-butyl)catechol and 4-methyl catechol to the corresponding quinones under aerobic conditions. A kinetic treatment on the basis of the Michaelis-Menten model has been applied for the kinetic study. The complex is found to be selective for the substrates with higher Vmax = 8.2726x10−8 M s−1 and Km = 0.0107 M for 3,5-DTBC at 30 °C as compared to Vmax = 5.0371x10−8 M s−1 and Km = 0.027 M for 4-methyl catechol at 50 °C while it is found to be practically inactive for dopamine, 2,3-dihydroxy naphthalene and pyrocatechol oxidation.

Cover Feature: DFT Analysis of Methane C−H Activation and Over‐Oxidation by [Cu2O]2+ and [Cu2O2]2+ Sites in Zeolite Mordenite: Intra‐ versus Inter‐site Over‐Oxidation (ChemPhysChem 24/2021)

The Cover Feature illustrates the inter-site nature of methane over-oxidation by dicopper sites in zeolites used for direct methane-to-methanol conversion. Intermediates from methane oxidation can be stabilized at the immediate active site or at Brønsted acid sites, without over-oxidation. This ensures high methanol selectivities. More information can be found in the Article by Samuel O. Odoh and co-workers.

DFT Analysis of Methane C-H Activation and Over-Oxidation by [Cu2 O]2+ and [Cu2 O2 ]2+ Sites in Zeolite Mordenite: Intra- versus Inter-site Over-Oxidation.

Methane over-oxidation by copper-exchanged zeolites prevents realization of high-yield catalytic conversion. However, there has been little description of the mechanism for methane over-oxidation at the copper active sites of these zeolites. Using density functional theory (DFT) computations, we reported that tricopper [Cu3 O3 ]2+ active sites can over-oxidize methane. However, the role of [Cu3 O3 ]2+ sites in methane-to-methanol conversion remains under debate. Here, we examine methane over-oxidation by dicopper [Cu2 O]2+ and [Cu2 O2 ]2+ sites using DFT in zeolite mordenite (MOR). For [Cu2 O2 ]2+ , we considered the μ-(η2 :η2 ) peroxo-, and bis(μ-oxo) motifs. These sites were considered in the eight-membered (8MR) ring of MOR. μ-(η2 :η2 ) peroxo sites are unstable relative to the bis(μ-oxo) motif with a small interconversion barrier. Unlike [Cu2 O]2+ which is active for methane C-H activation, [Cu2 O2 ]2+ has a very large methane C-H activation barrier in the 8MR. Stabilization of methanol and methyl at unreacted dicopper sites however leads to over-oxidation via sequential hydrogen atom abstraction steps. For methanol, these are initiated by abstraction of the CH3 group, followed by OH and can proceed near 200 °C. Thus, for [Cu2 O]2+ and [Cu2 O2 ]2+ species, over-oxidation is an inter-site process. We discuss the implications of these findings for methanol selectivity, especially in comparison to the intra-site process for [Cu3 O3 ]2+ sites and the role of Brønsted acid sites.

Coordination of the Copper Centers in Particulate Methane Monooxygenase: Comparison between Methanotrophs and Characterization of the CuC Site by EPR and ENDOR Spectroscopies.

In nature, methane is oxidized to methanol by two enzymes, the iron-dependent soluble methane monooxygenase (sMMO) and the copper-dependent particulate MMO (pMMO). While sMMO's diiron metal active site is spectroscopically and structurally well-characterized, pMMO's copper sites are not. Recent EPR and ENDOR studies have established the presence of two monocopper sites, but the coordination environment of only one has been determined, that within the PmoB subunit and denoted CuB. Moreover, this recent work only focused on a type I methanotrophic pMMO, while previous observations of the type II enzyme were interpreted in terms of the presence of a dicopper site. First, this report shows that the type II Methylocystis species strain Rockwell pMMO, like the type I pMMOs, contains two monocopper sites and that its CuB site has a coordination environment identical to that of type I enzymes. As such, for the full range of pMMOs this report completes the refutation of prior and ongoing suggestions of multicopper sites. Second, and of primary importance, EPR/ENDOR measurements (a) for the first time establish the coordination environment of the spectroscopically observed site, provisionally denoted CuC, in both types of pMMO, thereby (b) establishing the assignment of this site observed by EPR to the crystallographically observed metal-binding site in the PmoC subunit. Finally, these results further indicate that CuC is the likely site of biological methane oxidation by pMMO, a conclusion that will serve as a foundation for proposals regarding the mechanism of this reaction.

Role of Amino Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMO.

Formation of an active oxygen species at the dicopper site of pMMO is studied by using density functional theory (DFT) calculations. The role of the amino acid residues of tyrosine (Tyr374) and glutamate (Glu35) located in the second coordination sphere of the dicopper site is discussed in detail. The phenolic proton of the tyrosine residue is transferred to the Cu2O2 core in a two-step manner via the glutamate residue, and an electron is directly transferred to the Cu2O2 core. These proton- and electron-transfer processes induce the O-O bond cleavage of the μ-η2:η2-peroxodicopper(II) species to form the (μ-oxo)(μ-hydroxo)CuIICuIII species, which is able to play a key role of methane hydroxylation at the dicopper site of pMMO ( Inorg. Chem. 2013 , 52 , 7907 ). This proton-coupled electron-transfer mechanism is a little different from that in tyrosinase in that the proton of substrate tyrosine is directly transferred to the dicopper site ( J. Am. Chem. Soc. 2006 , 128 , 9873 ) because there is no proton acceptor in the vicinity of the dicopper site of tyrosinase. The rate-determining step for the formation of the (μ-oxo)(μ-hydroxo)CuIICuIII species is determined to be the O-O bond cleavage. These results shed new light on the interpretation of the role of the tyrosine and glutamate residues located in the second coordination sphere of the dicopper site of pMMO.

The PmoB subunit of particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath): The CuI sponge and its function

In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward CuI ions. To elucidate the high copper affinity of the subunit, the full-length PmoB, and the N-terminal truncated mutants PmoB33–414 and PmoB55–414, each fused to the maltose-binding protein (MBP), are cloned and over-expressed into Escherichia coli (E. coli) K12 TB1 cells. The Y374F, Y374S and M300L mutants of these protein constructs are also studied. When this E. coli is grown with the pmoB gene in 1.0 mM CuII, it behaves like M. capsulatus (Bath) cultured under high copper stress with abundant membrane accumulation and high CuI content. The recombinant PmoB proteins are verified by Western blotting of antibodies directed against the MBP sub-domain in each of the copper-enriched PmoB proteins. Cu K-edge X-ray absorption near edge spectroscopy (XANES) of the copper ions confirms that all the PmoB recombinants are CuI proteins. All the PmoB proteins show evidence of a “dicopper site” according to analysis of the Cu extended X-ray absorption edge fine structure (EXAFS) of the membranes. No specific activities toward methane and propene oxidation are observed with the recombinant membrane-bound PmoB proteins. However, significant production of hydrogen peroxide is observed in the case of the PmoB33–414 mutant. Reaction of the dicopper site with dioxygen produces hydrogen peroxide and leads to oxidation of the CuI ions residing in the C-terminal sub-domain of the PmoB subunit.

The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment.

The direct conversion of methane to methanol (MTM) is a reaction that has the potential to disrupt a great part of the synthesis gas-derived chemical industry. However, despite many decades of research, active enough catalysts and suitable processes for industrial application are still not available. Recently, several copper-exchanged zeolites have shown considerable activity and selectivity in the direct MTM reaction. Understanding the nature of the active site in these materials is essential for any further development in the field. Herein, we apply multivariate curve resolution analysis of X-ray absorption spectroscopy data to accurately quantify the fraction of active Cu in Cu-MOR (MOR = mordenite), allowing an unambiguous determination of the active site nuclearity as a dicopper site. By rationalizing the compositional parameters and reaction conditions, we achieve the highest methanol yield per Cu yet reported for MTM over Cu-zeolites, of 0.47 mol/mol.

Hydration facilitates oxygenation of hemocyanin: perspectives from molecular dynamics simulations.

Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein. The oxygenation effect on the overall structure of the protein or polypeptide subunit was further explored via gyration radii evaluated for the metal-binding domain and for the whole subunit. The evaluation of hydration dynamics was carried out to understand the water mediated role of amino acid residues of the solvent tunnel facilitating the entry of oxygen molecule to the dicopper site of hemocyanin.

Roles of Water Molecules in Modulating the Reactivity of Dioxygen-Bound Cu-ZSM-5 toward Methane: A Theoretical Prediction

We propose theoretically that the reactivity of O2-bound Cu-ZSM-5 toward methane is enhanced by the presence of one water molecule near a dinuclear copper site inside a 10-membered ring of the zeolite cavity. The current study employed density functional theory (DFT) calculations with the B3LYP functional to elucidate reaction intermediates during dioxygen activation by Cu-ZSM-5 in the presence of one water molecule attached to a dicopper site. The initial event is the formation of a hydroperoxo species bridged by the dicopper site via an H atom transfer from an attached water to the bound dioxygen. After the formation of the intermediate, the hydroperoxo O–O bond is completely cleaved to form radical oxygen containing intermediates, such as a Cu–O–Cu species bound by two OH groups (HO–Cu–O–Cu–OH), as well as a copper oxyl group containing intermediate (HO–Cu–OH–CuO). The radical oxygen containing intermediates can cleave a methane C–H bond in a homolytic fashion. Examining the barrier for the C–H bond ac...