Oxidation of a [Cu2S] complex by N2O and CO2: insights into a role of tetranuclearity in the CuZ site of nitrous oxide reductase

Cu site differentiation in tetracopper(i) sulfide clusters enables biomimetic N2O reduction

Copper clusters feature prominently in both metalloenzymes and synthetic nanoclusters that mediate catalytic redox transformations of gaseous small molecules. Such reactions are critical to biological energy conversion and are expected to be crucial parts of renewable energy economies. However, the precise roles of individual metal atoms within clusters are difficult to elucidate, particularly for cluster systems that are dynamic under operating conditions. Here, we present a metal site-specific analysis of synthetic Cu4(μ4-S) clusters that mimic the Cu Z active site of the nitrous oxide reductase enzyme. Leveraging the ability to obtain structural snapshots of both inactive and active forms of the synthetic model system, we analyzed both states using resonant X-ray diffraction anomalous fine structure (DAFS), a technique that enables X-ray absorption profiles of individual metal sites within a cluster to be extracted independently. Using DAFS, we found that a change in cluster geometry between the inactive and active states is correlated to Cu site differentiation that is presumably required for efficient activation of N2O gas. More precisely, we hypothesize that the Cu δ+⋯Cu δ- pairs produced upon site differentiation are poised for N2O activation, as supported by computational modeling. These results provide an unprecedented level of detail on the roles of individual metal sites within the synthetic cluster system and how those roles interplay with cluster geometry to impact the reactivity function. We expect this fundamental knowledge to inform understanding of metal clusters in settings ranging from (bio)molecular to nanocluster to extended solid systems involved in energy conversion.

Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus

Copper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N2O to yield N2. It contains two metal centers, the binuclear electron transfer site CuA, and the unique, tetranuclear CuZ center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N2OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The CuA site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the CuZ cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca2+, K+, and Cl-. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] CuZ site, a mechanistic model is presented, with a structurally flexible CuZ center that does not require the complete dissociation of a sulfide prior to N2O binding.

A mesoionic carbene stabilized nickel(II) hydroxide complex: a facile precursor for C-H activation chemistry

We report the synthesis of a new nickel(II) hydroxide complex 2 supported by a rigid, tridentate triazolylidene-carbazolid ligand. The complex can be accessed in high yields following a simple and stepwise extraction protocol using dichloromethane and aqueous ammonium chloride followed by aqeous sodium hydroxide solution. We found that complex 2 is highly basic, undergoing various deprotonation/desilylation reactions with E-H and C-H acidic and silylated compounds. In this context we synthesized a variety of novel, functionalized nickel(II) complexes with trimethylsilylolate (3), trityl sulfide (4), tosyl amide (5), azido (6), pyridine (7), acetylide (8, 9), fluoroarene (10 & 11) and enolate (12) ligands. We furthermore found that 2 reacts with malonic acid dimethyl ester in a knoevennagel-type condensation reaction, giving access to a new enolate ligand in complex 13, consisting of two malonic acid units. Furthermore, complex 2 reacts with acetonitrile to form the cyanido complex 14. The formation of complexes 13 and 14 is particularly interesting, as they underline the potential of complex 2 in both C-C bond formation and cleavage reactions.

Divergent CO2 Activation by Tuning the Lewis Acid in Iron-Based Bimetallic Systems

Bimetallic motifs mediate the selective activation and functionalization of CO2 in metalloenzymes and some recent synthetic systems. In this work, we build on the nascent concept of bimetallic frustrated Lewis pairs (FLPs) to investigate the activation and reduction of CO2 . Using the Fe0 fragment [(depe)2 Fe] (depe=1,2-bis(diethylphosphino)ethane) as base, we modify the nature of the partner Lewis acid to accomplish a divergent and highly chemoselective reactivity towards CO2 . [Au(PMe2 Ar)]+ irreversibly dissociates CO2 , Zn(C6 F5 )2 and B(C6 F5 )3 yield different CO2 adducts stabilized by push-pull interactions, while Al(C6 F5 )3 leads to a rare heterobimetallic C-O bond cleavage, and thus to contrasting reduced products after exposure to dihydrogen. Computational investigations provide a rationale for the divergent reactivity, while Energy Decomposition Analysis-Natural Orbital for Chemical Valence (EDA-NOCV) method substantiates the heterobimetallic bonding situation.

Recent advances in cooperative activation of CO2 and N2O by bimetallic coordination complexes or binuclear reaction pathways

The gaseous small molecules, CO₂ and N₂O, play important roles in climate change and ozone layer depletion, and they hold promise as underutilized reagents and chemical feedstocks. However, productive transformations of these heteroallenes are difficult to achieve because of their inertness. In nature, these gases are cycled through ecological systems by metalloenzymes featuring multimetallic active sites that employ cooperative mechanisms. Thus, cooperative bimetallic chemistry is an important strategy for synthetic systems, as well. In this Perspective, recent advances (since 2010) in cooperative activation of CO₂ and N₂O are reviewed, including examples involving s-block, p-block, d-block, and f-block metals and different combinations thereof.

Aromaticity-promoted CS2 activation by heterocycle-bridged P/N-FLPs: a comparative DFT study with CO2 capture

Carbon dioxide (CO₂) capture has attracted considerable attention from both experimental and theoretical chemists. In comparison, carbon disulfide (CS₂) activation is less developed. Here, we carry out a thorough comparative density functional theory study to examine the reaction mechanisms of CS₂ activation by five-membered heterocycle-bridged P/N frustrated Lewis pairs (FLPs). Calculations suggest that despite a weaker carbon-sulfur bond, all the CS₂ activations have higher reaction barriers than the CO₂ capture, which could be attributed to electrostatic repulsion between FLPs and CS₂ caused by the reversed polarity of CS in CS₂ rather than the electrostatic attraction in CO₂ capture. In addition, aromaticity is found to play an important role in CS₂ capture as it stabilizes both the transition states and products in heterocycle-bridged FLPs. All these findings could be useful for experimentalists to realize small molecule activations by FLPs.

Coordination chemistry of the CuZ site in nitrous oxide reductase and its synthetic mimics

Atmospheric nitrous oxide (N2O) has garnered significant attention recently due to its dual roles as an ozone depletion agent and a potent greenhouse gas. Anthropogenic N2O emissions occur primarily through agricultural disruption of nitrogen homeostasis causing N2O to build up in the atmosphere. The enzyme responsible for N2O fixation within the geochemical nitrogen cycle is nitrous oxide reductase (N2OR), which catalyzes 2H+/2e- reduction of N2O to N2 and H2O at a tetranuclear active site, CuZ. In this review, the coordination chemistry of CuZ is reviewed. Recent advances in the understanding of biological CuZ coordination chemistry is discussed, as are significant breakthroughs in synthetic modeling of CuZ that have emerged in recent years. The latter topic includes both structurally faithful, synthetic [Cu4(µ4-S)] clusters that are able to reduce N2O, as well as dicopper motifs that shed light on reaction pathways available to the critical CuI-CuIV cluster edge of CuZ. Collectively, these advances in metalloenzyme studies and synthetic model systems provide meaningful knowledge about the physiologically relevant coordination chemistry of CuZ but also open new questions that will pose challenges in the near future.

A [3Cu:2S] cluster provides insight into the assembly and function of the CuZ site of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme reducing environmentally critical nitrous oxide (N₂O) to dinitrogen (N₂) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu_Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N₂OR in Escherichia coli. While no copper ion was found in the Cu_Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S_Z2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S_Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu_Z and is thus of high mechanistic interest.

Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.

Impact of Electronic and Steric Changes of Ligands on the Assembly, Stability, and Redox Activity of Cu4(μ4-S) Model Compounds of the CuZ Active Site of Nitrous Oxide Reductase (N2OR)

Model compounds have been widely utilized in understanding the structure and function of the unusual Cu₄(μ₄-S) active site (Cu_Z) of nitrous oxide reductase (N₂OR). However, only a limited number of model compounds that mimic both structural and functional features of Cu_Z are available, limiting insights about Cu_Z that can be gained from model studies. Our aim has been to construct Cu₄(μ₄-S) clusters with tailored redox activity and chemical reactivity via modulating the ligand environment. Our synthetic approach uses dicopper(I) precursor complexes (Cu₂L₂) that assemble into a Cu₄(μ₄-S)L₄ cluster with the addition of an appropriate sulfur source. Here, we summarize the features of the ligands L that stabilize precursor and Cu₄(μ₄-S) clusters, along with the alternative products that form with inappropriate ligands. The precursors are more likely to rearrange to Cu₄(μ₄-S) clusters when the Cu(I) ions are supported by bidentate ligands with 3-atom bridges, but steric and electronic features of the ligand also play crucial roles. Neutral phosphine donors have been found to stabilize Cu₄(μ₄-S) clusters in the 4Cu(I) oxidation state, while neutral nitrogen donors could not stabilize Cu₄(μ₄-S) clusters. Anionic formamidinate ligands have been found to stabilize Cu₄(μ₄-S) clusters in the 2Cu(I):2Cu(II) and 3Cu(I):1Cu(II) states, with both the formation of the dicopper(I) precursors and subsequent assembly of clusters being governed by the steric factor at the ortho positions of the N-aryl substituents. Phosphaamidinates, which combine a neutral phosphine donor and an anionic nitrogen donor in the same ligand, form multinuclear Cu(I) clusters unless the negative charge is valence-trapped on nitrogen, in which case the resulting dicopper precursor is unable to rearrange to a multinuclear cluster. Taken together, the results presented in this study provide design criteria for successful assembly of synthetic model clusters for the Cu_Z active site of N₂OR, which should enable future insights into the chemical behavior of Cu_Z.

Probing the electronic and mechanistic roles of the μ4-sulfur atom in a synthetic CuZ model system

Nitrous oxide (N2O) contributes significantly to ozone layer depletion and is a potent greenhouse agent, motivating interest in the chemical details of biological N2O fixation by nitrous oxide reductase (N2OR) during bacterial denitrification. In this study, we report a combined experimental/computational study of a synthetic [4Cu:1S] cluster supported by N-donor ligands that can be considered the closest structural and functional mimic of the CuZ catalytic site in N2OR reported to date. Quantitative N2 measurements during synthetic N2O reduction were used to determine reaction stoichiometry, which in turn was used as the basis for density functional theory (DFT) modeling of hypothetical reaction intermediates. The mechanism for N2O reduction emerging from this computational modeling involves cooperative activation of N2O across a Cu/S cluster edge. Direct interaction of the μ4-S ligand with the N2O substrate during coordination and N-O bond cleavage represents an unconventional mechanistic paradigm to be considered for the chemistry of CuZ and related metal-sulfur clusters. Consistent with hypothetical participation of the μ4-S unit in two-electron reduction of N2O, Cu K-edge and S K-edge X-ray absorption spectroscopy (XAS) reveal a high degree of participation by the μ4-S in redox changes, with approximately 21% S 3p contribution to the redox-active molecular orbital in the highly covalent [4Cu:1S] core, compared to approximately 14% Cu 3d contribution per copper. The XAS data included in this study represent the first spectroscopic interrogation of multiple redox levels of a [4Cu:1S] cluster and show high fidelity to the biological CuZ site.

Synthesis and Characterization of Cu(II) and Mixed-Valence Cu(I)Cu(II) Clusters Supported by Pyridylamide Ligands

A group of copper complexes supported by polydentate pyridylamide ligands H₂bpda and H₂ppda were synthesized and characterized. The two Cu(II) dimers [Cu^II₂(Hbpda)₂(ClO₄)₂] (1) and [Cu^II₂(ppda)₂(DMF)₂] (2) were constructed by using neutral ligands to react with Cu(II) salts. Although the dimers showed similar structural features, the second-sphere interactions affect the structures differently. With the application of Et₃N, the tetranuclear cluster (HNEt₃)[Cu^II₄(bpda)₂(μ₃-OH)₂(ClO₄)(DMF)₃](ClO₄)₂ (3) and hexanuclear cluster (HNEt₃)₂[Cu^II₆(ppda)₆(H₂O)₂(CH₃OH)₂](ClO₄)₂ (4) were prepared under similar reaction conditions. The symmetrical and unsymmetrical arrangement of the ligand donors in ligands H₂bpda and H₂ppda led to the dramatic conformation difference of the two Cu(II) complexes. As part of our effort to explore mixed-valence copper chemistry, the triple-decker pentanuclear cluster [Cu^II₃Cu^I₂(bpda)₃(μ₃-O)] (5) was prepared. XPS examination demonstrated the localized mixed-valence properties of complex 5. Magnetic studies of the clusters with EPR evidence showed either weak ferromagnetic or antiferromagnetic interactions among copper centers. Due to the trigonal-planar conformation of the trinuclear Cu(II) motif with the μ₃-O center, complex 5 exhibits geometric spin frustration and engages in antisymmetric exchange interactions. DFT calculations were also performed to better interpret spectroscopic evidence and understand the electronic structures, especially the mixed-valence nature of complex 5.

N2 O Reductase Activity of a [Cu4 S] Cluster in the 4CuI Redox State Modulated by Hydrogen Bond Donors and Proton Relays in the Secondary Coordination Sphere

The model complex [Cu₄ (μ₄ -S)(dppa)₄ ]²⁺ (1, dppa=μ₂ -(Ph₂ P)₂ NH) has N₂ O reductase activity in methanol solvent, mediating 2 H⁺ /2 e^- reduction of N₂ O to N₂ +H₂ O in the presence of an exogenous electron donor (CoCp₂ ). A stoichiometric product with two deprotonated dppa ligands was characterized, indicating a key role of second-sphere N-H residues as proton donors during N₂ O reduction. The activity of 1 towards N₂ O was suppressed in solvents that are unable to provide hydrogen bonding to the second-sphere N-H groups. Structural and computational data indicate that second-sphere hydrogen bonding induces structural distortion of the [Cu₄ S] active site, accessing a strained geometry with enhanced reactivity due to localization of electron density along a dicopper edge site. The behavior of 1 mimics aspects of the Cu_Z catalytic site of nitrous oxide reductase: activity in the 4Cu^I :1S redox state, use of a second-sphere proton donor, and reactivity dependence on both primary and secondary sphere effects.

N-Heterocyclic Carbene Complexes of Copper, Nickel, and Cobalt

The emergence of N-heterocyclic carbenes as ligands across the Periodic Table had an impact on various aspects of the coordination, organometallic, and catalytic chemistry of the 3d metals, including Cu, Ni, and Co, both from the fundamental viewpoint but also in applications, including catalysis, photophysics, bioorganometallic chemistry, materials, etc. In this review, the emergence, development, and state of the art in these three areas are described in detail.

Lewis Acid-Mediated One-Electron Reduction of Nitrous Oxide

The one-electron reduction of nitrous oxide (N₂ O) was achieved using strong Lewis acids E(C₆ F₅ )₃ (E=B or Al) in combination with metallocenes. In the case of B(C₆ F₅ )₃ , electron transfer to N₂ O required a powerful reducing agent such as Cp*₂ Co (Cp*=pentamethylcyclopentadienyl). In the presence of Al(C₆ F₅ )₃ , on the other hand, the reactions could be performed with weaker reducing agents such as Cp*₂ Fe or Cp₂ Fe (Cp=cyclopentadienyl). The Lewis acid-mediated electron transfer from the metallocene to N₂ O resulted in cleavage of the N-O bond, generating N₂ and the oxyl radical anion [OE(C₆ F₅ )₃ ]^⋅- . The latter is highly reactive and engages in C-H activation reactions. It was possible to trap the radical by addition of the Gomberg dimer, which acts as a source of the trityl radical.

Chalcogen Impact on Covalency within Molecular [Cu3(μ3-E)]3+ Clusters (E = O, S, Se): A Synthetic, Spectroscopic, and Computational Study

Reaction of the tricopper(I)-dinitrogen tris(β-diketiminate) cyclophane, Cu3(N2)L, with O-atom-transfer reagents or elemental Se affords the oxido-bridged tricopper complex Cu3(μ3-O)L (2) or the corresponding Cu3(μ3-Se)L (4), respectively. For 2 and 4, incorporation of the bridging chalcogen donor was supported by electrospray ionization mass spectrometry and K-edge X-ray absorption spectroscopy (XAS) data. Cu L2,3-edge X-ray absorption data quantify 49.5% Cu 3d character in the lowest unoccupied molecular orbital of 2, with Cu 3d participation decreasing to 33.0% in 4 and 40.8% in the related sulfide cluster Cu3(μ3-S)L (3). Multiedge XAS and UV/visible/near-IR spectra are employed to benchmark density functional theory calculations, which describe the copper-chalcogen interactions as highly covalent across the series of [Cu3(μ-E)]3+ clusters. This result highlights that the metal-ligand covalency is not reserved for more formally oxidized metal centers (i.e., CuIII + O2- vs CuII + O-) but rather is a significant contributor even at more typical ligand-field cases (i.e., Cu3II/II/I + E2-). This bonding is reminiscent of that observed in p-block elements rather than in early-transition-metal complexes.

Synthesis and reactivity of a nickel(ii) thioperoxide complex: demonstration of sulfide-mediated N2O reduction

The “masked” terminal nickel sulfide [K(18-crown-6)][L^tBuNi^II(S)] mediates the reduction of N₂O by CO, via the thioperoxide complex [K(18-crown-6)][L^tBuNi^II(η²-SO)].

The thiohyponitrite ([SNNO]^2–) complex, [K(18-crown-6)][L^tBuNi^II(κ²-SNNO)] (L^tBu = {(2,6-ⁱPr₂C₆H₃)NC(^tBu)}₂CH), extrudes N₂ under mild heating to yield [K(18-crown-6)][L^tBuNi^II(η²-SO)] (1), along with minor products [K(18-crown-6)][L^tBuNi^II(η²-OSSO)] (2) and [K(18-crown-6)][L^tBuNi^II(η²-S₂)] (3). Subsequent reaction of 1 with carbon monoxide (CO) results in the formation of [K(18-crown-6)][L^tBuNi^II(η²-SCO)] (4), [K(18-crown-6)][L^tBuNi^II(S,O:κ²-SCO₂)] (5), [K(18-crown-6)][L^tBuNi^II(κ²-CO₃)] (6), carbonyl sulfide (COS) (7), and [K(18-crown-6)][L^tBuNi^II(S₂CO)] (8). To rationalize the formation of these products we propose that 1 first reacts with CO to form [K(18-crown-6)][L^tBuNi^II(S)] (I) and CO₂, via O-atom abstraction. Subsequently, complex I reacts with CO or CO₂ to form 4 and 5, respectively. Similarly, the formation of complex 6 and COS can be rationalized by the reaction of 1 with CO₂ to form a putative Ni(ii) monothiopercarbonate, [K(18-crown-6)][L^tBuNi^II(κ²-SOCO₂)] (11). The Ni(ii) monothiopercarbonate subsequently transfers a S-atom to CO to form COS and [K(18-crown-6)][L^tBuNi^II(κ²-CO₃)] (6). Finally, the formation of 8 can be rationalized by the reaction of COS with I. Critically, the observation of complexes 4 and 5 in the reaction mixture reveals the stepwise conversion of [K(18-crown-6)][L^tBuNi^II(κ²-SNNO)] to 1 and then I, which represents the formal reduction of N₂O by CO.