Open Coordination Site Research Articles

Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.

Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine as a sacrificial sulfur donor, and the other one that uses a [4Fe-4S] cluster as a cofactor. Only the crystal structure of LarE from Lactobacillus plantarum (LpLarE) from the first class has been solved. We report here the crystal structure of LarE from Methanococcus maripaludis (MmLarE), belonging to the second class, in the cluster-free (apo-) and cluster-bound (holo-) forms. The structure of holo-MmLarE shows that the [4Fe-4S] cluster is chelated by three cysteines only, leaving an open coordination site on one Fe atom. Moreover, the fourth nonprotein-bonded iron atom was able to bind an anionic ligand such as a phosphate group or a chloride ion. Together with the spectroscopic analysis of holo-MmLarE and the previously reported biochemical investigations of holo-LarE from Thermotoga maritima, these crystal structures support the hypothesis of a reaction mechanism, in which the [4Fe-4S] cluster binds a hydrogenosulfide ligand in place of the chloride anion, thus generating a [4Fe-5S] intermediate, and transfers it to the substrate, as in the case of [4Fe-4S]-dependent tRNA thiolation enzymes.

Size matters: altering the metal-surface coordination in micropores via structural confinement effects

NMR experiments reveal how surface curvature can impact metal coordination. It was observed that under extreme confinement, secondary support–metal interactions are prevented, leading to a dynamic complex with an open coordination site.

Coordinatively Unsaturated Metallates of Cobalt(II), Nickel(II), and Zinc(II) Guarded by a Rigid and Narrow Void.

Both natural enzymatic systems and synthetic porous material catalysts utilize well-defined and uniform channels to dictate reaction selectivities on the basis of size or shape. Mimicry of this design element in homogeneous systems is generally difficult owing to the flexibility inherent in most small molecular species. Herein, we report the synthesis of a tripodal ligand scaffold that orients a narrow and rigid cavity atop accessible metal coordination space. The permanent void is formed through a macrocyclization reaction whereby the 3,5-dihydroxyphenyl arms are covalently linked through methylene bridges. Deprotonative metallation leads to anionic and coordinatively unsaturated complexes of divalent cobalt, nickel, and zinc. An analogous series of trigonal monopyramidal complexes bearing a nonmacrocyclized variant of the tripodal ligand are also reported. Physical characterization of the coordination complexes has been carried out using multiple spectroscopic techniques (NMR, EPR, and UV-vis), cyclic voltammetry, and X-ray diffraction. Complexes of the macrocyclized [LOCH2O]3- ligand retain a rigid cavity upon metallation, with this cavity guarding the entrance to the open axial coordination site. Through a combination of spectroscopic and computational studies, it is shown that acetonitrile entry into the void is sterically precluded, disrupting anticipated coordination at the intracavity site.

Stepwise O2-Induced Rearrangement and Disassembly of the [NiFe4(OH)(µ3-S)4] Active Site Cluster of CO Dehydrogenase.

Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of carbon dioxide to carbon monoxide. CODHs are found in anaerobic microorganisms and can rapidly lose their activity when exposed to air. What causes the loss of activity is unclear. Here, we analyzed the time-dependent structural changes induced by the presence of air on the metal centers of CODH-II. We show that inactivation is a multistep process. In a reversible step, the open coordination site on the Ni ion is blocked by a Ni,Fe-bridging µ-sulfido or chlorido ligand. Blocking this open coordination site with a cyanide ligand stabilizes the cluster against O2-induced decomposition, indicating that O2 attacks at the Ni ion. In the subsequent irreversible phase, nickel is lost, the Fe ions rearrange and the sulfido ligands disappear. Our data are consistent with a reversible reductive reactivation mechanism to protect CODHs from transient over-oxidation.

Stepwise O2‐Induced Rearrangement and Disassembly of the [NiFe4(OH)(μ3‐S)4] Active Site Cluster of CO Dehydrogenase

AbstractNi,Fe‐containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of carbon dioxide to carbon monoxide. CODHs are found in anaerobic microorganisms and can rapidly lose their activity when exposed to air. What causes the loss of activity is unclear. In this study, we analyzed the time‐dependent structural changes induced by the presence of air on the metal centers of CODH‐II. We show that inactivation is a multistep process. In a reversible step, the open coordination site on the Ni ion is blocked by a Ni,Fe‐bridging μ‐sulfido or chlorido ligand. Blocking this open coordination site with a cyanide ligand stabilizes the cluster against O2‐induced decomposition, indicating that O2 attacks at the Ni ion. In the subsequent irreversible phase, nickel is lost, the Fe ions rearrange and the sulfido ligands disappear. Our data are consistent with a reversible reductive reactivation mechanism to protect CODHs from transient over‐oxidation.

Structure and Site Evolution of Framework Ni Species in MIL-127 MOFs for Propylene Oligomerization Catalysis

A mixed-valence oxotrimer metal-organic framework (MOF), Ni-MIL-127, with a fully coordinated nickel atom and two iron atoms in the inorganic node, generates a missing linker defect upon thermal treatment in helium (>473 K) to engender an open coordination site on nickel which catalyzes propylene oligomerization devoid of any cocatalysts or initiators. This catalyst is stable for ∼20 h on stream at 500 kPa and 473 K, unprecedented for this chemistry. The number of missing linkers on synthesized and activated Ni-MIL-127 MOFs is quantified using temperature-programmed oxidation, 1H nuclear magnetic resonance spectroscopy, and X-ray absorption spectroscopy to be ∼0.7 missing linkers per nickel; thus, a majority of Ni species in the MOF framework catalyze propylene oligomerization. In situ NO titrations under reaction conditions enumerate ∼62% of the nickel atoms as catalytically relevant to validate the defect density upon thermal treatment. Propylene oligomerization rates on Ni-MIL-127 measured at steady state have activation energies of 55-67 kJ mol-1 from 448 to 493 K and are first-order in propylene pressures from 5 to 550 kPa. Density functional theory calculations on cluster models of Ni-MIL-127 are employed to validate the plausibility of the missing linker defect and the Cossee-Arlman mechanism for propylene oligomerization through comparisons between apparent activation energies from steady-state kinetics and computation. This study illustrates how MOF precatalysts engender defective Ni species which exhibit reactivity and stability characteristics that are distinct and can be engineered to improve catalytic activity for olefin oligomerization.

Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway.

Hydrogenases are H2 converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN- ) ligands. Extrinsic CO and CN- , however, inhibit hydrogenases. The mechanism by which CN- binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN- -treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Å allowed us to distinguish intrinsic CN- and CO ligands and to show that extrinsic CN- binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN- treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally.

Basal Plane Functionalization of Niobium Disulfide Nanosheets with Cyclopentadienyl Manganese(I) Dicarbonyl.

Basal plane-functionalized NbS2 nanosheets were obtained using in situ photolysis to generate the coordinatively unsaturated organometallic fragment cyclopentadienyl manganese(I) dicarbonyl (CpMn(CO)2). Under UV irradiation, a labile carbonyl ligand dissociates from the tricarbonyl complex, creating an open coordination site for bonding between the Mn atom and the electron-rich sulfur atoms on the surface of the NbS2 nanosheets. In contrast, no reaction is observed with 2H-MoS2 nanosheets under the same reaction conditions. This difference in reactivity is consistent with the electronic structure calculations, which indicate stronger bonding of the organometallic fragment to electron-poor, metallic NbS2 than to semiconducting, electron-rich MoS2. X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared (FTIR) spectroscopy, and powder X-ray diffraction (PXRD) were used to characterize the bonding between Mn and S atoms on the surface-functionalized nanosheets.

A Combined Experimental and Theoretical Investigation of Arene-Supported Actinide and Ytterbium Tetraphenolate Complexes.

Modular tetraphenolate ligands tethered with a protective arene platform (para-phenyl or para-terphenyl) are used to support mononuclear An(IV) (An = Th, U) complexes with an exceptionally large and open axial coordination site at the metal. The base-free complexes and a series of neutral donor adducts were synthesized and characterized by spectroscopies and single-crystal X-ray diffraction. Anionic Th(IV) -ate complexes with an additional axial aryloxide ligand were also synthesized and characterized. The para-phenyl-tethered mononuclear complexes exhibit rare An(IV)-arene interactions, and the An(IV)-arene distance broadly increases with axial donor strength. The para-terphenyl-tethered complexes have almost no interaction with the arene base, isolating the central metal cation. Computational analysis of the mononuclear complexes and their reduced analogues, and Yb(III) congeners, as well as the effect of additional donor ligand binding, seek to elucidate the electronic structure of the metal-arene interactions and establish whether they, or their reduced or oxidized counterparts, could function as molecular qubits.

Electrocatalytic CO2 Reduction and H2 Evolution by a Copper (II) Complex with Redox-Active Ligand.

The process of electrocatalytic CO2 reduction and H2 evolution from water, regarding renewable energy, has become one of the global solutions to problems related to energy consumption and environmental degradation. In order to promote the electrocatalytic reactivity, the study of the role of ligands in catalysis has attracted more and more attention. Herein, we have developed a copper (II) complex with redox-active ligand [Cu(L1)2NO3]NO3 (1, L1 = 2-(6-methoxypyridin-2-yl)-6-nitro-1h-benzo [D] imidazole). X-ray crystallography reveals that the Cu ion in cation of complex 1 is coordinated by two redox ligands L1 and one labile nitrate ligand, which could assist the metal center for catalysis. The longer Cu-O bond between the metal center and the labile nitrate ligand would break to provide an open coordination site for the binding of the substrate during the catalytic process. The electrocatalytic investigation combined with DFT calculations demonstrate that the copper (II) complex could homogeneously catalyze CO2 reduction towards CO and H2 evolution, and this could occur with great performance due to the cooperative effect between the central Cu (II) ion and the redox- active ligand L1. Further, we discovered that the added proton source H2O and TsOH·H2O (p-Toluenesulfonic acid) could greatly enhance its electrocatalytic activity for CO2 reduction and H2 evolution, respectively.

Kinetics of halide exchange in cyclopentadienylruthenium bis(triarylphosphine)halides

The kinetics of halide exchange in cyclopentadienylruthenium bis(triarylphosphine) halide complexes CpRu(PAr3)2X (1a X = Cl, 1b X = Br, 1c X = I; X′= Cl, Br, Ar = C6H5, 2 Ar = p-CH3OC6H4, X = Cl, X′= Br and 3 Ar = p-FC6H4, X = Cl, X′ = Br) have been measured and the results interpreted with respect to two possible mechanisms: halide dissociation vs phosphine dissociation. Halide exchange between nBu4NX′ and 1–3 in fluorobenzene under pseudo-first order conditions is found to be first order in 1–3. Relative rates of halide exchange follow the order: 1a > 1b > 1c > 2 ≈ 3 with activation parameters ΔH† = 117 ± 6 kJ/mol and ΔS† = 44 ± 18 J/mol-K (1a, X′ = Br) and ΔH† = 120 ± 14 kJ/mol ΔS† = 50 ± 45 J/mol-K (1b, X′ = Cl). Plots of kobs vs [X′–] for 1 and 2 are consistent with a two-term rate law where kobs = (k1 + k2[X′–]) while reactions of 3 are independent of the halide concentration. The rate data are consistent with phosphine dissociation as the rate determining step followed by a slightly faster reaction with halide ions where the dissociated phosphine competes effectively with halide for the open coordination site in a CpRu(PAr3)X intermediate.

Isolation of a Side-On V(III)-(η2-O2) through the Intermediacy of a Low-Valent V(II) in a Metal-Organic Framework.

We report the isolation of vanadium(II) in a metal-organic framework (MOF) by the reaction of the chloride-capped secondary building unit in the all-vanadium(III) V-MIL-101 (1) with 1,4-bis(trimethylsilyl)-2,3,5,6-tetramethyl-1,4-dihydropyrazine. The reduced material, 2, has a secondary building unit with the formal composition [VIIV2III], with each metal ion presenting one open coordination site. Subsequent reaction with O2 yields a side-on η2 vanadium-superoxo species, 3. The MOF featuring V(III)-superoxo moieties exhibits a mild enhancement in the isosteric enthalpy of adsorption for methane compared to the parent V-MIL-101. We present this synthetic methodology as a potentially broad way to access low-valent open metal sites within MOFs without causing a loss of crystallinity or porosity. The low-valent sites can serve as isolable intermediates to access species otherwise inaccessible by direct synthesis.

Spectroscopic investigation of iron(III) cysteamine dioxygenase in the presence of substrate (analogs): implications for the nature of substrate-bound reaction intermediates.

Thiol dioxygenases (TDOs) are a class of metalloenzymes that oxidize various thiol-containing substrates to their corresponding sulfinic acids. Originally established by X-ray crystallography for cysteine dioxygenase (CDO), all TDOs are believed to contain a 3-histidine facial triad that coordinates the necessary Fe(II) cofactor. However, very little additional information is available for cysteamine dioxygenase (ADO), the only other mammalian TDO besides CDO. Previous spectroscopic characterizations revealed that ADO likely binds substrate cysteamine in a monodentate fashion, while a mass spectrometry study provided evidence that a thioether crosslink can form between Cys206 and Tyr208 (mouse ADO numbering). In the present study, we have used electronic absorption and electron paramagnetic resonance (EPR) spectroscopies to investigate the species formed upon incubation of Fe(III)ADO with sulfhydryl-containing substrates and the superoxide surrogates azide and cyanide. Our data reveal that azide is unable to coordinate to cysteamine-bound Fe(III)ADO, suggesting that the Fe(III) center lacks an open coordination site or azide competes with cysteamine for the same binding site. Alternatively, cyanide binds to either cysteamine- or Cys-bound Fe(III)ADO to yield a low-spin (S = 1/2) EPR signal that is distinct from that observed for cyanide/Cys-bound Fe(III)CDO, revealing differences in the active-site pockets between ADO and CDO. Finally, EPR spectra obtained for cyanide/cysteamine adducts of wild-type Fe(III)ADO and its Tyr208Phe variant are superimposable, implying that either an insignificant fraction of as-isolated wild-type enzyme is crosslinked or that formation of the thioether bond has minimal effects on the electronic structure of the iron cofactor.

Iron(II) Complexes Featuring a Redox-Active Dihydrazonopyrrole Ligand.

Nature uses control of the secondary coordination sphere to facilitate an astounding variety of transformations. Similarly, synthetic chemists have found metal-ligand cooperativity to be a powerful strategy for designing complexes that can mediate challenging reactivity. In particular, this strategy has been used to facilitate two electron reactions with first row transition metals that more typically engage in one electron redox processes. While NNN pincer ligands feature prominently in this area, examples which can potentially engage in both proton and electron transfer are less common. Dihydrazonopyrrole (DHP) ligands have been isolated in a variety of redox and protonation states when complexed to Ni. However, the redox-state of this ligand scaffold is less obvious when complexed to metal centers with more accessible redox couples. Here, we synthesize a new series of Fe-DHP complexes in two distinct oxidation states. Detailed characterization supports that the redox-chemistry in this set is still primarily ligand based. Finally, these complexes exist as 5-coordinate species with an open coordination site offering the possibility of enhanced reactivity.

Electrochemical behaviors of a pincer-type NNN-Fe complex and catalytic H2 evolution activity.

We describe electrochemical reactivity of a pincer-type [NNN-Fe(tBuNC)3](ClO4)2 complex. Upon electron reduction, the Fe(i) species experienced disproportionation to Fe(0) and Fe(ii). An electron-reduced Fe center dissociated a tBuNC ligand to make an open coordination site, where a proton could be transferred. The low-spin Fe center, assisted by isocyanide and a pyridine-based NNN-pincer ligand, catalyzed efficiently the proton reduction reaction. Also, a Lewis basic amine site in the side 'arm' of the NNN-pincer ligand lowered the free energy for the protonation of an Fe center during the proton reduction process. DFT calculations provided insight into a plausible catalytic pathway.

De Novo Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species.

De novo protein design offers the opportunity to test our understanding of how metalloproteins perform difficult transformations. Attaining high-resolution structural information is critical to understanding how such designs function. There have been many successes in the design of porphyrin-binding proteins; however, crystallographic characterization has been elusive, limiting what can be learned from such studies as well as the extension to new functions. Moreover, formation of highly oxidizing high-valent intermediates poses design challenges that have not been previously implemented: (1) purposeful design of substrate/oxidant access to the binding site and (2) limiting deleterious oxidation of the protein scaffold. Here we report the first crystallographically characterized porphyrin-binding protein that was programmed to not only bind a synthetic Mn-porphyrin but also maintain binding site access to form high-valent oxidation states. We explicitly designed a binding site with accessibility to dioxygen units in the open coordination site of the Mn center. In solution, the protein is capable of accessing a high-valent Mn(V)-oxo species which can transfer an O atom to a thioether substrate. The crystallographic structure is within 0.6 Å of the design and indeed contained an aquo ligand with a second water molecule stabilized by hydrogen bonding to a Gln side chain in the active site, offering a structural explanation for the observed reactivity.

Tunable Cobalt-Polypyridyl Catalysts Supported on Metal-Organic Layers for Electrochemical CO2 Reduction at Low Overpotentials.

The Co center is active in electrochemical CO2 reduction (CO2RR), and its activity can be tuned by changing its coordination environment. However, the coordination number around the Co center cannot be readily changed in homogeneous systems owing to bimolecular decomposition of reduced low-coordinate Co species. Herein we report the systematic tuning of N atom numbers from 2 to 5 in the first coordination sphere around Co centers supported on two-dimensional metal-organic layers (MOLs) for the electrochemical CO2RR. The N atoms come from a combination of bipyridine, terpyridine, and phenylpyridine ligands. The Co centers are isolated and stabilized on the MOL to prevent bimolecular decomposition. All of the catalysts, denoted MOL-Co-Nx (x = 2-5), are active in reducing CO2 to CO electrochemically, but their activities are highly dependent on the number of coordinating N atoms. MOL-Co-N3 showed the highest current density of 2.3 A mg-1 with a CO Faradaic efficiency of 99% at an overpotential of only 380 mV. Density functional theory calculations attribute the high activity of the Co-N3 center to a balance of ligand field strength and open coordination site: the high ligand field strength promotes back-bonding, while the open coordination site allows HCO3- assistance, both of which accelerate C-O cleavage. MOLs thus provide a unique platform to systematically study the relationship between the coordination environment and the reactivity of open metal sites in electrocatalysis.

Saccharomyces cerevisiae and Candida albicans Yeast Cells Labeled with Fe(III) Complexes as MRI Probes

The development of MRI probes is of interest for labeling antibiotic-resistant fungal infections based on yeast. Our work showed that yeast cells can be labeled with high-spin Fe(III) complexes to produce enhanced T2 water proton relaxation. These Fe(III)-based macrocyclic complexes contained a 1,4,7-triazacyclononane framework, two pendant alcohol groups, and either a non-coordinating ancillary group and a bound water molecule or a third coordinating pendant. The Fe(III) complexes that had an open coordination site associated strongly with Saccharomyces cerevisiae upon incubation, as shown by screening using Z-spectra analysis. The incubation of one Fe(III) complex with either Saccharomyces cerevisiae or Candida albicans yeast led to an interaction with the β-glucan-based cell wall, as shown by the ready retrieval of the complex by the bidentate chelator called maltol. Other conditions, such as a heat shock treatment of the complexes, produced Fe(III) complex uptake that could not be reversed by the addition of maltol. Appending a fluorescence dye to Fe(TOB) led to uptake through secretory pathways, as shown by confocal fluorescence microscopy and by the incomplete retrieval of the Fe(III) complex by the maltol treatment. Yeast cells that were labeled with these Fe(III) complexes displayed enhanced water proton T2 relaxation, both for S. cerevisiae and for yeast and hyphal forms of C. albicans.

Caught in the Hinact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O2 -stable State of [FeFe] Hydrogenase.

[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2‐stable state called Hinact. To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in‐depth spectroscopic characterization by X‐ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2‐stable hydrogenases and molecular catalysts.

Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.