Probing Variable Amine/Amide Ligation in NiIIN2S2 Complexes Using Sulfur K-Edge and Nickel L-Edge X-ray Absorption Spectroscopies: Implications for the Active Site of Nickel Superoxide Dismutase

A Series of Ni Complexes Based on a Versatile ATCUN-Like Tripeptide Scaffold to Decipher Key Parameters for Superoxide Dismutase Activity

The cellular level of reactive oxygen species (ROS) has to be controlled to avoid some pathologies, especially those linked to oxidative stress. One strategy for designing antioxidants consists of modeling natural enzymes involved in ROS degradation. Among them, nickel superoxide dismutase (NiSOD) catalyzes the dismutation of the superoxide radical anion, O₂^•-, into O₂ and H₂O₂. We report here Ni complexes with tripeptides derived from the amino-terminal Cu^II- and Ni^II-binding (ATCUN) motif that mimics some structural features found in the active site of the NiSOD. A series of six mononuclear Ni^II complexes were investigated in water at physiological pH with different first coordination spheres, from compounds with a N3S to N2S2 set, and also complexes that are in equilibrium between the N-coordination (N3S) and S-coordination (N2S2). They were fully characterized by a combination of spectroscopic techniques, including ¹H NMR, UV-vis, circular dichroism, and X-ray absorption spectroscopy, together with theoretical calculations and their redox properties studied by cyclic voltammetry. They all display SOD-like activity, with a k_cat ranging between 0.5 and 2.0 × 10⁶ M^-1 s^-1. The complexes in which the two coordination modes are in equilibrium are the most efficient, suggesting a beneficial effect of a nearby proton relay.

A Bioinspired NiII Superoxide Dismutase Catalyst Designed on an ATCUN-like Binding Motif

Nickel superoxide dismutase (NiSOD) is an enzyme that protects cells against O₂^·-. While the structure of its active site is known, the mechanism of the catalytic cycle is still not elucidated. Its active site displays a square planar Ni^II center with two thiolates, the terminal amine and an amidate. We report here a bioinspired Ni^II complex built on an ATCUN-like binding motif modulated with one cysteine, which demonstrates catalytic SOD activity in water (k_cat = 8.4(2) × 10⁵ M^-1 s^-1 at pH = 8.1). Its reactivity with O₂^·- was also studied in acetonitrile allowing trapping two different short-lived species that were characterized by electron paramagnetic resonance or spectroelectrochemistry and a combination of density functional theory (DFT) and time-dependent DFT calculations. Based on these observations, we propose that O₂^·- interacts first with the complex outer sphere through a H-bond with the peptide scaffold in a [Ni^IIO₂^·-] species. This first species could then evolve into a Ni^III hydroperoxo inner sphere species through a reaction driven by protonation that is thermodynamically highly favored according to DFT calculations.

[(MeCN)Ni(CF3)3]- and [Ni(CF3)4]2-: Foundations toward the Development of Trifluoromethylations at Unsupported Nickel

Nickel anions [(MeCN)Ni(CF₃)₃]^- and [Ni(CF₃)₄]^2- were prepared by the formal addition of 3 and 4 equiv, respectively, of AgCF₃ to [(dme)NiBr₂] in the presence of the [PPh₄]⁺ counterion. Detailed insights into the electronic properties of these new compounds were obtained through the use of density functional theory (DFT) calculations, spectroscopy-oriented configuration interaction (SORCI) calculations, X-ray absorption spectroscopy, and cyclic voltammetry. The data collectively show that trifluoromethyl complexes of nickel, even in the most common oxidation state of nickel(II), are highly covalent systems whereby a hole is distributed on the trifluoromethyl ligands, surprisingly rendering the metal to a physically more reduced state. In the cases of [(MeCN)Ni(CF₃)₃]^- and [Ni(CF₃)₄]^2-, these complexes are better physically described as d⁹ metal complexes. [(MeCN)Ni(CF₃)₃]^- is electrophilic and reacts with other nucleophiles such as phenoxide to yield the unsupported [(PhO)Ni(CF₃)₃]^2- salt, revealing the broader potential of [(MeCN)Ni(CF₃)₃]^- in the development of "ligandless" trifluoromethylations at nickel. Proof-in-principle experiments show that the reaction of [(MeCN)Ni(CF₃)₃]^- with an aryl iodonium salt yields trifluoromethylated arene, presumably via a high-valent, unsupported, and formal organonickel(IV) intermediate. Evidence of the feasibility of such intermediates is provided with the structurally characterized [PPh₄]₂[Ni(CF₃)₄(SO₄)], which was derived through the two-electron oxidation of [Ni(CF₃)₄]^2-.

pH Dependent Reversible Formation of a Binuclear Ni2 Metal-Center Within a Peptide Scaffold

A disulfide-bridged peptide containing two Ni2+ binding sites based on the nickel superoxide dismutase protein, {Ni2(SODmds)}, has been prepared. At physiological pH (7.4) it was found that the metal sites are mononuclear with a square planar NOS2 coordination environment with the two sulfur-based ligands derived from cysteinate residues, the nitrogen ligand derived from the amide backbone and a water ligand. Furthermore, S K-edge X-ray absorption spectroscopy indicated that the two cysteinate sulfur atoms ligated to nickel are each protonated. Elevation of the pH to 9.6 results in the deprotonation of the cysteinate sulfur atoms, and yields a binuclear, cysteinate bridged Ni22+ center with each nickel contained in a distorted square planar geometry. At both pH = 7.4 and 9.6 the nickel sites are moderately air sensitive, yielding intractable oxidation products. However, at pH = 9.6 {Ni2(SODmds)} reacts with O2 at an ~3.5-fold faster rate than at pH = 7.4. Electronic structure calculations indicate the reduced reactivity at pH = 7.4 is a result of a reduction in S(3p) character and deactivation of the nucleophilic frontier molecular orbitals upon cysteinate sulfur protonation.

The Role of Mixed Amine/Amide Ligation in Nickel Superoxide Dismutase

Superoxide dismutases (SODs) utilize a ping-pong mechanism in which a redox-active metal cycles between oxidized and reduced forms that differ by one electron to catalyze the disproportionation of superoxide to dioxygen and hydrogen peroxide. Nickel-dependent SOD (NiSOD) is a unique biological solution for controlling superoxide levels. This enzyme relies on the use of cysteinate ligands to bring the Ni(III/II) redox couple into the range required for catalysis (∼300 mV vs. NHE). The use of cysteine thiolates, which are not found in any other SOD, is a curious choice because of their well-known oxidation by peroxide and dioxygen. The NiSOD active site cysteinate ligands are resistant to oxidation, and prior studies of synthetic and computational models point to the backbone N-donors in the active site (the N-terminal amine and the amide N atom of Cys2) as being involved in stabilizing the cysteines to oxidation. To test the role of the backbone N-donors, we have constructed a variant of NiSOD wherein an alanine residue was added to the N-terminus (Ala0-NiSOD), effectively altering the amine ligand to an amide. X-ray absorption, electronic absorption, and magnetic circular dichroism (MCD) spectroscopic analyses of as-isolated Ala0-NiSOD coupled with density functional theory (DFT) geometry optimized models that were evaluated on the basis of the spectroscopic data within the framework of DFT and time-dependent DFT computations are consistent with a diamagnetic Ni(II) site with two cysteinate, one His1 amide, and one Cys2 amidate ligands. The variant protein is catalytically inactive, has an altered electronic absorption spectrum associated with the nickel site, and is sensitive to oxidation. Mass spectrometric analysis of the protein exposed to air shows the presence of a mixture of oxidation products, the principal ones being a disulfide, a bis-sulfenate, and a bis-sulfinate derived from the active site cysteine ligands. Details of the electronic structure of the Ni(III) site available from the DFT calculations point to subtle changes in the unpaired spin density on the S-donors as being responsible for the altered sensitivity of Ala0-NiSOD to O₂.

Steric Enforcement about One Thiolate Donor Leads to New Oxidation Chemistry in a NiSOD Model Complex

Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to the presence of oxygen-sensitive Ni-SCys bonds at its active site. Reported in this account is the synthesis and properties of the Ni^II complex of the N₃S₂ ligand [N₃S₂^Me2]^3- ([N₃S₂^Me2]^3- = deprotonated form of 2-((2-mercapto-2-methylpropyl)(pyridin-2-ylmethyl)amino)-N-(2-mercaptoethyl)acetamide), namely Na[Ni(N₃S₂^Me2)] (2), as a NiSOD model that features sterically robust gem-(CH₃)₂ groups on the thiolate α-C positioned trans to the carboxamide. The crystal structure of 2, coupled with spectroscopic measurements from ¹H NMR, X-ray absorption, IR, UV-vis, and mass spectrometry (MS), reveal a planar Ni^II (S = 0) ion coordinated by only the N₂S₂ basal donors of the N₃S₂ ligand. While the structure and spectroscopic properties of 2 resemble those of NiSOD_red and other models, the asymmetric S ligands open up new reaction paths upon chemical oxidation. One unusual oxidation product is the planar Ni^II-N₃S complex [Ni(L^ox)] (5; L^ox = 2-(5,5-dimethyl-2-(pyridin-2-yl)thiazolidin-3-yl)-N-(2-mercaptoethyl)acetamide), where two-electron oxidation takes place at the substituted thiolate and py-CH₂ carbon to generate a thiazolidine heterocycle. Electrochemical measurements of 2 reveal irreversible events wholly consistent with thiolate redox, which were identified by comparison to the Zn^II complex Na[Zn(N₃S₂^Me2)] (3). Although no reaction is observed between 2 and azide, reaction of 2 with superoxide produces multiple products on the basis of UV-vis and MS data, one of which is 5. Density functional theory (DFT) computations suggest that the HOMO in 2 is π* with primary contributions from Ni-dπ/S-pπ orbitals. These contributions can be modulated and biased toward Ni when electron-withdrawing groups are placed on the thiolate α-C. Analysis of the oxidized five-coordinate species 2^ox* by DFT reveal a singly occupied spin-up (α) MO that is largely thiolate based, which supports the proposed Ni^III-thiolate/Ni^II-thiyl radical intermediates that ultimately yield 5 and other products.

Reinventing the Wheel: The NiSOD Story

The most recently discovered SOD requires nickel in its active site – NiSOD. Among the available metals, nickel seems an unlikely redox center. This chapter discusses the protein adaptations required in order to use nickel for SOD catalysis. Cysteine ligands are employed for the first time in an SOD, to suppress the potential of the Ni(ii/iii) couple. However, this adaptation alone is not sufficient to produce an SOD, since thiolate ligands are sensitive to oxidation by H2O2 and O2. Additional adaptations include the use of two unusual backbone N-donor ligands, an amidate and the N-terminal amine. Yet merely producing a stable Ni redox center is not sufficient for SOD catalysis. A source of protons is needed to produce H2O2 and the pH-independent catalysis that is characteristic of SODs. Thus, the cysteine thiolates were also employed to provide a site for protonation. In restricting active site access, NiSOD appears to have utilized the same strategy employed by MnSOD and FeSOD – a “gateway” formed by Tyr residues. Thus, NiSOD represents evolution that converged on the same criteria for catalysis as other SODs, where the adaptations to the metal site are uniquely suited to using nickel as a redox center.

A Semisynthetic Strategy Leads to Alteration of the Backbone Amidate Ligand in the NiSOD Active Site

Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ∼1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ∼11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. (14)N-hyperfine is observed on gz, confirming the addition of the apical histidine ligand in the Ni(III) complex. The altered electronic properties and implications for redox catalysis are discussed in light of predictions based on synthetic and computational models.

Accessing Ni(III)-thiolate versus Ni(II)-thiyl bonding in a family of Ni-N2S2 synthetic models of NiSOD

Superoxide dismutase (SOD) catalyzes the disproportionation of superoxide (O2(• -)) into H2O2 and O2(g) by toggling through different oxidation states of a first-row transition metal ion at its active site. Ni-containing SODs (NiSODs) are a distinct class of this family of metalloenzymes due to the unusual coordination sphere that is comprised of mixed N/S-ligands from peptide-N and cysteine-S donor atoms. A central goal of our research is to understand the factors that govern reactive oxygen species (ROS) stability of the Ni-S(Cys) bond in NiSOD utilizing a synthetic model approach. In light of the reactivity of metal-coordinated thiolates to ROS, several hypotheses have been proffered and include the coordination of His1-Nδ to the Ni(II) and Ni(III) forms of NiSOD, as well as hydrogen bonding or full protonation of a coordinated S(Cys). In this work, we present NiSOD analogues of the general formula [Ni(N2S)(SR')](-), providing a variable location (SR' = aryl thiolate) in the N2S2 basal plane coordination sphere where we have introduced o-amino and/or electron-withdrawing groups to intercept an oxidized Ni species. The synthesis, structure, and properties of the NiSOD model complexes (Et4N)[Ni(nmp)(SPh-o-NH2)] (2), (Et4N)[Ni(nmp)(SPh-o-NH2-p-CF3)] (3), (Et4N)[Ni(nmp)(SPh-p-NH2)] (4), and (Et4N)[Ni(nmp)(SPh-p-CF3)] (5) (nmp(2-) = dianion of N-(2-mercaptoethyl)picolinamide) are reported. NiSOD model complexes with amino groups positioned ortho to the aryl-S in SR' (2 and 3) afford oxidized species (2(ox) and 3(ox)) that are best described as a resonance hybrid between Ni(III)-SR and Ni(II)-(•)SR based on ultraviolet-visible (UV-vis), magnetic circular dichroism (MCD), and electron paramagnetic resonance (EPR) spectroscopies, as well as density functional theory (DFT) calculations. The results presented here, demonstrating the high percentage of S(3p) character in the highest occupied molecular orbital (HOMO) of the four-coordinate reduced form of NiSOD (NiSODred), suggest that the transition from NiSODred to the five-coordinate oxidized form of NiSOD (NiSODox) may go through a four-coordinate Ni-(•)S(Cys) (NiSODox-Hisoff) that is stabilized by coordination to Ni(II).

X-ray absorption spectroscopy of dinuclear metallohydrolases

In this mini-review, we briefly discuss the physical origin of x-ray absorption spectroscopy (XAS) before illustrating its application using dinuclear metallohydrolases as exemplary systems. The systems we have selected for illustrative purposes present a challenging problem for XAS, one that is ideal to demonstrate the potential of this methodology for structure/function studies of metalloenzymes in general. When the metal ion is redox active, XAS provides a sensitive measure of oxidation-state-dependent differences. When the metal ion is zinc, XAS is the only spectroscopic method that will provide easily accessible structural information in solution. In the case of heterodimetallic sites, XAS has the unique ability to interrogate each metal site independently in the same sample. One of the strongest advantages of XAS is its ability to examine metal ion site structures with crystallographic precision, without the need for a crystal. This is key for studying flexible metal ion sites, such as those described in the selected examples, because it allows one to monitor structural changes that occur during substrate turnover.

Cysteinate protonation and water hydrogen bonding at the active-site of a nickel superoxide dismutase metallopeptide-based mimic: implications for the mechanism of superoxide reduction

Nickel-containing superoxide dismutase (NiSOD) is a mononuclear cysteinate-ligated nickel metalloenzyme that catalyzes the disproportionation of superoxide into dioxygen and hydrogen peroxide by cycling between Ni(II) and Ni(III) oxidation states. All of the ligating residues to nickel are found within the first six residues from the N-terminus, which has prompted several research groups to generate NiSOD metallopeptide-based mimics derived from the first several residues of the NiSOD sequence. To assess the viability of using these metallopeptide-based mimics (NiSOD maquettes) to probe the mechanism of SOD catalysis facilitated by NiSOD, we computationally explored the initial step of the O2(-) reduction mechanism catalyzed by the NiSOD maquette {Ni(II)(SOD(m1))} (SOD(m1) = HCDLP CGVYD PA). Herein we use spectroscopic (S K-edge X-ray absorption spectroscopy, electronic absorption spectroscopy, and circular dichroism spectroscopy) and computational techniques to derive the detailed active-site structure of {Ni(II)(SOD(m1))}. These studies suggest that the {Ni(II)(SOD(m1))} active-site possesses a Ni(II)-S(H(+))-Cys(6) moiety and at least one associated water molecule contained in a hydrogen-bonding interaction to the coordinated Cys(2) and Cys(6) sulfur atoms. A computationally derived mechanism for O2(-) reduction using the formulated active-site structure of {Ni(II)(SOD(m1))} suggests that O2(-) reduction takes place through an apparent initial outersphere hydrogen atom transfer (HAT) from the Ni(II)-S(H(+))-Cys(6) moiety to the O2(-) molecule. It is proposed that the water molecule aids in driving the reaction forward by lowering the Ni(II)-S(H(+))-Cys(6) pK(a). Such a mechanism is not possible in NiSOD itself for structural reasons. These results therefore strongly suggest that maquettes derived from the primary sequence of NiSOD are mechanistically distinct from NiSOD itself despite the similarities in the structure and physical properties of the metalloenzyme vs the NiSOD metallopeptide-based models.

Insight into the structure and mechanism of nickel-containing superoxide dismutase derived from peptide-based mimics

Nickel superoxide dismutase (NiSOD) is a nickel-containing metalloenzyme that catalyzes the disproportionation of superoxide through a ping-pong mechanism that relies on accessing reduced Ni(II) and oxidized Ni(III) oxidation states. NiSOD is the most recently discovered SOD. Unlike the other known SODs (MnSOD, FeSOD, and (CuZn)SOD), which utilize "typical" biological nitrogen and oxygen donors, NiSOD utilizes a rather unexpected ligand set. In the reduced Ni(II) oxidation state, NiSOD utilizes nitrogen ligands derived from the N-terminal amine and an amidate along with two cysteinates sulfur donors. These are unusual biological ligands, especially for an SOD: amine and amidate donors are underrepresented as biological ligands, whereas cysteinates are highly susceptible to oxidative damage. An axial histidine imidazole binds to nickel upon oxidation to Ni(III). This bond is long (2.3-2.6 Å) owing to a tight hydrogen-bonding network. All of the ligating residues to Ni(II) and Ni(III) are found within the first 6 residues from the NiSOD N-terminus. Thus, small nickel-containing metallopeptides derived from the first 6-12 residues of the NiSOD sequence can reproduce many of the properties of NiSOD itself. Using these nickel-containing metallopeptide-based NiSOD mimics, we have shown that the minimal sequence needed for nickel binding and reproduction of the structural, spectroscopic, and functional properties of NiSOD is H2N-HCXXPC. Insight into how NiSOD avoids oxidative damage has also been gained. Using small NiN2S2 complexes and metallopeptide-based mimics, it was shown that the unusual nitrogen donor atoms protect the cysteinates from oxidative damage (both one-electron oxidation and oxygen atom insertion reactions) by fine-tuning the electronic structure of the nickel center. Changing the nitrogen donor set to a bis-amidate or bis-amine nitrogen donor led to catalytically nonviable species owing to nickel-cysteinate bond oxidative damage. Only the amine/amidate nitrogen donor atoms within the NiSOD ligand set produce a catalytically viable species. These metallopeptide-based mimics have also hinted at the detailed mechanism of SOD catalysis by NiSOD. One such aspect is that the axial imidazole likely remains ligated to the Ni center under rapid catalytic conditions (i.e., high superoxide loads). This reduces the degree of structural rearrangement about the nickel center, leading to higher catalytic rates. Metallopeptide-based mimics have also shown that, although an axial ligand to Ni(III) is required for catalysis, the rates are highest when this is a weak interaction, suggesting a reason for the long axial His-Ni(III) bond found in NiSOD. These mimics have also suggested a surprising mechanistic insight: O2(-) reduction via a "H(•)" tunneling event from a R-S(H(+))-Ni(II) moiety to O2(-) is possible. The importance of this mechanism in NiSOD has not been verified.

Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase

Cobalt nitrile hydratases (Co-NHase) contain a catalytic cobalt(III) ion coordinated in an N2S3 first coordination sphere composed of two amidate nitrogens and three cysteine-derived sulfur donors: a thiolate (-SR), a sulfenate (-S(R)O(-)), and a sulfinate (-S(R)O2(-)). The sequence of biosynthetic reactions that leads to the post-translational oxidations of the metal and the sulfur ligands is unknown, but the process is believed to be initiated directly by oxygen. Herein we utilize cobalt bound in an N2S2 first coordination sphere by a seven amino acid peptide known as SODA (ACDLPCG) to model this oxidation process. Upon exposure to oxygen, Co-SODA is oxidized in two steps. In the first fast step (seconds), magnetic susceptibility measurements demonstrated that the metallocenter remains paramagnetic, that is, Co(2+), and sulfur K-edge X-ray absorption spectroscopy (XAS) is used to show that one of the thiolates is oxidized to sulfinate. In a second process on a longer time scale (hours), magnetic susceptibility measurements and Co K-edge XAS show that the metal is oxidized to Co(3+). Unlike other model complexes, additional slow oxidation of the second thiolate in Co-SODA is not observed, and a catalytically active complex is never formed. The likely reason is the absence of the axial thiolate ligand. In essence, the reactivity of Co-SODA can be described as between previously described models which either quickly convert to final product or are stable in air, and it offers a first glimpse into a possible oxidation pathway for nitrile hydratase biosynthesis.

Embedding the Ni-SOD mimetic Ni-NCC within a polypeptide sequence alters the specificity of the reaction pathway

The unique metal abstracting peptide asparagine-cysteine-cysteine (NCC) binds nickel in a square planar 2N:2S geometry and acts as a mimic of the enzyme nickel superoxide dismutase (Ni-SOD). The Ni-NCC tripeptide complex undergoes rapid, site-specific chiral inversion to dld-NCC in the presence of oxygen. Superoxide scavenging activity increases proportionally with the degree of chiral inversion. Characterization of the NCC sequence within longer peptides with absorption, circular dichroism (CD), and magnetic CD (MCD) spectroscopies and mass spectrometry (MS) shows that the geometry of metal coordination is maintained, though the electronic properties of the complex are varied to a small extent because of bis-amide, rather than amine/amide, coordination. In addition, both Ni-tripeptide and Ni-pentapeptide complexes have charges of -2. This study demonstrates that the chiral inversion chemistry does not occur when NCC is embedded in a longer polypeptide sequence. Nonetheless, the superoxide scavenging reactivity of the embedded Ni-NCC module is similar to that of the chirally inverted tripeptide complex, which is consistent with a minor change in the reduction potential for the Ni-pentapeptide complex. Together, this suggests that the charge of the complex could affect the SOD activity as much as a change in the primary coordination sphere. In Ni-NCC and other Ni-SOD mimics, changes in chirality, superoxide scavenging activity, and oxidation of the peptide itself all depend on the presence of dioxygen or its reduced derivatives (e.g., superoxide), and the extent to which each of these distinct reactions occurs is ruled by electronic and steric effects that emenate from the organization of ligands around the metal center.

Influence of sequential thiolate oxidation on a nitrile hydratase mimic probed by multiedge X-ray absorption spectroscopy

Nitrile hydratases (NHases) are Fe(III)- and Co(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N(2)S(3) coordination motif with two post-translationally modified cysteinates contained in a cis arrangement, which have been converted into a sulfinate (R-SO(2)(-)) and a sulfenate (R-SO(-)) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru(II) complexes ((bmmp-TASN)RuPPh(3), (bmmp-O(2)-TASN)RuPPh(3), and (bmmp-O(3)-TASN)RuPPh(3)). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)RuPPh(3) to the sulfenato species (bmmp-O(2)-TASN)RuPPh(3) and then to the mixed sulfenato/sulfinato speices (bmmp-O(3)-TASN)RuPPh(3) the complexes become progressively more ionic, and hence the Ru(II) center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B(38HF)P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis.

Dipeptide-based models of nickel superoxide dismutase: solvent effects highlight a critical role to Ni-S bonding and active site stabilization

Nickel superoxide dismutase (Ni-SOD) catalyzes the disproportionation of the superoxide radical to O(2) and H(2)O(2) utilizing the Ni(III/II) redox couple. The Ni center in Ni-SOD resides in an unusual coordination environment that is distinct from other SODs. In the reduced state (Ni-SOD(red)), Ni(II) is ligated to a primary amine-N from His1, anionic carboxamido-N/thiolato-S from Cys2, and a second thiolato-S from Cys6 to complete a NiN(2)S(2) square-planar coordination motif. Utilizing the dipeptide N(2)S(2-) ligand, H(2)N-Gly-l-Cys-OMe (GC-OMeH(2)), an accurate model of the structural and electronic contributions provided by His1 and Cys2 in Ni-SOD(red), we constructed the dinuclear sulfur-bridged metallosynthon, [Ni(2)(GC-OMe)(2)] (1). From 1 we prepared the following monomeric Ni(II)-N(2)S(2) complexes: K[Ni(GC-OMe)(SC(6)H(4)-p-Cl)] (2), K[Ni(GC-OMe)(S(t)Bu)] (3), K[Ni(GC-OMe)(SC(6)H(4)-p-OMe)] (4), and K[Ni(GC-OMe)(SNAc)] (5). The design strategy in utilizing GC-OMe(2-) is analogous to one which we reported before (see Inorg. Chem. 2009, 48, 5620 and Inorg. Chem. 2010, 49, 7080) where Ni-SOD(red) active site mimics can be assembled at will with electronically variant RS(-) ligands. Discussed herein is our initial account pertaining to the aqueous behavior of isolable, small-molecule Ni-SOD model complexes (non-maquette based). Spectroscopic (FTIR, UV-vis, ESI-MS, XAS) and electrochemical (CV) measurements suggest that 2-5 successfully simulate many of the electronic features of Ni-SOD(red). Furthermore, the aqueous studies reveal a dynamic behavior with regard to RS(-) lability and bridging interactions, suggesting a stabilizing role brought about by the protein architecture.

MAPping the chiral inversion and structural transformation of a metal-tripeptide complex having ni-superoxide dismutase activity

The metal abstraction peptide (MAP) tag is a tripeptide sequence capable of abstracting a metal ion from a chelator and binding it with extremely high affinity at neutral pH. Initial studies on the nickel-bound form of the complex demonstrate that the tripeptide asparagine-cysteine-cysteine (NCC) binds metal with 2N:2S, square planar geometry and behaves as both a structural and functional mimic of Ni superoxide dismutase (Ni-SOD). Electronic absorption, circular dichroism (CD), and magnetic CD (MCD) data collected for Ni-NCC are consistent with a diamagnetic Ni(II) center. It is apparent from the CD signal of Ni-NCC that the optical activity of the complex changes over time. Mass spectrometry data show that the mass of the complex is unchanged. Combined with the CD data, this suggests that chiral rearrangement of the complex occurs. Following incubation of the nickel-containing peptide in D(2)O and back-exchange into H(2)O, incorporation of deuterium into non-exchangeable positions is observed, indicating chiral inversion occurs at two of the α carbon atoms in the peptide. Control peptides were used to further characterize the chirality of the final nickel-peptide complex, and density functional theory (DFT) calculations were performed to validate the hypothesized position of the chiral inversions. In total, these data indicate Ni-SOD activity is increased proportionally to the degree of structural change in the complex over time. Specifically, the relationship between the change in CD signal and change in SOD activity is linear.

Use of metallopeptide based mimics demonstrates that the metalloprotein nitrile hydratase requires two oxidized cysteinates for catalytic activity

Nitrile hydratases (NHases) are non-heme Fe(III) or non-corrin Co(III) containing metalloenzymes that possess an N(2)S(3) ligand environment with nitrogen donors derived from amidates and sulfur donors derived from cysteinates. A closely related enzyme is thiocyanate hydrolase (SCNase), which possesses a nearly identical active-site coordination environment as CoNHase. These enzymes are redox inactive and perform hydrolytic reactions; SCNase hydrolyzes thiocyanate anions while NHase converts nitriles into amides. Herein an active CoNHase metallopeptide mimic, [Co(III)NHase-m1] (NHase-m1 = AcNH-CCDLP-CGVYD-PA-COOH), that contains Co(III) in a similar N(2)S(3) coordination environment as CoNHase is reported. [Co(III)NHase-m1] was characterized by electrospray ionization-mass spectrometry (ESI-MS), gel-permeation chromatography (GPC), Co K-edge X-ray absorption spectroscopy (Co-S: 2.21 Å; Co-N: 1.93 Å), vibrational, and optical spectroscopies. We find that [Co(III)NHase-m1] will perform the catalytic conversion of acrylonitrile into acrylamide with up to 58 turnovers observed after 18 h at 25 °C (pH 8.0). FTIR data used in concert with calculated vibrational data (mPWPW91/aug-cc-TZVPP) demonstrates that the active form of [Co(III)NHase-m1] has a ligated SO(2) (ν = 1091 cm(-1)) moiety and a ligated protonated SO(H) (ν = 928 cm(-1)) moiety; when only one oxygenated cysteinate ligand (i.e., a mono-SO(2) coordination motif) or the bis-SO(2) coordination motif are found within [Co(III)NHase-m1] no catalytic activity is observed. Calculations of the thermodynamics of ligand exchange (B3LYP/aug-cc-TZVPP) suggest that the reason for this is that the SO(2)/SO(H) equatorial ligand motif promotes both water dissociation from the Co(III)-center and nitrile coordination to the Co(III)-center. In contrast, the under- or overoxidized motifs will either strongly favor a five coordinate Co(III)-center or strongly favor water binding to the Co(III)-center over nitrile binding.

Versatile methodology toward NiN(2)S(2) complexes as nickel superoxide dismutase models: structure and proton affinity

Structural features of the reduced form of the nickel superoxide dismutase (Ni-SOD) active site have been modeled with asymmetric NiN(2)S(2) complexes (Et(4)N)[Ni(nmp)(SR)] (R = C(6)H(4)-p-Cl (2) and (S(t)Bu) (3)) obtained via S,S-bridge splitting of the dimeric metallosynthon, [Ni(2)(nmp)(2)] (1). Complexes 2 and 3 are irreversibly oxidized at potentials within the window needed for SOD activity, 236 and 75 mV versus Ag/AgCl, respectively. The exogenous thiolato-S in 2 and 3 serves as a proton acceptor, suggesting potential involvement of Cys6 in Ni-SOD for H(+) storage between SOD half reactions.

Bisamidate and mixed amine/amidate NiN2S2 complexes as models for nickel-containing acetyl coenzyme A synthase and superoxide dismutase: an experimental and computational study

The distal nickel site of acetyl-CoA synthase (Ni(d)-ACS) and reduced nickel superoxide dismutase (Ni-SOD) display similar square-planar Ni(II)N(2)S(2) coordination environments. One difference between these two sites, however, is that the nickel ion in Ni-SOD contains a mixed amine/amidate coordination motif while the Ni(d) site in Ni-ACS contains a bisamidate coordination motif. To provide insight into the consequences of the different coordination environments on the properties of the Ni ions, we systematically examined two square-planar Ni(II)N(2)S(2) complexes, one with bisthiolate-bisamidate ligation (Et(4)N)(2)(Ni(L1)).2H(2)O (2) [H(4)L1 = N-(2-mercaptoacetyl)-N'-(2-mercaptoethyl)glycinamide] and another with bisthiolate-amine/amidate ligation K(Ni(HL2)) (3) [H(4)L2 = N-(2''-mercaptoethyl)-2-((2'-mercaptoethyl)amino)acetamide]. Although these two complexes differ only by a single amine versus amidate ligand, their chemical properties are quite different. The stronger in-plane ligand field in the bisamidate complex (Ni(II)(L1))(2-) (2) results in an increase in the energies of the d --> d transitions and a considerably more negative oxidation potential. Furthermore, while the bisamidate complex (Ni(II)(L1))(2-) (2) readily forms a trinuclear species (Et(4)N)(2)({Ni(L1)}(2)Ni).H(2)O (1) and reacts rapidly with O(2), presumably via sulfoxidation, the mixed amine/amidate complex (Ni(II)(HL2))(-) (3) remains monomeric and is stable for days in air. Interestingly, the Ni(III) species of the bisamidate complex formed by chemical oxidation with I(2) can be detected by electron paramagnetic resonance (EPR) spectroscopy while the mixed amine/amidate complex immediately decomposes upon oxidation. To explain these experimentally observed properties, we performed S K-edge X-ray absorption spectroscopy and low-temperature (77 K) electronic absorption measurements as well as both hybrid density functional theory (hybrid-DFT) and spectroscopy oriented configuration interaction (SORCI) calculations. These studies demonstrate that the highest occupied molecular orbital (HOMO) of the bisamidate complex (Ni(II)(L1))(2-) (2) has more Ni character and is significantly destabilized relative to the mixed amine/amidate complex (Ni(II)(HL2))(-) (3) by approximately 6.2 kcal mol(-1). The consequence of this destabilization is manifested in the nucleophilic activation of the doubly filled HOMO, which makes (Ni(II)(L1))(2-) (2) significantly more reactive toward electrophiles such as O(2).

Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues

Nickel-dependent superoxide dismutase (NiSOD) is a member of a class of metalloenzymes that protect aerobic organisms from the damaging superoxide radical (O(2) (.-)). A distinctive and fascinating feature of NiSOD is the presence of active-site nickel-thiolate interactions involving the Cys2 and Cys6 residues. Mutation of one or both Cys residues to Ser prevents catalysis of O(2) (.-), demonstrating that both residues are necessary to support proper enzymatic activity (Ryan et al., J Biol Inorg Chem, 2010). In this study, we have employed a combined spectroscopic and computational approach to characterize three Cys-to-Ser (Cys --> Ser) mutants (C2S, C6S, and C2S/C6S NiSOD). Similar electronic absorption and magnetic circular dichroism spectra are observed for these mutants, indicating that they possess nearly identical active-site geometric and electronic structures. These spectroscopic data also reveal that the Ni(2+) ion in each mutant adopts a high-spin (S = 1) configuration, characteristic of a five- or six-coordinate ligand environment, as opposed to the low-spin (S = 0) configuration observed for the four-coordinate Ni(2+) center in the native enzyme. An analysis of the electronic absorption and magnetic circular dichroism data within the framework of density functional theory computations performed on a series of five- and six-coordinate C2S/C6S NiSOD models reveals that the active site of each Cys --> Ser mutant possesses an essentially six-coordinate Ni(2+) center with a rather weak axial bonding interaction. Factors contributing to the lack of catalytic activity displayed by the Cys --> Ser NiSOD mutants are explored.

Imidazole-containing (N3S)-Ni(II) complexes relating to nickel containing biomolecules

Dimeric (N(2)S)Ni complexes and the monomeric N(2)S(2) bismercaptodiazacycloheptane nickel complex, (bme-dach)Ni, serve as precursors to two N(2)-, N'-/ S- complexes where N(2) = diazacycloheptane, N' = imidazole and S = thiolate. As rare examples of nickel complexes containing a mixed thiolate/imidazole ligand set, these complexes are characterized by X-ray diffraction, UV/vis, and variable temperature (1)H NMR spectroscopies, and electrochemistry. Density functional theory computations relate the orientation of the imidazole with respect to the N(2)N'SNi square plane to the VT NMR observed fluxionality and activation parameters. The superoxide dismutase activity of the imidazole complexes was investigated by the nitroblue tetrazolium assay.

Universal spectrochemical series of six-coordinate octahedral metal complexes for modifying the ligand field splitting

We studied a novel universal spectrochemical series of six-coordinated octahedral 3d transition metal complexes, which can be used for any combination of central metal atom and ligand molecules. A two dimensional spectrochemical series could be used to estimate the ligand field splitting energy of not only known compounds but also the unknown compounds. Therefore, it should be possible to control the physical properties, such as the electronic and magnetic properties and the optical phenomena of octahedral transition metal complexes by modifying the ligand field splitting.

Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases

We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.