Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.

Superoxide Oxidation by a Thiolate-Ligated Iron Complex and Anion Inhibition

Superoxide (O₂^•-) is a toxic radical, generated via the adventitious reduction of dioxygen (O₂), which has been implicated in a number of human disease states. Nonheme iron enzymes, superoxide reductase (SOR) and superoxide dismutase (SOD), detoxify O₂^•- via reduction to afford H₂O₂ and disproportionation to afford O₂ and H₂O₂, respectively. The former contains a thiolate in the coordination sphere, which has been proposed to prevent O₂^•- oxidation to O₂. The work described herein shows that, in contrast to this, oxidized thiolate-ligated [Fe^III(S^Me2N₄(tren)(THF)]²⁺ (1^ox-THF) is capable of oxidizing O₂^•- to O₂. Coordinating anions, Cl^- and OAc^-, are shown to inhibit dioxygen evolution, implicating an inner-sphere mechanism. Previously we showed that the reduced thiolate-ligated [Fe^II(S^Me2N₄(tren))]⁺ (1) is capable of reducing O₂^•- via a proton-dependent inner-sphere mechanism involving a transient Fe(III)-OOH intermediate. A transient ferric-superoxo intermediate, [Fe^III(S^Me2N₄(tren))(O₂)]⁺ (3), is detected by electronic absorption spectroscopy at -130 °C in the reaction between 1^ox-THF and KO₂ and shown to evolve O₂ upon slight warming to -115 °C. The DFT calculated O-O (1.306 Å) and Fe-O (1.943 Å) bond lengths of 3 are typical of ferric-superoxo complexes, and the time-dependent DFT calculated electronic absorption spectrum of 3 reproduces the experimental spectrum. The electronic structure of 3 is shown to consist of two antiferromagnetically coupled (J^calc = -180 cm^-1) unpaired electrons, one in a superoxo π*(O-O) orbital and the other in an antibonding π*(Fe(d_yz)-S(p_y)) orbital.

Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies

Superoxide reductases (SORs) are mononuclear non-heme iron enzymes involved in superoxide radical detoxification in some microorganisms. Their atypical active site is made of an iron atom pentacoordinated by four equatorial nitrogen atoms from histidine residues and one axial sulfur atom from a cysteinate residue, which plays a central role in catalysis. In most SORs, the residue immediately following the cysteinate ligand is an asparagine, which belongs to the second coordination sphere and is expected to have a critical influence on the properties of the active site. In this work, in order to investigate the role of this asparagine residue in the Desulfoarculus baarsii enzyme (Asn117), we carried out, in comparison with the wild-type enzyme, absorption and resonance Raman (RR) studies on a SOR mutant in which Asn117 was changed into an alanine. RR analysis was developed in order to assign the different bands using excitation in the (Cys116)-S^-→ Fe³⁺ charge transfer band. By investigating the correlation between the (Cys116)-S^-→ Fe³⁺ charge transfer band maximum with the frequency of each RR band in different SOR forms, we assessed the contribution of the ν(Fe-S) vibration among the different RR bands. The data showed that Asn117, by making hydrogen bond interactions with Lys74 and Tyr76, allows a rigidification of the backbone of the Cys116 ligand, as well as that of the neighboring residues Ile118 and His119. Such a structural role of Asn117 has a deep impact on the S-Fe bond. It results in a tight control of the H-bond distance between the Ile118 and His119 NH peptidic moiety with the cysteine sulfur ligand, which in turn enables fine-tuning of the S-Fe bond strength, an essential property for the SOR active site. This study illustrates the intricate roles of second coordination sphere residues to adjust the ligand to metal bond properties in the active site of metalloenzymes.

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy

The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.

How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes

Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O₂ and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O₂ and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.

How Do Ring Size and π-Donating Thiolate Ligands Affect Redox-Active, α-Imino-N-heterocycle Ligand Activation?

Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L^•-), initially suggested that the electron-donating thiolate had reduced the N-heterocycle. Sulfur K-edge X-ray absorption spectroscopic (XAS) data, however, provides evidence for direct communication, via backbonding, between the thiolate sulfur and the formally orthogonal (α-imino)-N-heterocycle ligand π*-orbitals. DFT calculations provide evidence for extensive delocalization of bonds over the sulfur, iron, and (α-imino)-N-heterocycle, and TD-DFT shows that the intense optical CT bands involve transitions between a mixed Fe/S donor, and (α-imino)-N-heterocycle π*-acceptor orbital. The energies and intensities of the optical and S K-edge pre-edge XAS transitions are shown to correlate with N-heterocycle ring size, as do the redox potentials. When the thiolate is replaced with a thioether, or when the low-spin S = 0 Fe(II) is replaced with a high-spin S = 3/2 Co(II), the N-heterocycle ligand metrical parameters and electronic structure do not change relative to the neutral L⁰ ligand. With respect to the development of future catalysts containing redox-active ligands, the energy cost of storing reducing equivalents is shown to be lowest when a quinoline, as opposed to imidazole or pyridine, is incorporated into the ligand backbone of the corresponding Fe complex.

Light-Induced Radical Formation and Isomerization of an Aromatic Thiol in Solution Followed by Time-Resolved X-ray Absorption Spectroscopy at the Sulfur K-Edge

We applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ∼70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemical reaction pathways and transient products of sulfur-containing molecules in solution.

Multiconfigurational and DFT analyses of the electromeric formulation and UV-vis absorption spectra of the superoxide adduct of ferrous superoxide reductase

The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer. In an attempt to clarify the electromeric formulation of this adduct, we report a computational study using a multiconfigurational complete active space self-consistent field (MC-CASSCF) wave function approach as well as modelling the UV-vis absorption spectra with time-dependent density functional theory (TD-DFT). The MC-CASSCF calculations disclose a weak interaction between iron and the dioxygenic ligand and a dominant configuration with an essentially ferrous-superoxo character. The computed UV-vis absorption spectra reveal a marked dependence on the choice of density functional - both in terms of location of bands and in terms of orbital contributors. For the main band in the visible region, besides the recently reported thiolate-to-superoxide charge transfer, a more salient, and less functional-dependent, feature is a thiolate-to-ferric iron charge transfer, consistent with a ferric-peroxo electromer. By contrast, the computed UV-vis spectra of a ferric-hydroperoxo SOR model match distinctly better (and with no qualitative dependence on the DFT methodology) the 600-nm band as due to a mainly thiolate-to-ferric character - supporting the assignment of the SOR "600-nm intermediate" as a S=5/2 ferric-hydroperoxo species.

Valence tautomerism in synthetic models of cytochrome P450

CytP450s have a cysteine-bound heme cofactor that, in its as-isolated resting (oxidized) form, can be conclusively described as a ferric thiolate species. Unlike the native enzyme, most synthetic thiolate-bound ferric porphyrins are unstable in air unless the axial thiolate ligand is sterically protected. Spectroscopic investigations on a series of synthetic mimics of cytP450 indicate that a thiolate-bound ferric porphyrin coexists in organic solutions at room temperature (RT) with a thiyl-radical bound ferrous porphyrin, i.e., its valence tautomer. The ferric thiolate state is favored by greater enthalpy and is air stable. The ferrous thiyl state is favored by entropy, populates at RT, and degrades in air. These ground states can be reversibly interchanged at RT by the addition or removal of water to the apolar medium. It is concluded that hydrogen bonding and local electrostatics protect the resting oxidized cytP450 active site from degradation in air by stabilizing the ferric thiolate ground state in contrast to its synthetic analogs.

Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue

Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the -EKHVP- motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (-E23T24HVP-), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild-type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.

Iron-sulfur bond covalency from electronic structure calculations for classical iron-sulfur clusters

The covalent character of iron-sulfur bonds is a fundamental electronic structural feature for understanding the electronic and magnetic properties and the reactivity of biological and biomimetic iron-sulfur clusters. Conceptually, bond covalency obtained from X-ray absorption spectroscopy (XAS) can be directly related to orbital compositions from electronic structure calculations, providing a standard for evaluation of density functional theoretical methods. Typically, a combination of functional and basis set that optimally reproduces experimental bond covalency is chosen, but its dependence on the population analysis method is often neglected, despite its important role in deriving theoretical bond covalency. In this study of iron tetrathiolates, and classical [2Fe-2S] and [4Fe-4S] clusters with only thiolate ligands, we find that orbital compositions can vary significantly depending on whether they are derived from frontier orbitals, spin densities, or electron sharing indexes from "Átoms in Molecules" (ÁIM) theory. The benefits and limitations of Mulliken, Minimum Basis Set Mulliken, Natural, Coefficients-Squared, Hirshfeld, and AIM population analyses are described using ab initio wave function-based (QCISD) and experimental (S K-edge XAS) bond covalency. We find that the AIM theory coupled with a triple-ζ basis set and the hybrid functional B(5%HF)P86 gives the most reasonable electronic structure for the studied Fe-S clusters.

Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials

The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.

EPR, resonance Raman, and DFT calculations on thiolate- and imidazole-bound iron(III) porphyrin complexes: role of the axial ligand in tuning the electronic structure

Iron(III) porphyrin complexes bearing covalently attached imidazole and thiolate axial ligands are investigated using resonance Raman, electron paramagnetic resonance, and cyclic voltammetry. The thiolate ligand stabilizes a low-spin ground state in solvent-bound six-coordinate species, weakens the Fe-N(pyr) bonds, and shifts the Fe(III/II) potential more negative by ~500 mV relative to an imidazole-bound species. Density functional theory calculations reproduce the experimental observation and indicate that the covalent charge donation from thiolate to iron reduces the Z(eff) on the iron. This increases the Fe(3d) orbital energies, which changes the bonding interaction present in these complexes significantly. In particular, the increase of the Fe(3d) energies activates an iron-to-porphyrin π*-back-bonding interaction not present in the imidazole-bound complex.

Characterization of a thiolato iron(III) Peroxy dianion complex

Nucleophilic oxidant: The reaction between a thiolato iron(II) complex 1 and superoxide in aprotic solvent at -90 °C yields a novel thiolato iron(III) peroxide intermediate 2, which exhibits unusually high nucleophilic reactivity. Compound 2 is an isomer of the thiolato iron(II) superoxide intermediate that is invoked in the reaction between superoxide reductase and superoxide.

Mechanism of S-oxygenation by a cysteine dioxygenase model complex

In this work, we present the first computational study on a biomimetic cysteine dioxygenase model complex, [Fe(II)(LN(3)S)](+), in which LN(3)S is a tetradentate ligand with a bis(imino)pyridyl scaffold and a pendant arylthiolate group. The reaction mechanism of sulfur dioxygenation with O(2) was examined by density functional theory (DFT) methods and compared with results obtained for cysteine dioxygenase. The reaction proceeds via multistate reactivity patterns on competing singlet, triplet, and quintet spin state surfaces. The reaction mechanism is analogous to that found for cysteine dioxygenase enzymes (Kumar, D.; Thiel, W.; de Visser, S. P. J. Am. Chem. Soc. 2011, 133, 3869-3882); hence, the computations indicate that this complex can closely mimic the enzymatic process. The catalytic mechanism starts from an iron(III)-superoxo complex and the attack of the terminal oxygen atom of the superoxo group on the sulfur atom of the ligand. Subsequently, the dioxygen bond breaks to form an iron(IV)-oxo complex with a bound sulfenato group. After reorganization, the second oxygen atom is transferred to the substrate to give a sulfinic acid product. An alternative mechanism involving the direct attack of dioxygen on the sulfur, without involving any iron-oxygen intermediates, was also examined. Importantly, a significant energetic preference for dioxygen coordinating to the iron center prior to attack at sulfur was discovered and serves to elucidate the function of the metal ion in the reaction process. The computational results are in good agreement with experimental observations, and the differences and similarities of the biomimetic complex and the enzymatic cysteine dioxygenase center are highlighted.

Influence of thiolate ligands on reductive N-O bond activation. Probing the O2(-) binding site of a biomimetic superoxide reductase analogue and examining the proton-dependent reduction of nitrite

Nitric oxide (NO) is frequently used to probe the substrate-binding site of "spectroscopically silent" non-heme Fe(2+) sites of metalloenzymes, such as superoxide reductase (SOR). Herein we use NO to probe the superoxide binding site of our thiolate-ligated biomimetic SOR model [Fe(II)(S(Me(2))N(4)(tren))](+) (1). Like NO-bound trans-cysteinate-ligated SOR (SOR-NO), the rhombic S = 3/2 EPR signal of NO-bound cis-thiolate-ligated [Fe(S(Me(2))N(4)(tren)(NO)](+) (2; g = 4.44, 3.54, 1.97), the isotopically sensitive ν(NO)(ν((15)NO)) stretching frequency (1685(1640) cm(-1)), and the 0.05 Å decrease in Fe-S bond length are shown to be consistent with the oxidative addition of NO to Fe(II) to afford an Fe(III)-NO(-) {FeNO}(7) species containing high-spin (S = 5/2) Fe(III) antiferromagnetically coupled to NO(-) (S = 1). The cis versus trans positioning of the thiolate does not appear to influence these properties. Although it has yet to be crystallographically characterized, SOR-NO is presumed to possess a bent Fe-NO similar to that of 2 (Fe-N-O = 151.7(4)°). The N-O bond is shown to be more activated in 2 relative to N- and O-ligated {FeNO}(7) complexes, and this is attributed to the electron-donating properties of the thiolate ligand. Hydrogen-bonding to the cysteinate sulfur attenuates N-O bond activation in SOR, as shown by its higher ν(NO) frequency (1721 cm(-1)). In contrast, the ν(O-O) frequency of the SOR peroxo intermediate and its analogues is not affected by H-bonds to the cysteinate sulfur or other factors influencing the Fe-SR bond strength; these only influence the ν(Fe-O) frequency. Reactions between 1 and NO(2)(-) are shown to result in the proton-dependent heterolytic cleavage of an N-O bond. The mechanism of this reaction is proposed to involve both Fe(II)-NO(2)(-) and {FeNO}(6) intermediates similar to those implicated in the mechanism of NiR-promoted NO(2)(-) reduction.

Investigation of the mechanism of formation of a thiolate-ligated Fe(III)-OOH

Kinetic studies aimed at determining the most probable mechanism for the proton-dependent [Fe(II)(S(Me2)N(4)(tren))](+) (1) promoted reduction of superoxide via a thiolate-ligated hydroperoxo intermediate [Fe(III)(S(Me2)N(4)(tren))(OOH)](+) (2) are described. Rate laws are derived for three proposed mechanisms, and it is shown that they should conceivably be distinguishable by kinetics. For weak proton donors with pK(a(HA)) > pK(a(HO(2))) rates are shown to correlate with proton donor pK(a), and display first-order dependence on iron, and half-order dependence on superoxide and proton donor HA. Proton donors acidic enough to convert O(2)(-) to HO(2) (in tetrahydrofuran, THF), that is, those with pK(a(HA)) < pK(a(HO(2))), are shown to display first-order dependence on both superoxide and iron, and rates which are independent of proton donor concentration. Relative pK(a) values were determined in THF by measuring equilibrium ion pair acidity constants using established methods. Rates of hydroperoxo 2 formation displays no apparent deuterium isotope effect, and bases, such as methoxide, are shown to inhibit the formation of 2. Rate constants for p-substituted phenols are shown to correlate linearly with the Hammett substituent constants σ(-). Activation parameters ((ΔH(++) = 2.8 kcal/mol, ΔS(++) = -31 eu) are shown to be consistent with a low-barrier associative mechanism that does not involve extensive bond cleavage. Together, these data are shown to be most consistent with a mechanism involving the addition of HO(2) to 1 with concomitant oxidation of the metal ion, and reduction of superoxide (an "oxidative addition" of sorts), in the rate-determining step. Activation parameters for MeOH- (ΔH(++) = 13.2 kcal/mol and ΔS(++) = -24.3 eu), and acetic acid- (ΔH(++) = 8.3 kcal/mol and ΔS(++) = -34 eu) promoted release of H(2)O(2) to afford solvent-bound [Fe(III)(S(Me2)N(4)(tren))(OMe)](+) (3) and [Fe(III)(S(Me2)N(4)(tren))(O(H)Me)](+) (4), respectively, are shown to be more consistent with a reaction involving rate-limiting protonation of an Fe(III)-OOH, than with one involving rate-limiting O-O bond cleavage. The observed deuterium isotope effect (k(H)/k(D) = 3.1) is also consistent with this mechanism.

S K-edge X-ray absorption spectroscopy and density functional theory studies of high and low spin {FeNO}7 thiolate complexes: exchange stabilization of electron delocalization in {FeNO}7 and {FeO2}8

S K-edge X-ray absorption spectroscopy (XAS) is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and density functional theory (DFT) calculations indicates that the electronic structures of {FeNO}(7) (S = 3/2) (S(Me2)N4(tren)Fe(NO), complex I) and {FeNO}(7) (S = 1/2) ((bme-daco)Fe(NO), complex II) are Fe(III)(S = 5/2)-NO(-)(S = 1) and Fe(III)(S = 3/2)-NO(-)(S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes Fe(II)(S = 0)-NO•(S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}(7) and {FeO2}(8) sites.

Density Functional Theory Calculations on Fe-O and O-O Cleavage of Ferric Hydroperoxide Species: Role of axial ligand and spin state

Density Functional Theory (DFT) calculations are performed on thiolate bound hydroperoxide complexes. O-O and Fe-O cleavage reaction coordinates, relevant to the active sites of Cytocrome P450 and Superoxide Reductase enzymes, were investigated for both high and low spin states and for cis and trans orientations of the thiolate ligand with respect to the hydroperoxide ligand. The results indicate that the presence of a thiolate ligand produces significant elongation of the Fe-O bond and reduction of Fe-O vibrational frequency. While the fate of the O-O cleavage reaction is not significantly altered, the presence of a thiolate induces a heterolytic Fe-O cleavage irrespective of the spin state and orientation which is very different from results obtained with a trans ammine ligand.

Influence of the nitrogen donors on nonheme iron models of superoxide reductase: high-spin Fe(III)-OOR complexes

A new five-coordinate, (N(4)S(thiolate))Fe(II) complex, containing tertiary amine donors, [Fe(II)(Me(4)[15]aneN(4))(SPh)]BPh(4) (2), was synthesized and structurally characterized as a model of the reduced active site of superoxide reductase (SOR). Reaction of 2 with tert-butyl hydroperoxide (tBuOOH) at -78 degrees C led to the generation of the alkylperoxo-iron(III) complex [Fe(III)(Me(4)[15]aneN(4))(SPh)(OOtBu)](+) (2a). The nonthiolate-ligated complex, [Fe(II)(Me(4)[15]aneN(4))(OTf)(2)] (3), was also reacted with tBuOOH and yielded the corresponding alkylperoxo complex [Fe(III)(Me(4)[15]aneN(4))(OTf)(OOtBu)](+) (3a) at an elevated temperature of -23 degrees C. These species were characterized by low-temperature UV-vis, EPR, and resonance Raman spectroscopies. Complexes 2a and 3a exhibit distinctly different spectroscopic signatures than the analogous alkylperoxo complexes [Fe(III)([15]aneN(4))(SAr)(OOR)](+), which contain secondary amine donors. Importantly, alkylation at nitrogen leads to a change from low-spin (S = 1/2) to high-spin (S = 5/2) of the iron(III) center. The resonance Raman data reveal that this change in spin state has a large effect on the nu(Fe-O) and nu(O-O) vibrations, and a comparison between 2a and the nonthiolate-ligated complex 3a shows that axial ligation has an additional significant impact on these vibrations. To our knowledge this study is the first in which the influence of a ligand trans to a peroxo moiety has been evaluated for a structurally equivalent pair of high-spin/low-spin peroxo-iron(III) complexes. The implications of spin state and thiolate ligation are discussed with regard to the functioning of SOR.

S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity

Experimental covalencies of the Fe-S bond for the resting low-spin and substrate-bound high-spin active site of cytochrome P450 are reported. DFT calculations on the active site indicate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental values. The H-bonding to the thiolate from the backbone decreases the anisotropic pi covalency of the Fe-S bond lowering the barrier of free rotation of the exchangeable axial ligand, which is important for reactivity. The anionic axial thiolate ligand is calculated to lower the Fe(III/II) reduction potential of the active site by more than 1 V compared to a neutral imidazole ligand. About half of this derives from its covalent bonding and half from its electrostatic interaction with the oxidized Fe. This axial thiolate ligand increases the pK(a) of compound 0 (Fe(III)-hydroperoxo) favoring its protonation which promotes O-O bond heterolysis forming compound I. The reactivity of compound I is calculated to be relatively insensitive to the nature of the axial ligand due to opposing reduction potential and proton affinity contributions to the H-atom abstraction energy.

X-ray spectroscopic approaches to the investigation and characterization of photochemical processes

Despite a wealth of studies exemplifying the utility of the 2-5 keV X-ray range in speciation and electronic structure elucidation, the exploitation of this energy regime for the study of photochemical processes has not been forthcoming. Herein, a new endstation set-up for in situ photochemical soft X-ray spectroscopy in the 2-5 keV energy region at the Stanford Synchrotron Radiation Lightsource is described for continuous photolysis under anaerobic conditions at both cryogenic and ambient temperatures. Representative examples of this approach are used to demonstrate the potential information content in several fields of study, including organometallic chemistry, biochemistry and materials chemistry.

Substrate binding preferences and pka determinations of a nitrile hydratase model complex: variable solvent coordination to [(bmmp-TASN)Fe]OTf

The five-coordinate iron-dithiolate complex (N,N'-4,7-bis-(2'-methyl-2'-mercatopropyl)-1-thia-4,7-diazacyclononane)iron(III), [LFe]+, has been isolated as the triflate salt from reaction of the previously reported LFeCl with thallium triflate. Spectroscopic characterization confirms an S = 1/2 ground state in non-coordinating solvents with room temperature microeff = 1.78 microB and electron paramagnetic resonance (EPR) derived g-values of g1 = 2.04, g2 = 2.02 and g3 = 2.01. [LFe]+ binds a variety of coordinating solvents resulting in six-coordinate complexes [LFe-solvent]+. In acetonitrile the low-spin [LFe-NCMe]+ (g1 = 2.27, g2 = 2.18, and g3 = 1.98) is in equilibrium with [LFe]+ with a binding constant of Keq = 4.7 at room temperature. Binding of H2O, DMF, methanol, DMSO, and pyridine to [LFe]+ yields high-spin six-coordinate complexes with EPR spectra that display significant strain in the rhombic zero-field splitting term E/D. Addition of 1 equiv of triflic acid to the previously reported diiron species (LFe)2O results in the formation of [(LFe)2OH]OTf, which has been characterized by X-ray crystallography. The aqueous chemistry of [LFe]+ reveals three distinct species as a function of pH: [LFe-OH2]+, [(LFe)2OH]OTf, and (LFe)2O. The pKa values for [LFe-OH2]+ and [(LFe)2OH]OTf are 5.4 +/- 0.1 and 6.52 +/- 0.05, respectively.

Structural analysis of metal sites in proteins: non-heme iron sites as a case study

In metalloproteins, the protein environment modulates metal properties to achieve the required goal, which can be protein stabilization or function. The analysis of metal sites at the atomic level of detail provided by protein structures can thus be of benefit in functional and evolutionary studies of proteins. In this work, we propose a structural bioinformatics approach to the study of metalloproteins based on structural templates of metal sites that include the PDB coordinates of protein residues forming the first and the second coordination sphere of the metal. We have applied this approach to non-heme iron sites, which have been analyzed at various levels. Templates of sites located in different protein domains have been compared, showing that similar sites can be found in unrelated proteins as the result of convergent evolution. Templates of sites located in proteins of a large superfamily have been compared, showing possible mechanisms of divergent evolution of proteins to achieve different functions. Furthermore, template comparisons have been used to predict the function of uncharacterized proteins, showing that similarity searches focused on metal sites can be advantageously combined with typical whole-domain comparisons. Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases.

Rational tuning of the thiolate donor in model complexes of superoxide reductase: direct evidence for a trans influence in Fe(III)-OOR complexes

Iron peroxide species have been identified as important intermediates in a number of nonheme iron as well as heme-containing enzymes, yet there are only a few examples of such species either synthetic or biological that have been well characterized. We describe the synthesis and structural characterization of a new series of five-coordinate (N4S(thiolate))Fe(II) complexes that react with tert-butyl hydroperoxide ((t)BuOOH) or cumenyl hydroperoxide (CmOOH) to give metastable alkylperoxo-iron(III) species (N4S(thiolate)Fe(III)-OOR) at low temperature. These complexes were designed specifically to mimic the nonheme iron active site of superoxide reductase, which contains a five-coordinate iron(II) center bound by one Cys and four His residues in the active form of the protein. The structures of the Fe(II) complexes are analyzed by X-ray crystallography, and their electrochemical properties are assessed by cyclic voltammetry. For the Fe(III)-OOR species, low-temperature UV-vis spectra reveal intense peaks between 500-550 nm that are typical of peroxide to iron(III) ligand-to-metal charge-transfer (LMCT) transitions, and EPR spectroscopy shows that these alkylperoxo species are all low-spin iron(III) complexes. Identification of the vibrational modes of the Fe(III)-OOR unit comes from resonance Raman (RR) spectroscopy, which shows nu(Fe-O) modes between 600-635 cm(-1) and nu(O-O) bands near 800 cm(-1). These Fe-O stretching frequencies are significantly lower than those found in other low-spin Fe(III)-OOR complexes. Trends in the data conclusively show that this weakening of the Fe-O bond arises from a trans influence of the thiolate donor, and density functional theory (DFT) calculations support these findings. These results suggest a role for the cysteine ligand in SOR, and are discussed in light of the recent assessments of the function of the cysteine ligand in this enzyme.

Spin-state-dependent oxygen sensitivity of iron dithiolates: sulfur oxygenation or disulfide formation

The oxygen sensitivity of two related iron(III) dithiolate complexes of the ligand [4,7-bis-(2'-methyl-2'-mercatopropyl)-1-thia-4,7-diazacyclononane], (bmmp-TASN)FeCN (1) and (bmmp-TASN)FeCl (2), has been examined. Oxygen exposure of the low-spin complex 1 yields the disulfonate complex (bmmp-O6-TASN)FeCN (3) as an olive-green solid with characteristic peaks in the IR spectrum at 1262, 1221, 1111, 1021, 947, 800, and 477 cm(-1). The corresponding nickel dithiolate, (bmmp-TASN)Ni (4), yields the related disulfonato derivative, (bmmp-O6-TASN)Ni (5) upon addition of H2O2 (IR bands at 1258, 1143, 1106, 1012, 800, and 694 cm(-1). Oxygen exposure of the high-spin complex 2 results in disulfide formation and decomplexation of the metal with subsequent iron-oxo cluster formation. Complexes 1 and 2 were examined using density functional theory calculations. A natural bond order/natural localized molecular orbital covalency analysis reveals that the low-spin complex 1 contains Fe-Sthiolate bonds with calculated covalencies of 75 and 86%, while the high-spin complex 2 contains Fe-Sthiolate bonds with calculated covalencies of 11 and 40%. The results indicate the degree of covalency of the Fe-S bonds plays a major role in determining the reaction pathway associated with oxygen exposure of iron thiolates. The X-ray structures of 1, 4, and 5 are reported.

Structure and dynamics of metalloproteins in live cells

X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components, and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized to provide both a cellular image of the relative distribution of metals throughout the cell as well as a high-resolution picture of the structure of the metal. As these techniques continue to grow in their capabilities and ease of use, so too does the demand for their application by chemists and biochemists interested in studying the structure and dynamics of metals in cells, in cellular organelles, and in metalloproteins.