Formation of High‐Valent Iron–Oxo Species in Superoxide Reductase: Characterization by Resonance Raman Spectroscopy

Superoxide reductase (SOR), a non‐heme mononuclear iron protein that is involved in superoxide detoxification in microorganisms, can be used as an unprecedented model to study the mechanisms of O₂ activation and of the formation of high‐valent iron–oxo species in metalloenzymes. By using resonance Raman spectroscopy, it was shown that the mutation of two residues in the second coordination sphere of the SOR iron active site, K₄₈ and I₁₁₈, led to the formation of a high‐valent iron–oxo species when the mutant proteins were reacted with H₂O₂. These data demonstrate that these residues in the second coordination sphere tightly control the evolution and the cleavage of the O? O bond of the ferric iron hydroperoxide intermediate that is formed in the SOR active site.     

Activation of a Non‐Heme FeIII‐OOH by a Second FeIII to Hydroxylate Strong C−H Bonds: Possible Implications for Soluble Methane Monooxygenase

Non‐heme iron oxygenases contain either monoiron or diiron active sites, and the role of the second iron in the latter enzymes is a topic of particular interest, especially for soluble methane monooxygenase (sMMO). Herein we report the activation of a non‐heme Fe^III‐OOH intermediate in a synthetic monoiron system using Fe^III(OTf)₃ to form a high‐valent oxidant capable of effecting cyclohexane and benzene hydroxylation within seconds at ?40 °C. Our results show that the second iron acts as a Lewis acid to activate the iron–hydroperoxo intermediate, leading to the formation of a powerful Fe^V=O oxidant—a possible role for the second iron in sMMO.     

The Fe2(NO)2 Diamond Core: A Unique Structural Motif In Non‐Heme Iron–NO Chemistry

Non‐heme high‐spin (hs) {FeNO}⁸ complexes have been proposed as important intermediates towards N₂O formation in flavodiiron NO reductases (FNORs). Many hs‐{FeNO}⁸ complexes disproportionate by forming dinitrosyl iron complexes (DNICs), but the mechanism of this reaction is not understood. While investigating this process, we isolated a new type of non‐heme iron nitrosyl complex that is stabilized by an unexpected spin‐state change. Upon reduction of the hs‐{FeNO}⁷ complex, [Fe(TPA)(NO)(OTf)](OTf) ( 1 ), the N‐O stretching band vanishes, but no sign of DNIC or N₂O formation is observed. Instead, the dimer, [Fe₂(TPA)₂(NO)₂](OTf)₂ ( 2 ) could be isolated and structurally characterized. We propose that 2 is formed from dimerization of the hs‐{FeNO}⁸ intermediate, followed by a spin state change of the iron centers to low‐spin (ls), and speculate that 2 models intermediates in hs‐{FeNO}⁸ complexes that precede the disproportionation reaction.     

Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO

Molecular mechanisms underlying the repair of nitrosylated [Fe–S] clusters by the microbial protein YtfE remain poorly understood. The X‐ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and ¹⁷O‐labeling electron spin echo envelope modulation measurements, show that each iron of the oxo‐bridged Fe^II–Fe^III diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo‐bridge. Structural analysis reveals that there are two solvent‐accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced‐form Fe^II–Fe^II YtfE toward nitric oxide demonstrates that the prerequisite for N₂O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N₂O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO‐trapping scavenger to promote the NO to N₂O transformation under low NO flux, which precedes nitrosative stress.     

Biologically Inspired C−H and C=C Oxidations with Hydrogen Peroxide Catalyzed by Iron Coordination Complexes

The development of catalysts for the selective oxidation of readily available hydrocarbons or organic precursors into oxygenated products is a long‐standing goal in organic synthesis. In the last decade, some iron coordination complexes have shown the potential to fit this role. These catalysts can mimic the O?O activation mode of far more sophisticated iron oxygenase enzymes, generating powerful yet selective oxidants. In this review, we report state‐of‐the‐art C?H and C=C oxidations catalyzed by non‐heme iron complexes and H₂O₂ as the oxidant. Finally, we briefly describe some novel oxidative reactivity and the perspectives of this chemistry.     

Lewis Acid Coordination Redirects S‐Nitrosothiol Signaling Output

S‐Nitrosothiols (RSNOs) serve as air‐stable reservoirs for nitric oxide in biology. While copper enzymes promote NO release from RSNOs by serving as Lewis acids for intramolecular electron‐transfer, redox‐innocent Lewis acids separate these two functions to reveal the effect of coordination on structure and reactivity. The synthetic Lewis acid B(C₆F₅)₃ coordinates to the RSNO oxygen atom, leading to profound changes in the RSNO electronic structure and reactivity. Although RSNOs possess relatively negative reduction potentials, B(C₆F₅)₃ coordination increases their reduction potential by over 1 V into the physiologically accessible +0.1 V vs. NHE. Outer‐sphere chemical reduction gives the Lewis acid stabilized hyponitrite dianion trans‐[LA‐O‐N=N‐O‐LA]^2? [LA=B(C₆F₅)₃], which releases N₂O upon acidification. Mechanistic and computational studies support initial reduction to the [RSNO‐B(C₆F₅)₃] radical anion, which is susceptible to N?N coupling prior to loss of RSSR.     

CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y‐zeolite supported Rhn clusters

We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane‐wave density functional theory based CPMD code and the empirical force‐field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born–Oppenheimer and Car–Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α‐cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rh_n; n = 2 to 6) formed from Rh(C₂H₄)₂ complex adsorbed within a cavity of Y‐zeolite in a reducible atmosphere of H₂ gas. © 2016 Wiley Periodicals, Inc.     

Structure of Bromotrinitrosyl Iron, [Fe(NO)3Br], and DFT Calculations of the Structures of [Fe(NO)3X] (X = Cl,Br, I)

Bromotrinitrosyl iron was prepared by passing a stream of nitrogen monoxide over a mixture of iron dibromide and iron powder at elevated temperatures. It readily loses NO to give [(ON)₂Fe(μ‐Br)Fe(CO)₂]. The structure of freshly obtained [Fe(NO)₃Br] was determined by X‐ray diffraction at 200 K and shows (distorted) tetrahedral coordination with N–Fe–N and N–Fe–Br angles of 107.9(2)° and 111.0(2)° and bent Fe–N–O groups (162.5(6)°). The DFT calculations in the series [Fe(NO)₃X] (X = Cl, Br, I) reproduce well the experimental structural parameters and vibrational frequencies.     

Theoretical modeling of the heme group with a hybrid QM/MM method

The quality of the results obtained in calculations with the hybrid QM/MM method IMOMM on systems where the heme group is partitioned in QM and MM regions is evaluated through the performance of calculations on the 4‐coordinate [Fe(P)] (P = porphyrin), the 5‐coordinate [Fe(P)(1−(Me)Im)] (Im = imidazole) and the 6‐coordinate [Fe(P)(1−(Me)Im)(O₂)] systems. The results are compared with those obtained from much more expensive pure quantum mechanics calculations on model systems. Three different properties are analyzed—namely, the optimized geometries, the binding energies of the axial ligands to the heme group, and the energy cost of the biochemically relevant out‐of‐plane displacement of the iron atom. Agreement is especially good in the case of optimized geometries and energy cost of out‐of‐plane displacements, with larger discrepancies in the case of binding energies. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 282–294, 2000     

Unusual Stabilization of an Intermediate Spin State of Iron upon the Axial Phenoxide Coordination of a Diiron(III)–Bisporphyrin: Effect of Heme–Heme Interactions

The binding of a series of substituted phenols as axial ligands onto a diiron(III)? bisporphyrin framework have been investigated. Spectroscopic characterization revealed high‐spin states of the iron centers in all of the phenolate complexes, with one exception in the 2,4,6‐trinitrophenolate complex of diiron(III)? bisporphyrin, which only stabilized the pure intermediate‐spin (S=3/2) state of the iron centers. The average Fe? N (porphyrin) and Fe? O (phenol) distances that were observed with the 2,4,6‐trinitrophenolate complex were 1.972(3) Å and 2.000(2) Å, respectively, which are the shortest and longest distances reported so far for any Fe^III? porphyrin with phenoxide coordination. The alternating shift pattern, which shows opposite signs of the chemical shifts for the meta versus ortho/para protons, is attributed to negative and positive spin densities on the phenolate carbon atoms, respectively, and is indicative of π‐spin delocalization onto the bound phenolate. Electrochemical data reveals that the E_1/2 value for the Fe^III/Fe^II couple is positively shifted with increasing acidity of the phenol. However, a plot of the E_1/2 values for the Fe^III/Fe^II couple versus the pK_a values of the phenols shows a linear relationship for all of the complexes, except for the 2,4,6‐trinitrophenolate complex. The large deviation from linearity is probably due to the change of spin for the complex. Although 2,4,6‐trinitrophenol is the weakest axial ligand in the series, its similar binding with the corresponding Fe^III? monoporphyrin only results in stabilization of the high‐spin state. The porphyrin macrocycle in the 2,4,6‐trinitrophenolate complex of diiron(III)? bisporphyrin is the most distorted, whilst the “ruffling” deformation affects the energy levels of the iron d orbitals. The larger size and weaker binding of 2,4,6‐trinitrophenol, along with heme? heme interactions in the diiron(III)? bisporphyrin, are responsible for the larger ring deformations and eventual stabilization of the pure intermediate‐spin states of the iron centers in the complex.     

A non-radical mechanism for methane hydroxylation at the diiron active site of soluble methane monooxygenase

We propose a non‐radical mechanism for the conversion of methane into methanol by soluble methane monooxygenase (sMMO), the active site of which involves a diiron active center. We assume the active site of the MMOH_Q intermediate, exhibiting direct reactivity with the methane substrate, to be a bis(μ‐oxo)diiron(IV ) complex in which one of the iron atoms is coordinatively unsaturated (five‐coordinate). Is it reasonable for such a diiron complex to be formed in the catalytic reaction of sMMO? The answer to this important question is positive from the viewpoint of energetics in density functional theory (DFT) calculations. Our model thus has a vacant coordination site for substrate methane. If MMOH_Q involves a coordinatively unsaturated iron atom at the active center, methane is effectively converted into methanol in the broken‐symmetry singlet state by a non‐radical mechanism; in the first step a methane C? H bond is dissociated via a four‐centered transition state (TS1) resulting in an important intermediate involving a hydroxo ligand and a methyl ligand, and in the second step the binding of the methyl ligand and the hydroxo ligand through a three‐centered transition state (TS2) results in the formation of a methanol complex. This mechanism is essentially identical to that of the methane–methanol conversion by the bare FeO⁺ complex and relevant transition metal–oxo complexes in the gas phase. Neither radical species nor ionic species are involved in this mechanism. We look in detail at kinetic isotope effects (KIEs) for H atom abstraction from methane on the basis of transition state theory with Wigner tunneling corrections.     

Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity

Protein design is a useful strategy to interrogate the protein structure‐function relationship. We demonstrate using a highly modular 3‐stranded coiled coil (TRI‐peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H₂O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75‐fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three‐coordinate Cu^I in a site, which tends toward two‐coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal‐center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.     

N2O Reductase Activity of a [Cu4S] Cluster in the 4CuI Redox State Modulated by Hydrogen Bond Donors and Proton Relays in the Secondary Coordination Sphere

The model complex [Cu₄(μ₄‐S)(dppa)₄]²⁺ ( 1 , dppa=μ₂‐(Ph₂P)₂NH) has N₂O reductase activity in methanol solvent, mediating 2 H⁺/2 e^? reduction of N₂O to N₂+H₂O in the presence of an exogenous electron donor (CoCp₂). A stoichiometric product with two deprotonated dppa ligands was characterized, indicating a key role of second‐sphere N?H residues as proton donors during N₂O reduction. The activity of 1 towards N₂O was suppressed in solvents that are unable to provide hydrogen bonding to the second‐sphere N?H groups. Structural and computational data indicate that second‐sphere hydrogen bonding induces structural distortion of the [Cu₄S] active site, accessing a strained geometry with enhanced reactivity due to localization of electron density along a dicopper edge site. The behavior of 1 mimics aspects of the Cu_Z catalytic site of nitrous oxide reductase: activity in the 4Cu^I:1S redox state, use of a second‐sphere proton donor, and reactivity dependence on both primary and secondary sphere effects.     

Not Limited to Iron: A Cobalt Heme–NO Model Facilitates N–N Coupling with External NO in the Presence of a Lewis Acid to Generate N2O

Some bacterial heme proteins catalyze the coupling of two NO molecules to generate N₂O. We previously reported that a heme Fe–NO model engages in this N?N bond‐forming reaction with NO. We now demonstrate that (OEP)Co^II(NO) similarly reacts with 1 equiv of NO in the presence of the Lewis acids BX₃ (X=F, C₆F₅) to generate N₂O. DFT calculations support retention of the Co^II oxidation state for the experimentally observed adduct (OEP)Co^II(NO?BF₃), the presumed hyponitrite intermediate (P^.+)Co^II(ONNO?BF₃), and the porphyrin π‐radical cation by‐product of this reaction, and that the π‐radical cation formation likely occurs at the hyponitrite stage. In contrast, the Fe analogue undergoes a ferrous‐to‐ferric oxidation state conversion during this reaction. Our work shows that cobalt hemes are chemically competent to engage in the NO‐to‐N₂O conversion reaction.     

The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics,free energies,and excited state properties

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM–TURBOMOLE is well‐suited for extended QM/MM MD simulations using first principles methods with large (triple‐ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg²⁺(aq), where the MM outer sphere water molecules are represented using the SWM4‐NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg²⁺ and Zn²⁺ were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time‐averaged solution absorption spectrum of indole, the emission spectrum of the indole excited state, and the electronic circular dichroism spectrum of an oxacepham. © 2014 Wiley Periodicals, Inc.     

Synergistic Substrate and Oxygen Activation in Salicylate Dioxygenase Revealed by QM/MM Simulations

Salicylate 1,2‐dioxygenase (SDO) is the first enzyme to be discovered to catalyze the oxidative cleavage of a monohydroxylated aromatic compound, namely salicylate, instead of the well‐known electron‐rich substrates. We have investigated the mechanism of dioxygen activation in SDO by QM/MM calculations. Our study reveals that the non‐heme Fe^II center in SDO activates salicylate and O₂ synergistically through a strong covalent interaction to facilitate the reductive cleavage of O₂. A covalent salicylate–Fe^II–O₂ complex is the reactive oxygen species in this case, and its electronic structure is best described as being between the two limiting cases, Fe^II?O₂ and Fe^II?O₂^.?, with partial electron transfer from the activated salicylate to O₂ via the Fe center. Thus SDO employs a synergistic strategy of substrate and oxygen activation to carry out the catalytic reaction, which is unprecedented in the family of iron dioxygenases. Moreover, O₂ activation in SDO happens without the assistance of a proton source. Our study essentially shows a new mechanistic possibility for O₂ activation.     

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

The formation of the Hg–N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg²⁺ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H₂O)₆]²⁺, (2) T + [Hg(H₂O)₅(OH)]⁺, (3) T + Hg(H₂O)₄(OH)₂, and (4) N3-deprotonated T + Hg(H₂O)₄(OH)₂. The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4–5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg²⁺ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.     

Crystallographic Evidence for a Sterically Induced Ferryl Tilt in a Non‐Heme Oxoiron(IV) Complex that Makes it a Better Oxidant

Oxoiron(IV) units are often implicated as intermediates in the catalytic cycles of non‐heme iron oxygenases and oxidases. The most reactive synthetic analogues of these intermediates are supported by tetradentate tripodal ligands with N‐methylbenzimidazole or quinoline donors, but their instability precludes structural characterization. Herein we report crystal structures of two [Fe^IV(O)(L)]²⁺ complexes supported by pentadentate ligands incorporating these heterocycles, which show longer average Fe–N distances than the complex with only pyridine donors. These longer distances correlate linearly with log k₂′ values for O‐ and H‐atom transfer rates, suggesting that weakening the ligand field increases the electrophilicity of the Fe=O center. The sterically bulkier quinoline donors are also found to tilt the Fe=O unit away from a linear N‐Fe=O arrangement by 10°.