Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Reduction of molecular oxygen in flavodiiron proteins - Catalytic mechanism and comparison to heme-copper oxidases

The family of flavodiiron proteins (FDPs) plays an important role in the scavenging and detoxification of both molecular oxygen and nitric oxide. Using electrons from a flavin mononucleotide cofactor molecular oxygen is reduced to water and nitric oxide is reduced to nitrous oxide and water. While the mechanism for NO reduction in FDPs has been studied extensively, there is very little information available about O2 reduction. Here we use hybrid density functional theory (DFT) to study the mechanism for O2 reduction in FDPs. An important finding is that a proton coupled reduction is needed after the O2 molecule has bound to the diferrous diiron active site and before the OO bond can be cleaved. This is in contrast to the mechanism for NO reduction, where both NN bond formation and NO bond cleavage occurs from the same starting structure without any further reduction, according to both experimental and computational results. This computational result for the O2 reduction mechanism should be possible to evaluate experimentally. Another difference between the two substrates is that the actual OO bond cleavage barrier is low, and not involved in rate-limiting the reduction process, while the barrier connected with bond cleavage/formation in the NO reduction process is of similar height as the rate-limiting steps. We suggest that these results may be part of the explanation for the generally higher activity for O2 reduction as compared to NO reduction in most FDPs. Comparisons are also made to the O2 reduction reaction in the family of heme‑copper oxidases.

The flavodiiron protein from Syntrophomonas wolfei has five domains and acts both as an NADH:O2 or an NADH:H2 O2 oxidoreductase

Flavodiiron proteins (FDPs) are a family of enzymes with a significant role in O2 /H2 O2 and/or NO detoxification through the reduction of these species to H2 O or N2 O, respectively. All FDPs contain a minimal catalytic unit of two identical subunits, each one having a metallo-β-lactamase-like domain harboring the catalytic diiron site, and a flavodoxin-like domain. However, more complex and diverse arrangements in terms of domains are found in this family, of which the class H enzymes are among the most complex. One of such FDPs is encoded in the genome of the anaerobic bacterium Syntrophomonas wolfei subsp. wolfei str. Goettingen G311. Besides the core domains, this protein is predicted to have three additional ones after the flavodoxin core domain: two short-chain rubredoxins and a NAD(P)H:rubredoxin oxidoreductase-like domain. This enzyme, FDP_H, was produced and characterized and the presence of the predicted cofactors was investigated by a set of biochemical and spectroscopic methodologies. Syntrophomonas wolfei FDP_H exhibited a remarkable O2 reduction activity with a kcat  = 52.0 ± 1.2 s-1 and a negligible NO reduction activity (~ 100 times lower than with O2 ), with NADH as an electron donor, that is, it is an oxygen-selective FDP. In addition, this enzyme showed the highest turnover value for H2 O2 reduction (kcat  = 19.1 ± 2.2 s-1 ) ever observed among FDPs. Kinetic studies of site-directed mutants of iron-binding cysteines at the two rubredoxin domains demonstrated the essential role of these centers since their absence leads to a significant decrease or even abolishment of O2 and H2 O2 reduction activities.

Exploring second coordination sphere effects in flavodiiron nitric oxide reductase model complexes

Flavodiiron nitric oxide reductases (FNORs) equip pathogens with resistance to nitric oxide (NO), an important immune defense agent in mammals, allowing these pathogens to proliferate in the human body, potentially causing chronic infections. Understanding the mechanism of how FNORs mediate the reduction of NO contributes to the greater goal of developing new therapeutic approaches against drug-resistant strains. Recent density functional theory calculations suggest that a second coordination sphere (SCS) tyrosine residue provides a hydrogen bond that is critical for the reduction of NO to N2O at the active site of FNORs [J. Lu, B. Bi, W. Lai and H. Chen, Origin of Nitric Oxide Reduction Activity in Flavo-Diiron NO Reductase: Key Roles of the Second Coordination Sphere, Angew. Chem., Int. Ed., 2019, 58, 3795-3799]. Specifically, this H-bond stabilizes the hyponitrite intermediate and reduces the energetic barrier for the N-N coupling step. At the same time, the role of the Fe⋯Fe distance and its effect on the N-N coupling step has not been fully investigated. In this study, we equipped the H[BPMP] (= 2,6-bis[[bis(2-pyridylmethyl)amino]methyl]-4-methylphenol) ligand with SCS amide groups and investigated the corresponding diiron complexes with 0-2 bridging acetate ligands. These amide groups can form hydrogen bonds with the bridging acetate ligand(s) and potentially the coordinated NO groups in these model complexes. At the same time, by changing the number of bridging acetate ligands, we can systematically vary the Fe⋯Fe distance. The reactivity of these complexes with NO was then investigated, and the formation of stable iron(II)-NO complexes was observed. Upon one-electron reduction, these NO complexes form Dinitrosyl Iron Complexes (DNICs), which were further characterized using IR and EPR spectroscopy.

Nitrite Formation at a Diiron Dinitrosyl Complex

Pathogenic bacteria employ iron-containing enzymes to detoxify nitric oxide (NO•) produced by mammals as part of their immune response. Two classes of diiron proteins, flavodiiron nitric oxide reductases (FNORs) and the hemerythrin-like proteins from mycobacteria (HLPs), are upregulated in bacteria in response to an increased local NO• concentration. While FNORs reduce NO• to nitrous oxide (N2O), the HLPs have been found to either reduce nitrite to NO• (YtfE), or oxidize NO• to nitrite (Mka-HLP). Various structural and functional models of the diiron site in FNORs have been developed over the years. However, the NO• oxidation reactivity of Mka-HLP has yet to be replicated with a synthetic complex. Compared to the FNORs, the coordination environment of the diiron site in Mka-HLP contains one less carboxylate ligand and, therefore, is expected to be more electron-poor. Herein, we synthesized a new diiron complex that models the electron-poor coordination environment of the Mka-HLP diiron site. The diferrous precursor FeIIFeII reacts with NO• to form a diiron dinitrosyl species ({FeNO}72), which is in equilibrium with a mononitrosyl diiron species (FeII{FeNO}7) in solution. Both complexes can be isolated and fully characterized. However, only oxidation of {FeNO}72 produced nitrite in high yield (71%). Our study provides the first model that reproduces the NO• oxidase reactivity of Mka-HLP and suggests intermediacy of an {FeNO}6/{FeNO}7 species.

Trapping of a Mononitrosyl Nonheme Intermediate of Nitric Oxide Reductase by Cryo-Photolysis of Caged Nitric Oxide

Characterization of short-lived reaction intermediates is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes. Here, we demonstrated that the photolysis of a caged compound under cryogenic temperature followed by thermal annealing is an invaluable technique for trapping of short-lived reaction intermediates of metalloenzymes through the study of membrane-integrated nitric oxide reductase (NOR) that catalyzes reductive coupling of two NO molecules to N₂O at its heme/nonheme Fe_B binuclear center. Although NO produced by the photolysis of caged NO did not react with NOR under cryogenic temperature, annealing to ∼160 K allowed NO to diffuse and react with NOR, which was evident from the appearance of EPR signals assignable to the S = 3/2 state. This indicates that the nonheme Fe_B-NO species can be trapped as the intermediate. Time-resolved IR spectroscopy with the use of the photolysis of caged NO as a reaction trigger showed that the intermediate formed at 10 μs gave the NO stretching frequency at 1683 cm^-1 typical of nonheme Fe-NO, confirming that the combination of the cryo-photolysis of caged NO and annealing enabled us to trap the reaction intermediate. Thus, the cryo-photolysis of the caged compound has great potential for the characterization of short-lived reaction intermediates.

Reductive Coupling of Nitric Oxide by Cu(I): Stepwise Formation of Mono- and Dinitrosyl Species En Route to a Cupric Hyponitrite Intermediate

Transition-metal-mediated reductive coupling of nitric oxide (NO(g)) to nitrous oxide (N2O(g)) has significance across the fields of industrial chemistry, biochemistry, medicine, and environmental health. Herein, we elucidate a density functional theory (DFT)-supplemented mechanism of NO(g) reductive coupling at a copper-ion center, [(tmpa)CuI(MeCN)]+ (1) {tmpa = tris(2-pyridylmethyl)amine}. At -110 °C in EtOH (<-90 °C in MeOH), exposing 1 to NO(g) leads to a new binuclear hyponitrite intermediate [{(tmpa)CuII}2(μ-N2O22-)]2+ (2), exhibiting temperature-dependent irreversible isomerization to the previously characterized κ2-O,O'-trans-[(tmpa)2Cu2II(μ-N2O22-)]2+ (OOXray) complex. Complementary stopped-flow kinetic analysis of the reaction in MeOH reveals an initial mononitrosyl species [(tmpa)Cu(NO)]+ (1-(NO)) that binds a second NO molecule, forming a dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2). The decay of 1-(NO)2 requires an available starting complex 1 to form a dicopper-dinitrosyl species hypothesized to be [{(tmpa)Cu}2(μ-NO)2]2+ (D) bearing a diamond-core motif, en route to the formation of hyponitrite intermediate 2. In contrast, exposing 1 to NO(g) in 2-MeTHF/THF (v/v 4:1) at <-80 °C leads to the newly observed transient metastable dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2) prior to its disproportionation-mediated transformation to the nitrite product [(tmpa)CuII(NO2)]+. Our study furnishes a near-complete profile of NO(g) activation at a reduced Cu site with tripodal tetradentate ligation in two distinctly different solvents, aided by detailed spectroscopic characterization of metastable intermediates, including resonance Raman characterization of the new dinitrosyl and hyponitrite species detected.

Stable Bimetallic FeII/{Fe(NO)2}9 Moiety Derived from Reductive Transformations of a Diferrous-dinitrosyl Species

A dimeric dithiolate-bridged species, [Fe(NO)(PS2)]₂ (1) containing two {FeNO}⁷ units, can be isolated by treating [Fe(CO)₂(NO)₂] with PS2H₂ (PS2H₂ = bis(2-dimercaptophenyl)phenylphosphine). Crystallographic studies reveal the syn-configuration of NO units and the bridging thiolates in the butterfly shape of the 2Fe2S core. Addition of PPh₃ to the solution of dinuclear 1 leads to the formation of mononuclear {FeNO}⁷ [Fe(NO)(PS2)(PPh₃)] (2) that shows electrochemical responses similar to those of 1. One-electron reduction of 1 with Cp*₂Co or KC₈ results in the isolation of thiolate-bridged bimetallic DNIC, [(PS2)Fe(μ-PS2)Fe(NO)₂]^- ([3]^-), confirmed by several spectroscopies including single-crystal X-ray diffraction studies. The bimetallic DNIC [3]^- is a rare example obtained from the one-electron reduction of a dinuclear Fe-NO {FeNO}⁷ model complex. With the assistance of redox behaviors of 2, electrochemical studies imply that the reduction of 1 leads to the formation of a mononuclear {FeNO}⁸ [Fe(NO)(PS2)(THF)]^- intermediate, which involves disproportionation or NO^- transfer to yield [3]^-. Based on IR data and magnetic properties, the electronic structure of [3]^- can be described as a Fe^II/{Fe(NO)₂}⁹ state. Isolation of the {Fe(NO)₂}⁹ moiety coordinated by the Fe ancillary complex lends strong support to the NO scrambling behavior in the effectiveness of the activity of flavodiiron nitric oxide reductases (FNORs).

Direct Reduction of NO to N2O by a Mononuclear Nonheme Thiolate Ligated Iron(II) Complex via Formation of a Metastable {FeNO}7 Complex

Addition of NO to a nonheme dithiolate-ligated iron(II) complex, FeII(Me3TACN)(S2SiMe2) (1), results in the generation of N2O. Low-temperature spectroscopic studies reveal a metastable six-coordinate {FeNO}7 intermediate (S = 3/2) that was trapped at -135 °C and was characterized by low-temperature UV-vis, resonance Raman, EPR, Mössbauer, XAS, and DFT studies. Thermal decay of the {FeNO}7 species leads to the evolution of N2O, providing a rare example of a mononuclear thiolate-ligated {FeNO}7 that mediates NO reduction to N2O without the requirement of any exogenous electron or proton sources.

Spectroscopic Characterization of a Diferric Mycobacterial Hemerythrin-Like Protein with Unprecedented Reactivity toward Nitric Oxide

Hemerythrin-like proteins (HLPs) are broadly distributed across taxonomic groups and appear to play highly diverse functional roles in prokaryotes. Mycobacterial HLPs contribute to the survival of these pathogenic bacteria in mammalian macrophages, but their modes of action remain unclear. A recent crystallographic characterization of Mycobacterium kansasii HLP (Mka-HLP) revealed the unexpected presence of a tyrosine sidechain (Tyr54) near the coordination sphere of one of the two iron centers. Here, we show that Tyr54 is a true ligand to the Fe2(III) ion which, in conjunction with the presence of a μ-oxo group bridging the two iron(III), brings unique reactivity toward nitric oxide (NO). Monitoring the titration of Mka-HLP with NO by Fourier-transform infrared and electron paramagnetic resonance spectroscopies shows that both diferric and diferrous forms of Mka-HLP accumulate an uncoupled high-spin and low-spin {FeNO}⁷ pair. We assign the reactivity of the diferric protein to an initial radical reaction between NO and the μ-oxo bridge to form nitrite and a mixed-valent diiron center that can react further with NO. Amperometric measurements of NO consumption by Mka-HLP confirm that this reactivity can proceed at low micromolar concentrations of NO, before additional NO consumption, supporting a NO scavenging role for mycobacterial HLPs.

What Is the Right Level of Activation of a High-Spin {FeNO}7 Complex to Enable Direct N-N Coupling? Mechanistic Insight into Flavodiiron NO Reductases

Flavodiiron nitric oxide reductases (FNORs), found in pathogenic bacteria, are capable of reducing nitric oxide (NO) to nitrous oxide (N₂O) to detoxify NO released by the human immune system. Previously, we reported the first FNOR model system that mediates direct NO reduction (Dong, H. T.; J. Am. Chem. Soc. 2018, 140, 13429-13440), but no intermediate of the reaction could be characterized. Here, we present a new set of model complexes that, depending on the ligand substitution, can either mediate direct NO reduction or stabilize a highly activated high-spin (hs) {FeNO}⁷ complex, the first intermediate of the reaction. The precursors, [{Fe^II(MPA-(RPhO)₂)}₂] (1, R = H and 2, R = ^tBu, Me), were prepared first and fully characterized. Complex 1 (without steric protection) directly reduces NO to N₂O almost quantitatively, which constitutes only the second example of this reaction in model systems. Contrarily, the reaction of sterically protected 2 with NO forms the stable mononitrosyl complex 3, which shows one of the lowest N-O stretching frequencies (1689 cm^-1) observed so far for a mononuclear hs-{FeNO}⁷ complex. This study confirms that an N-O stretch ≤1700 cm^-1 represents the appropriate level of activation of the FeNO unit to enable direct NO reduction. The higher activation level of these hs-{FeNO}⁷ complexes required for NO reduction compared to those formed in FNORs emphasizes the importance of hydrogen bonding residues in the active sites of FNORs to activate the bound NO ligands for direct N-N coupling and N₂O formation. The implications of these results for FNORs are further discussed.

A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis

Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from H2O-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: H2O-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD+ while simultaneously removing O2 from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX-like enzyme and instead harbors three paralogous genes (FDPF1-3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a "stand-alone" FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions.

Mechanistic study on reduction of nitric oxide to nitrous oxide using a dicopper complex

A density functional theory study was carried out to investigate the reduction mechanisms of NO to N₂O using a dicopper complex reported by Zhang and coworkers (J. Am. Chem. Soc., 2019, 141, 10159-10164). The reaction mechanism consists of three steps: N-N bond formation, isomerization of the resultant N₂O₂ moiety, and cleavage of the N-O bond.

Distortion of the [FeNO]2 Core in Flavodiiron Nitric Oxide Reductase Models Inhibits N-N Bond Formation and Promotes Formation of Unusual Dinitrosyl Iron Complexes: Implications for Catalysis and Reactivity

Flavodiiron nitric oxide reductases (FNORs) carry out the reduction of nitric oxide (NO) to nitrous oxide (N₂O), allowing infectious pathogens to mitigate toxic levels of NO generated in the human immune response. We previously reported the model complex [Fe₂(BPMP)(OPr)(NO)₂](OTf)₂ (1, OPr^- = propionate) that contains two coplanar NO ligands and that is capable of quantitative NO reduction to N₂O [White et al. J. Am. Chem. Soc. 2018, 140, 2562-2574]. Here we investigate, for the first time, how a distortion of the active site affects the ability of the diiron core to mediate N₂O formation. For this purpose, we prepared several analogues of 1 that contain two monodentate ligands in place of the bridging carboxylate, [Fe₂(BPMP)(X)₂(NO)₂]^3+/1+ (2-X; X = triflate, 1-methylimidazole, or methanol). Structural data of 2-X show that without the bridging carboxylate, the diiron core expands, leading to elongated (O)N-N(O) distances (from 2.80 Å in 1 to 3.00-3.96 Å in 2-X) and distorted (O)N-Fe-Fe-N(O) dihedral angles (from coplanarity (5.9°) in 1 to 52.9-85.1° in 2-X). Whereas 1 produces quantitative amounts of N₂O upon one-electron reduction, N₂O production is substantially impeded in 2-X, to an initial 5-10% N₂O yield. The main products after reduction are unprecedented hs-Fe^II/{Fe(NO)₂}^9/10 dinitrosyl iron complexes (DNICs). Even though mononuclear DNICs are stable and do not show N-N coupling (since it is a spin-forbidden process), the hs-Fe^II/{Fe(NO)₂}^9/10 DNICs obtained from 2-X show unexpected reactivity and produce up to quantitative N₂O yields after 2 h. The implications of these results for the active site structure of FNORs are discussed.

Bioinspired Di-Fe Complexes: Correlating Structure and Proton Transfer over Four Oxidation States

Metalloproteins with active sites containing di-Fe cores exhibit diverse chemical reactivity that is linked to the precise transfer of protons and electrons which directly involve the di-Fe units. The redox conversions are commonly corroborated by spectroscopic methods, but the associated structural changes are often difficult to assess, particularly those related to proton movements. This report describes the development of di-Fe complexes in which the movements of protons and electrons are pinpointed during the stepwise oxidation of a di-Fe^II species to one with an Fe^IIIFe^IV core. Complex formation was promoted using the phosphinic amido tripodal ligand [poat]^3- (N,N',N″-[nitrilotris(ethane-2,1-diyl)]tris(P,P-diphenylphosphinic amido)) that provided dynamic coordination spheres that assisted in regulating both electron and proton transfer processes. Oxidation of an [Fe^II-(μ-OH)-Fe^III] complex led to the corresponding di-Fe^III species containing a hydroxido bridge that was not stable at room temperature and converted to a species containing an oxido bridging ligand and protonation of one phosphinic amido group to form [Hpoat]^2-. Deprotonation led to a new species with an [Fe^III-(μ-O)-Fe^III] core that could be further oxidized to its Fe^IIIFe^IV analogue. Reactions with phenols suggest homolytic cleavage of the O-H bond to give products that are consistent with the initial formation of a phenoxyl radical─spectroscopic studies indicated that the electron is transferred to the Fe^IV center, and the proton is initially transferred to the more sterically hindered oxido ligand but then relocates to [poat]^3-. These findings offer new mechanistic insights related to the stability of and the reactions performed by di-Fe enzymes.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

NO Reduction to N2O Triggered by a Dinuclear Dinitrosyl Iron Complex via the Associated Pathways of Hyponitrite Formation and NO Disproportionation

In spite of the comprehensive study of the metal-mediated conversion of NO to N2O disclosing the conceivable processes/mechanism in biological and biomimetic studies, in this study, the synthesis cycles and mechanism of NO reduction to N2O triggered by the electronically localized dinuclear {Fe(NO)2}10-{Fe(NO)2}9 dinitrosyl iron complex (DNIC) [Fe(NO)2(μ-bdmap)Fe(NO)2(THF)] (1) (bdmap = 1,3- bis(dimethylamino)-2-propanolate) were investigated in detail. Reductive conversion of NO to N2O triggered by complex 1 in the presence of exogenous ·NO occurs via the simultaneous formation of hyponitrite-bound {[Fe2(NO)4(μ-bdmap)]2(κ4-N2O2)} (2) and [NO2]--bridged [Fe2(NO)4(μ-bdmap)(μ-NO2)] (3) (NO disproportionation yielding N2O and complex 3). EPR/IR spectra, single-crystal X-ray diffraction, and the electrochemical study uncover the reversible redox transformation of {Fe(NO)2}9-{Fe(NO)2}9 [Fe2(NO)4(μ-bdmap)(μ-OC4H8)]+ (7) ↔ {Fe(NO)2}10-{Fe(NO)2}9 1 ↔ {Fe(NO)2}10-{Fe(NO)2}10 [Fe(NO)2(μ-bdmap)Fe(NO)2]- (6) and characterize the formation of complex 1. Also, the synthesis study and DFT computation feature the detailed mechanism of electronically localized {Fe(NO)2}10-{Fe(NO)2}9 DNIC 1 reducing NO to N2O via the associated hyponitrite-formation and NO-disproportionation pathways. Presumably, the THF-bound {Fe(NO)2}9 unit of electronically localized {Fe(NO)2}10-{Fe(NO)2}9 complex 1 served as an electron buffering reservoir for accommodating electron redistribution, and the {Fe(NO)2}10 unit of complex 1 acted as an electron-transfer channel to drive exogeneous ·NO coordination to yield proposed relay intermediate κ2-N,O-[NO]--bridged [Fe2(NO)4(μ-bdmap)(μ-NO)] (A) for NO reduction to N2O.

A Monohydrosulfidodinitrosyldiiron Complex That Generates N2O as a Model for Flavodiiron Nitric Oxide Reductases: Reaction Mechanism and Electronic Structure

Flavodiiron nitric oxide reductases (FNORs) protect microbes from nitrosative stress under anaerobic conditions by mediating the reduction of nitric oxide (NO) to nitrous oxide (N2O). The proposed mechanism for the catalytic reduction of NO by FNORs involves a dinitrosyldiiron intermediate with a [hs-{FeNO}7]2 formulation, which produces N2O and a diferric species. Moreover, both NO and hydrogen sulfide (H2S) have been implicated in several similar physiological functions in biology and are also known to cross paths in cell signaling. Here we report the synthesis, spectroscopic and theoretical characterization, and N2O production activity of an unprecedented monohydrosulfidodinitrosyldiiron compound, with a [(HS)hs-{FeNO}7/hs-{FeNO}7] formulation, that models the key dinitrosyl intermediate of FNORs. The generation of N2O from this unique compound follows a semireduced pathway, where one-electron reduction generates a reactive hs-{FeNO}8 center via the occupation of an Fe-NO antibonding orbital. In contrast to the well-known reactivity of H2S and NO, the coordinated hydrosulfide remains unreactive toward NO and acts only as a spectator ligand during the NO reduction process.

A Nonheme Mononuclear {FeNO}7 Complex that Produces N2 O in the Absence of an Exogenous Reductant

A new nonheme iron(II) complex, Fe^II (Me₃ TACN)((OSi^Ph2 )₂ O) (1), is reported. Reaction of 1 with NO_(g) gives a stable mononitrosyl complex Fe(NO)(Me₃ TACN)((OSi^Ph2 )₂ O) (2), which was characterized by Mössbauer (δ=0.52 mm s^-1 , |ΔE_Q |=0.80 mm s^-1 ), EPR (S=3/2), resonance Raman (RR) and Fe K-edge X-ray absorption spectroscopies. The data show that 2 is an {FeNO}⁷ complex with an S=3/2 spin ground state. The RR spectrum (λ_exc =458 nm) of 2 combined with isotopic labeling (¹⁵ N, ¹⁸ O) reveals ν(N-O)=1680 cm^-1 , which is highly activated, and is a nearly identical match to that seen for the reactive mononitrosyl intermediate in the nonheme iron enzyme FDPnor (ν(NO)=1681 cm^-1 ). Complex 2 reacts rapidly with H₂ O in THF to produce the N-N coupled product N₂ O, providing the first example of a mononuclear nonheme iron complex that is capable of converting NO to N₂ O in the absence of an exogenous reductant.

Reduction of NO by diiron complexes in relation to flavodiiron nitric oxide reductases

Reduction of nitric oxide (NO) to nitrous oxide (N₂O) is associated with immense biological and health implications. Flavodiiron nitric oxide reductases (FNORs) are diiron containing enzymes that catalyze the two electron reduction of NO to N₂O and help certain pathogenic bacteria to survive under "nitrosative stress" in anaerobic growth conditions. Consequently, invading bacteria can proliferate inside the body of mammals by bypassing the immune defense mechanism involving NO and may thus lead to harmful infections. Various mechanisms, namely the direct reduction, semireduction, superreduction and hyponitrite mechanisms, have been proposed over time for catalytic NO reduction by FNORs. Model studies in relation to the diiron active site of FNORs have immensely helped to replicate the minimal structure-reactivity relationship and to understand the mechanism of NO reduction. A brief overview of the FNOR activity and the proposed reaction mechanisms followed by a systematic description and detailed analysis of the model studies is presented, which describes the development in the area of NO reduction by diiron complexes and its implications. A great deal of successful modeling chemistry as well as the shortcomings related to the synthesis and reactivity studies is discussed in detail. Finally, future prospects in this particular area of research are proposed, which in due course may bring more clarity in the understanding of this important redox reaction.

Direct NO Reduction by a Biomimetic Iron(II) Pyrazolate MOF

A novel metal-organic framework (MOF) containing one-dimensional, Fe²⁺ chains bridged by dipyrazolate linkers and N,N-dimethylformamide (DMF) ligands has been synthesized. The unusual chain-type metal nodes feature accessible coordination sites on adjacent metal centers, resulting in motifs that are reminiscent of the active sites in non-heme diiron enzymes. The MOF facilitates direct reduction of nitric oxide (NO), producing nearly quantitative yields of nitrous oxide (N₂ O) and emulating the reactivity of flavodiiron nitric oxide reductases (FNORs). The ferrous form of the MOF can be regenerated via a synthetic cycle involving reduction with cobaltocene (CoCp₂ ) followed by reaction with trimethylsilyl triflate (TMSOTf).

The Amino Acids Motif -32GSSYN36- in the Catalytic Domain of E. coli Flavorubredoxin NO Reductase Is Essential for Its Activity

Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif, -G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release.

Tuning metal-metal interactions for cooperative small molecule activation

Cluster complexes have attracted interest for decades due to their promise of drawing analogies to metallic surfaces and metalloenzyme active sites, but only recently have chemists started to develop ligand scaffolds that are specifically designed to support multinuclear transition metal cores. Such ligands not only hold multiple metal centers in close proximity but also allow for fine-tuning of their electronic structures and surrounding steric environments. This Feature Article highlights ligand designs that allow for cooperative small molecule activation at cluster complexes, with a particular focus on complexes that contain metal-metal bonds. Two useful ligand-design elements have emerged from this work: a degree of geometric flexibility, which allows for novel small molecule activation modes, and the use of redox-active ligands to provide electronic flexibility to the cluster core. The authors have incorporated these factors into a unique class of dinucleating macrocycles (nPDI2). Redox-active fragments in nPDI2 mimic the weak-overlap covalent bonding that is characteristic of M-M interactions, and aliphatic linkers in the ligand backbone provide geometric flexibility, allowing for interconversion between a range of geometries as the dinuclear core responds to the requirements of various small molecule substrates. The union of these design elements appears to be a powerful combination for analogizing critical aspects of heterogeneous and metalloenzyme catalysts.

Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers

Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin-streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [Fe^III-(μ-OH)-Fe^III] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.

Exploring the Limits of Dative Boratrane Bonding: Iron as a Strong Lewis Base in Low-Valent Non-Heme Iron-Nitrosyl Complexes

We previously reported the synthesis and preliminary characterization of a unique series of low-spin (ls) {FeNO}8-10 complexes supported by an ambiphilic trisphosphineborane ligand, [Fe(TPB)(NO)]+/0/-. Herein, we use advanced spectroscopic techniques and density functional theory (DFT) calculations to extract detailed information as to how the bonding changes across the redox series. We find that, in spite of the highly reduced nature of these complexes, they feature an NO+ ligand throughout with strong Fe-NO π-backbonding and essentially closed-shell electronic structures of their FeNO units. This is enabled by an Fe-B interaction that is present throughout the series. In particular, the most reduced [Fe(TPB)(NO)]- complex, an example of a ls-{FeNO}10 species, features a true reverse dative Fe → B bond where the Fe center acts as a strong Lewis-base. Hence, this complex is in fact electronically similar to the ls-{FeNO}8 system, with two additional electrons "stored" on site in an Fe-B single bond. The outlier in this series is the ls-{FeNO}9 complex, due to spin polarization (quantified by pulse EPR spectroscopy), which weakens the Fe-NO bond. These data are further contextualized by comparison with a related N2 complex, [Fe(TPB)(N2)]-, which is a key intermediate in Fe(TPB)-catalyzed N2 fixation. Our present study finds that the Fe → B interaction is key for storing the electrons needed to achieve a highly reduced state in these systems, and highlights the pitfalls associated with using geometric parameters to try to evaluate reverse dative interactions, a finding with broader implications to the study of transition metal complexes with boratrane and related ligands.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Copper(I) Complex Mediated Nitric Oxide Reductive Coupling: Ligand Hydrogen Bonding Derived Proton Transfer Promotes N2O(g) Release

A cuprous chelate bearing a secondary sphere hydrogen bonding functionality, [(PV-tmpa)Cu^I]⁺, transforms ^•NO_(g) to N₂O_(g) in high-yields in methanol. Ligand derived proton transfer facilitates N-O bond cleavage of a putative hyponitrite intermediate releasing N₂O_(g), underscoring the crucial balance between H-bonding capabilities and acidities in (bio)chemical ^•NO_(g) coupling systems.

Diversity and complexity of flavodiiron NO/O2 reductases

Flavodiiron proteins (FDPs) are a family of enzymes endowed with nitric oxide (NO) or oxygen reductase activities, forming the innocuous nitrous oxide (N2O) or water molecules, respectively. FDPs are widespread in the three life kingdoms, and have a modular nature, being each monomer minimally constituted by a metallo-β-lactamase-like domain containing a catalytic diiron centre, followed by a flavodoxin one, with a flavin mononucleotide. Since their discovery, additional domains have been found in FDPs, attached to the C-terminus, and containing either extra metal (iron) centers or extra flavin binding modules. Following an extensive analysis of genomic databases, we identified novel domain compositions, and proposed a new classification of FDPs in eight classes based on the nature and number of extra domains.

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.

Spectroscopy and DFT Calculations of Flavo-Diiron Nitric Oxide Reductase Identify Bridging Structures of NO-Coordinated Diiron Intermediates

Flavo-diiron proteins (FDPs) are widespread in anaerobic bacteria, archaea, and protozoa, where they serve as the terminal components of dioxygen and nitric oxide reductive scavenging pathways. FDPs contain an N,O-ligated diiron site adjacent to a flavin mononucleotide (FMN) cofactor. The diiron site is structurally similar to those in hemerythrin, ribonucleotide reductase, and methane monooxygenase. However, only FDPs turn over NO to N2O at significant rates and yields. Previous studies revealed sequential binding of two NO molecules to the diferrous site, forming mono- and dinitrosyl intermediates leading to N2O formation. In the present work, these mono- and dinitrosyl intermediates have been characterized by EPR and Mössbauer spectroscopies and DFT calculations. Our results show that the iron proximal to the cofactor binds the first NO to form the diiron mononitrosyl complex, implying the iron distal to the FMN binds the second NO to form the diiron dinitrosyl intermediate. The exchange-coupling constants, J (H = JS1·S2), were found to differ substantially, +17 cm-1 for the diiron mononitrosyl and +60 cm-1 for the diiron dinitrosyl. Notwithstanding this large difference, our findings indicate retention of at least one hydroxo bridge throughout the NOR catalytic cycle. The Mossbauer hyperfine parameters and DFT calculations confirmed a semibridging NO- ligand in the mononitrosyl intermediate that lowers the exchange parameter. The DFT calculations on the dinitrosyl intermediate suggest a contribution to J from direct exchange between the S = 1 spins on the NO- ligands, which could initiate N-N bond formation. Our results provide insight into why FDPs are the only known nonheme diiron enzymes that competently turn over NO to N2O.

Nitric Oxide Reductase Activity in Heme-Nonheme Binuclear Engineered Myoglobins through a One-Electron Reduction Cycle

Fe_BMbs are structural and functional models of native bacterial nitric oxide reductases (NORs) generated through engineering of myoglobin. These biosynthetic models replicate the heme-nonheme diiron site of NORs and allow substitutions of metal centers and heme cofactors. Here, we provide evidence for multiple NOR turnover in monoformyl-heme-containing Fe_BMb1 proteins loaded with Fe^II, Co^II, or Zn^II metal ions at the Fe_B site (Fe^II/Co^II/Zn^II-Fe_BMb1(MF-heme)). FTIR detection of the ν(NNO) band of N₂O at 2231 cm^-1 provides a direct quantitative measurement of the product in solution. A maximum number of turnover is observed with Fe^II-Fe_BMb1(MF-heme), but the NOR activity is retained when the Fe_B site is loaded with Zn^II. These data support the viability of a one-electron semireduced pathway for the reduction of NO at binuclear centers in reducing conditions.

Non-heme High-Spin {FeNO}6-8 Complexes: One Ligand Platform Can Do It All

Heme and non-heme iron-nitrosyl complexes are important intermediates in biology. While there are numerous examples of low-spin heme iron-nitrosyl complexes in different oxidation states, much less is known about high-spin (hs) non-heme iron-nitrosyls in oxidation states other than the formally ferrous NO adducts ({FeNO}⁷ in the Enemark-Feltham notation). In this study, we present a complete series of hs-{FeNO}^6-8 complexes using the TMG₃tren coligand. Redox transformations from the hs-{FeNO}⁷ complex [Fe(TMG₃tren)(NO)]²⁺ to its {FeNO}⁶ and {FeNO}⁸ analogs do not alter the coordination environment of the iron center, allowing for detailed comparisons between these species. Here, we present new MCD, NRVS, XANES/EXAFS, and Mössbauer data, demonstrating that these redox transformations are metal based, which allows us to access hs-Fe(II)-NO^-, Fe(III)-NO^-, and Fe(IV)-NO^- complexes. Vibrational data, analyzed by NCA, directly quantify changes in Fe-NO bonding along this series. Optical data allow for the identification of a "spectator" charge-transfer transition that, together with Mössbauer and XAS data, directly monitors the electronic changes of the Fe center. Using EXAFS, we are also able to provide structural data for all complexes. The magnetic properties of the complexes are further analyzed (from magnetic Mössbauer). The properties of our hs-{FeNO}^6-8 complexes are then contrasted to corresponding, low-spin iron-nitrosyl complexes where redox transformations are generally NO centered. The hs-{FeNO}⁸ complex can further be protonated by weak acids, and the product of this reaction is characterized. Taken together, these results provide unprecedented insight into the properties of biologically relevant non-heme iron-nitrosyl complexes in three relevant oxidation states.

Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures

Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.

A Nonheme, High-Spin {FeNO}8 Complex that Spontaneously Generates N2O

One-electron reduction of [Fe(NO)-(N3PyS)]BF₄ (1) leads to the production of the metastable nonheme {FeNO}⁸ complex, [Fe(NO)(N3PyS)] (3). Complex 3 is a rare example of a high-spin (S = 1) {FeNO}⁸ and is the first example, to our knowledge, of a mononuclear nonheme {FeNO}⁸ species that generates N₂O. A second, novel route to 3 involves addition of Piloty's acid, an HNO donor, to an Fe^II precursor. This work provides possible new insights regarding the mechanism of nitric oxide reductases.

Structure/function correlations over binuclear non-heme iron active sites

Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.