Synthetic Models for Non-Heme Carboxylate-Bridged Diiron Metalloproteins: Strategies and Tactics

Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks

Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to predict the dynamics of initiation and propagation of blood clotting and tested these predictions with human blood plasma by using microfluidics. We discovered that both initiation and propagation of clotting are regulated by a threshold response to the concentration of activators of clotting, and that clotting is sensitive to the spatial localization of stimuli. To understand the dynamics of patterning of the Drosophila embryo, we used microfluidics to perturb the environment around a developing embryo and observe the effects of this perturbation on the expression of Hunchback, a protein whose localization is essential to proper development. We found that the mechanism that is responsible for Hunchback positioning is asymmetric, time-dependent, and more complex than previously proposed by studies of individual reactions. Overall, these approaches provide strategies for simplifying, modeling, and probing complex networks without sacrificing the functionality of the network. Such network-level strategies may be most useful for understanding systems with nonlinear interactions where spatial dynamics is essential for function. In addition, microfluidics provides an opportunity to investigate the mechanisms responsible for robust functioning of complex networks. By creating nonideal, stressful, and perturbed environments, microfluidic experiments could reveal the function of pathways thought to be nonessential under ideal conditions.

Iron complexes of dendrimer-appended carboxylates for activating dioxygen and oxidizing hydrocarbons

The active sites of metalloenzymes are often deeply buried inside a hydrophobic protein sheath, which protects them from undesirable hydrolysis and polymerization reactions, allowing them to achieve their normal functions. In order to mimic the hydrophobic environment of the active sites in bacterial monooxygenases, diiron(II) compounds of the general formula [Fe2([G-3]COO)4(4-RPy)2] were prepared, where [G-3]COO- is a third-generation dendrimer-appended terphenyl carboxylate ligand and 4-RPy is a pyridine derivative. The dendrimer environment provides excellent protection for the diiron center, reducing its reactivity toward dioxygen by about 300-fold compared with analogous complexes of terphenyl carboxylate ([G-1]COO-) ligands. An FeIIFeIII intermediate was characterized by electronic, electron paramagnetic resonance, Mössbauer, and X-ray absorption spectroscopic analyses following the oxygenation of [Fe2([G-3]COO)4(4-PPy)2], where 4-PPy is 4-pyrrolidinopyridine. The results are consistent with the formation of a superoxo species. This diiron compound, in the presence of dioxygen, can oxidize external substrates.

Copper-Sulfur Complexes Supported by N-Donor Ligands: Towards Models of the Cu(Z) Site in Nitrous Oxide Reductase

The distinctive structure of the [(his)(7)Cu(4)(μ-S)](n+) cluster in the "Cu(Z)" active site of nitrous oxide reductase and the intriguing mechanistic hypotheses for its catalytic reactivity provide inspiration for synthetic model studies aimed at characterizing relevant copper-sulfur compounds and obtaining fundamental insights into structure and bonding. In this brief review, we summarize such studies that have focused on the synthesis and characterization of a range of copper-sulfur complexes supported by N-donor ligands. Compounds with variable nuclearities and sulfur redox levels have been isolated, with the nature of the species obtained being dependent on the supporting ligand, sulfur source, and the reaction conditions. Spectroscopic data and theoretical calculations, often performed with a view toward drawing comparisons to oxygen analogs, have provided insight into the nature of the copper-sulfur bonding interactions in the complexes.

Iron(II) complexes of sterically bulky alpha-ketocarboxylates. structural models for alpha-ketoacid-dependent nonheme iron halogenases

Reaction of the sterically hindered alpha-ketocarboxylate 2,6-di(mesityl)benzoylformate (MesBF) with the iron(II) complexes LFeCl 2 [L = N, N, N', N'-tetramethylpropylenediamine (Me 4pda) or 6,6'-dimethyl-2,2'-bipyridine (dmby)] yielded LFe(Cl)(MesBF) ( 1 or 2). X-ray crystal structures of these complexes showed that they closely model the active site structure of the nonheme iron halogenase enzyme SyrB2. A similar synthetic procedure using benzoylformate with L = dmby yielded (dmby)Fe[(O 2CC(O)Ph)] 2 ( 3) instead, demonstrating the need for the sterically hindered alpha-ketocarboxylate to assemble the halogenase model compounds. In order to make reactivity comparisons among the structurally related iron(II) complexes of benzoylformates of varying steric properties, the complexes [LFe(O 2CC(O)Ar)] n ( 4- 6) were prepared, where L' = tris(pyridylmethyl)amine (tpa) and Ar = 2,6-dimesitylphenyl, 2,6-di p-tolylphenyl, or 2,4,6-trimethylphenyl, respectively. X-ray structures for the latter two cases ( 5 and 6) revealed dinuclear topologies ( n = 2), but UV-vis and (1)H NMR spectroscopy indicated that all three complexes dissociated in varying degrees to monomers in CH 2Cl 2 solution. Although compounds 1- 6 were oxidized by O 2, oxidative decarboxylation of the alpha-ketocarboxylate ligand(s) only occurred for 3. These results indicate that the steric hindrance useful for structural modeling of the halogenase active site prohibits functional mimicry of the enzyme.

Di-μ-thio-cyanato-κN:N-bis-({2,4-di-bromo-6-[2-(methyl-amino)ethyl-imino-meth-yl]-phenol-ato-κN,N',O}nickel(II))

The title complex, [Ni(2)(C(11)H(11)Br(2)N(2)O)(2)(NCS)(2)], is a thio-cyanate-bridged dinuclear nickel(II) complex. The asymmetric unit contains two molecules. Both Ni atoms in each molecule have a square-pyramidal coordination geometry, and each center is bound by one O and two N atoms of one Schiff base ligand and by one N atom of a bridging thio-cyanate ligand, which define the basal planes. N atoms from the bridging thio-cyanate ligands occupy the apical positions.

High-spin versus broken symmetry—Effect of DFT spin density representation on the geometries of three diiron (III) model compounds

Unrestricted density functional theory calculations have been conducted on three diiron(III) synthetic model compounds containing antiferromagnetically coupled high-spin (HS) irons for which crystallographic structures and Raman spectral data are available. Three density functionals have been employed: BPW91, PWC, and BOP. The study compares the effects on optimized geometries and harmonic vibrational frequencies of spin-paired (SP) low-spin, HS, and broken symmetry antiferromagnetically coupled singlet representations of the spin density distribution. The geometries around the diiron centers in the HS and broken symmetry (BS) representations are found to be similar, both markedly different from those arising from the SP representation. Small differences between the HS and BS results are seen in bond lengths, angles, Raman frequencies, and spin densities associated with oxo and peroxo bridges between the irons.

A predictably selective aliphatic C-H oxidation reaction for complex molecule synthesis

Realizing the extraordinary potential of unactivated sp3 C-H bond oxidation in organic synthesis requires the discovery of catalysts that are both highly reactive and predictably selective. We report an iron (Fe)-based small molecule catalyst that uses hydrogen peroxide (H2O2) to oxidize a broad range of substrates. Predictable selectivity is achieved solely on the basis of the electronic and steric properties of the C-H bonds, without the need for directing groups. Additionally, carboxylate directing groups may be used to furnish five-membered ring lactone products. We demonstrate that these three modes of selectivity enable the predictable oxidation of complex natural products and their derivatives at specific C-H bonds with preparatively useful yields. This type of general and predictable reactivity stands to enable aliphatic C-H oxidation as a method for streamlining complex molecule synthesis.

Unraveling the reactive species of a functional non-heme iron monooxygenase model using stopped-flow UV-vis spectroscopy

Low-temperature stopped-flow electronic spectroscopy was utilized to resolve the intermediates formed in the reaction of a diiron(II) compound, Fe2(H2Hbamb)2(N-MeIm)2 (H4HBamb = 2,3-bis(2-hydroxybenzamido)dimethylbutane), 1, with the oxygen atom donors 2,6-dimethyliodosylbenzene and p-cyanodimethylaniline N-oxide and the mechanistic probe hydroperoxide 2-methyl-1-phenylprop-2-yl hydroperoxide (MPPH). Previous studies showed that 1 is capable of catalytically oxidizing cyclohexane to cyclohexanol (300 turnovers) via a pathway involving the heterolytic cleavage of the O-O bond of MPPH (>98% peroxide utilization). We now report intimate details of the formation of the reactive intermediate and its subsequent decay in the absence of substrates. The reaction, which is independent of the nature of the oxidant, proceeds in three consecutive steps assigned as (i) oxygen-atom transfer to one of the iron centers of 1 to form an FeIV=O species, 2, (ii) ligand rearrangement to 3, and (iii) internal collapse of the terminal oxo group to generate a diferric, mu-oxo species, 4. Assignment of the second step as a ligand rearrangement was corroborated by stopped-flow spectroscopic studies of the one-electron oxidation of the starting diferrous 1, which is also known to undergo ligand rearrangement upon the formation of the [FeII, FeIII] mixed-valent complex. Observation of the reaction rates over a temperature range allowed for the determination of activation parameters for each of the three steps. The role of the ligand reorganization in the energetic profile for the formation of the catalytically competent intermediate is discussed, along with the potential biological significance of the internal conversion of the active oxidant to the inert, mu-oxo diiron(III) dimer, 4.

Synthesis and Metal Complexes of ChiralC2-Symmetric Diamino–Bisoxazoline Ligands

A synthetic route to tetradentate chiral N(4) ligands has been developed with the aim to study the potential of corresponding iron and manganese complexes as catalysts for enantioselective epoxidation. These ligands, which contain two oxazoline rings and two trialkylamino groups as coordinating units, are readily prepared in enantiomerically pure form by the reaction of chiral 2-chloromethyloxazolines with achiral N,N'-dimethylethane-1,2-diamine or chiral (R,R)-N,N'-dimethylcyclohexane-1,2-diamine. The ligands derived from N,N'-dimethylethane-1,2-diamine reacted with anhydrous metal halides MnCl(2) and FeCl(2) in a stereoselective manner to give octahedral mononuclear complexes that have the general formula Delta-[(L)MCl(2)]. In contrast, the ligands derived from N,N'-dimethylcyclohexane-1,2-diamine formed complexes with different coordination modes depending on the diastereomer employed: in one case the metal ion was found to be pentacoordinate, in the other case a hexacoordinated complex was observed. The structure of a series of Fe and Mn complexes was determined by X-ray analysis. The coordination chemistry of these ligands was further studied by X-ray and NMR analyses of the diamagnetic isostructural complexes [(L)ZnCl(2)]. Analogous ionic complexes, which were prepared by removing chloride with silver trifluoromethanesulfonate or hexafluoroantimonate, were tested as catalysts for the epoxidation of olefins.

A Mononuclear Cyclopentadiene–Iron Complex Grafted in the Supercages of HY Zeolite: Synthesis, Structure, and Reactivity

The reaction of ferrocene with the acidic hydroxy groups in the supercages of zeolite HY dehydrated at 673 K and the reactivity of the resultant surface species towards CO and O(2) were investigated by temperature-programmed decomposition (TPD) and reduction (TPR) and IR, X-ray absorption fine structure analysis (XAFS), and X-ray photoelectron (XP) spectroscopy. In situ FTIR, TPD, TPR, and chemical analysis reveal that the Cp(2)Fe molecule adsorbed on the zeolite surface loses one cyclopentadienyl group under vacuum at 423 K, which leads to the formation of a well-defined mononuclear surface Fe-C(5)H(6) complex grafted to two acidic sites and one ([triple bond]Si-O-Si[triple bond]) unit, as confirmed by the lack of Fe-Fe contributions in the EXAFS spectra. Each iron atom is coordinated, on average, to three oxygen atoms of the zeolite surface with a Fe--O distance of 2.00 A and to five carbon atoms with a Fe--C distance of 2.09 A. IR spectra indicate that the cyclopentadiene-iron species grafted on the surface of the zeolite is quite stable in vacuo or under an inert or hydrogen atmosphere below 423 K, and is also relatively stable under oxygen at room temperature. However, the cyclopentadiene ligand readily reacts with CO to form a compound containing carbonyl at 323 K, and even at room temperature. The single carbonyl band in the IR spectra provides evidence for the nearly uniform formation of a cyclopentadiene-iron species on the surface of the zeolite.

"Turn-on" fluorescent sensor for the selective detection of zinc ion by a sterically-encumbered bipyridyl-based receptor

A sterically-encumbered 5,5'-distyryl-2,2'-bipyridyl derivative that enforces a 1:1 metal-to-ligand ratio acts as a selective turn-on sensor for Zn(2+) in THF.

Dioxygen activation at non-heme iron: insights from rapid kinetic studies

One of the common biochemical pathways of binding and activation of dioxygen involves non-heme iron centers. The enzyme cycles usually start with an iron(II) or diiron(II) state and traverse via several intermediates (detected or postulated) such as (di)iron(III)-superoxo, (di)iron(III)-(hydro)peroxo, iron(III)iron(IV)-oxo, and (di)iron(IV)-oxo species, some of which are responsible for substrate oxidation. In this Account, we present results of kinetic and mechanistic studies of dioxygen binding and activation reactions of model inorganic iron compounds. The number of iron centers, their coordination number, and the steric and electronic properties of the ligands were varied in several series of well-characterized complexes that provided reactive manifolds modeling the function of native non-heme iron enzymes. Time-resolved cryogenic stopped-flow spectrophotometry permitted the identification of kinetically competent intermediates in these systems. Inner-sphere mechanisms dominated the chemistry of dioxygen binding, intermediate transformations, and substrate oxidation as most of these processes were controlled by the rates of ligand substitution at the iron centers.

High-valent iron(IV)-oxo complexes of heme and non-heme ligands in oxygenation reactions

High-valent iron(IV)-oxo species have been implicated as the key reactive intermediates in the catalytic cycles of dioxygen activation by heme and non-heme iron enzymes. Our understanding of the enzymatic reactions has improved greatly via investigation of spectroscopic and chemical properties of heme and non-heme iron(IV)-oxo complexes. In this Account, reactivities of synthetic iron(IV)-oxo porphyrin pi-cation radicals and mononuclear non-heme iron(IV)-oxo complexes in oxygenation reactions have been discussed as chemical models of cytochrome P450 and non-heme iron enzymes. These results demonstrate how mechanistic developments in biomimetic research can help our understanding of dioxygen activation and oxygen atom transfer reactions in nature.

Ligand effects on dioxygen activation by copper and nickel complexes: reactivity and intermediates

Copper and nickel complexes having various active-oxygen species M n -O 2 ( n = 1 or 2), such as trans-(micro-1,2-peroxo)Cu (II) 2, bis(micro-oxo)M (III) 2, bis(micro-superoxo)Ni (II) 2, and ligand-based alkylperoxo-M (II) n , can be produced by a series of tetradentate tripodal ligands (TMPA analogues) containing sterically demanding 6-methyl substituent(s) on the pyridyl group(s), where TMPA = tris(2-pyridylmethyl)amine. Roles of the methyl substituent(s) for the formation of the active-oxygen species and their oxidation reactivities are reported.

Synthesis, structure, and properties of a mixed-valent triiron complex of tetramethyl reductic acid, an ascorbic acid analogue, and its relationship to a functional non-heme iron oxidation catalyst system

The purple triiron(II,III,III) complex, [Fe(3)Cl(2)(TMRASQ)(4)(HTMRA)(2)] x C(5)H(12) (1 x C(5)H(12)), where H(2)TMRA is a tetramethyl reductic acid, 4,4,5,5-tetramethyl-2,3-dihydroxy-2-cyclopenten-1-one, and HTMRASQ is the semiquinone form of this ligand, was prepared from (Et(4)N)(2)[Fe(2)OCl(6)] and H(2)TMRA and characterized by X-ray crystallography, Mössbauer spectroscopy, and redox titrations. The physical properties of the complex in solution are consistent with its mixed-valent character, as delineated by a solid-state structure analysis. Assignments of the iron and ligand oxidation states in the crystal were made on the basis of a valence bond sum analysis and the internal ligand geometry. As the first well-characterized iron complex of an ascorbic acid H(2)AA analogue, 1 provides insight into the possible coordination geometry of the family of complexes containing H(2)AA and its analogues. In the presence of air and H(2)TMRA, 1 is able to catalyze the oxidation of cyclohexane to cyclohexanol with remarkable selectivity, but the nature of the true catalyst remains unknown.

Active-site models of bacterial nitric oxide reductase featuring tris-histidyl and glutamic acid mimics: influence of a carboxylate ligand on Fe(B) binding and the heme Fe/Fe(B) redox potential

Active-site models of bacterial nitric oxide reductase (NOR) featuring a heme Fe and a trisimidazole- and glutaric acid-bound non-heme Fe (Fe(B)) have been synthesized. These models closely replicate the proposed active site of native NORs. Examination of these models shows that the glutamic acid mimic is required for both Fe(B) retention in the distal binding site and proper modulation of the redox potentials of both the heme and non-heme Fe's.

Design and Synthesis of Binucleating Macrocyclic Clefts Derived from Schiff-Base Calixpyrroles

The syntheses, characterisation and complexation reactions of a series of binucleating Schiff-base calixpyrrole macrocycles are described. The acid-templated [2+2] condensations between meso-disubstituted diformyldipyrromethanes and o-phenylenediamines generate the Schiff-base pyrrolic macrocycles H(4)L(1) to H(4)L(6) upon basic workup. The single-crystal X-ray structures of both H(4)L(3).2 EtOH and H(4)L(6).H2O confirm that [2+2] cyclisation has occurred, with either EtOH or H2O hydrogen-bonded within the macrocyclic cleft. A series of complexation reactions generate the dipalladium [Pd2(L)] (L=L(1) to L(5)), dinickel [Ni2(L(1))] and dicopper [Cu2(L)] (L=L(1) to L(3)) complexes. All of these complexes have been structurally characterised in the solid state and are found to adopt wedged structures that are enforced by the rigidity of the aryl backbone to give a cleft reminiscent of the structures of Pacman porphyrins. The binuclear nickel complexes [Ni2(mu-OMe)2Cl2(HOMe)2(H(4)L(1))] and [Ni2(mu-OH)2Cl2(HOMe)(H(4)L(5))] have also been prepared, although in these cases the solid-state structures show that the macrocyclic ligand remains protonated at the pyrrolic nitrogen atoms, and the Ni(II) cations are therefore co-ordinated by the imine nitrogen atoms only to give an open conformation for the complex. The dicopper complex [Cu2(L(3))] was crystallised in the presence of pyridine to form the adduct [Cu2(py)(L(3))], in which, in the solid state, the pyridine ligand is bound within the binuclear molecular cleft. Reaction between H(4)L(1) and [Mn(thf){N(SiMe(3))2}2] results in clean formation of the dimanganese complex [Mn2(L(1))], which, upon crystallisation, formed the mixed-valent complex [Mn2(mu-OH)(L(1))] in which the hydroxo ligand bridges the metal centres within the molecular cleft.

μ-η1:η1-Peroxo-Bridged Dinuclear Peroxotungstate Catalytically Active for Epoxidation of Olefins

The reaction of the dinuclear peroxotungstate, [(n-C4H9)4N]2[{WO(O2)2}2(mu-O)] (II), with H2O2 gives the novel mu-eta1:eta1-peroxo-bridging dinuclear tungsten species, [(n-C4H9)4N]2[{WO(O2)2}2(mu-O2)] (I), which has been characterized by X-ray crystallography, elemental analysis, IR, Raman, UV-vis, and 183W NMR. Only I is active for the epoxidation of cyclic, internal, and terminal olefins, whereas II is inactive for each. The low XSO (XSO=(nucleophilic oxidation)/(total oxidation)) value of I (0.18+/-0.02) in comparison with that of II (0.39+/-0.01) for the stoichiometric oxidation of thianthrene 5-oxide, which is a mechanistic probe for determining the electronic character of an oxidant, reveals that I is more electrophilic than II. On the basis of the kinetic and spectroscopic results, the catalytic epoxidation proceeds by the reaction of I with an olefin to form II and the corresponding epoxide followed by the regeneration of I by the reaction of II with H2O2.

Computational study of iron(II) and -(III) complexes with a simple model human H ferritin ferroxidase center

Interaction of iron ions with a six-amino acid model of the ferroxidase center of human H chain ferritin has been examined in density functional theory calculations. The model, based on experimental studies of oxidation of Fe2+ at the center, consists of Glu27, Glu62, His65, Glu107, Gln141, and Ala144. Reasonable structures are obtained in a survey of types of iron complexes inferred to occur in the ferroxidase reaction. Structures of complexes of the model center with one and two Fe2+ ions, with diiron(III) bridged by peroxide and bridged by oxide-peroxide combinations, have been optimized. Calculations on diiron(III) complexes confirm that stable peroxide-bridged complexes can form and that the Fe-Fe distance in at least one is consistent with the experimental Fe-Fe distance observed in the blue peroxodiferric complex of ferritin.

Synthesis, structure, and magnetic properties of valence ambiguous dinuclear antiferromagnetically coupled cobalt and ferromagnetically coupled iron complexes containing the chloranilate(2-) and the significantly stronger coupling chloranilate(*3-) radical trianion

Dinuclear [(TPyA)MII(CA2-)MII(TPyA)]2+ [TPyA=tris(2-pyridylmethyl)amine; CA2-=chloranilate dianion; M=Co (1(2+)), Fe (2(2+))] complexes have been prepared by the reaction of M(BF4)(2).6H2O, TPyA, H2CA, and triethylamine in MeOH solution. Their reduced forms [(TPyA)MII(CA*3-)MII(TPyA)]+ [M=Co(1+), Fe (2+)] have been synthesized by using cobaltocene, and oxidized forms of 1, [(TPyA)CoIII(CAn)CoIII(TPyA)]z+ [z=3, n=3- (1(3+)); z=4, n=2- (1(4+))], have been obtained by using FcBF4 and ThianBF4 (Fc=ferrocenium; Thian=thianthrinium), respectively. The dinuclear compound bridged chloranilates (CA2- or CA*3-) were isolated and characterized by X-ray crystallography, electrochemistry, magnetism, and EPR spectroscopy. Unlike the other redox products, valence ambiguous 13+ forms via a complex redox-induced valence electron rearrangement whereby the one-electron oxidation of the [CoIICA2-CoII]2+ core forms [CoIIICA*3-CoIII]3+, not the expected simple 1-e- transfer mixed-valent [CoIICA2-CoIII]3+ core. The M ions in 1 and 2 have a distorted octahedral geometry by coordination with four nitrogens of a TPyA, two oxygens of a chloranilate. Due to the interdimer offset face-to-face pi-pi and/or herringbone interactions, all complexes show extended 1-D and/or 2-D supramolecular structures. The existence of CA*3- in 1(3+) is confirmed from both solid-state magnetic and solution EPR data. Co-based 1n+ exhibit antiferromagnetic interactions [1(2+): g=2.24, J/kB=-0.65 K (-0.45 cm-1); 1+: g=2.36, J/kB=-75 K (52 cm-1)], while Fe-based 2n+ exhibit ferromagnetic interactions [2(2+): g=2.08, J/kB=1.0 K (0.70 cm-1); 2+: g=2.03, J/kB=28 K (19 cm-1)] [H=-2JS1.S2 for 12+ and 2(2+); H=-2J(S1.S2+S2.S3) for 1+ and 2+]. Thus, due to direct spin exchange CA*3- is a much strong spin coupling linkage than the superexchange spin-coupling pathway provided by CA2-.