Modeling the Oxygen Activation Chemistry of Methane Monooxygenase and Ribonucleotide Reductase

Manganese catalysts for C-H activation: an experimental/theoretical study identifies the stereoelectronic factor that controls the switch between hydroxylation and desaturation pathways

We describe competitive C-H bond activation chemistry of two types, desaturation and hydroxylation, using synthetic manganese catalysts with several substrates. 9,10-Dihydrophenanthrene (DHP) gives the highest desaturation activity, the final products being phenanthrene (P1) and phenanthrene 9,10-oxide (P3), the latter being thought to arise from epoxidation of some of the phenanthrene. The hydroxylase pathway also occurs as suggested by the presence of the dione product, phenanthrene-9,10-dione (P2), thought to arise from further oxidation of hydroxylation intermediate 9-hydroxy-9,10-dihydrophenanthrene. The experimental work together with the density functional theory (DFT) calculations shows that the postulated Mn oxo active species, [Mn(O)(tpp)(Cl)] (tpp = tetraphenylporphyrin), can promote the oxidation of dihydrophenanthrene by either desaturation or hydroxylation pathways. The calculations show that these two competing reactions have a common initial step, radical H abstraction from one of the DHP sp(3) C-H bonds. The resulting Mn hydroxo intermediate is capable of promoting not only OH rebound (hydroxylation) but also a second H abstraction adjacent to the first (desaturation). Like the active Mn(V)=O species, this Mn(IV)-OH species also has radical character on oxygen and can thus give H abstraction. Both steps have very low and therefore very similar energy barriers, leading to a product mixture. Since the radical character of the catalyst is located on the oxygen p orbital perpendicular to the Mn(IV)-OH plane, the orientation of the organic radical with respect to this plane determines which reaction, desaturation or hydroxylation, will occur. Stereoelectronic factors such as the rotational orientation of the OH group in the enzyme active site are thus likely to constitute the switch between hydroxylase and desaturase behavior.

Orbitals in inorganic chemistry: metal rings and clusters, hydronitrogens, and heterocyles

A chemical orbital theory is useful in inorganic chemistry. Some applications are described for understanding and designing of inorganic molecules. Among the topics included are: (1) valence electron rules to predict stabilities of three- and four-membered ring metals and for those of regular octahedral M(6) metal clusters solely by counting the number of valence electrons; (2) pentagon stability (stability of five- relative to six-membered rings in some classes of molecules), predicted and applied for understanding and designing saturated molecules of group XV elements; (3) properties of unsaturated hydronitrogens N( m )H( n ) in contrast to those of hydrocarbons C( m )H( n ); (4) unusually short nonbonded distances between metal atoms in cyclic molecules.

Molecular recognition in Mn-catalyzed C-H oxidation. Reaction mechanism and origin of selectivity from a DFT perspective

Experimental studies have shown that the C-H oxidation of Ibuprofen and methylcyclohexane acetic acid can be carried out with high selectivities using [(terpy')Mn(OH(2))(mu-O)(2)Mn(OH(2))(terpy')](3+) as catalyst, where terpy' is a terpyridine ligand functionalized with a phenylene linker and a Kemp's triacid serving to recognize the reactant via H-bonding. Experiments, described here, suggest that the sulfate counter anion, present in stoichiometric amounts, coordinates to manganese in place of water. DFT calculations have been carried out using [(terpy')Mn(O)(mu-O)(2)Mn(SO(4))(terpy')](+) as a model catalyst, to analyze the origin of selectivity and its relation to molecular recognition, as well as the mechanism of catalyst inhibition by tert-butyl benzoic acid. The calculations show that a number of spin states, all having radical oxygen character, are energetically accessible. All these spin states promote C-H oxidation via a rebound mechanism. The catalyst recognizes the substrate by a double H bond. This interaction orients the substrate inducing highly selective C-H oxidation. The double hydrogen bond stabilizes the reactant, the transition state and the product to the same extent. Consequently, the reaction occurs at lower energy than without molecular recognition. The association of the catalyst with tert-butyl benzoic acid is shown to shield the access of unbound substrate to the reactive oxo site, hence preventing non-selective hydroxylation. It is shown that the two recognition sites of the catalyst can be used in a cooperative manner to control the access to the reactive centre.

A rational basis for the axial ligand effect in C-H oxidation by [MnO(porphyrin)(X)]+ (X = H2O, OH-, O2-) from a DFT study

Oxyl radical character in the MnO group of the title system is shown from a density functional theory study to be essential for efficient C-H cleavage, which is a key step in C-H oxidation. Since oxyl species have elongated Mn-O bonds relative to the more usual oxo species of type MnO, the normal expectation would be that high trans-influence ligands X should facilitate oxyl character by elongating the Mn-O bond and thus enhance both oxyl character and reactivity. Contrary to this expectation, but in line with the experimental data (Jin, N.; Ibrahim, M.; Spiro, T. G.; Groves, J. T. J. Am. Chem. Soc. 2007, 129, 12416), we find that reactivity increases along the series X = O(2-) < OH(-) < H2O for the following reasons. The ground-state singlet (S) is unreactive for all X, and only the higher-energy triplet (T) and quintet (Q) states have the oxyl character needed for reactivity, but the higher trans-influence X ligands are also shown to increase the S/T and S/Q gaps, thus making attainment of the needed T and Q states harder. The latter effect is dominant, and high trans-influence X ligands thus disfavor reaction. The higher reactivity in the presence of acid noted by Groves and co-workers is thus rationalized by the preference for having X = H2O over OH(-) or O(2-).

Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)-hydroxide

We report direct evidence for the existence of an iron(IV)-hydroxide. Resonance Raman measurements on chloroperoxidase compound II (CPO-II) reveal an isotope ((18)O and (2)H)-sensitive band at nu(Fe-O) = 565 cm(-1). Preparation of CPO-II in H(2)O using H(2)(18)O(2) results in a red-shift of 22 cm(-1), while preparation of CPO-II in (2)H(2)O using H(2)O(2) results in a red-shift of 13 cm(-1). These values are in good agreement with the isotopic shifts predicted (23 and 12 cm(-1), respectively) for an Fe-OH harmonic oscillator. The measured Fe-O stretching frequency is also in good agreement with the 1.82-A Fe-O bond reported for CPO-II. A Badger's rule analysis of this distance provides an Fe-O stretching frequency of nu(Badger) = 563 cm(-1). We also present X-band electron nuclear double resonance (ENDOR) data for cryoreduced CPO-II. Cryogenic reduction (77 K) of the EPR-silent Fe(IV)OH center in CPO-II results in an EPR-active Fe(III)OH species with a strongly coupled (13.4 MHz) exchangeable proton. Based on comparisons with alkaline myoglobin, we assign this resonance to the hydroxide proton of cryoreduced CPO-II.

Conversion of Methane to Methanol at the Mononuclear and Dinuclear Copper Sites of Particulate Methane Monooxygenase (pMMO): A DFT and QM/MM Study

Methane hydroxylation at the mononuclear and dinuclear copper sites of pMMO is discussed using quantum mechanical and QM/MM calculations. Possible mechanisms are proposed with respect to the formation of reactive copper-oxo and how they activate methane. Dioxygen is incorporated into the Cu(I) species to give a Cu(II)-superoxo species, followed by an H-atom transfer from a tyrosine residue near the monocopper active site. A resultant Cu(II)-hydroperoxo species is next transformed into a Cu(III)-oxo species and a water molecule by the abstraction of an H-atom from another tyrosine residue. This process is accessible in energy under physiological conditions. Dioxygen is also incorporated into the dicopper site to form a (mu-eta(2):eta(2)-peroxo)dicopper species, which is then transformed into a bis(mu-oxo)dicopper species. The formation of this species is more favorable in energy than that of the monocopper-oxo species. The reactivity of the Cu(III)-oxo species is sufficient for the conversion of methane to methanol if it is formed in the protein environment. Since the sigma orbital localized in the Cu-O bond region is singly occupied in the triplet state, this orbital plays a role in the homolytic cleavage of a C-H bond of methane. The reactivity of the bis(mu-oxo)dicopper species is also sufficient for the conversion of methane to methanol. The mixed-valent bis(mu-oxo)Cu(II)Cu(III) species is reactive to methane because the amplitude of the sigma singly occupied MO localized on the bridging oxo moieties plays an essential role in C-H activation.

Microsecond freeze-hyperquenching: development of a new ultrafast micro-mixing and sampling technology and application to enzyme catalysis

A novel freeze-quench instrument with a characteristic <<dead-time>> of 137 +/- 18 micros is reported. The prototype has several key features that distinguish it from conventional freeze-quench devices and provide a significant improvement in time resolution: (a) high operating pressures (up to 400 bar) result in a sample flow with high linear rates (up to 200 m s(-1)); (b) tangential micro-mixer with an operating volume of approximately 1 nl yields short mixing times (up to 20 micros); (c) fast transport between the mixer and the cryomedium results in short reaction times: the ageing solution exits the mixer as a free-flowing jet, and the chemical reaction occurs "in-flight" on the way to the cryomedium; (d) a small jet diameter (approximately 20 microm) and a high jet velocity (approximately 200 m s(-1)) provide high sample-cooling rates, resulting in a short cryofixation time (up to 30 micros). The dynamic range of the freeze-quench device is between 130 micros and 15 ms. The novel tangential micro-mixer efficiently mixes viscous aqueous solutions, showing more than 95% mixing at eta < or = 4 (equivalent to protein concentrations up to 250 mg ml(-1)), which makes it an excellent tool for the preparation of pre-steady state samples of concentrated protein solutions for spectroscopic structure analysis. The novel freeze-quench device is characterized using the reaction of binding of azide to metmyoglobin from horse heart. Reaction samples are analyzed using 77 K optical absorbance spectroscopy, and X-band EPR spectroscopy. A simple procedure of spectral analysis is reported that allows (a) to perform a quantitative analysis of the reaction kinetics and (b) to identify and characterize novel reaction intermediates. The reduction of dioxygen by the bo3-type quinol oxidase from Escherichia coli is assayed using the MHQ technique. In these pilot experiments, low-temperature optical absorbance measurements show the rapid oxidation of heme o3 in the first 137 micros of the reaction, accompanied by the formation of an oxo-ferryl species. X-band EPR spectroscopy shows that a short-living radical intermediate is formed during the oxidation of heme o3. The radical decays within approximately 1 ms concomitant with the oxidation of heme b, and can be attributed to the PM reaction intermediate converting to the oxoferryl intermediate F. The general field of application of the freeze-quench methodology is discussed.

Mixed metal bis(mu-oxo) complexes with [CuM(mu-O)2]n+(M = Ni(III) or Pd(II)) cores

Two highly reactive heterodinuclear bis(mu-oxo) complexes were prepared by combining mononuclear peroxo species with reduced metal precursors at -80 degrees C and were identified by UV-vis, EPR/NMR, and resonance Raman spectroscopy, with corroboration in the case of the CuPd system from density functional calculations.

Novel Iron(III) Complexes of Tripodal and Linear Tetradentate Bis(phenolate) Ligands: Close Relevance to Intradiol-Cleaving Catechol Dioxygenases

Four new iron(III) complexes of the bis(phenolate) ligands N,N-dimethyl-N',N'-bis(2-hydroxy-3,5-dimethylbenzyl)ethylenediamine [H2(L1)], N,N-dimethyl-N',N'-bis(2-hydroxy-4-nitrobenzyl)ethylenediamine [H2(L2)], N,N'-dimethyl-N,N'-bis(2-hydroxy-3,5-dimethylbenzyl)ethylenediamine [H2(L3)], and N,N'-dimethyl-N,N'-bis(2-hydroxy-4-nitrobenzyl)ethylenediamine [H2(L4)] have been isolated and studied as structural and functional models for the intradiol-cleaving catechol 1,2-dioxygenases (CTD). The complexes [Fe(L1)Cl] (1), [Fe(L2)(H2O)Cl] (2), [Fe(L3)Cl] (3), and [Fe(L4)(H2O)Cl] (4) have been characterized using absorption spectral and electrochemical techniques. The single-crystal X-ray structures of the ligand H2(L1) and the complexes 1 and 2 have been successfully determined. The tripodal ligand H2(L1) containing a N2O2 donor set represents the metal-binding region of the iron proteins. Complex 1 contains an FeN2O2Cl chromophore with a novel trigonal bipyramidal coordination geometry. While two phenolate oxygens and an amine nitrogen constitute the trigonal plane, the other amine nitrogen and chloride ion are located in the axial positions. In contrast, 2 exhibits a rhombically distorted octahedral coordination geometry for the FeN2O3Cl chromophore. Two phenolate oxygen atoms, an amine nitrogen atom, and a water molecule are located on the corners of a square plane with the axial positions being occupied by the other nitrogen atom and chloride ion. The interaction of the complexes with a few monodentate bases and phenolates and differently substituted catechols have been investigated using absorption spectral and electrochemical methods. The effect of substituents on the phenolate rings on the electronic spectral features and FeIII/FeII redox potentials of the complexes are discussed. The interaction of the complexes with catecholate anions reveals changes in the phenolate to iron(III) charge-transfer band and also the appearance of a low-energy catecholate to iron(III) charge-transfer band similar to catechol dioxygenase-substrate complexes. The redox behavior of the 1:1 adducts of the complexes with 3,5-di-tert-butylcatechol (H2DBC) has been also studied. The reactivities of the present complexes with H2DBC have been studied and illustrated. Interestingly, only 2 and 4 catalyze the intradiol-cleavage of H2DBC, the rate of oxygenation being much faster for 4. Also 2, but not 4, yields an extradiol cleavage product. The reactivity of the complexes could be illustrated not on the basis of the Lewis acidity of the complexes alone but by assuming that the product release is the rate-determining phase of the catalytic reaction.

Spectroscopic and computational studies on [(PhTt(tBu))2Ni2(mu-O)2]: nature of the bis-mu-oxo (Ni3+)2 diamond core

Spectroscopic and density functional theory (DFT) electronic structure computational studies on a binuclear bis-mu-oxo bridged (Ni(3+))(2) complex, [(PhTt(t(Bu))(2)Ni(2)(mu-O)(2)] (1), where (PhTt(t(Bu)) represents phenyl-tris((tert-butylthio)methyl)borate, are presented and discussed. These studies afford a detailed description of the Ni(2)O(2) core electronic structure in bis-mu-oxo (Ni(3+))(2) dimers and provide insight into the possible role of the (PhTt(t(Bu)) thioether ligand in the formation of 1 from a Ni(1+) precursor by O(2) activation. From a normal coordinate analysis of resonance Raman data, a value of k(Ni)(-)(O) = 2.64 mdyn/A is obtained for the Ni-O stretch force constant for 1. This value is smaller than k(Cu)(-)(O) = 2.82-2.90 mdyn/A obtained for bis-mu-oxo (Cu(3+))(2) dimers possessing nitrogen donor ligands, indicating a reduced metal-oxo bond strength in 1. Electronic absorption and magnetic circular dichroism spectroscopic techniques permit identification of several O-->Ni and S-->Ni charge transfer (CT) transitions that are assigned on the basis of DFT calculations. The dominant O-->Ni CT transition of 1 occurs at 17 700 cm(-)(1), red-shifted by approximately 7000 cm(-)(1) relative to the corresponding transition in bis-mu-oxo (Ni(3+))(2) dimers with nitrogen donor ligands. This red-shift along with the relatively low value of k(Ni)(-)(O) are due primarily to the presence of the thioether ligands in 1 that greatly affect the compositions of the Ni(2)O(2) core MOs. This unique property of the thioether ligand likely contributes to the reactivity of the Ni center in the precursor [(PhTt(t(Bu))Ni(1+)CO] toward O(2). DFT computations reveal that conversion of a hypothetical side-on peroxo (Ni(2+))(2) dimer, [(PhTt(t(Bu))(2)Ni(2)(mu-eta(2):eta(2)-O(2))], to the bis-mu-oxo (Ni(3+))(2) dimer 1 is energetically favorable by 32 kcal/mol and occurs without a significant activation energy barrier (DeltaH++) = 2 kcal/mol).

Computational de novo design, and characterization of an A(2)B(2) diiron protein

Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.

Bis(mu-oxo)dimetal "diamond" cores in copper and iron complexes relevant to biocatalysis

Although quite a familiar feature in high-valent manganese chemistry, the M(2)(mu-O)(2) diamond core motif has only recently been found in synthetic complexes for M=Cu or Fe. Structural and spectroscopic characterization of these more reactive Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) compounds has been possible through use of appropriately designed supporting ligands, low-temperature handling methods, and techniques such as electrospray ionization mass spectrometry and X-ray crystallography with area detector instrumentation for rapid data collection. Despite differences in electronic structures that have been revealed through experimental and theoretical studies, Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) cores exhibit analogously covalent metal-oxo bonding, remarkably congruent Raman and extended X-ray absorption fine structure (EXAFS) signatures, and similar tendencies to abstract hydrogen atoms from substrates. Core isomerization is another common reaction attribute, although different pathways are traversed; for Fe, bridge-to-terminal oxo migration has been discovered, while for Cu, reversible formation of an O-O bond to yield a peroxo isomer has been identified. Our understanding of biocatalysis has been enhanced significantly through the isolation and comprehensive characterization of the Cu(2)(mu-O)(2) and Fe(2)(mu-O)(2) complexes. In particular, it has led to the development of new mechanistic notions about how non-heme multimetal enzymes, such as methane monooxygenases, fatty acid desaturase, and tyrosinase, may function in the activation of dioxygen to catalyze a diverse array of organic transformations.