C-H bond activation by a ferric methoxide complex: modeling the rate-determining step in the mechanism of lipoxygenase.

Lipoxygenases are mononuclear non-heme iron enzymes that regio- and stereospecifcally convert 1,4-pentadiene subunit-containing fatty acids into alkyl peroxides. The rate-determining step is generally accepted to be hydrogen atom abstraction from the pentadiene subunit of the substrate by an active ferric hydroxide species to give a ferrous water species and an organic radical. Reported here are the synthesis and characterization of a ferric model complex, [Fe(III)(PY5)(OMe)](OTf)(2), that reacts with organic substrates in a manner similar to the proposed enzymatic mechanism. The ligand PY5 (2,6-bis(bis(2-pyridyl)methoxymethane)pyridine) was developed to simulate the histidine-dominated coordination sphere of mammalian lipoxygenases. The overall monoanionic coordination provided by the endogenous ligands of lipoxygenase confers a strong Lewis acidic character to the active ferric site with an accordingly positive reduction potential. Incorporation of ferrous iron into PY5 and subsequent oxidation yields a stable ferric methoxide species that structurally and chemically resembles the proposed enzymatic ferric hydroxide species. Reactivity with a number of hydrocarbons possessing weak C-H bonds, including a derivative of the enzymatic substrate linoleic acid, scales best with the substrates' bond dissociation energies, rather than pK(a)'s, suggesting a hydrogen atom abstraction mechanism. Thermodynamic analysis of [Fe(III)(PY5)(OMe)](OTf)(2) and the ferrous end-product [Fe(II)(PY5)(MeOH)](OTf)(2) estimates the strength of the O-H bond in the metal bound methanol in the latter to be 83.5 +/- 2.0 kcal mol(-1). The attenuation of this bond relative to free methanol is largely due to the high reduction potential of the ferric site, suggesting that the analogously high reduction potential of the ferric site in LO is what allows the enzyme to perform its unique oxidation chemistry. Comparison of [Fe(III)(PY5)(OMe)](OTf)(2) to other coordination complexes capable of hydrogen atom abstraction shows that, although a strong correlation exists between the thermodynamic driving force of reaction and the rate of reaction, other factors appear to further modulate the reactivity.     

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study

The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.     

The pyrolytic graphite surface as an enzyme substrate: microscopic and spectroscopic studies

We have conducted a series of experiments to explore the surface of the polished pyrolytic graphite ‘edge’ electrode as routinely prepared for use in protein film voltammetry. Our investigations have included nitrogen porosimetry and scanning electron microscopy. The nitrogen adsorption revealed a Brunauer–Emmett–Teller surface area ∼10⁴ times greater than the geometric surface area of the electrode. The pore-size distribution calculated by the Horváth–Kawazoe method showed that 10–18% of the pore volume arises from pores having widths >10 nm and, thus, should be accessible to enzymes, although much of the exposed ‘wall’ surface may be inactive for enzyme binding or electron transfer: for example, it may be mainly basal plane. Scanning electron micrographs of the abraded pyrolytic graphite edge showed differing scales of surface damage caused by the abrasion and the presence of many cracks in the surface where thin platelets had been removed.This work is dedicated to Prof. Alan Bond on the occasion of his 60th birthday. Alan’s enthusiasm for the complexities of diffusion control persuaded one of us (F.A. Armstrong) to try and avoid it altogether in protein electrochemical studies.     

Hydrogen atom abstraction by a mononuclear ferric hydroxide complex: insights into the reactivity of lipoxygenase

The lipoxygenase mimic [Fe(III)(PY5)(OH)](CF3SO3)2 is synthesized from the reaction of [Fe(II)(PY5)(MeCN)](CF3SO3)2 with iodosobenzene, with low-temperature studies suggesting the possible intermediacy of an Fe(IV) oxo species. The Fe(III)-OH complex is isolated and identified by a combination of solution and solid-state methods, including EPR and IR spectroscopy. [Fe(III)(PY5)(OH)](2+) reacts with weak X-H bonds in a manner consistent with hydrogen-atom abstraction. The composition of this complex allows meaningful comparisons to be made with previously reported Mn(III)-OH and Fe(III)-OMe lipoxygenase mimics. The bond dissociation energy (BDE) of the O-H bond formed upon reduction to [Fe(II)(PY5)(H2O)]2+ is estimated to be 80 kcal mol(-1), 2 kcal mol(-1) lower than that in the structurally analogous [Mn(II)(PY5)(H2O)]2+ complex, supporting the generally accepted idea that Mn(III) is the thermodynamically superior oxidant at parity of coordination sphere. The identity of the metal has a large influence on the entropy of activation for the reaction with 9,10-dihydroanthracene; [Mn(III)(PY5)(OH)]2+ has a 10 eu more negative DeltaS++ value than either [Fe(III)(PY5)(OH)]2+ or [Fe(III)(PY5)(OMe)]2+, presumably because of the increased structural reorganization that occurs upon reduction to [Mn(II)(PY5)(H2O)]2+. The greater enthalpic driving force for the reduction of Mn(III) correlates with [Mn(III)(PY5)(OH)]2+ reacting more quickly than [Fe(III)(PY5)(OH)]2+. Curiously, [Fe(III)(PY5)(OMe)]2+ reacts with substrates only about twice as fast as [Fe(III)(PY5)(OH)]2+, despite a 4 kcal mol(-1) greater enthalpic driving force for the methoxide complex.     

Kinetic analysis of the mechanism of plasminogen activation by streptokinase

A kinetic study is made of plasminogen activation to plasmin catalyzed by streptokinase. The goal of the present paper is the resolution of the mechanism corresponding to the activation process by a global way, considering the mechanism as a whole and under less restrictive assumptions that those used by other authors. The kinetic equations describing the evolution with time of species involved in the system have been obtained. These equations are valid for both the transient phase and the steady state of the reaction. A kinetic data analysis procedure to evaluate the kinetic parameters, based on the derived kinetic equations has been suggested, for the first time, in the present paper. The validity of the results obtained has been checked by using simulated progress curves of the species involved. Finally, we have demonstrated that the time course equations obtained can be applied directly to different mechanisms of zymogen activation that could be considered to be particular cases of the general studied mechanism.     

Kinetic energy release of C70(+) and its endohedral cation N@C70(+): activation energy for N extrusion

Unimolecular decomposition of C70(+) and its endohedral cation N@C70(+) were studied by high-resolution mass-analyzed ion kinetic energy (MIKE) spectrometry. Information on the energetics and dynamics of these reactions was extracted. C70(+) dissociates unimolecularly by loss of a C2 unit, whereas N@C70(+) expels the endohedral N atom. Kinetic energy release distributions (KERDs) in these reactions were measured. By use of finite heat bath theory (FHBT), the binding energy for C2 emission from C70(+) and the activation energy for N elimination from N@C70(+) were deduced from KERDs in the light of a recent finding that fragmentation of fullerene cations proceeds via a very loose transition state. The activation energy measured for N extrusion from N@C70(+) was found to be lower than that for C2 evaporation, higher than the value from its neutral molecule N@C70 obtained on the basis of thermal stability measurements, and coincident with the theoretical value. The results provide confirmation that the proposed extrusion mechanism in which the N atom escapes from the cage via formation of an aza-bridged intermediate is correct.     

In situ characterisation of the aqueous gold colloid interface using CO as a surface probe: IR spectroscopic studies

Fourier transform infrared (FTIR) spectra are presented of CO gas-treated protected gold colloids prepared from hydrazinium hydrate reduction of an Au(III) precursor which reproducibly feature a weak, shortlived peak at ca. 2169 cm(-1). When the gold colloid was treated with 99% isotopically enriched (13)CO gas, the IR peak shifted to a frequency of 2114 cm(-1) which indicated that it represented a simple gold monocarbonyl species. The value of 2169 cm(-1) for the CO stretching frequency suggests the peak represents CO physisorbed on oxidised gold atoms on the colloid surface. The peak is not observed when the concentration of the colloidally dispersed gold is reduced either by use of lower starting salt concentrations or by aggregation. It is also not observed when solutions of the protecting agent or reducing agent or the dispersion medium (water) or even the starting Au(III) salts are CO-treated individually. This confirms that the spectral feature is uniquely associated with colloidally dispersed gold. In general, the work has shown that the surfaces of Au colloids in situ have partially oxidised Au character which is of interest in systems where supported nanoparticulate gold derived from colloid preparations are considered for low temperature oxidation catalysts for CO.     

Insights into the mechanism of N2O reduction by reductively activated N2O reductase from kinetics and spectroscopic studies of pH effects

Nitrous oxide reductase (N2OR) from Achromobacter cycloclastes (Ac) can be reductively activated with reduced methyl viologen over a broad range of pH. Activated Ac N2OR displays a complex activity profile as a function of the pH at which catalytic turnover is measured. Spectroscopic and steady-state kinetics data suggest that [H+] has multiple effects on both the activation and the catalytic reactions. These experimental results are in good agreement with previous theoretical studies, which suggested that the transition state is stabilized by H-bonding interactions between the active site and an N2O-derived intermediate bound to the catalytic CuZ cluster.     

Kinetic investigation of redox reaction between vitamin C and ferric chloride hexahydrate in acidic medium

The kinetics of the reaction between vitamin C (l-ascorbic acid) and ferric chloride hexahydrate was investigated in acidic medium at pH 3 spectrophotometrically. The order of the reaction was established by applying different methods, such as initial rate method, integration method and half-life method. The results obtained from each method were correlated with each other and consistency in all methods was observed. The order of the reaction with respect to each reactant was found first and the overall second order was recommended for the reaction.     

Kinetic and theoretical studies on the mechanism of alkaline hydrolysis of DNA

The reaction mechanism of alkaline hydrolysis of DNA has been investigated by kinetic analysis and density-functional-theory calculation. The rates of hydrolysis of thymidine 3'-monophosphate esters (including thymidylyl(3'-5')thymidine (Tp-OT)) monotonically decrease as the leaving groups get poorer. According to the theoretical calculation in which the solvent effects are incorporated, no intermediate is formed in the course of the reaction. In the alkaline hydrolysis of the activated Tp-OT analogues having good leaving groups, the 3',5'-cyclic monophosphate of thymidine is concurrently formed through the intramolecular attack by the 5'-alkoxide ion. In the hydrolysis of the native dinucleotide, however, this side reaction does not occur, since the transition state leading to the departure of its poor leaving group cannot be formed due to conformational restraint. These arguments are supported by the theoretical analysis on the hydrolysis of both dimethyl phosphate and its O(bridging)-->S substituted analogue.     

Kinetic and equilibrium studies of urea adsorption onto activated carbon: Adsorption mechanism

We found that activated carbon effectively removed urea from solution and that urea adsorption onto activated carbon followed a pseudo-second-order kinetic model. We classified the urea adsorption on activated carbon as physical adsorption and found that it was best described by the Halsey adsorption isotherm, suggesting that the multilayer adsorption of urea molecules on the adsorption sites of activated carbon best characterized the adsorption system. The mechanism of adsorption of urea by activated carbon involved two steps. First, an amino (–NH₂) group of urea interacted with a carbonyl (–C?O) group and a hydroxyl (?OH) group on the surface of activated carbon via dipole–dipole interactions. Next, the –C?O group of the urea molecule adsorbed to the activated carbon interacted with another –NH₂ group from a second urea molecule, leading to multilayer adsorption.     

Kinetic and spectroscopic studies of the [palladium(Ar-bian)]-catalyzed semi-hydrogenation of 4-octyne

The kinetics of the stereoselective semi-hydrogenation of 4-octyne in THF by the highly active catalyst [Pd{(m,m'-(CF(3))(2)C(6)H(3))-bian}(ma)] (2) (bian = bis(imino)acenaphthene; ma = maleic anhydride) has been investigated. The rate law under hydrogen-rich conditions is described by r = k[4-octyne](0.65)[Pd][H(2)], showing first order in palladium and dihydrogen and a broken order in substrate. Parahydrogen studies have shown that a pairwise transfer of hydrogen atoms occurs in the rate-limiting step. In agreement with recent theoretical results, the proposed mechanism consists of the consecutive steps: alkyne coordination, heterolytic dihydrogen activation (hydrogenolysis of one Pd-N bond), subsequent hydro-palladation of the alkyne, followed by addition of N-H to palladium, reductive coupling of vinyl and hydride and, finally, substitution of the product alkene by the alkyne substrate. Under hydrogen-limiting conditions, side reactions occur, that is, formation of catalytically inactive palladacycles by oxidative alkyne coupling. Furthermore, it has been shown that (Z)-oct-4-ene is the primary reaction product, from which the minor product (E)-oct-4-ene is formed by an H(2)-assisted, palladium-catalyzed isomerization reaction.     

Chemical and spectroscopic studies of a new palladium(II) complex with N -acetyl-L-cysteine

Chemical and spectroscopic studies of a new palladium(II) N-acetyl-L-cysteine complex are described. Elemental analyses for the solid complex are consistent with the formula [Pd(C₅H₈NO₃S)₂]?·?H₂O or [Pd(NAC)₂]?·?H₂O. Solid-state ¹³C nuclear magnetic resonance (NMR), UV–Visible (UV–Vis) and infrared (IR) spectroscopic analyses are consistent with coordination of the ligand to palladium(II) through the nitrogen and sulfur atoms in a square-planar geometry. Thermogravimetric and differential thermal analyses confirmed the composition; final residue was identified as metallic palladium.     

NMR studies of the dynamics of a bifunctional rhodamine probe attached to troponin C

Fluorescence polarization measurements of bifunctional rhodamine (BR) probes provide a powerful approach to determine the in situ orientation of proteins within ordered complexes such as muscle fibers. For accurate interpretation of fluorescence measurements, it is important to understand the probe dynamics relative to the protein to which it is attached. We previously determined the structure of the N-domain of chicken skeletal troponin C, BR-labeled on the C helix, in complex with the switch region of troponin I, and demonstrated that the probe does not perturb the structure or dynamics of the protein. In this study, the motion of the fluorescence label relative to the protein has been characterized using NMR relaxation measurements of 13C-labeled methyl groups on the BR probe and 15N-labeled backbone amides of the protein. Probe dynamics were monitored using off-resonance 13C-R(1rho), 13C-R(1) and {1H}-13C NOE at magnetic field strengths of 500, 600, and 800 MHz. Relaxation data were interpreted in terms of the overall rotational correlation time of the protein and a two-time scale model for internal motion of the BR methyl groups, using a numerical optimization with Monte Carlo parameter error estimation. The analysis yields a 1.5 +/- 0.4 ps correlation time for rotation around the three-fold methyl symmetry axis, and a 0.8 +/- 0.4 ns rotational correlation time for reorientation of the 13C-14N bond with an associated S2s of 0.79 +/- 0.03. Order parameters of the backbone NH vectors in the helix to which the probe is attached average S2 approximately 0.85, implying that the amplitude of independent reorientation of the BR probe is small in magnitude, consistent with results from fluorescence polarization measurements in reconstituted muscle fibers.     

Kinetic and quantum chemical studies of the mechanism of formation of 1,2-dialkyldiaziridines

The regularities of AlkNHBr consumption in the reaction of formation of 1,2-dialkyldiaziridines in aqueous media were studied for the first time by UV spectrometry. The rate constants of particular steps of the reaction were estimated starting from the possibility of formation of the precursor of 1,2-dialkyldiaziridine, N-halogenaminal, due to the amination of the intermediate iminium cation along with the parallel halogenation of the intermediate gem-diamine. The quantum chemical calculations (DFT, B3LYP, 6–31++G(d,p) and 3–21G basis sets) were performed for the spatial and electronic structures of the compounds and indices of the local reactivity and global electrophilicity of the key intermediates of the reactions. The results of the calculations allowed us to explain the retardation of the reaction when using EtNHBr instead of MeNHBr.     

Matrix isolation IR spectroscopic and ab initio studies of C(3)N(-) and related species

Coupled cluster calculations were carried out for C(3)N(-), CCNC(-), C(3)N, CCNC, C(3)N(+), and C(3)O. They support the experimental identification of the C(3)N(-) ion by means of matrix isolation infrared (IR) spectroscopy. The anion was generated in electric discharges through the cyanoacetylene isotopomers HC(3) (14)N, HC(3) (15)N, and (2)HC(3)N, trapped in cryogenic rare gas matrices (Ne, Ar, Kr), and detected via its two most intense IR absorption bands, assigned to the nu(1) and nu(2) stretching vibrations. C(3)N(-) appears to be quite a stable anion, with a vertical detachment energy predicted to be as high as 4.42 eV. A large equilibrium electric dipole moment of 3.10 D facilitates the investigation of C(3)N(-) by microwave spectroscopy and radio astronomy. Various structural parameters and spectroscopic properties have been calculated for all tetra-atomic species considered.     

NMR spectroscopic studies on the mechanism of cellulose dissolution in alkali solutions

It was considered that the dissolution of cellulose in alkali solutions is mainly due to the breakage of hydrogen bonds. As an alkali hydroxide, KOH can provide OH^? just like LiOH and NaOH; but it is well known that LiOH and NaOH can dissolve cellulose, whereas KOH can only swell cellulose. The inability of KOH to dissolve cellulose was investigated and the mechanism of cellulose dissolving in alkali solutions was proposed. The dissolution behavior of cellulose and cellobiose in LiOH, NaOH and KOH were studied by means of ¹H and ¹³C NMR as well as longitudinal relaxation times. The structure and properties of the three alkali solutions were compared. The results show that alkali share the same interaction mode with cellobiose and with the magnitude of LiOH > NaOH > KOH; the alkalis influence the structure of water also in the same order LiOH > NaOH > KOH. The different behavior of the three alkalis lies in the different structure of the cation hydration ions. Li⁺ and Na⁺ can form two hydration shells, while K⁺ can only form loose first hydration shell. The key to the alkali solution can or cannot dissolve cellulose is whether the cation hydration ions can form stable complex with cellulose or not. K⁺ cannot form stable complex with cellulose result in the KOH solution can only swell cellulose.