Peroxy Anion Research Articles

An Automated Thermochemistry Protocol Based on Explicitly Correlated Coupled-Cluster Theory: The Methyl and Ethyl Peroxy Families.

An automated computational thermochemistry protocol based on explicitly correlated coupled-cluster theory was designed to produce highly accurate enthalpies of formation and atomization energies for small- to medium-sized molecular species (3-12 atoms). Each potential source of error was carefully examined, and the sizes of contributions to the total atomization enthalpies were used to generate uncertainty estimates. The protocol was first used to generate total atomization enthalpies for a family of four molecular species exhibiting a variety of charges, multiplicities, and electronic ground states. The new protocol was shown to be in good agreement with the Active Thermochemical Tables database for the four species: the methyl peroxy radical, methoxyoxoniumylidene (methyl peroxy cation), methyl peroxy anion, and methyl hydroperoxide. Updating the Active Thermochemical Tables to include those results yielded significantly improved accuracy for the formation enthalpies of those species. The derived protocol was then used to predict formation enthalpies for the larger ethyl peroxy family of species.

QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins.

Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecular mechanics (QM/MM) and site-directed mutagenesis studies to investigate the details of the catalytic mechanism in berovin, a member of the ctenophore family. In the absence of a crystal structure of the berovin-substrate complex, molecular docking was used to determine the binding mode of the protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) forms of the substrate to berovin. A total of 13 mutants predicted to surround the binding site were targeted by site-directed mutagenesis which revealed their relative importance in substrate binding and catalysis. Molecular dynamics simulations and MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) calculations showed that electrostatic and polar solvation energy are +115.65 and -100.42 kcal/mol in the deprotonated form, respectively. QM/MM calculations and pKa analysis revealed the deprotonated form of substrate is unstable due to the generation of a dioxetane intermediate caused by nucleophilic attack of the substrate peroxy anion at its C3 position. This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent.

Acyl-Carbon Bond Cleaving Cytochrome P450 Enzymes: CYP17A1, CYP19A1 and CYP51A1.

Cytochrome P450 (P450 or CYP) enzymes in their resting state contain the heme-iron in a high-spin FeIII state. Binding of a substrate to a P450 enzyme allows transfer of the first electron, producing a Fe(II) species that reacts with oxygen to generate a low-spin iron superoxide intermediate (FeIII-O-O•) ready to accept the second electron to produce an iron peroxy anion intermediate (a, FeIII-O-O-). In classical monooxygenation reactions, the peroxy anion upon protonation fragments to form the reactive Compound I intermediate (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). However, when the substrate projects a carbonyl functionality, of the type b, at the active site as is the case for reactions catalyzed by CYP17A1, CYP19A1 and CYP51A1, the peroxy anion (FeIII-O-O-) is trapped, yielding a tetrahedral intermediate (c) that fragments to an acyl-carbon cleavage product (d plus an acid). Analogous acyl-carbon cleavage reactions are also catalyzed by certain hepatic P450s and CYP125A1 from Mycobacterium tuberculosis. A further improvisation on the theme is provided by aldehyde deformylases that convert long-chain aliphatic aldehydes to hydrocarbons. CYP17A1 is involved in the biosynthesis of corticoids as well as androgens. The flux toward these two classes of hormones seems to be regulated by cytochrome b 5, at the level of the acyl-carbon cleavage reaction. It is this regulation of CYP17A1 that provides a safety mechanism, ensuring that during corticoid biosynthesis, which requires 17α-hydroxylation by CYP17A1, androgen formation is avoided (Fig. 4.1).

Oxygen Activation of Apo‐obelin–Coelenterazine Complex

Ca(2+) -regulated photoproteins use a noncovalently bound 2-hydroperoxycoelenterazine ligand to emit light in response to Ca(2+) binding. To better understand the mechanism of formation of active photoprotein from apoprotein, coelenterazine and molecular oxygen, we investigated the spectral properties of the anaerobic apo-obelin-coelenterazine complex and the kinetics of its conversion into active photoprotein after exposure to air. Our studies suggest that coelenterazine bound within the anaerobic complex might be a mixture of N7-protonated and C2(-) anionic forms, and that oxygen shifts the equilibrium in favor of the C2(-) anion as a result of peroxy anion formation. Proton removal from N7 and further protonation of peroxy anion and the resulting formation of 2-hydroperoxycoelenterazine in obelin might occur with the assistance of His175. It is proposed that this conserved His residue might play a key role both in formation of active photoprotein and in Ca(2+) -triggering of the bioluminescence reaction.

DFT calculations of the anomeric and exo-anomeric effect of the hydroperoxy and peroxy groups

DFT calculations were carried out on axially and equatorially oriented 2-hydroperoxy and 2-peroxy tetrahydropyran, cyclohexyl hydroperoxide, hydroperoxides of 2,3-unsaturated hexapyranoses, and hydroperoxides of OMe and OBn substituted derivatives of 2-deoxy-glucopyranose and 2-deoxy-galactopyranose to investigate the anomeric and exo-anomeric effects of these groups. The structure and energy of the conformers were calculated at the B3LYP/6-311++G ∗∗ level. Calculations showed that the peroxy anion group exhibits a strong anomeric effect, comparable in magnitude to the methoxy group, and that the anomeric effect of the hydroperoxy group is similar to the hydroxyl group. These results revealed that hydroperoxy and peroxy anion groups display an exo-anomeric effect, but the orientation around the C1–O1 bond is also affected by hydrogen bonding and electrostatic interactions.

Synthesis of DNA using a new two-step cycle.

For the first time a new, two-step method is described for synthesizing deoxyribonucleic acid. The approach uses 5'-carbonate protected 2'-deoxynucleoside-3'-phosphoramidites as synthons and a peroxy anion buffer that removes the carbonate protecting group and oxidizes the internucleotide linkage. Following synthesis via this two-step cycle, oligomers are isolated by standard procedures.

Column: Polymer Supports in Synthesis

This month's column will describe the recent development of a novel sucrose-based polymer support for both solid-phase peptide synthesis and affinity chromatography. Secondly, a solid-phase oligodeoxynucleotide two-step synthetic cycle, using peroxy anion deprotection, will be intruduced. These two developments underscore the continuing rich development in organic synthesis that is based on using polymer supports. A novel SUcrose-Based Polymer support (SUBPOL), with a morphology tailored for use in solid-phase peptide synthesis (SPPS), and its use as a hydrophilic affinity matrix for the specific removal of fibrinogen from human plasma, has just been reported by an Austrian and French team (A. Poschalko, T. Rohr et al., J. Am. Chem. Soc., 2003, 125, 13,415-13,426).

Solid-phase oligodeoxynucleotide synthesis: a two-step cycle using peroxy anion deprotection.

A novel solid-phase phosphoramidite based oligodeoxynucleotide two-step synthesis method has been developed. Keys to this method are replacement of the 5'-dimethoxytrityl blocking group with an aryloxycarbonyl and the use of N-dimethoxytrityl protection for the exocyclic amines of adenine and cytosine. With these modifications, coupling of each 2'-deoxynucleoside 3'-phosphoramidite to the growing oligodeoxynucleotide on the solid support can be followed by treatment with an aqueous mixture of peroxy anions buffered at pH 9.6. This reagent effectively removes the carbonate protecting group and simultaneously oxidizes the phosphite internucleotide linkage. As a consequence a new two-step synthesis cycle is possible. Oligodeoxynucleotides synthesized using this approach are identical to authentic samples when tested by a variety of analytical techniques.

Expression, purification, and characterization of AknX anthrone oxygenase, which is involved in aklavinone biosynthesis in Streptomyces galilaeus.

In streptomycete anthracycline biosynthetic gene clusters, small open reading frames are located just upstream of minimal polyketide synthase genes. aknX is such a gene found in the aklavinone-aclacinomycin biosynthetic gene cluster of Streptomyces galilaeus. In order to identify its function, the aknX gene was expressed in Escherichia coli. The cell extract prepared from E. coli cells overexpressing AknX protein exhibited anthrone oxygenase activity, which converted emodinanthrone to anthraquinone emodin. This indicates that AknX and related gene products such as DnrG and SnoaB are involved in the formation of aklanonic acid from its anthrone precursor, as suggested by their homology with TcmH and ActVA6. The AknX protein fused with a His(6) tag was efficiently purified to homogeneity by Ni(2+) affinity and anion-exchange column chromatography. The native molecular mass of AknX was estimated to be 42 kDa by gel filtration. Thus, native AknX is considered to have a homotrimeric subunit structure. AknX, like TcmH and ActVA6, possesses no apparent prosthetic group for oxygen activation. Site-directed mutagenesis was carried out to identify the key amino acid residue(s) involved in the oxygenation reaction. Of seven AknX mutants expressed, the W67F mutant showed significantly reduced oxygenase activity, suggesting the important role of the W67 residue in the AknX reaction. A possible mechanism for the reaction via peroxy anion intermediate is proposed.

Rapid Nucleophilic/Oxidative Decontamination of Chemical Warfare Agents

Simple solutions of hydrogen peroxide; peroxide activators such as carbonate, bicarbonate, and molybdate; and organic cosolvents afford rapid, broad-spectrum decontamination of chemical warfare agents, even at low temperatures (−30 °C). Such solutions are nontoxic, noncorrosive, and environmentally friendly. With bicarbonate activator, the decon solution can be comprised solely using food-grade materials. In situ generation of peroxy anion OOH- effects perhydrolysis of the nerve agents O-ethyl-S-[2-(diisopropylamino)ethyl]-methylphosphonothioate (VX) and pinacolyl methylphosphonofluoridate (GD or Soman) to yield nontoxic products. For the blister agent bis(2-chloroethyl) sulfide (HD or mustard), peroxo species HCO4- and Mo(OO)42- afford oxidation, initially, to the nonvesicant sulfoxide.

β‐Cyclodextrin‐catalyzed decomposition of Caro's acid

AbstractThe kinetics and mechanism of decomposition of peroxomonosulphate (PMS) in aqueous sodium hydroxide medium in the presence β‐cyclodextrin has been investigated. The rate of decomposition of PMS is considerably enhanced by the added β‐cyclodextrin. The reaction follows first order kinetics with respect to [PMS]. The experimental results suggest the formation of β‐cyclodextrin peroxy anion by the interaction between SO52−, and β‐cyclodextrin anion (BCDO−). β‐Cyclodextrin peroxy anion subsequently reacts with PMS to give O2, SO42− and β‐cyclodextrin anion. The rate constant for the β‐cyclodextrin‐catalyzed decomposition of SO52− (BCD + SO52−) is of the same order of magnitude as that of the reaction HSO52− + SO52− products. © 2002 Wiley Periodic mals, Inc. Int J Chem Kinet 34: 508–513, 2002

Mechanism of oxygenation of naphthoquinone derivative

Vitamin K in its hydroquinone form, vitamin KH 2, is transformed to vitamin K oxide concurrent with the abstraction of the γ-hydrogen of Glu leading to Gla. The nonenzymatic model supports that oxygenation of the monoanion of vitamin KH 2 can produce the peroxy anion at the 4-position yielding vitamin K oxide.

Electron Transfer. 133. Copper Catalysis in the Sulfite Reduction of Peroxynitrite1

Peroxynitrite (ONOO-) is formed by the reaction of cold aqueous solutions of hydrogen peroxide and nitrous acid, followed by rapid quenching with base. Reduction of this peroxy anion with sulfite (ONOO- + SO32- → NO2- + SO42-) at pH 12−14 is slow but is catalyzed markedly by dissolved Cu(II), which, in this medium, exists predominantly as Cu(OH)42-. Nonexponential kinetic profiles for 10 runs, carried out with [OH-] = 0.005−0.50 M, [ONOO-] = 0.16−0.58 mM, [SO32-] = 7.5−75 mM, and [CuII] = 1.0−4.0 μM, are consistent with a sequence (eqs 8−13 in the text) in which Cu(I) is generated from the one-electron reduction of Cu(II) by SO32-, after which Cu(I) reduces peroxynitrite to NO2 by competing protonated and nonprotonated paths. Subsequent reduction of NO2 is taken to be rapid. The proposed sequence then attributes the catalytic role of copper, in this system, to its ability to support a single-electron route to supplement the uncatalyzed path, which has been taken to entail direct oxygen atom transfer. Vana...

Autoxidation of Intermediary Mesoionic 1,3-Oxazolium-5-olates Generated from Cyclic N-Acyl .ALPHA.-Amino Acids.

Mesoionic 1, 3-oxazolium-5-olates (munchnones) react fairly rapidly with oxygen to give the autoxidation products when the C-4 substituent is aromatic. The autoxidation occurred in the munchnones generated from N-acyl tetrahydroisoquinoline-1-carboxylic acids or tetrahydro-β-carboline-1-carboxylic acids. The mechanism was elucidated by 18O labeling experiments and involved a series of well-precedented autoxidative processes including oxygenation, cyclization of the resulting peroxy anion, and oxidative cleavage.

Studies on the mechanism of aromatase and other cytochrome P450 mediated deformylation reactions

Aromatase is a microsomal cytochrome P450 that converts androgens to estrogens by three sequential oxidations. The isolation of the 19-hydroxy and 19-oxo androgens suggests that the first two oxidations occur at the C 19 carbon. However, the mechanism of the third oxidation, which results in C 10C 19 bond cleavage, has not been determined. Two proposed mechanisms which remain viable involve either initial 1β-hydrogen atom abstraction or addition of the ferric peroxy anion from aromatase to the C 19 aldehyde. Semiempirical molecular orbital calculations (AM1) were used to study potential reaction mechanisms initiated by initial 1β-hydrogen atom abstraction. Initially, the energetics of carboncarbon bond cleavage of the keto and enol forms of C1-radicals were studied and were found to be energetically similar. A mechanism was proposed in which the 19-oxo intermediate is subject to initial nucleophilic attack by the protein. The geometry of the A-ring in the androgens is between that for the 1-radicals and estrogen, suggesting that some transition state stabilization for the homolytic cleavage reaction can occur. More recently, studies on liver microsomal cytochrome P450 mediated deformylation of xenobiotic aldehydes supports mechanisms involving an alkyl peroxy intermediate formed by addition of the ferric peroxy anion from aromatase to the C 19 aldehyde. Although this intermediate could proceed through several different concerted or non-concerted pathways, one non-concerted pathway involves the heterolytic cleavage of the dioxygen bond resulting in an active oxygenating species (iron-oxene) and a diol. The diol could then undergo hydrogen atom abstraction followed by homolytic carboncarbon bond cleavage as in the mechanisms modeled previously. When this cleavage was modeled for seven aldehydes, a good correlation with reported experimental aldehyde turnover numbers was obtained. However, when dialkoxy derivatives of the aldehydes are subject to microsomal metabolism, the rates of carboncarbon cleavage products do not approach the rates of deformylation of the aldehyde analog.

Carbon in oxides and silicates — dissolution versus exsolution

Carbon seems to be an ubiquitous impurity in high-melting oxides and silicates which have been exposed to CO/CO 2 during crystal growth. The study of synthetic MgO crystals has provided insight into the dissolution mechanism of CO/CO 2 and the diffusion mechanism of solute carbon through a dense oxide matrix. Treating the dissolution of CO 2 in MgO as a solid solution between the majority divalent oxide and a minority tetravalent oxide, two Mg 2+ vacancies are introduced for each CO 2 molecule dissolved. Carbon, sitting off-center in one cation vacancy, forms an anion complex, CO 2- 2. This complex corresponds formally to a dissolved CO molecule: CO+ O 2= CO 2- 2. The second cation vacancy is chargewise compensated by two O - undergoing spin pairing to give a peroxy anion, O 2- 2, which formally corresponds to a dissolved oxygen atom: O+ O 2-= O 2- 2. Chemically the dissolution of CO 2 can be described as redox process producing reduced and oxidized solute species, e.g. CO 2- 2 and O 2- 2. When the solute carbon passes from the cation vacancy site to interstitial sites, the CO 2- 2 anion complex dissociates into CO - and O -. While one O - remains with the cation vacancy forming a V - center, the C atom diffuses with the other O - state, e.g. a positive hole or defect electron on the O 2- sublattice. Because an O - is much smaller than an O 2- the local lattice contraction associated with the CO - lowers the activation energy barrier for the C diffusion through the dense MgO matrix. This makes C a very mobile solute species, capable of diffusing already at low temperatures when cation vacancy diffusion is not yet activated. At the same time the C diffusion is coupled to the diffusion of an electric charge. Therefore, when the MgO-CO 2 solid solution turns supersaturated during cooling, C segregation builds up a space charge layer near the surface. Its bias counteracts further segregation. This leads to the prediction that the exsolution of the MgO-CO 2 solid solution (e.g. degassing) may be controlled by space charges rather than by the carbon mobility. Experimental support is derived from SIMS measurements. However, if C-C bonds can form at the surface, CO -+ CO -= C 2 O -+ O -, the positive holes, e.g. O - states, may retrodiffuse to the bulk. This reduces the space charge at the surface, while reconverting V - centers in the bulk into peroxy anions which compensate the extrinsic cation vacancies introduced initially. If the C-C polymerization goes on, C n O -=C n+1O -+O -, with n å 1, the exsolution can procede and the solu te CO 2 component eventually splits into graphitic carbon which precipitates at the surface and solute oxygen which remains in the bulk in the form of peroxy defects.

Kinetics of yeast cytochrome c peroxidase compound I formation with modified substrates (peroxybenzoic acids)

The kinetics of formation of Compound I of yeast cytochrome c peroxidase (ferrocytochrome c:hydrogen-peroxide oxidoreductase, EC 1.11.1.5) with a series of peroxybenzoic acids were studied. Reactivity is affected not only by protein ionization, as in the reaction with H 2O 2, but also by substrate ionization. The reactivity of negatively charged substrates is markedly lower than that of uncharged species, implying that electrostatic factors profoundly influence substrate binding. The rate constants for neutral peroxybenzoic acids carrying electron-withdrawing substituents increase with increasing peroxy acid p K a. This behaviour suggests that, as previously discussed for reactions of turnip peroxidases, formation of peroxy anion by ionization of substrate within the active site is kinetically important. The results support the mechanism of cytochrome c peroxidase Compound I formation which has been proposed by Poulos and Kraut (J. Biol. Chem. 225 (1980), 8199–8205) on the basis of enzyme structural studies.

A new source of carbon oxides in biochemical systems. Implications regarding dioxetane intermediates

The peroxidase catalyzed aerobic oxidation of aromatic pyruvates produces the aromatic aldehyde, oxalate, CO and CO 2 and a weak light emission. This indicates the preliminary formation of a peroxy anion which can cyclizes to a four-membered ring dioxetane and to a five membered ring α-keto-β-peroxylactone intermediates. The possible importance of this new source of carbon oxides in biological systems is pointed out. The results considerably strengthen the view that a dioxetane is formed in side chain of the plant hormone indoleacetic acid during the oxidation catalyzed by peroxidase.

BIOLUMINESCENCE FROM THE REACTION OF FMN, H2O2 AND LONG CHAIN ALDEHYDE WITH BACTERIAL LUCIFERASE

Abstract— The bioluminescent oxidation of reduced flavin mononucleotide by bacterial luciferase involves a long‐lived flavoenzyme intermediate whose chromophore has been postulated to be the 4a‐sub‐stituted peroxy anion of reduced flavin. Reaction of long chain aldehyde with this intermediate results in light emission and formation of the corresponding acid. These experiments show that the typical aldehyde‐dependent, luciferase‐catalyzed bioluminescence can also be obtained starting with FMN and H2O2 instead of FMNH2 and O2. We postulate that the 4a‐peroxy anion intermediate is formed directly by attack of H2O2 on FMN. The latter may be bound to luciferase. An enzyme bound intermediate is formed which by kinetic analysis, flavin specificity for luminescence, aldehyde dependence, and bioluminescent emission spectrum appears to be identical with the species generated by reaction of FMNH, and O2 with luciferase. The quantum yield of the H2O2‐‐ and FMN‐initiated biolumlnescence is low but can be enhanced by certain metal ions, which also stimulate a chemiluminescent reaction of oxidized flavin with H2O2. The peak of this chemiluminescence. however, appears to be at a shorter wavelength than that (490 nm) of the bioluminescence.

Compound I formation with turnip peroxidases and peroxybenzoic acids.

The kinetics of formation of the compounds I of the turnip peroxidase isoenzymes 1 and 7 with peroxybenzoic acid and a series of substituted peroxybenzoic acids (p‐OCH3, p‐CH3, p‐Cl, m‐Cl, m‐NO2 and p‐NO2) were studied at 25°C. The pH profiles of the observed second‐order rate constants, after correction for the alkaline transitions of the enzymes, indicate that isoenzyme 1 reacts exclusively with unionized peroxy acids whereas with isoenzyme 7, although the major contribution involves reaction with unionized peroxy acid, an additional reaction with peroxy anion is observed. In contrast to the behaviour of horse‐radish peroxidase, (where the rate constants for unhindered unionized peroxybenzoic acids exceed that with H2O2 and the reactions are probably diffusion controlled) the rate constants, kHA, for isoenzyme 1 reaction with unionized peroxy acids are all lower than that with H2O2 and the activation energies indicate chemical control. For isoenzyme 7 the value of kHA with the most weakly acidic peroxybenzoic acids exceeds the rate constant with H2O2. For both isoenzyme 1 and isoenzyme 7 the values of kHA are very sensitive to peroxy acid acidity and in both cases log kHA shows good correlation with pKHA.The results are compared with each other and with previous data for both turnip and horse radish peroxidases. It is suggested that the multifactorial influences upon the kinetics of compound I formation include (a) diffusion, (b) substrate hydrophobicity, the hydrophobic binding affinity of the active sites of the enzymes and perhaps hydrogen bonding interactions, (c) a substrate‐charge‐type discrimination elicited by the protein at the entrance to the active site, (d) substrate substituent inductive effects which suggest the importance of the generation of highly nucleophilic peroxy anions from neutral hydroperoxides within the active site. These influences are of very variable relative importance in enzymes from different sources and in different isoenzymes from the same source.