Oxidation of methanol by FeO2+ in water: DFT calculations in the gas phase and ab initio MD simulations in water solution

We investigate the mechanism of methanol oxidation to formaldehyde by ironoxido ([Fe(IV)O]2+), the alleged active intermediate in the Fenton reaction. The most likely reaction mechanisms are explored with density functional theory (DFT) calculations on microsolvated clusters in the gas phase and, for a selected set of mechanisms, with constrained Car-Parrinello molecular dynamics (CPMD) simulations in water solution. Helmholtz free energy differences are calculated using thermodynamic integration in a simulation box with 31 water molecules at 300 K. The mechanism of the reaction is investigated with an emphasis on whether FeO2+ attacks methanol at a C-H bond or at the O-H bond. We conclude that the most likely mechanism is attack by the oxido oxygen at the C-H bond ("direct CH mechanism"). We calculate an upper bound for the reaction Helmholtz free energy barrier in solution of 50 kJ/mol for the C-H hydrogen transfer, after which transfer of the O-H hydrogen proceeds spontaneously. An alternative mechanism, starting with coordination of methanol directly to Fe ("coordination OH mechanism"), cannot be ruled out, as it involves a reaction Helmholtz free energy barrier in solution of 44 +/- 10 kJ/mol. However, this coordination mechanism has the disadvantage of requiring a prior ligand substitution reaction, to replace a water ligand by methanol. Because of the strong acidity of [FeO(H2O)5]2+, we also investigate the effect of deprotonation of a first-shell water molecule. However, this is found to increase the barriers for all mechanisms.     

Theoretical study of the mechanism of alkane hydroxylation and ethylene epoxidation reactions catalyzed by diiron bis-oxo complexes. The effect of substrate molecules

The hybrid density functional method B3LYP was used to study the mechanism of the hydrocarbon (methane, ethane, methyl fluoride, and ethylene) oxidation reaction catalyzed by the complexes cis-(H(2)O)(NH(2))Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(NH(2))(H(2)O), I, and cis-(HCOO)(Imd)Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(Imd)(HCOO) (Imd = Imidazole), I_m, the "small" and "medium" model of compound Q of the methane monooxygenase (MMO). The improvement of the model from "small" to "medium" did not change the qualitative conclusions but significantly changed the calculated energetics. As in the case of methane oxidation reported by the authors previously, the reaction of all the substrates studied here is shown to start by coordination of the substrate molecule to the bridging oxygen atom, O(1) of I, an Fe(IV)-Fe(IV) complex, followed by the H-atom abstraction at the transition state III leading to the bound hydroxy alkyl intermediate IV of Fe(III)-Fe(IV) core. IV undergoes a very exothermic coupling of alkyl and hydroxy groups to give the alcohol complex VI of Fe(III)-Fe(III) core, from which alcohol dissociates. The H(b)-atom abstraction (or C-H bond activation) barrier at transition state III is found to be a few kcal/mol lower for C(2)H(6) and CH(3)F than for CH(4). The calculated trend in the H(b)-abstraction barrier, CH(4) (21.8 kcal/mol) > CH(3)F (18.8 kcal/mol) > or = C(2)H(6) (18.5 kcal/mol), is consistent with the C-H(b) bond strength in these substrates. Thus, the weaker the C-H(b) bond, the lower is the H(b)-abstraction barrier. It was shown that the replacement of a H-atom in a methane molecule with a more electronegative group tends to make the H(b)-abstraction transition state less "reactant-like". In contrast, the replacement of the H-atom in CH(4) with a less electronegative group makes the H(b)-abstraction transition state more "reactant-like". The epoxidation of ethylene by complex I is found to proceed without barrier and is a highly exothermic process. Thus, in the reaction of ethylene with complex I the only product is expected to be ethylene oxide, which is consistent with the experiment.     

Theoretical study of C-H and N-H sigma-bond activation reactions by titinium(IV)-imido complex. Good understanding based on orbital interaction and theoretical proposal for N-H sigma-bond activation of ammonia

The C-H sigma-bond activation of methane and the N-H sigma-bond activation of ammonia by (Me3SiO)2Ti(=NSiMe3) 1 were theoretically investigated with DFT, MP2 to MP4(SDQ), and CCSD(T) methods. The C-H sigma-bond activation of methane takes place with an activation barrier (Ea) of 14.6 (21.5) kcal/mol and a reaction energy (DeltaE) of -22.7 (-16.5) kcal/mol to afford (Me3SiO)2Ti(Me)[NH(SiMe3)], where DFT- and MP4(SDQ)-calculated values are given without and in parentheses, respectively, hereafter. The electron population of the CH3 group increases, but the H atomic population decreases upon going to the transition state from the precursor complex, which indicates that the C-H sigma-bond activation occurs in heterolytic manner unlike the oxidative addition. The Ti atomic population considerably increases upon going to the transition state from the precursor complex, which indicates that the charge transfer (CT) occurs from methane to Ti. These population changes are induced by the orbital interactions among the d(pi)-p(pi) bonding orbital of the Ti=NSiMe3 moiety, the Ti d(z2) orbital and the C-H sigma-bonding and sigma*-antibonding orbitals of methane. The reverse regioselective C-H sigma-bond activation which leads to formation of (Me3SiO)2Ti(H)[NMe(SiMe3)] takes place with a larger Ea value and smaller exothermicity. The reasons are discussed in terms of Ti-H, Ti-CH3, Ti-NH3, N-H, and N-CH3 bond energies and orbital interactions in the transition state. The N-H sigma-bond activation of ammonia takes place in a heterolytic manner with a larger Ea value of 19.0 (27.9) kcal/mol and considerably larger exothermicity of -45.0 (-39.4) kcal/mol than those of the C-H sigma-bond activation. The N-H sigma-bond activation of ammonia by a Ti-alkylidyne complex, [(PNP)Ti(CSiMe3)] 3 (PNP = N-[2-(PH2)2-phenyl]2-]) ,was also investigated. This reaction takes place with a smaller E(a) value of 7.5 (15.3) kcal/mol and larger exothermicity of -60.2 (-56.1) kcal/mol. These results lead us to predict that the N-H sigma-bond activation of ammonia can be achieved by these complexes.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

The "somersault" mechanism for the p-450 hydroxylation of hydrocarbons. The intervention of transient inverted metastable hydroperoxides

A series of model theoretical calculations are described that suggest a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. A new class of metastable metal hydroperoxides is described that involves the rearrangement of the ground-state metal hydroperoxide to its inverted isomeric form with a hydroxyl radical hydrogen bonded to the metal oxide (MO-OH --> MO....HO). The activation energy for this somersault motion of the FeO-OH group is 20.3 kcal/mol for the P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] to produce the isomeric ferryl oxygen hydrogen bonded to an *OH radical [Por(SH)Fe(III)-O....HO(-)]. This isomeric metastable hydroperoxide, the proposed primary oxidant in the P450 hydroxylation reaction, is calculated to be 17.8 kcal/mol higher in energy than the ground-state iron(III) hydroperoxide Cpd 0. The first step of the proposed mechanism for isobutane oxidation is abstraction of a hydrogen atom from the C-H bond of isobutane by the hydrogen-bonded hydroxyl radical to produce a water molecule strongly hydrogen bonded to anionic Cpd II. The hydroxylation step involves a concerted but nonsynchronous transfer of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concomitant rebound of the incipient *OH radical to the carbon radical of isobutane to produce the C-O bond of the final product, tert-butyl alcohol. The TS for the oxygen rebound step is 2 kcal/mol lower in energy than the hydrogen abstraction TS (DeltaE() = 19.5 kcal/mol). The overall proposed new mechanism is consistent with a lot of the ancillary experimental data for this enzymatic hydroxylation reaction.     

Theoretical study of the Cp2Zr-catalyzed hydrosilylation of ethylene. Reaction mechanism including new sigma-bond activation

The Cp(2)Zr-catalyzed hydrosilylation of ethylene was theoretically investigated with DFT and MP2-MP4(SDQ) methods, to clarify the reaction mechanism and the characteristic features of this reaction. Although ethylene insertion into the Zr-SiH(3) bond of Cp(2)Zr(H)(SiH(3)) needs a very large activation barrier of 41.0 (42.3) kcal/mol, ethylene is easily inserted into the Zr-H bond with a very small activation barrier of 2.1 (2.8) kcal/mol, where the activation barrier and the energy of reaction calculated with the DFT(B3LYP) method are given and in parentheses are those values which have been corrected for the zero-point energy, hereafter. Not only this ethylene insertion reaction but also the coupling reaction between Cp(2)Zr(C(2)H(4)) and SiH(4) easily takes place to afford Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with activation barriers of 0.3 (0.7) and 5.0 (5.4) kcal/mol, respectively. This coupling reaction involves a new type of Si-H sigma-bond activation which is similar to metathesis. The important interaction in the coupling reaction is the bonding overlap between the d(pi)-pi bonding orbital of Cp(2)Zr(C(2)H(4)) and the Si-H sigma orbital. The final step is neither direct C-H nor Si-C reductive elimination, because both reductive eliminations occur with a very large activation barrier and significantly large endothermicity. This is because the d orbital of Cp(2)Zr is at a high energy. On the other hand, ethylene-assisted C-H reductive elimination easily occurs with a small activation barrier, 5.0 (7.5) kcal/mol, and considerably large exothermicity, -10.6 (-7.1) kcal/mol. Also, ethylene-assisted Si-C reductive elimination and metatheses of Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with SiH(4) take place with moderate activation barriers, 26.5 (30.7), 18.4 (20.5), and 28.3 (31.5) kcal/mol, respectively. From these results, it is clearly concluded that the most favorable catalytic cycle of the Cp(2)Zr-catalyzed hydrosilylation of ethylene consists of the coupling reaction of Cp(2)Zr(C(2)H(4)) with SiH(4) followed by the ethylene-assisted C-H reductive elimination.     

On the effect of low-energy electron induced DNA strand break in aqueous solution: a theoretical study indicating guanine as a weak link in DNA

In this theoretical study we have investigated the effect of low-energy electrons attached onto a 3'-guanine monophosphate, 3'-GMP, in the gas phase and in aqueous solution. DFT calculations with B3LYP/DZP++ were performed to study the C3'-O3' bond break of a 3'-GMP radical anion. Our results show that low-energy electrons, if attached to a 3'-GMP with a neutrally charged phosphate group, can easily induce a C3'-3' bond break in both the gas phase and aqueous solution. The activation energy was found here to be 10.3 kcal/mol in the gas phase and, even lower, 5.3 kcal/mol in aqueous solution. In comparison with calculated activation energies for other nucleotides the 3'-GMP has the lowest energy barrier in aqueous solution.     

On the mechanism of (PCP)Ir-catalyzed acceptorless dehydrogenation of alkanes: a combined computational and experimental study

Pincer complexes of the type ((R)PCP)IrH(2), where ((R)PCP)Ir is [eta(3)-2,6-(R(2)PCH(2))(2)C(6)H(3)]Ir, are the most effective catalysts reported to date for the "acceptorless" dehydrogenation of alkanes to yield alkenes and free H(2). We calculate (DFT/B3LYP) that associative (A) reactions of ((Me)PCP)IrH(2) with model linear (propane, n-PrH) and cyclic (cyclohexane, CyH) alkanes may proceed via classical Ir(V) and nonclassical Ir(III)(eta(2)-H(2)) intermediates. A dissociative (D) pathway proceeds via initial loss of H(2), followed by C-H addition to ((Me)PCP)Ir. Although a slightly higher energy barrier (DeltaE(+ +)) is computed for the D pathway, the calculated free-energy barrier (DeltaG(+ +)) for the D pathway is significantly lower than that of the A pathway. Under standard thermodynamic conditions (STP), C-H addition via the D pathway has DeltaG(o)(+ +) = 36.3 kcal/mol for CyH (35.1 kcal/mol for n-PrH). However, acceptorless dehydrogenation of alkanes is thermodynamically impossible at STP. At conditions under which acceptorless dehydrogenation is thermodynamically possible (for example, T = 150 degrees C and P(H)2 = 1.0 x 10(-7) atm), DeltaG(+ +) for C-H addition to ((Me)PCP)Ir (plus a molecule of free H(2)) is very low (17.5 kcal/mol for CyH, 16.7 kcal/mol for n-PrH). Under these conditions, the rate-determining step for the D pathway is the loss of H(2) from ((Me)PCP)IrH(2) with DeltaG(D)(+ +) approximately DeltaH(D)(+ +) = 27.2 kcal/mol. For CyH, the calculated DeltaG(o)(+ +) for C-H addition to ((Me)PCP)IrH(2) on the A pathway is 35.2 kcal/mol (32.7 kcal/mol for n-PrH). At catalytic conditions, the calculated free energies of C-H addition are 31.3 and 33.7 kcal/mol for CyH and n-PrH addition, respectively. Elimination of H(2) from the resulting "seven-coordinate" Ir-species must proceed with an activation enthalpy at least as large as the enthalpy change of the elimination step itself (DeltaH approximately 11-13 kcal/mol), and with a small entropy of activation. The free energy of activation for H(2) elimination (DeltaG(A)(+ +)) is hence found to be greater than ca. 36 kcal/mol for both CyH and n-PrH under catalytic conditions. The overall free-energy barrier of the A pathway is calculated to be higher than that of the D pathway by ca. 9 kcal/mol. Reversible C-H(D) addition to ((R)PCP)IrH(2) is predicted to lead to H/D exchange, because the barriers for hydride scrambling are extremely low in the "seven-coordinate" polyhydrides. In agreement with calculation, H/D exchange is observed experimentally for several deuteriohydrocarbons with the following order of rates: C(6)D(6) > mesitylene-d(12) > n-decane-d(22) > cyclohexane-d(12). Because H/D exchange in cyclohexane-d(12) solution is not observed even after 1 week at 180 degrees C, we estimate that the experimental barrier to cyclohexane C-D addition is greater than 36.4 kcal/mol. This value is considerably greater than the experimental barrier for the full catalytic dehydrogenation cycle for cycloalkanes (ca. 31 kcal/mol). Thus, the experimental evidence, in agreement with calculation, strongly indicates that the A pathway is not kinetically viable as a segment of the "acceptorless" dehydrogenation cycle.     

Quantum mechanical and molecular mechanics approach with a multilayered-quantum representation study of solvent effects and potentials of mean force for the CH<Subscript>3</Subscript>CH<Subscript>2</Subscript>Cl + ClO<Superscript>−</Superscript> S<Subscript>N</Subscript>2 reaction in aqueous solution

The bimolecular nucleophilic substitution reaction of CH₃CH₂Cl + ClO^? in aqueous solution was investigated using a multilayered-quantum representation, quantum mechanical and molecular mechanics approach with an explicit water model. Ten configurations along the reaction pathway including reactant complex, transition state and product complex were analyzed in the presence of the aqueous solution. The obtained free energy activation barrier under the CCSD(T)/MM representation is 13.2 kcal/mol, while it is 11.7 kcal/mol under the DFT/MM representation which agrees very well with the DFT calculation, at 11.0 kcal/mol, with a polarizable continuum solvent model. The solvent effects including the solvation free energy contribution and the polarization effect raise the free activation barrier by 9.8 kcal/mol. The rate constant, at 298 K, is 5.27 × 10^?17 cm³/molecule/s which is about seven orders of magnitude smaller than that in the gas phase (1.10 × 10^?10 cm³/molecule/s). All in all, the aqueous solution plays an essential role in shaping the reaction pathway for this reaction in water.     

Methane activation on Pt and Pt4: a density functional theory study

The activation mechanisms of a methane molecule on a Pt atom (CH4-Pt) and on a Pt tetramer (CH4-Pt4) were investigated using density functional theory (B3LYP and PW91) calculations. The results from these two functionals are different mostly in predicting the reaction barrier, in particular for the CH4-Pt system. A new lower energy pathway was identified for the CH4 dehydrogenation on a Pt atom. In the new pathway, the PtCH2 + H2 products were formed via a transition state, in which the Pt atom forms a complex with carbene and both dissociated hydrogen atoms. We report here the first theoretical study of methane activation on a Pt4 cluster. Among the five single steps toward dehydrogenation, our results show that the rate-limiting step is the third step, that is, breaking the second C-H bond, which requires overcoming an energy barrier of 28 kcal/mol. On the other hand, the cleavage of the first C-H bond, that is, the first reaction step, requires overcoming an energy barrier of 4 kcal/mol.     

Theoretical study on the nitration of methane by acyl nitrate catalyzed by H-ZSM5 zeolite

A theoretical study on the nitration of methane by acyl nitrate catalyzed by HZSM-5 zeolite is reported. The zeolite was represented by a "double ring" 20T cluster. The calculations were performed at the DFT/X3LYP/6-31G** and MP2/6-31G** levels. The first step of the mechanism involves the protonation of the acyl nitrate by the zeolite and the formation of a nitronium-like ion. The reaction proceeds through a concerted step with the attack of the methane molecule by the nitronium-like ion and the simultaneous transfer of a proton from the methane molecule to the zeolite, thus reconstructing the acidic site. The activation energies for the first and second steps of this reaction are, respectively, 14.09 and 10.14 kcal/mol at X3LYP/6-31G** level and 16.68 and 13.85 kcal/mol at the MP2/6-31G**.     

Reaction mechanism and tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution: a combined Monte Carlo and quantum mechanics study

A combined Monte Carlo and quantum mechanical study was carried out to analyze the tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution. Second- and fourth-order M?ller-Plesset perturbation theory calculations indicate that in the gas phase thiol (Pym-SH) is more stable than the thione (Pym-NH) by ca. 8 kcal/mol. In aqueous solution, thermodynamic perturbation theory implemented on a Monte Carlo NpT simulation indicates that both the differential enthalpy and Gibbs free energy favor the thione form. The calculated differential enthalpy is DeltaH(SH)(-->)(NH)(solv) = -1.7 kcal/mol and the differential Gibbs free energy is DeltaG(SH)(-->)(NH)(solv) = -1.9 kcal/mol. Analysis is made of the contribution of the solute-solvent hydrogen bonds and it is noted that the SH group in the thiol and NH group in the thione tautomers act exclusively as a hydrogen bond donor in aqueous solution. The proton transfer reaction between the tautomeric forms was also investigated in the gas phase and in aqueous solution. Two distinct mechanisms were considered: a direct intramolecular transfer and a water-assisted mechanism. In the gas phase, the intramolecular transfer leads to a large energy barrier of 34.4 kcal/mol, passing through a three-center transition state. The proton transfer with the assistance of one water molecule decreases the energy barrier to 17.2 kcal/mol. In solution, these calculated activation barriers are, respectively, 32.0 and 14.8 kcal/mol. The solvent effect is found to be sizable but it is considerably more important as a participant in the water-assisted mechanism than the solvent field of the solute-solvent interaction. Finally, the calculated total Gibbs free energy is used to estimate the equilibrium constant.     

Hybrid quantum mechanical and molecular mechanics study of the S(N)2 Reaction of CCl4 + OH- in aqueous solution: the potential of mean force, reaction energetics, and rate constants

The bimolecular nucleophilic substitution reaction of CCl(4) and OH(-) in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 × 10(-28) cm(3) molecule(-1) s(-1) at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH(3)Cl, CH(2)Cl(2), CHCl(3), and CCl(4)), CCl(4) has the lowest free energy activation barrier for the reaction with OH(-) in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.     

A theoretical study of alcohol oxidation by ferrate

The conversion of methanol to formaldehyde mediated by ferrate (FeO(4)2-), monoprotonated ferrate (HFeO4-), and diprotonated ferrate (H2FeO4) is discussed with the hybrid B3LYP density functional theory (DFT) method. Diprotonated ferrate is the best mediator for the activation of the O-H and C-H bonds of methanol via two entrance reaction channels: (1) an addition-elimination mechanism that involves coordination of methanol to diprotonated ferrate; (2) a direct abstraction mechanism that involves H atom abstraction from the O-H or C-H bond of methanol. Within the framework of the polarizable continuum model (PCM), the energetic profiles of these reaction mechanisms in aqueous solution are calculated and investigated. In the addition-elimination mechanism, the O-H and C-H bonds of ligating methanol are cleaved by an oxo or hydroxo ligand, and therefore the way to the formation of formaldehyde is branched into four reaction pathways. The most favorable reaction pathway in the addition-elimination mechanism is initiated by an O-H cleavage via a four-centered transition state that leads to intermediate containing an Fe-O bond, followed by a C-H cleavage via a five-centered transition state to lead to formaldehyde complex. In the direct abstraction mechanism, the oxidation reaction can be initiated by a direct H atom abstraction from either the O-H or C-H bond, and it is branched into three pathways for the formation of formaldehyde. The most favorable reaction pathway in the direct abstraction mechanism is initiated by C-H activation that leads to organometallic intermediate containing an Fe-C bond, followed by a concerted H atom transfer from the OH group of methanol to an oxo ligand of ferrate. The first steps in both mechanisms are all competitive in energy, but due to the significant energetical stability of the organometallic intermediate, the most likely initial reaction in methanol oxidation by ferrate is the direct C-H bond cleavage.     

Insights into the mechanism of methionine oxidation catalyzed by metal (Cu2+, Zn2+, and Fe3+)—Amyloid beta (Aβ) peptide complexes: A computational study

In this DFT study, a mechanism of the oxidation of methionine (Met) amino acid residue catalyzed by the metal (Cu²⁺, Zn²⁺, and Fe³⁺) bound amyloid beta (Aβ) peptide has been proposed. Based on experimental information, two different mechanisms: (1) stepwise and (2) concerted mechanisms for this important process have been investigated. The B3LYP calculations suggest that in the stepwise mechanism, the two separate pathways leading to the same sulfoxide product [Met(O)] go through prohibitively high barriers of 27.3 and 35.1 kcal/mol, therefore it is ruled out. In the concerted mechanism, the Cu²⁺‐Aβ complex has been found to be the most efficient catalyst with the computed barrier of 14.3 kcal/mol. The substitutions of Cu²⁺ by Zn²⁺ and Fe³⁺ increase barriers to 19.6 and 16.9 kcal/mol, respectively and make the reaction thermodynamically less favorable. It was also found that, in comparison with the cysteine (Cys) residue, Met is more susceptible toward oxidation. Its substitution with Cys slightly increased the barrier to 15.8 kcal/mol for the Cu²⁺‐Aβ complex. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Role of the somersault rearrangement in the oxidation step for flavin monooxygenases (FMO). A comparison between FMO and conventional xenobiotic oxidation with hydroperoxides

Model quantum mechanical calculations presented for C-4a-flavin hydroperoxide (FlHOOH) at the B3LYP/6-311+G(d,p) level suggest a new mechanism for flavoprotein monooxygenase (FMO) oxidation involving a concerted homolytic O-O bond cleavage in concert with hydroxyl radical transfer from the flavin hydroperoxide rather than an S(N)2-like displacement by the substrate on the C-4a-hydroperoxide OOH group. Homolytic O-O bond cleavage in a somersault-like rearrangement of hydroperoxide C-4a-flavinhydroperoxide (1) (FLHO-OH → FLHO···HO) produces an internally hydrogen-bonded HO(?) radical intermediate with a classical activation barrier of 27.0 kcal/mol. Model hydroperoxide 1 is used to describe the transition state for the key oxidation step in the paradigm aromatic hydroxylase, p-hydroxybenzoate hydroxylase (PHBH). A comparison of the electron distribution in the transition structures for the PHBH hydroxylation of p-hydroxybenzoic acid (ΔE(?) = 23.0 kcal/mol) with that of oxidation of trimethylamine (ΔE(?) = 22.3 kcal/mol) and dimethyl sulfide (ΔE? = 14.1 kcal/mol) also suggests a mechanism involving a somersault mechanism in concert with transfer of an HO(?) radical to the nucleophilic heteroatom center with a hydrogen transfer back to the FLH-O residue after the barrier is crossed to produce the final product, FLH-OH. In each case the hydroxylation barrier was less than that of the O-O rearrangement barrier in the absence of a substrate supporting an overall concerted process. All three transition structures bear a resemblance to the TS for the comparable hydroxylation of isobutane (ΔE(?) = 29.2 kcal/mol) and for simple Fenton oxidation by aqueous iron(III) hydroperoxides. To our surprise the oxidation of N- and S-nucleophiles with conventional oxidants such as alkyl hydroperoxides and peracids also proceeds by HO(?) radical transfer in a manner quite similar to that for tricyclic hydroperoxide 1. Stabilization of the developing oxyradical produced by somersault rearrangement for concerted enzymatic oxidation with tricyclic hydroperoxide 1 results in a reduced overall activation barrier.     

Selenocysteine versus cysteine reactivity: a theoretical study of their oxidation by hydrogen peroxide

The cysteine and selenocysteine oxidation by H2O2 in vacuo and in aqueous solution was studied using the integrated molecular orbital + molecular orbital (IMOMO) method combining the quadratic configuration method QCISD(T) and the spin projection of second-order perturbation theory PMP2. It is shown that including in the model system of cysteine (selenocysteine) residue up to 20 atoms has significant consequences upon the calculated reaction energy barrier. On the other hand, it is demonstrated that free cysteine and selenocysteine have very similar reaction energy barriers, 77-79 kJ mol(-1) in aqueous solution. It is thus concluded that the high experimental reaction rate constant reported for the oxidation of the selenocysteine residue in the glutathione peroxidase (GPx) active center is due to an important interaction between selenocysteine and its molecular environment. The sensitivity of the calculated energy barrier to the dielectric constant of the molecular environment observed for both cysteine and selenocysteine as well as the catalytic effect of the NH group emphasized in the case of cysteine supports this hypothesis.     

Separation and detection of oxidation products of fluorodeoxyglucose and glucose by high-performance liquid chromatography-electrospray ionisation mass spectrometry

2-Deoxy-2-[18F]fluoro-D-glucose ([18F] FDG), the most popular positron emitting radiopharmaceutical, may oxidise by autoradiolysis in aqueous solution. The aim of this work was to use LC-MS for determination of the oxidation products of fluorodeoxyglucose and glucose (Glc) obtained by oxidation with Fenton's reagent. Asahipak NH2P-50 polyamide silica column and acetonitrile-0.025% aqueous ammonium formate (80:20 (v/v)) eluent were utilised with an Agilent 1100 HPLC-MS instrument. Ten major oxidation products of FDG and Glc were separated and identified by mass spectrometry: 2-fluorogluconic acid, 2-fluoroglucuronic acid, 2-oxoerythronic acid, arabinose, arabonic acid, araburonic acid, erythrose, erythrulose, gluconic acid, and glucuronic acid. The most intensive electrospray ionisation signals were found in the negative ion spectra and were due to HCOO- adducts, the other acids being in their lactone forms.     

Influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine. A theoretical study

The influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine has been studied using density functional theory (DFT) methods. For the neutral system, two different pathways (with retention and inversion of configuration at the C1' anomeric carbon) have been found, both of them consisting of two steps and involving the formation of a dihydrofurane-like intermediate. The Gibbs free energy barrier for the first step is very high in both cases (53 and 46 kcal/mol for the process with inversion and with retention, respectively). However, the N7-protonated system shows a very different mechanism which consists of two steps. The first one leads to the formation of an oxacarbenium ion intermediate, with a Gibbs free energy barrier of 27 kcal/mol, and the second one corresponds to the nucleophilic attack of the water molecule to the oxacarbenium ion and takes place with a barrier of 1.3 kcal/mol. Thus, these results agree with a stepwise SN1 mechanism (DN*AN), with a discrete intermediate formed between the leaving group and the nucleophile approach, and show that N7 protonation strongly catalyzes the hydrolysis of the N-glycosidic bond, making the guanine a better leaving group. Finally, kinetic isotope effects have been calculated for the protonated system, and the results obtained are in very good agreement with experimental data for analogous systems.