Electrochemical oxygen reduction mechanism on FeN<Subscript>2</Subscript>-graphene

Metal-coordinated nitrogen-doped carbons are highly active in promoting electrochemical oxygen reduction reactions (ORR). The detailed kinetic and thermodynamic ORR behavior on three different FeN₂-graphene [FeN₂–G (A), (B) and (C)] structures was investigated in this work. The results show that formation of these FeN₂–G configurations is energetically favorable; however, not all of them are effective for ORR. The higher HOMO energy and smaller HOMO–LUMO gap of FeN₂–G (A) and (C) make them have strong adsorption strengths to ORR intermediates, which leads to occupation the active sites on the catalysts during ORR, and thus loss of catalytic activity. Examination of the results of ?G of each reduction step also drew the same conclusion. The ?G of the elementary steps of the ORR at zero electrode potential vs. standard hydrogen electrode are downhill only on FeN₂–G (B). Throughout the entire four-electron ORR, the reduction of O to OH displays the highest reaction barrier. When the potential is >0.19 V, the reduction of OH species into water is uphill. Therefore, ORR activity is limited by two rate-determining steps on FeN₂–G (B) at high potential: O and OH reduction steps.     

Stoichiometry of microsomal oxidation reactions. Distribution of redox-equivalents in monooxygenase and oxidase reactions catalyzed by cytochrome P-450

The stoichiometry of NADPH oxidation in rabbit liver microsomes was studied. It was shown that in uncoupled reactions cytochrome P-450, besides O2- generation catalyzes direct two- and four-electron reduction of O2 to produce H2O2 and water, respectively. With an increase in pH and ionic strength, the amount of O2 reduced via an one-electron route increases at the expense of the two-electron reaction. In parallel, with a rise in pH the steady-state concentration of the oxy-complex of cytochrome P-450 increases, while the synergism of NADPH and NADH action in the H2O2 formation reaction is replaced by competition. The four-electron reduction is markedly accelerated and becomes the main pathway of O2 reduction in the presence of a pseudo-substrate--perfluorohexane. Treatment of rabbit with phenobarbital, which induces the cytochrome P-450 isozyme specific to benzphetamine results in a 2-fold increase in the degree of coupling of NADPH and benzphetamine oxidation. The experimental results suggest that the ratio of reactions of one- and two-electron reduction of O2 is controlled by the ratio of rates of one- and two-electron reduction of cytochrome P-450. In the presence of pseudo-substrates cytochrome P-450 acts predominantly as a four-electron oxidase; one of possible reasons for the uncoupling of microsomal monooxygenase reactions is the multiplicity of cytochrome P-450 isozymes.     

Triptan partition in model membranes

The development of fuel cells as clean-energy technologies is largely limited by the prohibitive cost of the noble-metal catalysts needed for catalyzing the oxygen reduction reaction (ORR) in fuel cells. A fundamental understanding of catalyst design principle that links material structures to the catalytic activity can accelerate the search for highly active and abundant bimetallic catalysts to replace platinum. Here, we present a first-principles study of ORR on Ag₁₂Cu cluster in alkaline environment. The adsorptions of O₂, OOH, and OH on Cu-doped Ag₁₃ are stronger than on Ag₁₃. The d-band centers of adsorption sites show the Cu-doping makes d-electrons transferred to higher energy state, and improves O₂ dissociation. ORR processes on Ag₁₂Cu and Ag₁₃ indicate Cu-doping can strongly promote ORR, and ORR process can be better preformed on Ag₁₂Cu than on Ag₁₃. For four-electron transfer, the effective reversible potential is 0.401 V/RHE on Ag₁₂Cu in alkaline medium.     

A density functional theory study of the decomposition mechanism of nitroglycerin

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO₂ (a product obtained following the abstraction of three H atoms from NG by NO₂) include O–NO₂ cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO₂ concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O–NO₂ cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO₂ concentration. However, when a threshold NO₂ concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.     

QM/MM investigation on the catalytic mechanism of Bacteroides thetaiotaomicron α-glucosidase BtGH97a

Bacteroides thetaiotaomicron α-glucosidase BtGH97a is an inverting enzyme. In this paper, the hydrolysis mechanism of p-nitro-phenyl α-d-glucopyranoside (pNP-Glc) catalyzed by BtGH97a was firstly studied by using quantum mechanical/molecular mechanical (QM/MM) approach. Two possible reaction pathways were considered. In the first pathway, a water molecule deprotonated by a nucleophilic base (here E439 or E508) attacks firstly on the anomeric carbon of pNP-Glc, then a proton from an acid residue (E532) attacks on the glycosidic oxygen to finish the hydrolysis reaction (named as nucleophilic attack-first pathway). In the second pathway, the proton from E532 attacks firstly on the glycosidic oxygen, then the water deprotonated by the nucleophilic base attacks on the anomeric carbon of pNP-Glc (named as proton attack-first pathway). Our calculation results indicate that the nucleophilic attack-first pathway is favorable in energy, in which the nucleophilic attack process is the rate-determining step with an energy barrier of 15.4 kcal/mol in the case of residue E508 as nucleophilic base. In this rate-determining step, the deprotonation of water and the attack on the anomeric carbon are concerted. In the proton attack-first pathway, the proton attack on the glycosidic oxygen is the rate-determining step, and the energy barrier is 24.1 kcal/mol. We conclude that the hydrolysis mechanism would follow nucleophilic attack-first pathway.     

The reduction of trimethylarsine oxide to trimethylarsine by thiols: a mechanistic model for the biological reduction of arsenicals

Trimethylarsine oxide is reduced to trimethylarsine in aqueous solution by a variety of thiols and dithiols including cysteine, glutathione, and lipoic acid. Kinetic results and other observations suggest that the rate-determining step is the production of [Me₃AsSR]⁺ from an initially formed Me₃As(SR)OH species, and that the reduction occurs via a two-electron transfer from Me₃As(SR)₂ affording Me₃As and RS-SR. A simple model for the biological methylation of arsenic is proposed based on oxidative methylation of arsenic(III) by S-adenosylmethionine and reduction by a thiol such as lipoic acid.     

QM/MM investigation on the catalytic mechanism of Bacteroides thetaiotaomicron α-glucosidase BtGH97a

Bacteroides thetaiotaomicron α-glucosidase BtGH97a is an inverting enzyme. In this paper, the hydrolysis mechanism of p-nitro-phenyl α-d-glucopyranoside (pNP-Glc) catalyzed by BtGH97a was firstly studied by using quantum mechanical/molecular mechanical (QM/MM) approach. Two possible reaction pathways were considered. In the first pathway, a water molecule deprotonated by a nucleophilic base (here E439 or E508) attacks firstly on the anomeric carbon of pNP-Glc, then a proton from an acid residue (E532) attacks on the glycosidic oxygen to finish the hydrolysis reaction (named as nucleophilic attack-first pathway). In the second pathway, the proton from E532 attacks firstly on the glycosidic oxygen, then the water deprotonated by the nucleophilic base attacks on the anomeric carbon of pNP-Glc (named as proton attack-first pathway). Our calculation results indicate that the nucleophilic attack-first pathway is favorable in energy, in which the nucleophilic attack process is the rate-determining step with an energy barrier of 15.4kcal/mol in the case of residue E508 as nucleophilic base. In this rate-determining step, the deprotonation of water and the attack on the anomeric carbon are concerted. In the proton attack-first pathway, the proton attack on the glycosidic oxygen is the rate-determining step, and the energy barrier is 24.1kcal/mol. We conclude that the hydrolysis mechanism would follow nucleophilic attack-first pathway.     

Gadolinium‐Induced Valence Structure Engineering for Enhanced Oxygen Electrocatalysis

Rare earth doped materials with unique electronic ground state configurations are considered emerging alternatives to conventional Pt/C for the oxygen reduction reaction (ORR). Herein, gadolinium (Gd)‐induced valence structure engineering is, for the first, time investigated for enhanced oxygen electrocatalysis. The Gd₂O₃–Co heterostructure loaded on N‐doped graphene (Gd₂O₃–Co/NG) is constructed as the target catalyst via a facile sol–gel assisted strategy. This synthetic strategy allows Gd₂O₃–Co nanoparticles to distribute uniformly on an N‐graphene surface and form intimate Gd₂O₃/Co interface sites. Upon the introduction of Gd₂O₃, the ORR activity of Gd₂O₃–Co/NG is significantly increased compared with Co/NG, where the half‐wave potential (E_1/2) of Gd₂O₃–Co/NG is 100 mV more positive than that of Co/NG and even close to commercial Pt/C. The density functional theory calculation and spectroscopic analysis demonstrate that, owing to intrinsic charge redistribution at the engineered interface of Gd₂O₃/Co, the coupled Gd₂O₃–Co can break the OOH*–OH* scaling relation and result in a good balance of OOH* and OH* binding on Gd₂O₃–Co surface. For practical application, a rechargeable Zn–air battery employing Gd₂O₃–Co/NG as an air–cathode achieves a large power density and excellent charge–discharge cycle stability.     

Mechanistic studies of cyclohexanone monooxygenase: chemical properties of intermediates involved in catalysis

Cyclohexanone monooxygenase (CHMO), a bacterial flavoenzyme, carries out an oxygen insertion reaction on cyclohexanone to form a seven-membered cyclic product, epsilon-caprolactone. The reaction catalyzed involves the four-electron reduction of O2 at the expense of a two-electron oxidation of NADPH and a two-electron oxidation of cyclohexanone to form epsilon-caprolactone. Previous studies suggested the participation of either a flavin C4a-hydroperoxide or a flavin C4a-peroxide intermediate during the enzymatic catalysis [Ryerson, C. C., Ballou, D. P., and Walsh, C. (1982) Biochemistry 21, 2644-2655]. However, there was no kinetic or spectral evidence to distinguish between these two possibilities. In the present work we used double-mixing stopped-flow techniques to show that the C4a-flavin-oxygen adduct, which is formed rapidly from the reaction of oxygen with reduced enzyme in the presence of NADP, can exist in two states. When the reaction is carried out at pH 7.2, the first intermediate is a flavin C4a-peroxide with maximum absorbance at 366 nm; this intermediate becomes protonated at about 3 s(-1) to form what is believed to be the flavin C4a-hydroperoxide with maximum absorbance at 383 nm. These two intermediates can be interconverted by altering the pH, with a pK(a) of 8.4. Thus, at pH 9.0 the flavin C4a-peroxide persists mainly in the deprotonated form. Further kinetic studies also demonstrated that only the flavin C4a-peroxide intermediate could oxygenate the substrate, cyclohexanone. The requirement in catalysis of the deprotonated flavin C4a-peroxide, a nucleophile, is consistent with a Baeyer-Villiger rearrangement mechanism for the enzymatic oxygenation of cyclohexanone. In the course of these studies, the Kd for cyclohexanone to the C4a-peroxyflavin form of CHMO was determined to be approximately 1 microM. The rate-determining step in catalysis was shown to be the release of NADP from the oxidized enzyme.     

Thermodynamic considerations on the generation of hydroxyl radicals from nitrous oxide--no laughing matter.

The one-electron reduction of nitrous oxide is a possible pathway to the hydroxyl radical. The one- and two-electron reduction potentials EO' (N2O/OH,N2) and EO' (N2O/H2O, N2) are calculated to be 0.32 V and 1.32 V at pH 7, respectively, for all species dissolved in water. Although nitrous oxide is thermodynamically capable of oxidising a variety of biomolecules, it is kinetically rather inert. The reason that nitrous oxide does not produce hydroxyl radicals readily might be that the one-electron reduction proceeds through an N2O- intermediate which is energetically very unfavourable: EO (N2O/N2O-) = -1.1 V.     

Theoretical study of the reduction of nitric oxide in an A-type flavoprotein

The mechanism for the reduction of nitric oxide to nitrous oxide and water in an A-type flavoprotein (FprA) in Moorella thermoacetica, which has been proposed to be a scavenging type of nitric oxide reductase, has been investigated using density functional theory (B3LYP). A dinitrosyl complex, [{FeNO}⁷]₂, has previously been proposed to be a key intermediate in the NO reduction catalyzed by FprA. The electrons and protons involved in the reduction were suggested to “super-reduce” the dinitrosyl intermediate to [{FeNO}⁸]₂ or the corresponding diprotonated form, [{FeNO(H)}⁸]₂. In this type of mechanism the electron and/or proton transfers will be a part of the rate-determining step. In the present study, on the other hand, a reaction mechanism is suggested in which N₂O can be formed before the protons and electrons enter the catalytic cycle. One of the irons in the diiron center is used to stabilize the formation of a hyponitrite dianion, instead of binding a second NO. Cleaving the N–O bond in the hyponitrite dianion intermediate is the rate-determining step in the proposed reaction mechanism. The barrier of 16.5 kcal mol⁻¹ is in good agreement with the barrier height of the experimental rate-determining step of 14.8 kcal mol⁻¹. The energetics of some intermediates in the “super-reduction” mechanism and the mechanism proceeding via a hyponitrite dianion are compared, favoring the latter. It is also discussed how to experimentally discriminate between the two mechanisms. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Catalytic activity of iron phthalocyanine for the oxidation of thiocyanate and L-cysteine anchored on Au(111) clusters

ABSTRACT

We studied the oxidation reactions of thiocyanate and L-cysteine on iron phthalocyanine (FePc) coupled via a bridging ligand of the 4-mercatopyridine (4MP) type to a gold cluster (Au₂₆), aiming to simulate a modified gold electrode. Theoretical models have been used based on the framework of density functional theory. Several mechanistic pathways are explored for the study of these reactions, finding that the most favorable mechanism involves an electron transfer process as the rate-determining step. Along the process, the ability of the gold cluster to act as an electron acceptor facilitating the reactions was detected. In addition, the proposed models presented a correlation between the energy obtained for the rate-determining step of the reaction and the experimental oxidation potentials of the thiocyanate and L-cysteine.     

Decomposition of water by cerium oxide of δ-phase

Reduced cerium dioxide (CeO_2?x) can reduce water, producing hydrogen at ?298 K. Kinetic studies were focused on the stoichiometric reaction of δ-phase cerium oxide (CeO_1.818) with water vapor. Different activation energies of 18.1 and 33.4 kJ mol^?1 were observed for the reactions at the temperature ranges above and below ca. 453 K, respectively. Rate equations observed in the two temperature ranges were also different. These results strongly suggest that the rate-determining steps are different between the two temperature ranges. Rapid oxygen exchange observed between H₂¹⁸O and lattice oxygen in cerium oxide of δ- phase at ? 298 K indicated that neither the adsorption of water molecules not the diffusion of oxygen ions in the bulk of the oxide can be the rate-determining step. H₂D₂ exchange occurred rapidly at 373 K compared to the rate of water decomposition, suggesting that the recombination of hydrogen atoms on the surface is not rate- determining either. A tentative reaction mechanism was proposed to explain the results of the kinetic studies. The rate-determining step at high temperatures (>453 K) is the reduction of OH^? by the six-coordinated Ce³⁺ which is present in the nonstoichiometric cerium oxide, while that at low temperatures (<453 K) is the subsequent reduction of H⁺ by the seven-coordinated Ce³⁺.     

A DFT study on the mechanism of the organocatalytic synthesis of a benzoxazine-substituted indolizine derivative

A series of theoretical computations were conducted via density functional theory at the B3LYP/6–31 + G(d,p) level to study the mechanism of the organocatalytic synthesis of a benzoxazine-substituted indolizine derivative. Four possible alternative pathways were considered in this work. The calculated results show that the formation of an N-ylide precursor from 4-dimethylaminopyridine (DMAP) is a key step as it provides the necessary nucleophilic centre for the subsequent H-migration and H-elimination processes. The precursor N-ylide and Schiff base isomers with the most favourable activities in the preliminary work were identified theoretically by analysing the reaction mechanism. The synthetic mechanism to obtain the indolizine derivative was found to be a two-step reaction, with the rate-determining step being the first H migration to form a transition state with a four-membered ring. The catalytic activity of DMAP in the first H-migration step in the overall synthetic process greatly reduces the reaction barrier height. The chiral selectivity of the synthesis is dominated by the spatial geometry of the Schiff base functional group.     

The secondary coordination sphere and axial ligand effects on oxygen reduction reaction by iron porphyrins: a DFT computational study

Oxygen reduction reaction (ORR) catalyzed by a bio-inspired iron porphyrin bearing a hanging carboxylic acid group over the porphyrin ring, and a tethered axial imidazole ligand was studied by DFT calculations. BP86 free energy calculations of the redox potentials and pK _a’s of reaction components involved in the proton coupled electron transfer (PCET) reactions of the ferric-hydroxo and -superoxo complexes were performed based on Born–Haber thermodynamic cycle in conjunction with a continuum solvation model. The comparison was made with iron porphyrins that lack either in the hanging acid group or axial ligand, suggesting that H-bond interaction between the carboxylic acid and iron-bound hydroxo, aquo, superoxo, and peroxo ligands (de)stabilizes the Fe–O bonding, resulting in the increase in the reduction potential of the ferric complexes. The axial ligand interaction with the imidazole raises the affinity of the iron-bound superoxo and peroxo ligands for proton. In addition, a low-spin end-on ferric-hydroperoxo intermediate, a key precursor for O–O cleavage, can be stabilized in the presence of axial ligation. Thus, selective and efficient ORR of iron porphyrin can be achieved with the aid of the secondary coordination sphere and axial ligand interactions.     

Iron phthalocyanine supported on amino-functionalized multi-walled carbon nanotube as an alternative cathodic oxygen catalyst in microbial fuel cells

Amino-functionalized multi-walled carbon nanotube (a-MWCNT)-supported iron phthalocyanine (FePc) (a-MWCNT/FePc) has been investigated as a catalyst for the oxygen reduction reaction (ORR) in an air-cathode single-chambered microbial fuel cell (MFC). Cyclic and linear sweep voltammogram are employed to investigate the electrocatalytic activity of the a-MWCNT/FePc for ORR. The maximum power density of 601 mW m⁻² is achieved from a MFC with the a-MWCNT/FePc cathode, which is the highest energy output compared to those MFCs with other materials supported FePc, such as carbon black, pristine MWCNT (p-MWCNT), carboxylic acid functionalized MWCNT (c-MWCNT), and even with a Pt/C cathode. Furthermore, cyclic voltammetry performed on the a-MWCNT/FePc electrode suggests that the a-MWCNT/FePc has an electrochemical activity for ORR via a four-electron pathway in a neutral pH solution. This work provides a potential alternative to Pt in MFCs for sustainable energy generation.     

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release

A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H₂O molecule is easily adsorbed onto the Al₁₃ surface, forming adlayers. The dissociation of the first H₂O molecule from the bimolecular H₂O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O–H bond breaking. The elimination of H₂ in the reaction of an H₂O molecule with a hydrogen atom on the Al cluster via the Eley–Rideal mechanism has a lower activation barrier than the elimination of H₂ in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H₂O, the structure of Al₁₃ is distorted to varying degrees.

Quantitative structure-activity relationships in two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H:nitroreductase

Enterobacter cloacae NAD(P)H:nitroreductase (NR; EC 1.6.99.7) catalyzes the reduction of a series of nitroaromatic compounds with steady-state bimolecular rate constants (kcat/Km) ranging from 10(4) to 10(7) M(-1) s(-1). In agreement with a previously proposed scheme of two-step four-electron reduction of nitroaromatics by NR (Koder, R. L., and Miller, A.-F. (1998) Biochim. Biophys. Acta 1387, 395-405), 2 mol NADH per mole mononitrocompound were oxidized. An oxidation of excess NADH by polinitrobenzenes, including explosives 2,4,6-trinitrotoluene (TNT) and 2,4,6-trinitrophenyl-N-methylnitramine (tetryl), has been observed as a slower secondary process, accompanied by O2 consumption. This type of "redox cycling" was not related to reactions of nitroaromatic anion-radicals, but was caused by the autoxidation of relatively stable reaction products. The initial reduction of tetryl and other polinitrophenyl-N-nitramines by E. cloacae NR was analogous to a two-step four-electron reduction mechanism of TNT and other nitroaromatics. The logs kcat/Km of all the compounds examined exhibited parabolic dependence on their enthalpies of single-electron or two-electron (hydride) reduction, obtained by quantum mechanical calculations. This type of quantitative structure-activity relationship shows that the reactivity of nitroaromatics towards E. cloacae nitroreductase depends mainly on their hydride accepting properties, but not on their particular structure, and does not exclude the possibility of multistep hydride transfer.     

The fully oxidized form of the cytochrome bd quinol oxidase from E. coli does not participate in the catalytic cycle: direct evidence from rapid kinetics studies

Cytochrome bd catalyzes the two-electron oxidation of either ubiquinol or menaquinol and the four-electron reduction of O(2) to H(2)O. In the current work, the rates of reduction of the fully oxidized and oxoferryl forms of the enzyme by the 2-electron donor ubiquinol-1 and single electron donor N,N,N',N'-tetramethyl-p-phenylendiamine (TMPD) have been examined by stopped-flow techniques. Reduction of the all-ferric form of the enzyme is 1000-fold slower than required for a step in the catalytic cycle, whereas the observed rates of reduction of the oxoferryl and singly-reduced forms of the cytochrome are consistent with the catalytic turnover. The data support models of the catalytic cycle which do not include the fully oxidized form of the enzyme as an intermediate.     

Theoretical discussion on the mechanism of binding CO2 by DBU and alcohol

Quantum chemical studies on the reaction of binding CO₂ by amidine base diazabicyclo [5.4.0]-undec-7-ene (DBU) and alcohol were carried out at the B3LYP/6-31g(d) level in order to find the reaction mechanism. The structures of reactants and product were optimised, and thermodynamic analyses were also carried out using the single point energy calculation and frequency analyses. It is noted that the reaction of binding CO₂ by DBU and propanol is thermodynamically feasible and qualitatively in accordance with the experimental observations. The results of thermodynamic and kinetic analyses demonstrate that the possible reaction mechanisms can be a two-step bimolecular reaction and a one-step trimolecular reaction. In the two-step bimolecular mechanism, the first step is the formation of intermediate by DBU and CO₂, and the second step is the nucleophilic attack of propanol on the intermediate. In the one-step trimolecular mechanism, O and H atoms of hydroxyl in propanol form an O–C bond with CO₂ and an H–N bond with DBU, respectively. The one-step trimolecular reaction seems a more reasonable mechanism because of the consideration of kinetic parameters.