Direct Hydride Transfer Mechanism Research Articles

Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction.

p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallography, were exploited to reach these conclusions and provide additional insights.

Hydrogenation of CO2 to Methanol Catalyzed by Cp*Co Complexes: Mechanistic Insights and Ligand Design.

A direct hydride transfer mechanism with three cascade cycles for the conversion of carbon dioxide and dihydrogen to methanol (CO2 + 3H2 → CH3OH + H2O) catalyzed by a half-sandwich cobalt complex [Cp*Co(bpy-Me)OH2]2+ (1) is proposed based on density functional theory calculations. The formation of methanediol via hydride transfer from Co to formic acid (4 → TS8,11) is the rate-determining step with a total barrier of 26.0 kcal/mol in free energy. Furthermore, 15 analogues of 1 are constructed by replacing the hydrogen atoms at the two meta and para positions of the bipyridine ligand with different functional groups (1b-1l), the carbon atoms in the bipyridine ligand with nitrogen atoms (1m-1o), and one pyridine ligand with N-heterocyclic carbene (1p). Among all newly proposed complexes, [Cp*Co(2,2'-bipyrazine)OH2]2+ (1n) is the most active one with a total barrier of 19.6 kcal/mol in free energy. Such a low barrier indicates 1n is a promising catalyst for efficient conversion of CO2 and H2 to methanol at room temperature.

A Computational Study on the Hydride Transfer Mechanism between Nicotinamide and Menadione

AbstractMenadione (MD) or vitamin K3 is a component of multivitamin drugs, which exhibits a wide range of pharmacological effects relevant to human health. Nicotinamide adenine dinucleotide (NAD) catalyzes the oxidation process of MD through hydride transfer from nicotinamide (NA) to MD. In the present study, the hydride transfer mechanism between NA and MD was investigated using the quantum mechanical calculations at the M06‐2X/6‐31G (d,p) level of theory in the gas‐phase and solution media. Two mechanisms were proposed to clarify the cyclic redox of MD via NA: one includes direct hydride transfer (DHT) in one step and other includes single electron and proton transfer (SET‐PT) in two steps through an intermediate. Although the energy barrier is almost equal on two pathways, the results of natural bond orbital (NBO), and the molecular electrostatic potential (MEP) are clearly in agreement with the SET‐PT mechanism, which is preferred to the DHT mechanism for hydride transfer from NA to MD. The cation and anion radicals of NA and MD facilitate the proton transfer from NA to MD in the SET‐PT pathway. In addition, the binding energy between NA and MD and the energy barrier of proton transfer increase by the electron‐withdrawing substituents (EWSs) and decrease by electron‐donating substituents (EDSs) located at the C3 position of NA. A higher binding energy makes the intermediate more stable, which is accompanied with the increase in the energy barrier of proton transfer step.

Frontispiece: Unexpected Direct Hydride Transfer Mechanism for the Hydrogenation of Ethyl Acetate to Ethanol Catalyzed by SNS Pincer Ruthenium Complexes

Frontispiece: Unexpected Direct Hydride Transfer Mechanism for the Hydrogenation of Ethyl Acetate to Ethanol Catalyzed by SNS Pincer Ruthenium Complexes

Unexpected Direct Hydride Transfer Mechanism for the Hydrogenation of Ethyl Acetate to Ethanol Catalyzed by SNS Pincer Ruthenium Complexes.

The hydrogenation of ethyl acetate to ethanol catalyzed by SNS pincer ruthenium complexes was computationally investigated by using DFT. Different from a previously proposed mechanism with fac-[(SNS)Ru(PPh3 )(H)2 ] (5') as the catalyst, an unexpected direct hydride transfer mechanism with a mer-SNS ruthenium complex as the catalyst, and two cascade catalytic cycles for hydrogenations of ethyl acetate to aldehyde and aldehyde to ethanol, is proposed base on our calculations. The new mechanism features ethanol-assisted proton transfer for H2 cleavage, direct hydride transfer from ruthenium to the carbonyl carbon, and C-OEt bond cleavage. Calculation results indicate that the rate-determining step in the whole catalytic reaction is the transfer of a hydride from ruthenium to the carbonyl carbon of ethyl acetate, with a total free energy barrier of only 26.9 kcal mol-1 , which is consistent with experimental observations and significantly lower than the relative free energy of an intermediate in a previously postulated mechanism with 5' as the catalyst.

Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations

Monoamine oxidases are two isozymic flavoenzymes which are the important targets for drugs used in the treatment of depression, Parkinson and Alzheimer's diseases. The catalytic reaction taking place between the cofactor FAD and amine substrate is still not completely understood. Herein we employed quantum chemical methods on the recently proposed direct hydride transfer mechanism including full active site residues of MAO isoforms in the calculations. Activation free energy barriers of direct hydride transfer mechanism for MAO-A and MAO-B were calculated by ONIOM (our own n-layered integrated molecular orbital + molecular mechanics) method with QM/QM (quantum mechanics:quantum mechanics) approach employing several density functional theory functionals, B3LYP, WB97XD, CAM-B3LYP and M06-2X, for the high layer. The formation of very recently proposed αC-flavin N5 adduct inside the enzyme has been investigated. ONIOM (M06-2X/6-31+G(d,p):PM6) results revealed that such an adduct may form only in MAO-B suggesting slightly different hydride transfer mechanisms for MAO-A and MAO-B.

Catalytic Mechanism Investigation of Lysine-Specific Demethylase 1 (LSD1): A Computational Study

Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes.

Use of pH and Kinetic Isotope Effects To Establish Chemistry as Rate-Limiting in Oxidation of a Peptide Substrate by LSD1

The mechanism of oxidation of a peptide substrate by the flavoprotein lysine-specific demethylase (LSD1) has been examined using the effects of pH and isotopic substitution on steady-state and rapid-reaction kinetic parameters. The substrate contained the 21 N-terminal residues of histone H3, with a dimethylated lysyl residue at position 4. At pH 7.5, the rate constant for flavin reduction, k(red), equals k(cat), establishing the reductive half-reaction as rate-limiting at physiological pH. Deuteration of the lysyl methyls results in identical kinetic isotope effects of 3.1 +/- 0.2 on the k(red), k(cat), and k(cat)/K(m) values for the peptide, establishing C-H bond cleavage as rate-limiting with this substrate. No intermediates between oxidized and reduced flavin can be detected by stopped-flow spectroscopy, consistent with the expectation for a direct hydride transfer mechanism. The k(cat)/K(m) value for the peptide is bell-shaped, consistent with a requirement that the nitrogen at the site of oxidation be uncharged and that at least one of the other lysyl residues be charged for catalysis. The (D)(k(cat)/K(m)) value for the peptide is pH-independent, suggesting that the observed value is the intrinsic deuterium kinetic isotope effect for oxidation of this substrate.

Insights into the Mechanism of Flavoprotein-Catalyzed Amine Oxidation from Nitrogen Isotope Effects on the Reaction of N-Methyltryptophan Oxidase

The mechanism of N-methyltryptophan oxidase, a flavin-dependent amine oxidase from Escherichia coli, was studied using a combination of kinetic isotope effects and theoretical calculations. The 15(kcat/Km) kinetic isotope effect for sarcosine oxidation is pH-dependent with a limiting value of 0.994-0.995 at high pH. Density functional theory calculations on model systems were used to interpret these isotope effects. The isotope effects are inconsistent with proposed mechanisms involving covalent amine-flavin adducts but cannot by themselves conclusively distinguish between some discrete electron-transfer mechanisms and a direct hydride-transfer mechanism, although the latter mechanism is more consistent with the energetics of the reaction.

Mechanism of photoreduction of diethyl benzylidene malonates by NAD(P)H model and comparison with thermal reaction

Photoreduction of diethyl benzylidene malonates by NAD(P)H model has been investigated. The reduction of the carbon–carbon double bond occurs and is enhanced by electron-withdrawing groups on the benzene ring. Deuteriation experiments in [2H4]methanol showed that the deuterium which originated from the solvent was mainly incorporated at the β-carbon. The mechanism of photoreduction is discussed in terms of sequential electron-hydrogen atom transfer from NAD(P)H model to the substrate in the solvent cage. On the other hand, thermal reduction of NAD(P)H model with the substrates in methan-[2H]-ol and/or [2H4]methanol gave the reduced products with deuterium incorporated at the α-carbon. Reduction of diethyl benzylidene malonates with [4,4-2H2]-1-benzyl-1,4-dihydronicotinamide (BNAH) led to the direct transfer of deuterium from C-4 to the β-carbon. These results have been interpreted as support for the direct hydride transfer mechanism.

ChemInform Abstract: Solvent and Micellar Effects upon the Reaction of NADH Models with Methylene Blue.

AbstractThe oxidation of the NADH model compounds (I) and (II) by methylene blue to give the corresponding pyridinium or quinolinium compounds proceeds via a direct hydride transfer mechanism.

Solvent and micellar effects upon the reaction of NADH models with methylene blue

AbstractThe oxidation of the NADH‐model compounds 1‐R‐1,4‐dihydronicotinamide (R = benzyl, octyl or cetyl) and 1‐benzyl‐1,4‐dihydroquinoline‐3‐carboxamide by methylene blue proceeds via a direct hydride transfer mechanism. In the transition state of this reaction, a considerable fraction of positive charge is developed in the dihydronicotinamide ring. Effects of solvents and effects of NaLS micelles upon the reaction have been investigated. In organic solvents, the oxidation proceeds ca. 1.5–50 times more slowly than in water. Interestingly, the reaction rate in organic solvents increases with decreasing polarity of the solvents. In aqueous NaLS solution, the oxidation of the NADH models proceeds 9‐80 times more rapidly than in water. The kinetic data in micellar solution are analyzed in terms of the pseudophase model, taking into account partitioning of the reactants between micellar and aqueous pseudophase. It appears that the observed rate enhancements in micellar solution are completely due to an increase of the reactant concentrations in the micellar pseudophase. The second‐order rate constants for oxidation in the micellar pseudophase are 35‐150 times smaller than those in the aqueous phase. It is suggested that both a decrease of the micropolarity and a unfavourable orientation of the reactants contribute to the low values of the second‐order rate constants in the micellar pseudophase.