Sialic acid biosynthesis: stereochemistry and mechanism of the reaction catalyzed by the mammalian UDP-N-acetylglucosamine 2-epimerase

The bifunctional enzyme, UDP-N-acetylglucosamine 2-epimerase/ManNAc kinase, catalyzes the first two steps in the biosynthesis of the sialic acids in mammals. The epimerase domain converts UDP-GlcNAc into ManNAc and UDP. This paper demonstrates that alpha-ManNAc is the first formed anomer and therefore the reaction proceeds with a net retention of configuration at C-1. Studies in deuterated buffer show that solvent-derived deuterium is quantitatively incorporated into the C-2 position of the product during catalysis, but it is not incorporated into the remaining pool of substrate. This indicates that the inversion of stereochemistry is ultimately brought about by the removal and replacement of a proton at C-2 and is consistent with a two-base mechanism. Studies with (18)O-labeled UDP-GlcNAc show that the anomeric oxygen of the glycosyl phosphate bond departs with the UDP product and therefore the net hydrolysis reaction involves C-O bond cleavage. Incubation of the putative intermediate, 2-acetamidoglucal, with the enzyme resulted in a slow hydration reaction to give the product, ManNAc. Additional kinetic isotope effect and positional isotope exchange (PIX) experiments address the nature of the rate-determining step of the reaction and show that C-H bond cleavage is not rate limiting. Overall, these results support a reaction mechanism involving an anti-elimination of UDP to give 2-acetamidoglucal, followed by a syn-addition of water.     

Kinetics and mechanism of bromate-bromide reaction catalyzed by acetate

The initial rate of the bromate-bromide reaction, BrO3- + 5Br- + 6H+ --> 3Br2 + 3H2O, has been measured at constant ionic strength, I = 3.0 mol L(-1), and at several initial concentrations of acetate, bromate, bromide, and perchloric acid. The reaction was followed at the Br2/Br3- isosbestic point (lambda = 446 nm) by the stopped-flow technique. A very complex behavior was found such that the results could be fitted only by a six term rate law, nu = k1[BrO3-][Br-][H+]2 + k2[BrO3-][Br-]2[H+]2 + k3[BrO3-][H+]2[acetate]2 + k4[BrO3-][Br-]2[H+]2[acetate] + k5[BrO3-][Br-][H+]3[acetate]2 + k6[BrO3-][Br-][H+]2[acetate], where k1 = 4.12 L3 mol(-3) s(-1), k2 = 0.810 L4 mol(-4) s(-1), k3 = 2.80 x 10(3) L4 mol(-4) s(-1), k4 = 278 L5 mol(-5) s(-1), k5 = 5.45 x 10(7) L6 mol(-6) s(-1), and k6 = 850 L4 mol(-4) s(-1). A mechanism, based on elementary steps, is proposed to explain each term of the rate law. This mechanism considers that when acetate binds to bromate it facilitates its second protonation.     

DFT investigation on the mechanism of the deacetylation reaction catalyzed by LpxC

LpxC is a key enzyme in the biochemical synthesis of Lipid A, an important outer cell-membrane component found in a number of pathogenic bacteria. Using DFT, we have investigated the binding of the substrate within its active site as well as the deacetylation mechanism it catalyzes. The substrate is found to preferentially coordinate to the active site Zn2+ via its carbonyl oxygen between a Zn2+-bound H2O and an adjacent threonine (Thr191). Furthermore, upon substrate binding a nearby Glu78 residue is found to readily deprotonate the remaining Zn2+-bound H2O. Unlike several related metallopeptidases, the mechanism of LpxC is found to proceed via four steps; (i) initial hydroxylation of the substrates' carbonyl carbon to give a gem-diolate intermediate, (ii) protonation of the amide nitrogen by the histidine His265-H+, (iii) a barrier-less change in the active site-intermediate hydrogen-bond network and finally, (iv) C-N bond cleavage. Notably, the rate-determining step of the mechanism of LpxC is found to be the initial hydroxylation while the final C-N bond cleavage occurs with an overall barrier of 23.6 kJ mol-1. Furthermore, LpxC uses a general acid/base pair mechanism as indicated by the fact that both His265-H+ and Glu78 are accordingly involved.     

On the mechanism of the Kharash reaction catalyzed by Fe(CO)5

Fe(CO)₅ is sufficiently stable at 80 °C in benzene solution and its thermal decomposition is not accelerated in the presence of phenyl cinnamate or/and DMF. The decomposition is accelerated by CCl₃Br (drastically) and by CCl₄ (to a lesser extent). DMF accelerates the reaction of Fe(CO)₅ with CCl₄. The (FeCl(DMF)₅]²⁺[Cl₃FeOFeCl₃]^2– complex has been isolated as a product; its composition and structure have been determined by X-ray analysis. The obtained data indicate the absence of coordination of DMF or/and an olefin with Fe⁰ species at the stage preceding oxidation. The mechanisms of the generation of CCl₃ radicals in thermal and photochemical Kharash reactions in the presence of Fe(CO)₅ are basically different. The probable pathways of the effect of DMF on the rate of the oxidative decomposition of Fe(CO)₅ are discussed.For Part 2, see Ref. 1.Translated from IzvestiyaAkademii Nauk. Seriya Khimicheskaya, No. 4, pp. 916–919, April, 1996.     

Theoretical study on the reaction mechanism of NO and CO catalyzed by Rh atom

The gas-phase reaction mechanism of NO and CO catalyzed by Rh atom has been systematically investigated on the ground and first excited states at CCSD(T)//B3LYP/6-311+G(2d), SDD level. This reaction is mainly divided into two reaction stages, NO deoxygenation to generate N₂O and then the deoxygenation of N₂O with CO to form N₂ and CO₂. The crucial reaction step deals with the NO deoxygenation to generate N₂O catalyzed by Rh atom, in which the self-deoxygenation of NO reaction pathway is kinetically more preferable than that in the presence of CO. The minimal energy reaction pathway includes the rate-determining step about N–N bond formation. Once the NO deoxygenation with CO catalyzed by rhodium atom takes place, the reaction results in the intermediate RhN. Then, the reaction of RhN with CO is kinetically more favorable than that with NO, while both of them are thermodynamically preferable. These results can qualitatively explain the experimental finding of N₂O, NCO, and CN species in the NO + CO reaction. For the N₂O deoxygenation with CO catalyzed by rhodium atom, the reaction goes facilely forward, which involves the rate-determining step concerning CO₂ formation. CO plays a dominating role in the RhO reduction to regenerate Rh atom. The complexes, OCRhNO, RhON₂, RhNNO, ORhN₂, RhCO₂, RhNCO, and ORhCN, are thermodynamically preferred. Rh atom possesses stronger capability for the N₂O deoxygenation than Rh⁺ cation.     

On the mechanism of stereoselection in direct Mannich reaction catalyzed by BINOL-derived phosphoric acids

Associates between the chiral phosphoric acids and Boc-protected imine were characterized computationally and by NMR; the primary importance of the bulky protecting group in imine for the high enantioselectivity in the direct Mannich reaction is rationalized via the analysis of the stereodiscriminating intermediates.     

An investigation into the mechanism of the imidazolidinone catalyzed cascade reaction

The cascade reaction of α,β-unsaturated butyric aldehydes with 2-methyl furan and chlorinated quinone catalyzed by a (2S,5S)-5-benzyl-2-tert-butyl-3-methylimidazolidin-4-one·TFA was investigated by using density functional theory (DFT) calculations at the PCM(EtOAc)/B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level to (a) confirm the detailed reaction mechanism and key factors controlling the enantioselectivity; and (b) check the models of the iminium ion formation and hydrolysis process that were carried out in another reaction. Two favorable reaction channels, corresponding to the enantioselectivity of the (2R,3S)-product and (2S,3S)-product, have been characterized. The enantioselectivity is controlled by the steps involved in the formation of the C–C bond and the C–Cl bond in the iminium catalysis and the enamine catalysis, respectively. The calculated results explain the reaction mechanism and the enantioselectivity, which are in agreement with experimental observations, and may be helpful for understanding the reaction mechanism of similar cascade reactions.     

Theoretical study on the mechanism of the reaction for alkene hydroaminations catalyzed by chiral aldehyde

Alkene hydroamination catalyzed by chiral aldehyde relying only on temporary intramolecularity is a new concept reaction. In this article, the reaction mechanism was investigated using density functional theory. The calculation results show that: (1) The reaction can be divided into two parts. The first part is a dehydration process involving a hemiaminal formation. The nitrone catalyst forms through rapid intermolecular nucleophilic addition of benzylhydroxylamine to chiral aldehyde precatalyst. The second part is a catalytic cycle, which involves an aminal formation—hydroamination—ring opening—product release process. (2) There are four enantioselective pathways related to the products of S and R configurations. Enantioselectivity is attributed to the different forming ways of a planar five‐membered ring. The preferred pathways for the S‐configuration product ( S3 ) and R‐configuration product ( R3 ) are confirmed. © 2013 Wiley Periodicals, Inc.     

The oxidative mannich reaction catalyzed by dirhodium caprolactamate

Dirhodium caprolactamate [Rh2(cap)4] is a highly effective catalyst for the oxidative Mannich reaction. The reaction proceeds via C-H oxidation of a tertiary amine followed by nucleophilic capture. This green transformation is conducted in protic solvent using inexpensive T-HYDRO (70% t-BuOOH in water). Synthetically valuable gamma-aminoalkyl butenolides are obtained.     

Kinetics and reaction mechanism of phenol hydroxylation catalyzed by La-Cu_4FeAlCO_3

Phenol hydroxylation is an industrially important reaction, whose main products are catechol and hy-droquinone being diverse applications which are im-portant intermediates for perfumes, drugs, and phar-maceuticals and so on[1]. The processes using H2O2 a…     

水催化HBrO与OH自由基反应的微观机理

采用密度泛函理论,分别在B3LYP/6-311++g(d,p)和B3LYP/aug-cc-PVTZ理论水平下,系统研究了无水和水催化的OH自由基与HBrO反应,即HBrO+OH和HBrO+OH+H_2O 2个反应的微观反应机理,给出了所有可能发生的反应路径,并指出能量最低的反应通道.对于没有水参与的反应,由于OH自由基进攻HBrO方式不同,存在顺式方向和反式方向2种进攻方式的反应路径;当有一分子水参与反应时,考虑HBrO H_2O复合物与OH自由基的反应和HBrO与H_2O OH复合物2种反应情况,共发现4条不同的反应路径.这2种反应的所有路径均是在OH自由基提取氢之前以氢键复合物形式存在,反应过程均为无势垒加合过程,总反应为放热反应.水对目标反应起催化作用,有效地降低了反应的势垒,可以加快OH自由基和HBrO的消耗速度.     

The reaction mechanism for dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica

The fundamental reaction mechanism for the dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica has been studied by density functional theory calculations. The results indicate that the dehydration process undergoes a two-step cis-elimination mechanism, which is different from the previously proposed one. The catalytic roles of both the highly conserved residue His143 and the Schiff base formed between the substrate and Lys170 have also been elucidated. The structural and mechanistic insight presented here may direct the design of type I dehydroquinate dehydratase enzyme inhibitors as non-toxic antimicrobials, anti-fungals, and herbicides.     

Thermochemistry of the reaction catalyzed by malate dehydrogenase

The heat of reason for the process

has been determined to be ?21.4±0.2 kcal mol^?1. The similar reactions catalyzed by lactate dehydrogenase (IUB No. 1.1.1.27) and alcohol dehydrogenase (IUB No. 1.1.1.1) are compared with reference to their Gibbs-Helmholtz thermodynamic parameters.     

Thermochemistry of the reaction catalyzed by lactate dehydrogenase

The thermochemistry of the reduction of pyruvate to lactate, in the presence of nicotinamide adenine dinucleotide (reduced form); catalyzed by the enzyme lactate dehydrogenase, has been studied. After approximately 120 experiments, a best value for the enthalpy of reaction has been determined to be ?14.80±0.30 kcal mol^?1. This reveals that the driving force for the reaction is almost completely enthalpic in nature. In addition, using the current methodology, it is possible to determine lactate dehydrogenase activity as low as 0.15 international units (325 Wroblewski units) per sample.     

A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II

The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II has been investigated using molecular mechanics and quantum mechanics methods.Molecular dynamics(MD) simulations were carried out using the TIP3 water model and generalized solvent boundary potential(GSBP) by CHARMM based on the X-ray crystal structure.Two models of the ternary elongation complex were constructed based on CHARMM MD calculations.All the species including reactants,transition states,intermediates,and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2.Three pathways were explored using the DFT method.The most favorable reaction pathway involves indirect proton migration from the RNA primer 3’-OH to the oxygen atom of-phosphate via a solvent water molecule,proton rotation from the oxygen atom of-phosphate to the-phosphate side,the RNA primer 3’-O nucleophilic attack on the-phosphorus atom,and P-O bond breakage.The corresponding reaction potential profile was obtained.The rate limiting step,with a barrier height of 21.5 kcal/mol,is the RNA primer 3’-O nucleophilic attack,rather than the commonly considered proton transfer process.A high-resolution crystal structure including crystallographic water molecules is required for further studies.     

Generation of chemical reaction mechanism. CO hydrogenation catalyzed by meaal atoms in the gas phase

An approach to determine the catalytic properties of metal atoms for the hydrogenation of CO in the gas phase is suggested. This approach has been developed using an algorithm based on a mathematical model for structural chemistry. Structural and energetic characteristics for intermediates and possible products of the catalytic hydrogenation of CO to C₁ and C₂ organic compounds and metals established as catalysts for the formation of various products are presented.

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A new mechanism of acyl group transfer in the reaction catalyzed by D-glyceraldehyde-3-phosphate dehydrogenase

D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12) catalyzes the oxidative phosphorylation of its substrate in a two-step reaction. Asa result of the first, oxidativestep, the covalent intermediate where in 3-phosphoglyceroyl moiety is bound to Cys149 of the active center is subjected to nucleophilic attack by inorganic phosphate, but remains resistant to hydrolytic decomposition. This ensures tight coupling of oxidation with phosphorylation in glycolysis. In this article, we present the experimental evidence for the conversion of GAPDH into a form capable of performing the reaction in the absence of inorganic phosphate. The structural basis for this conversion is the oxidation of a cysteine residue (probably Cys 153) into a sulfenic acid derivative under mild conditions to affect the integrity of the essential Cys 149. As a result, an intram olecular transfer of 3-phosphoglyceroyl group from the active center Cys 149 to Cys 153 becomes possible with subsequent hydrolysis of the sulfenyl carboxylate intermediate.     

Ca+催化的N2O+CO反应机理的理论研究

采用B3LYP/cc-pVTZ理论水平系统研究了Ca+离子催化N2O+CO→N2+CO2反应的微观机理.反应分两步进行:第一步Ca+夺取N2O中的O原子有两条反应通道,其中优势通道为Ca+金属离子与N2O分子中O作用,形成线性分子复合物,活化N2O分子中的N-O键,之后的反应路径为O-N键断裂机理;第二步为CaO+金属...     

The kinetics and mechanism of polymer-based NHC-Pd-pyridine catalyzed heterogeneous Suzuki reaction in aqueous media

One of the most important challenges of the Suzuki reaction is a green synthesis of reaction products. In terms of economy and ecology, the Suzuki reaction details must be characterized for the industrial-scale Suzuki reaction processes. In this paper, for the first time, a kinetic and mechanistic study on the Suzuki reaction catalyzed with hydrogel-supported PEPPSI (pyridine-enhanced precatalyst preparation stabilization (and) initiation) type NHC-Pd-pyridine composite has been investigated. To determine the rate-limiting step, the effects of reactants and experimental conditions on the heterogeneous Suzuki reaction have been experimentally defined. The experimental results demonstrated that it is possible to reach 100% yield under the optimum reaction conditions, which were found as 75 × 10⁻³ mol/L of phenylboronic acid (FBA), 50 × 10⁻³ mol/L of bromoacetophenone (Brac), 125 × 10⁻³ mol/L of K₂CO₃, 1 g/L of catalyst, 80°C of reaction temperature, 400 rpm of mixing rate, and 3 h of reaction time. The transmetalation step in the cycle was defined as the rate-limiting step. On the basis of kinetic results, a mathematical reaction rate expression was presented assuming the steady-state approach to steps of the catalytic cycle. The activation energy (E_a) of the reaction was estimated to be 34.88 kJ/mol.