scholarly journals Catalytic reaction profile for NADH-dependent reduction of aromatic aldehydes by xylose reductase from Candida tenuis

2002 ◽  
Vol 366 (3) ◽  
pp. 889-899 ◽  
Author(s):  
Peter MAYR ◽  
Bernd NIDETZKY
Keyword(s):  
Transition State ◽  
Catalytic Reaction ◽  
Dissociation Constants ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Xylose Reductase ◽  
Hydride Transfer ◽  
Aromatic Aldehydes ◽  
Relationship Analysis ◽  
Reaction Profile

Kinetic substituent effects have been used to examine the catalytic reaction profile of xylose reductase from the yeast Candida tenuis, a representative aldo/keto reductase of primary carbohydrate metabolism. Michaelis—Menten parameters (kcat and Km) for NADH-dependent enzymic aldehyde reductions have been determined using a homologous series of benzaldehyde derivatives in which substituents in meta and para positions were employed to systematically perturb the properties of the reactive carbonyl group. Kinetic isotope effects (KIEs) on kcat and kcat/Km for enzymic reactions with meta-substituted benzaldehydes have been obtained by using NADH 2H-labelled in the pro-R C4-H position, and equilibrium constants for the conversion of these aldehydes into the corresponding alcohols (Keq) have been measured in the presence of NAD(H) and enzyme. Aldehyde dissociation constants (Kd) and the hydride transfer rate constant (k7) have been calculated from steady-state rate and KIE data. Quantitative structure—activity relationship analysis was used to factor the observed substituent dependence of kcat/Km into a major electronic effect and a productive positional effect of the para substituent. kcat/Km (after correction for substituent position) and Keq obeyed log-linear correlations over the substituent parameter, Hammett sigma, giving identical slope values (ρ) of +1.4 to +1.7, whereas the same Hammett plot for logKd yielded ρ =-1.5. This leads to the conclusion that electron-withdrawing substituents facilitate the reaction and increase binding to about the same extent. KIE values for kcat (1.8) and kcat/Km (2.7), and likewise k7, showed no substituent dependence. Therefore, irrespective of the observed changes in reactivity over the substrate series studied no shift in the character of the rate-limiting transition state of hydride transfer occurred. The signs and magnitudes of ρ values suggest this transition state to be product-like in terms of charge development at the reactive carbon. Structure—reactivity correlations reveal active-site homologies among NADPH-specific and dual NADPH/NADH-specific yeast xylose reductases and across two aldo/keto reductase families in spite of the phylogenetic separation of the host organisms producing xylose reductase (family 2B) and aldehyde reductase (family 1A).

Isotope Effects on Chemical Equilibria. Part II. Some Further Secondary Isotope Effects of the Second Kind

1974 ◽  
Vol 52 (10) ◽  
pp. 1966-1972 ◽  
Author(s):  
Douglas James Barnes ◽  
Peter David Golding ◽  
John Marshall William Scott
Keyword(s):  
Isotope Effect ◽  
Dissociation Constants ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Chemical Equilibria

The ratio of the dissociation constants Ka(H)/Ka(D) has been measured conductimetrically for the isotopic pairs XCH2COOH/XCD2COOH where X = Cl, PhO, and PhS. Methods of calculating the ratio of the equilibrium constants are considered in some detail. Since the isotope effect varies with the nature of the X substituent it is concluded that the simple inductive description of these effects is not tenable.

The nature of the transition state in diarylmethyl cation – nucleophile combination reactions as probed by secondary α-deuterium isotope effects

2001 ◽  
Vol 79 (12) ◽  
pp. 1887-1897
Author(s):  
Thuy Van Pham ◽  
Robert A McClelland
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Rate Constant ◽  
Rate Constants ◽  
Flash Photolysis ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Bond Formation ◽  
Kinetic Isotope ◽  
Rate Limiting

Transition-state structures for the carbocation–nucleophile combination reactions of (4-substituted-4'- methoxydiphenyl)methyl cations with water, chloride, and bromide ions in acetonitrile–water mixtures have been investigated by measuring the secondary α-deuterium kinetic and equilibrium isotope effects. Rate constants in the combination direction were measured with laser flash photolysis. Equilibrium constants were measured for the water reaction by a comparison method in moderately concentrated sulfuric acid solutions, for the bromide reaction via the observation of reversible combination, and for the chloride reaction from the ratio of the combination rate constant and the rate constant for the ionization of the diarylmethyl chloride product. The fraction of bond making in the transition state has been calculated as the ratio log (kinetic isotope effect):log (equilibrium isotope effect). For the water reaction, there is 50–65% bond making in the transition state; this is also true for cations that are many orders of magnitude less reactive. The same conclusions, 50–65% bond formation in the transition state independent of reactivity, have previously been made in correlations of log kw vs. log KR. Thus, two quite different measures of transition structure provide the same result. The kH:kD values for the halide combinations in 100% acetonitrile are within experimental error of unity. This is consistent with suggestions that these reactions are occurring with diffusional encounter as the rate-limiting step. Addition of water has a dramatic retarding effect on the halide reactions, with rate constants decreasing steadily with increased water content. Small inverse kinetic isotope effects are observed (in 20% acetonitrile:80% water) indicating that carbon—halogen bond formation is rate-limiting. Comparison of the kinetic and equilibrium isotope effects shows ~25 and ~40% bond formation in the transition states for the reactions with bromide and chloride, respectively.Key words: carbocation, isotope effect, transition state, halide.

Berechnung kinetischer Isotopeneffekte für die Reaktion von Methyljodid mit Cyanid-Ion

1966 ◽  
Vol 21 (9) ◽  
pp. 1377-1384
Author(s):  
A. V. Willi
Keyword(s):  
Transition State ◽  
Secular Equation ◽  
Isotope Effects ◽  
Force Constants ◽  
Bond Breaking ◽  
Bending Force ◽  
A Value ◽  
Order Of Magnitude ◽  
Deuterium Isotope Effects ◽  
The Difference

Kinetic carbon-13 and deuterium isotope effects are calculated for the SN2 reaction of CH3I with CN-. The normal vibrational frequencies of CH3I, the transition state I · · · CH3 · · · CN, and the corresponding isotope substituted reactants and transition states are evaluated from the force constants by solving the secular equation on an IBM 7094 computer.Values for 7 force constants of the planar CH3 moiety in the transition state (with an sp2 C atom) are obtained by comparison with suitable stable molecules. The stretching force constants related to the bonds being broken or newly formed (fCC, fCC and the interaction between these two stretches, /12) are chosen in such a way that either a zero or imaginary value for νʟ≠ will result. Agreement between calculated and experimental methyl-C13 isotope effects (k12/ k13) can be obtained only in sample calculations with sufficiently large values of f12 which lead to imaginary νʟ≠ values. Furthermore, the difference between fCI and fCC must be small (in the order of 1 mdyn/Å). The bending force constants, fHCI and fHCC, exert relatively little influence on k12/k13. They are important for the D isotope effect, however. As soon as experimental data on kH/kD are available it will be possible to derive a value for fHCC in the transition state if fHCI is kept constant at 0.205 mdynA, and if fCI, fCC and f12 are held in a reasonable order of magnitude. There is no agreement between experimental and calculated cyanide-C13 isotope effects. Possible explanations are discussed. — Since fCI and fCC cannot differ much it must be concluded that the transition state is relatively “symmetric”, with approximately equal amounts of bond making and bond breaking.

scholarly journals The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase

2006 ◽  
Vol 361 (1472) ◽  
pp. 1307-1315 ◽  
Author(s):  
Lin Wang ◽  
Nina M Goodey ◽  
Stephen J Benkovic ◽  
Amnon Kohen
Keyword(s):  
Temperature Dependence ◽  
Dihydrofolate Reductase ◽  
Isotope Effects ◽  
Hydride Transfer ◽  
Activation Parameters ◽  
Physical Nature ◽  
Enzyme Dynamics ◽  
Temperature Dependences ◽  
Donor Acceptor ◽  
Significant Temperature

Residues M42 and G121 of Escherichia coli dihydrofolate reductase ( ec DHFR) are on opposite sides of the catalytic centre (15 and 19 Å away from it, respectively). Theoretical studies have suggested that these distal residues might be part of a dynamics network coupled to the reaction catalysed at the active site. The ec DHFR mutant G121V has been extensively studied and appeared to have a significant effect on rate, but only a mild effect on the nature of H-transfer. The present work examines the effect of M42W on the physical nature of the catalysed hydride transfer step. Intrinsic kinetic isotope effects (KIEs), their temperature dependence and activation parameters were studied. The findings presented here are in accordance with the environmentally coupled hydrogen tunnelling. In contrast to the wild-type (WT), fluctuations of the donor–acceptor distance were required, leading to a significant temperature dependence of KIEs and deflated intercepts. A comparison of M42W and G121V to the WT enzyme revealed that the reduced rates, the inflated primary KIEs and their temperature dependences resulted from an imperfect potential surface pre-arrangement relative to the WT enzyme. Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry.

The Importance of Anharmonicity of The Vibrational Excited States in Chemical Kinetics

1975 ◽  
Vol 53 (20) ◽  
pp. 3069-3074 ◽  
Author(s):  
Jan Bron
Keyword(s):  
Transition State ◽  
Excited States ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Vibrational States ◽  
Vibrational Anharmonicity ◽  
Kinetic Isotope ◽  
Large Correction ◽  
Lower Temperature ◽  
Lower Temperature Region

The corrections to rate constants for an harmonicity of vibrational excited states have been evaluated over the temperature range of 200–1100 K. The reaction O2 + X, where X is H or D, has been chosen as the model system. Only the influence of vibrational anharmonicity of the triatomic transition state has been determined. Two geometric shapes for the transition state, bent and isosceles configurations, have been investigated in detail by the bond order method.It is found that the correction can be large, depending upon the geometry and force field of the transition state and the temperature. The magnitude of the correction for anharmonicity of the vibrational excited states depends mainly, at a particular temperature, on the strength of the O—X bond in the transition state. In the case of a large correction, anharmonicity may lead to a nonlinear Arrhenius plot.Because of cancellation effects, the correction for anharmonicity of the excited vibrational states in kinetic isotope effects can be ignored in the lower temperature region. It has also been found that anharmonicity of the vibrational groundstate can explain unexpected large isotope effects.

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