Semiempirical calculations of the oxygen equilibrium isotope effect on binding of oxamate to lactate dehydrogenase

A new scheme to calculate isotope effects

We present a new scheme to calculate isotope effects. Only selected frequencies at the target level of theory are calculated. The frequencies are selected by an analysis of the Hessian from a lower level of theory. We obtain accurate isotope effects without calculating the full Hessian at the target level of theory. The calculated frequencies are very accurate. The scheme converges to the correct isotope effect.

Path integral evaluation of equilibrium isotope effects

A general and rigorous methodology to compute the quantum equilibrium isotope effect is described. Unlike standard approaches, ours does not assume separability of rotational and vibrational motions and does not make the harmonic approximation for vibrations or rigid rotor approximation for the rotations. In particular, zero point energy and anharmonicity effects are described correctly quantum mechanically. The approach is based on the thermodynamic integration with respect to the mass of isotopes and on the Feynman path integral representation of the partition function. An efficient estimator for the derivative of free energy is used whose statistical error is independent of the number of imaginary time slices in the path integral, speeding up calculations by a factor of approximately 60 at 500 K and more at room temperature. We describe the implementation of the methodology in the molecular dynamics package AMBER 10. The method is tested on three [1,5] sigmatropic hydrogen shift reactions. Because of the computational expense, we use ab initio potentials to evaluate the equilibrium isotope effects within the harmonic approximation and then the path integral method together with semiempirical potentials to evaluate the anharmonicity corrections. Our calculations show that the anharmonicity effects amount up to 30% of the symmetry reduced reaction free energy. The numerical results are compared with recent experiments of Doering et al., [J. Am. Chem. Soc. 128, 9080 (2006); J. Am. Chem. Soc.129, 2488 (2007)] confirming the accuracy of the most recent measurement on 2,4,6,7,9-pentamethyl-5-(5,5-(2)H(2))methylene-11,11a-dihydro-12H-naphthacene as well as concerns about compromised accuracy, due to side reactions, of another measurement on 2-methyl-10-(10,10-(2)H(2))methylenebicyclo[4.4.0]dec-1-ene.

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction

We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.

13C and (15)N Kinetic Isotope Effects on the Decarboxylation of 3-Carboxybenzisoxazole. Theory vs Experiment

Nitrogen and carbon kinetic isotope effects were measured on the decarboxylation of 3-carboxybenzisoxazole at room temperature. The nitrogen isotope effect in acetone is 1.0312 +/- 0.0006. The carbon isotope effect shows no dependence on the solvent polarity: 1.0448 +/- 0.0007 in 1,4-dioxane, 1.0445 +/- 0.0001 in acetonitrile, 1.0472 +/- 0.0013 in DMF, and 1.0418 +/- 0.0027 in water. These isotope effects were modeled theoretically at the semiempirical (AM1, PM3, SAM1) and ab initio (up to B3LYP/6-31++G) levels. The comparison of the theoretical and experimental results leads to the conclusion that none of the theory levels employed is capable of quantitatively predicting these isotope effects.

Theoretical calculations of heavy-atom isotope effects

An overview of calculations of isotope effects on biochemical and chemical reactions using quantum chemistry methods is presented . Usefulness of different levels of theoretical scrutiny for such calculations is critically discussed.