Molecular modeling of the kinetic isotope effect for the [1,5]-sigmatropic rearrangement of cis-1,3-pentadiene

Liu, Yi Ping; Lynch, Gillian C.; Truong, Thanh N.; Lu, Da Hong; Truhlar, Donald G.; Garrett, Bruce C.

doi:10.1021/ja00059a041

Cited by 913 publications

(786 citation statements)

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“…4 and Table I. The temperature dependence of the QI result is compared with the experimental results by Roth and König, 19 conventional transition state theory ͑TST͒ calculations by Dormans and Buck, 20 and the canonical variational TST with multidimensional SC tunneling ͑CVT/SCT͒ by Liu et al 22 Calculation by Dormans and Buck used Hessian information about the potential at the reactant minimum and at the saddle point obtained by ab initio calculations at the 3-21G level. Liu et al used a semiempirical AM1 potential.…”

Section: Numerical Resultsmentioning

confidence: 99%

“…This system has been studied by several authors both experimentally ͑by Roth and König 19 ͒ and theoretically. [20][21][22][23] On one hand, this 13-atom system is much smaller than an enzyme; on the other hand, the pentadiene reaction exhibits certain properties believed to play a role in real enzymatic reactions.…”

Section: Kinetic Isotope Effects In Cis-pentadienementioning

confidence: 99%

“…In our calculation, the ab initio Hessian of the potential for the pentadiene at the transition state was obtained at MP2 / 6-31g͑d͒ level, using the GAUSSIAN 03 software package. 27 For the nonreactive potentials V 11 and V 22 we chose the general AMBER force field 28 ͑GAFF͒ from the AMBER ͑assisted model building with energy refinement͒ software package. 29 The GAFF potential has the form…”

Section: ͑43͒mentioning

confidence: 99%

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Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Vaníček

Miller

2007

The Journal of Chemical Physics

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The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient "virial" estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum mechanically and uses an empirical valence bond potential based on a molecular mechanics force field.

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Section: Numerical Resultsmentioning

confidence: 99%

Section: Kinetic Isotope Effects In Cis-pentadienementioning

confidence: 99%

Section: ͑43͒mentioning

confidence: 99%

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Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Vaníček

Miller

2007

The Journal of Chemical Physics

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“…60,61 This method takes into account the corner cutting tendency of the tunneling for problems with a curved minimum energy path (MEP) near the TS. Since the recalculation of the MEP at many values of θ proved to be a laborious chore, we adopted the following streamlined procedure.…”

Section: Quantum Tunnelingmentioning

confidence: 99%

Theoretical Determination of the Rate Coefficient for the HO₂+ HO₂→ H₂O₂+O₂Reaction: Adiabatic Treatment of Anharmonic Torsional Effects

et al. 2012

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ABSTRACT:The HO 2 + HO 2 → H 2 O 2 + O 2 chemical reaction is studied using statistical rate theory in conjunction with high level ab initio electronic structure calculations. A new theoretical rate coefficient is generated that is appropriate for both high and low temperature regimes. The transition state region for the ground triplet potential energy surface is characterized using the CASPT2/CBS/aug-cc-pVTZ method with 14 active electrons and 10 active orbitals. The reaction is found to proceed through an intermediate complex bound by approximately 9.79 kcal/mol. There is no potential barrier in the entrance channel, although the free energy barrier was determined using a large Monte Carlo sampling of the HO 2 orientations. The inner (tight) transition state lies below the entrance threshold. It is found that this inner transition state exhibits two saddle points corresponding to torsional conformations of the complex. A unified treatment based on vibrational adiabatic theory is presented that permits the reaction to occur on an equal footing for any value of the torsional angle. The quantum tunneling is also reformulated based on this new approach. The rate coefficient obtained is in good agreement with low temperature experimental results but is significantly lower than the results of shock tube experiments for high temperatures.

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“…In each case, rate constants were computed at the CVT/SCT level using an adiabatic PE surface propagated from each TS structure. Primary deuterium KIEs were then calculated and are presented in table 2 together with their representative tunnelling energies (RTEs) (Liu et al 1993b) below the peak of the classical adiabatic PE barrier. Unexpectedly, since a large KIE is observed experimentally, very few of the configurations resulted in a large KIE, e.g.…”

Section: Coordination Of Asp428mentioning

confidence: 99%

An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

Núñez

Tresadern

Hillier

et al. 2006

Phil. Trans. R. Soc. B

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Computational methods have now become a valuable tool to understand the way in which enzymes catalyse chemical reactions and to aid the interpretation of a diverse set of experimental data. This study focuses on the influence of the condensed-phase environment structure on proton transfer mechanisms, with an aim to understand how C-H bond cleavage is mediated in enzymatic reactions. We shall use a combination of molecular simulation, ab initio or semi-empirical quantum chemistry and semi-classical multidimensional tunnelling methods to consider the primary kinetic isotope effects of the enzyme methylamine dehydrogenase (MADH), with reference to an analogous application to triosephosphate isomerase. Analysis of potentially reactive conformations of the system, and correlation with experimental isotope effects, have highlighted that a quantum tunnelling mechanism in MADH may be modulated by specific amino acid residues, such as Asp428, Thr474 and Asp384.Keywords: proton tunnelling; methylamine dehydrogenase; enzyme catalysis; kinetic isotope effects; triosephosphate isomerase; quantum mechanical and molecular mechanical computational methods

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Molecular modeling of the kinetic isotope effect for the [1,5]-sigmatropic rearrangement of cis-1,3-pentadiene

Cited by 913 publications

References 3 publications

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Theoretical Determination of the Rate Coefficient for the HO₂+ HO₂→ H₂O₂+O₂Reaction: Adiabatic Treatment of Anharmonic Torsional Effects

An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

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Molecular modeling of the kinetic isotope effect for the [1,5]-sigmatropic rearrangement of cis-1,3-pentadiene

Cited by 913 publications

References 3 publications

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Theoretical Determination of the Rate Coefficient for the HO2 + HO2→ H2O2+O2Reaction: Adiabatic Treatment of Anharmonic Torsional Effects

An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

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Theoretical Determination of the Rate Coefficient for the HO₂+ HO₂→ H₂O₂+O₂Reaction: Adiabatic Treatment of Anharmonic Torsional Effects