Direct dynamics calculation of the kinetic isotope effect for an organic hydrogen-transfer reaction, including corner-cutting tunneling in 21 dimensions

Liu, Yi Ping; Lu, Da Hong; González‐Lafont, Àngels; Truhlar, Donald G.; Garrett, Bruce C.

doi:10.1021/ja00070a029

Cited by 363 publications

(445 citation statements)

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“…In EA-VTST calculations (3,17,37), we used the microcanonically optimized multidimensional tunneling path, in which the small curvature tunneling and large curvature tunneling paths are optimized, to determine the tunneling coefficient and the dominant tunneling energy (40,41). The transition-state ensemble was obtained during the free-energy simulations for determining the PMF, and the tunneling transmission coefficient for the enzyme was averaged over 19 reaction trajectories.…”

Section: Methodsmentioning

confidence: 99%

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Major

Héroux

Orville

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.PI-FEP/UM simulations ͉ enzyme catalysis ͉ kinetic isotope effects ͉ X-ray structure A lthough the dominant factor in enzyme catalysis is the lowering of the quasiclassical free energy barrier of the enzymatic reaction in comparison with the uncatalyzed process (1-3), quantum mechanical tunneling has been recognized to also play a role in enzymatic hydrogen transfer reactions (2, 3). An intriguing, yet unanswered, question is whether enzymes have evolved to enhance tunneling to accelerate the reaction rate because quantum effects on rate acceleration are much smaller than hydrogen bonding and electrostatic stabilization of the transition state (1, 4, 5). Nevertheless, a small factor of two in rate enhancement can have important physiological impacts. Although it appears straightforward to address this question by comparing the enzymatic and the uncatalyzed reaction in solution, the difficulty is to design a model system that mimics exactly the same enzymatic reaction and mechanism. The present study examines the structure of nitroalkane oxidase (NAO) complex with nitroethane and kinetic isotope effects at the primary and secondary sites for the enzymatic and the uncatalyzed reaction. The computational findings are consistent with experimental data, suggesting that there is a differential tunneling effect for the proton transfer reaction in NAO and in water. Analysis of tunneling paths reveals that the enzyme reduces both the free energy of activation and the width of the effective potential, resulting in enhanced proton tunneling in the active site.The flavoenzyme NAO catalyzes the conversion of nitroalkanes to nitrite and aldehydes or ketones (Fig. S1) (6). The ␣-proton abstraction of the small substrate nitroethane by Asp-402 is rate-limiting, which is accelerated by a factor of 10 9 over the uncatalyzed reaction between n...

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Section: Methodsmentioning

confidence: 99%

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Major

Héroux

Orville

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…17 In the present case, the ICVT/µOMT results were computed using the harmonic approximation for both the bound stretching mode and the nondegenerate bend. In the µOMT method, the larger of the centrifugal-dominant small-curvature adiabatic ground-state (CD-SCSAG) transmission further in previous papers.…”

Section: Iic Tunneling Contributionsmentioning

confidence: 99%

“…[12][13][14][15] From among the range of algorithms that may be employed for the latter, we choose the improved canonical variational theory (ICVT) 13,14 as implemented in the program POLYRATE. 16 In category II, we consider ICVT calculations that incorporate semiclassically calculated tunneling contributions, obtained using the microcanonical optimized multidimensional tunneling (µOMT) 17 approximation for transmission coefficients. This method has been widely validated.…”

Section: Introductionmentioning

confidence: 99%

Thermal and State-Selected Rate Coefficients for the O(³P) + HCl Reaction and New Calculations of the Barrier Height and Width

et al. 2001

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This paper compares several approximate methods for calculating rate coefficients for the O( 3 P) + HCl reaction to presumably more accurate quantum mechanical calculations based on applying the J-shifting approximation (QM/JS) to an accurate cumulative reaction probability for J = 0.All calculations for this work employ the recent S4 potential energy surface, which presents a number of challenges for the approximate methods. The O + HCl reaction also poses a significant challenge to computational dynamics because of the heavy-light-heavy mass combination and the broad noncollinear reaction path. The approximate methods for calculating 2 the thermal rate coefficient that are examined in this article are quasiclassical trajectories (QCT), conventional transition state theory (TST), variational transition state theory employing the improved canonical variational theory (ICVT), ICVT with the microcanonical optimized multidimensional tunneling correction (ICVT/µOMT), and reduced dimensionality quantum mechanical calculations based on adiabatic bend and J-shifting (QM/AB-JS) approximations. It is seen that QCT, TST, and ICVT rate coefficients agree with each other within a factor of 2.7 at 250 K and 1.6 at l000 K, whereas inclusion of tunneling by the ICVT/µOMT, QM/AB-JS, or QM/JS methods increases the rate coefficients considerably. However, the ICVT/µOMT and QM/AB-JS methods yield significantly lower rate coefficients than the QM/JS calculations, especially at lower temperatures. We also report and discuss calculations for the state-selected reaction of O( 3 P) with HCl in the first excited vibrational state. In addition to the dynamics calculations, we report new electronic structure calculations by the multi-coefficient Gaussian-3 (MCG3) method that indicate that one possible source of disagreement between the QM/JS rate coefficients and experiment is that the barrier on the S4 surface may be too narrow.

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“…VTST calculations with microcanonically optimized multidimensional tunneling (49) were presented by Troya et al (48). Their rate constants are larger than the present converged rate constants by 54%, 40%, and 75% at 300, 500, and 1,000 K, respectively.…”

Section: Resultsmentioning

confidence: 99%

Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H₂→H₂O + H reaction as a function of temperature

Chakraborty

Truhlar

2005

Proc. Natl. Acad. Sci. U.S.A.

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The thermal rate constant of the 3D OH ؉ H23 H2O ؉ H reaction was computed by using the flux autocorrelation function, with a time-independent square-integrable basis set. Two modes that actively participate in bond making and bond breaking were treated by using 2D distributed Gaussian functions, and the remaining (nonreactive) modes were treated by using harmonic oscillator functions. The finite-basis eigenvalues and eigenvectors of the Hamiltonian were obtained by solving the resulting generalized eigenvalue equation, and the flux autocorrelation function for a dividing surface optimized in reduced-dimensionality calculations was represented in the basis formed by the eigenvectors of the Hamiltonian. The rate constant was obtained by integrating the flux autocorrelation function. The choice of the final time to which the integration is carried was determined by a plateau criterion. The potential energy surface was from Wu, Schatz, Lendvay, Fang, and Harding (WSLFH). We also studied the collinear H ؉ H2 reaction by using the Liu-Siegbahn-Truhlar-Horowitz (LSTH) potential energy surface. The calculated thermal rate constant results were compared with reported values on the same surfaces. The success of these calculations demonstrates that time-independent vibrational configuration interaction can be a very convenient way to calculate converged quantum mechanical rate constants, and it opens the possibility of calculating converged rate constants for much larger reactions than have been treated until now.flux autocorrelation ͉ chemical kinetics ͉ dynamics ͉ localized basis functions ͉ many-body problem T he evaluation of the thermal reaction rate constant k(T) from the quantum mechanical flux provides an efficient alternative to the computation of rate constants by means of the scattering matrix. The quantum mechanical formulation of k(T) in terms of flux autocorrelation functions C f (t) was presented by Yamamoto (1) and Miller et al. (2,3), and there have been several applications to calculate thermal rate constants for specific systems. The flux operator can be used to compute the cumulative reaction probability N(E) or the flux autocorrelation function, and either of these functions can be used to compute the thermal rate constant. Various approaches (4-24) involving basis functions, path integrals, and wave packet propagation methods have been used. Recently, Manthe and coworkers (19,22) have calculated the thermal rate constants for the CH 4 ϩ H3CH 3 ϩ H 2 and CH 4 ϩ O3CH 3 ϩ OH reactions by calculating N(E) as a function of energy E by using the multiconfiguration time-dependent Hartree (MCTDH) method. Earlier work on triatomic reactions showed that accurate results can be obtained with an approach based on diagonalizing the time-independent Hamiltonian (4, 8, 10). One advantage of this formulation is that the variational principle is used to identify the relevant subspace of the basis set. This approach is appealing in terms of its generality and straightforward extension to larger systems, and it is exte...

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Direct dynamics calculation of the kinetic isotope effect for an organic hydrogen-transfer reaction, including corner-cutting tunneling in 21 dimensions

Cited by 363 publications

References 5 publications

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Thermal and State-Selected Rate Coefficients for the O(³P) + HCl Reaction and New Calculations of the Barrier Height and Width

Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H₂→H₂O + H reaction as a function of temperature

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Direct dynamics calculation of the kinetic isotope effect for an organic hydrogen-transfer reaction, including corner-cutting tunneling in 21 dimensions

Cited by 363 publications

References 5 publications

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Thermal and State-Selected Rate Coefficients for the O(3P) + HCl Reaction and New Calculations of the Barrier Height and Width

Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H2→H2O + H reaction as a function of temperature

Contact Info

Product

Resources

About

Thermal and State-Selected Rate Coefficients for the O(³P) + HCl Reaction and New Calculations of the Barrier Height and Width

Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H₂→H₂O + H reaction as a function of temperature