MORATE: a program for direct dynamics calculations of chemical reaction rates by semiempirical molecular orbital theory

Truong, Thanh N.; Lu, Da Hong; Lynch, Gillian C.; Liu, Yi Ping; Melissas, Vasilios S.; Stewart, James J. P.; Steckler, Rozeanne; Garrett, Bruce C.; Isaacson, Alan D.; González‐Lafont, Àngels; Sachchida, N.; Hancock, Gene C.; Joseph, Tomi; Truhlar, Donald G.

doi:10.1016/0010-4655(93)90172-9

Cited by 109 publications

(58 citation statements)

References 51 publications

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“…The progress variable along the MEP becomes the reaction coordinate, denoted as s to be distinguished from z used in the PMF calculation. The calculation yields a generalized transition-state free energy of activation G GT (T, s i ) and a semiclassical transmission coefficient κ(T ) by methods fully described in previous work (5,(180)(181)(182)(183)(184)(185)(186)(187)(188)(189)(190). In a canonical ensemble of primary systems interacting with its frozen environment the minimum-flux dividing hypersurface is the one with maximum G GT (T, s i ), which is located at…”

Section: Dynamics and Tunnelingmentioning

confidence: 99%

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Gao

Truhlar

2002

Annu. Rev. Phys. Chem.

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771

632

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This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

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Section: Dynamics and Tunnelingmentioning

confidence: 99%

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Gao

Truhlar

2002

Annu. Rev. Phys. Chem.

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771

632

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“…The potential curve is obtained using the ground-state-transmission-coefficient approximation 416,417 for the 3N 1 − 1 primary-subsystem modes transverse to the reaction path and using the zero-order canonical-mean-shape approximation 394 for the other modes. In the LCT approximation, the effective potential for tunneling is given by in adiabatic regions of coordinate space and by a state-specific diabatic extension 351,353,354,418 elsewhere.…”

Section: Author Manuscriptmentioning

confidence: 99%

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

2006

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“…In the present work, the semiclassical probability P X (E) at every tunneling energy E has been calculated by the microcanonically optimized multidimensional tunneling (μOMT) approximation, 76 which chooses the largest value between the small-curvature tunneling [77][78][79][80] (SCT) probability, P SCT (E), and the large-curvature tunneling 50,53,76,79,[81][82][83][84][85] (LCT) probability P LCT (E); the latter being evaluated with the version 4 of the LCT method, 85…”

Section: Iib Reaction Ratesmentioning

confidence: 99%

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen

Meana-Pañeda

Truhlar

Fernández‐Ramos

2011

The Journal of Chemical Physics

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We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.

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MORATE: a program for direct dynamics calculations of chemical reaction rates by semiempirical molecular orbital theory

Cited by 109 publications

References 51 publications

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen

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