Activation to the transition state: reactant and solvent energy flow for a model SN2 reaction in water

Gertner, Bradley J.; Whitnell, Robert M.; Wilson, Kent R.; Hynes, James T.

doi:10.1021/ja00001a014

Cited by 154 publications

(111 citation statements)

References 54 publications

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“…16,19,41 The work done by solvent atom i on reagent atom j up to time following the barrier crossing ͑at tϭ0͒ is…”

Section: Resultsmentioning

confidence: 99%

“…For example, the dynamics of energy flow into the reactants is much more complex for S N 2 reactions involving polar and charged species: a larger number of solvent atoms simultaneously take part in the energy transfer to the reactants compared with the ClϩCl 2 model system. 16,19 A substantial reorganization of the solvent structure always precedes the reaction for the strongly interacting system while such effect is not observed for the weakly coupled case. Moreover the constraints imposed on the relative diffusion of the reactants could further level off the differences between the silicates and the liquid solvent.…”

Section: Computer Simulationsmentioning

confidence: 99%

“…Previous theoretical studies 13 show that reactions of this kind ͑e.g. neutral atom exchange in rare gas solvents [14][15][16] ͒ are usually characterized by smaller solvent effects compared to exchange reactions in which long-range, strong interactions ͑both of Coulombic and ion-dipole nature, like bimolecular substitutions of alkyl halides by anions in polar solvents [17][18][19][20] ͒ are active. For example, the dynamics of energy flow into the reactants is much more complex for S N 2 reactions involving polar and charged species: a larger number of solvent atoms simultaneously take part in the energy transfer to the reactants compared with the ClϩCl 2 model system.…”

Section: Computer Simulationsmentioning

confidence: 99%

See 2 more Smart Citations

Molecular dynamics simulation of an activated transfer reaction in zeolites

Demontis

Suffritti

Tilocca

1999

The Journal of Chemical Physics

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The activated transfer of a light particle between two heavier species in the micropores of silicalite and ZK4 zeolites has been studied through molecular dynamics ͑MD͒ simulations. A three-body potential controls the exchange of the light particle between the heavier ones; an effective barrier of a few k B T separates the two stable regions corresponding to symmetric ''reactant'' and ''product'' species. Harmonic forces always retain the reactants at favorable distances so that in principle only the energetic requirement must be fulfilled for the transfer to occur. The rate constant for the process ͑obtained from a correlation analysis of equilibrium MD trajectories͒ decreases by more than one order of magnitude when the barrier height is increased from 2k B T to 5k B T following an Arrhenius-type behavior. The transfer rates are always lower in ZK4. When the reaction is studied in a liquid solvent the calculated rate constants are closer to those obtained in silicalite. Since with this model the diffusive approach of the reactants is almost irrelevant on the reactive dynamics, only the different ability of each environment to transfer the appropriate energy amount to the reactants and then promote the barrier passage could be invoked to explain the observed behavior. We found that structural, rather than energetic, effects are mainly involved on this point. The lower efficiency of ZK4 seems to arise from the frequent trapping of the reactive complex in the narrow ZK4 windows in which the transfer is forbidden and from the weaker interaction of the reactive complex with the host framework compared to silicalite.

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“…16,19,41 The work done by solvent atom i on reagent atom j up to time following the barrier crossing ͑at tϭ0͒ is…”

Section: Resultsmentioning

confidence: 99%

Section: Computer Simulationsmentioning

confidence: 99%

Section: Computer Simulationsmentioning

confidence: 99%

See 1 more Smart Citation

Molecular dynamics simulation of an activated transfer reaction in zeolites

Demontis

Suffritti

Tilocca

1999

The Journal of Chemical Physics

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“…[6][7][8][9] In 1991, Hynes and co-workers provided a detailed molecular dynamics description of the mechanism by which vibrational activation on the reactantside of the transition state gives rise to barrier crossing for thermal SN2 reactions in solution. 10 The extent to which chemical reactions under thermal conditions can lead to vibrationally excited products is an area which, until recently, has been less well studied. Over the last few years, a handful of experimental and theoretical studies have highlighted solution-phase chemical reactions which give rise to products with observable vibrational excitation beyond that which would be expected at thermal equilibrium.…”

Section: Introductionmentioning

confidence: 99%

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model

Glowacki

Orr-Ewing

Harvey

2015

The Journal of Chemical Physics

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We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol−1 localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.

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“…This exchange and its time scale are critical in a wide range of chemical and biochemical processes. For aqueous reactions such as substitution processes (1) or acid-base mechanisms (2) or for reactions at aqueous interfaces (3), it can be the rate-determining step. It is also key for transport of ionic solutes in water; ionic mobility, for example, depends not only on the ion size but also on the hydration shell lability, which determines whether the ion travels alone or accompanied by its hydration layer (4).…”

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confidence: 99%