Removing the barrier to the calculation of activation energies

Mesele, Oluwaseun O.; Thompson, Ward H.

doi:10.1063/1.4964284

Cited by 20 publications

(32 citation statements)

References 22 publications

(33 reference statements)

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“…The TCF including the energy fluctuation, C 2,H (t), is also shown (solid red line) along with the fit (dashed blue line) to Eq. (14). that our results give uncertainties that encompass zero activation energy: E a,iner = 1.6 ± 1.7 kcal/mol and E a,lib = 1.0 ± 1.2 kcal/mol.…”

Section: B Reorientation Time Activation Energymentioning

confidence: 66%

“…12, and the related fit to C 2,H (t), Eq. (14). The former gives the three time scales for the reorientational dynamics as 25 fs, 0.49 ps, and 2.6 ps, corresponding to inertial, librational, and H-bonding breaking and making dynamics, respectively.…”

Section: B Reorientation Time Activation Energymentioning

confidence: 99%

“…12,13 We have recently generalized this beyond transition path sampling and to other TCFs from which rate constants can be obtained, including those based on a quantum description. 14 The measurement and calculation of activation energies by an Arrhenius analysis can raise significant issues due to the need to consider multiple temperatures. For example, many systems have a structure that is highly dependent on temperature, e.g., folded proteins, bilayer membranes or vesicles, and self-assembled structures.…”

Section: Introductionmentioning

confidence: 99%

“…As noted above, an analogous result has already been obtained in the context of reactive flux and other TCFs that can be directly related to rate constants. 8,14 However, there are many contexts in which time scale or transport coefficients are calculated from a TCF and possess an activation energy, or even simply a dependence on temperature, that is of physical interest. In the following, we show how the general result in Eq.…”

Section: Introductionmentioning

confidence: 99%

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Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water

Piskulich

Mesele

Thompson

2017

The Journal of Chemical Physics

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General approaches for directly calculating the temperature dependence of dynamical quantities from simulations at a single temperature are presented. The method is demonstrated for self-diffusion and OH reorientation in liquid water. For quantities which possess an activation energy, e.g., the diffusion coefficient and the reorientation time, the results from the direct calculation are in excellent agreement with those obtained from an Arrhenius plot. However, additional information is obtained, including the decomposition of the contributions to the activation energy. These results are discussed along with prospects for additional applications of the direct approach.

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Section: B Reorientation Time Activation Energymentioning

confidence: 66%

Section: B Reorientation Time Activation Energymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water

Piskulich

Mesele

Thompson

2017

The Journal of Chemical Physics

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“…For example, taking the derivative of the log ratio of the conditioned path partition functions with respect to β, − d dβ ln Ω AB (t, y) Ω AB (t, y ) = E † (y) − E † (y ) + ∆F (18) we obtain the y dependence on the activation barrier, E † (y), which can be evaluated via a simple average within the conditioned path ensembles. 64,65 Finally, generalizations beyond those discussed here could be envisioned. For example, rather than conditioning the reactive ensemble on different regions in space, we could condition on different product states in order to compute branching ratios without having to independently compute the rate of formation for each product.…”

Section: Liquid-liquid Interfacesmentioning

confidence: 95%

Rate constants in spatially inhomogeneous systems

Schile

Limmer

2019

The Journal of Chemical Physics

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We present a theory and accompanying importance sampling method for computing rate constants in spatially inhomogeneous systems. Using the relationship between rate constants and path space partition functions, we illustrate that the relative change in the rate of a rare event through space is isomorphic to the calculation of a free energy difference, albeit in a trajectory ensemble. Like equilibrium free energies, relative rate constants can be estimated by importance sampling. An extension to transition path sampling is proposed that combines biased path ensembles and weighted histogram analysis to accomplish this estimate. We show that rate constants can also be decomposed into different contributions, including relative changes in stability, barrier height and flux. This decomposition provides a means of interpretation and insight into rare processes in complex environments. We verify these ideas with a simple model of diffusion with spatially varying diffusivity and illustrate their utility in a model of ion pair dissociation near an electrochemical interface.Macroscopic rate constants quantify the characteristic timescale for an ensemble of components to transition between two stable states. These states may be the reactants and products of a chemical transformation or the collective reorganizations accompanying a phase transformation. Microscopically, rate constants are related to dynamical fluctuations as codified in timecorrelation functions of populations of the stable states. 1 In the presence of spatial inhomogenieties, such as extended interfaces, dynamical fluctuations need not be the same throughout space, and rate constants may obtain a spatial dependence. 2 With the advent of interfacial sensitive measurements, 3-6 single molecule experiments, 7-9 and precision electrochemical techniques, 10,11 quantifying how reactivity changes spatially at a molecular level is now possible. Theoretical work has trailed behind these advances, with few methods to efficiently study such processes and consequently few guiding principles for understanding how reactivity is altered in inhomogeneous systems. Here, we detail a theory and numerical technique to compute rate constants in the presence of spatial inhomogenieties without assuming that the mechanism of the transition is conserved at different points in space. This theory relies on the relationship between rate constants and trajectory space partition functions, and the method it motivates is general, capable of application to complex environments and processes.Rare dynamical events often take place in environments that are complex and inhomogeneous. Heterogeneous catalysis relies on the increase of the rate of a chemical reaction near an extended fluid-solid interface relative to the rate in the fluid. 12 Moreover, heterogeneities along the interface like defects or grain boundaries can act as active sites for catalysis and have tremendous impact on reactivity. 13 Reactivity can be influenced analogously by extended liquid-vapor interfaces, or by a) Electron...

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Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water

Piskulich

Thompson

2021

J. Chem. Theory Comput.

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There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogenbond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.

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Removing the barrier to the calculation of activation energies

Cited by 20 publications

References 22 publications

Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water

Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water

Rate constants in spatially inhomogeneous systems

Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water

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