Grid−Flux Method for Learning the Solvent Contribution to the Mechanisms of Reactions

McCormick, Thomas A.; Chandler, David

doi:10.1021/jp027290l

Cited by 24 publications

(51 citation statements)

References 8 publications

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“…To expand the basis set, linear combinations of projections onto principal component axes may be useful for peptides and proteins (39,40); nonlinear functions can be optimized in the same way if required. In addition, inclusion of solvent coordinates (9,15,41) may be necessary to construct a search space that covers degrees of freedom essential for the reaction kinetics and mechanism. Applications of our approach to more complex systems are expected to aid in the development of novel and unanticipated reaction coordinates.…”

Section: Discussionmentioning

confidence: 99%

Reaction coordinates and rates from transition paths

Best

Hummer

2005

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

459

581

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The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting onedimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.carbon nanotubes ͉ chemical kinetics ͉ protein folding ͉ transition-state theory ͉ Grotthuss mechanism I dentifying the molecular mechanism of a reaction in solution, such as protein folding or enzyme-catalyzed chemistry, poses serious challenges because of the large number of coupled degrees of freedom (1-5). The identification and characterization of populated intermediate states along reaction paths is only a first step. Understanding the mechanism at a molecular level requires in addition the characterization of the transitions between those populated intermediates. The goal then is (i) to identify what is common to the transitions in a rare molecular reaction (or significant subsets thereof), and (ii) to find coordinates that not only measure the progress of the reaction but also are useful to characterize the reaction dynamics. The former leads to the concept of a transition state, the latter to that of a reaction coordinate.Transition states can be thought of as configurations ''intermediate'' between reactants and products. In one widely used definition (6-11), the ensemble of transition states comprises those configurations that have an equal probability of reaching reactant and product regions. The chance of proceeding to reactants or products first can be quantified by the splitting (or commitment) probability introduced by Onsager for ion-pair recombination (12). The splitting probability is defined as the fraction of trajectories reaching the reactant region first when initiated from a given configuration with random MaxwellBoltzmann velocities, and possibly averaged over noise for stochastic dynamics. We note that one of the difficulties arising from the above definition of transition states is that splitting probabilities cannot be measured experimentally, not even in a single-molecule measurement with atomic resolution. The reason is that multiple initializations with precise atomic positions, including those of solvent molecules, are required. Here, we will show how this difficulty can be circumvented by calculating average splitting probabilities (13) from transitionpath and equilibrium ensembles that can also be measured experimentally.Fro...

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Section: Discussionmentioning

confidence: 99%

Reaction coordinates and rates from transition paths

Best

Hummer

2005

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

459

581

View full text Add to dashboard Cite

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“…While there are a large number of such studies in the literature [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17], in this section the focus is set to our recent work on helium incorporation in C 60 fullerenes [13]. Despite its apparent simplicity, the formation of endohedral fullerenes may be taken as exemplary for the crossing of a large reaction barrier in a complex system.…”

Section: Transition Path Sampling Of Reactions In Complex Systemsmentioning

confidence: 99%

Extending the scope of ‘in silico experiments’: Theoretical approaches for the investigation of reaction mechanisms, nucleation events and phase transitions

Zahn¹,

Kawska²,

Seifert

et al. 2007

Science and Technology of Advanced Materials

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The investigation of the atomistic mechanisms of processes in complex systems constitutes a major challenge to both theory and experiment. While experimental studies offer a wide variety of insights at the macroscopic scale, the atomistic level of detail often remains elusive. On the other hand, molecular simulation approaches may easily achieve microscopic resolution and hence appear particularly suited for detailed mechanistic analyses. However, the computational effort is typically quite considerable and in many cases special simulation strategies are needed to make simulations possible. This review is dedicated to special approaches for tackling the time/lengthscale problem inherent to molecular dynamics simulations. Employing these techniques opened a series of new perspectives. The latter are illustrated with the example of recent simulation studies of the atomistic mechanisms involved in complex processes like crystal nucleation, phase transitions and reactions in solution. Along this line, we discuss the reaction mechanisms for He insertion into C 60 fullerenes, nucleation events and domain morphogenesis in pressure-induced phase transitions in solids and ion aggregation from solution. r

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“…Such "trial-and-error" procedures are labor intensive and thus restricted to simple systems. 16,17 Ma and Dinner developed the first automatic method for identifying reaction coordinates out of a large pool of candidates. 18 They combined a genetic algorithm and a neural network (GNN) to find an optimal combination of a pre-determined number of coordinates that can predict the committor most accurately.…”

Section: Introductionmentioning

confidence: 99%

A benchmark for reaction coordinates in the transition path ensemble

2016

The Journal of Chemical Physics

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The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. C 2016 AIP Publishing LLC. [http://dx

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Grid−Flux Method for Learning the Solvent Contribution to the Mechanisms of Reactions

Cited by 24 publications

References 8 publications

Reaction coordinates and rates from transition paths

Reaction coordinates and rates from transition paths

Extending the scope of ‘in silico experiments’: Theoretical approaches for the investigation of reaction mechanisms, nucleation events and phase transitions

A benchmark for reaction coordinates in the transition path ensemble

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