Kinetic Pathways of Ion Pair Dissociation in Water

Geissler, Phillip L.; Dellago, Christoph; Chandler, David

doi:10.1021/jp984837g

Cited by 328 publications

(415 citation statements)

References 16 publications

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“…72 In the former study, considering solvent relaxation to a flip of dipole in a solute diatomic, nonlinear solvation manifested itself in the deviation between the time-dependent Stokes shift and the equilibrium time correlation function of the ET energy gap. The second study 72 of the same system has shown that the width of the energy gap distribution evolves with time. Solvation nonlinearities in both cases were a result of a strong electrostatic coupling of water protons to the negative side of the solute diatomic.…”

Section: Resultsmentioning

confidence: 99%

Solvent Reorganization Entropy of Electron Transfer in Polar Solvents

2006

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We report the results of molecular dynamics simulations of the solvent reorganization energy of intramolecular electron transfer in a charge-transfer molecule dissolved in water and acetonitrile at varying temperatures. The simulations confirm the prediction of microscopic solvation theories of a positive reorganization entropy in polar solvents. The results of simulations are analyzed in terms of the splitting of the reorganization entropy into the contributions from the solute-solvent interaction and from the alteration of the solvent structure induced by the solute. These two contributions mutually cancel each other, resulting in the reorganization entropy amounting to only a fraction of each component.

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Section: Resultsmentioning

confidence: 99%

Solvent Reorganization Entropy of Electron Transfer in Polar Solvents

2006

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“…For example, the Nudged Elastic Band (NEB) method 20,21 and related approaches, [22][23][24] the zero-and finite-temperature string (FTS) methods, 25,26 and the growing string approach 27 all aim to search for a reaction path given an initial guess path connecting specified reactant and product configurations; the constraint of generating a good initial guess is removed in methods such as Gradient Extremal Following (GEF), 28,29 Scaled Hypersphere Searching (SHS [30][31][32], and reduced gradient following (RGF). 33 Rather than focussing on the search for single reaction paths, methods such as transition path sampling [34][35][36][37][38][39][40][41][42][43] and Onsager-Machlup path sampling 44,45 can instead generate ensembles of reaction pathways; subsequent analysis of the path ensemble, for example, by calculation of commitor probabilities, allows further identification of important features associated with transition states (TSs). More recently, the Artificial Force-Induced Reaction (AFIR) method, 46,47 in which a biasing force is used to drive chemical bond breaking and formation, has been developed as an automated approach to generating reaction pathways and stationary points.…”

Section: Introductionmentioning

confidence: 99%

Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis

Habershon

2015

The Journal of Chemical Physics

120

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Automatically generating chemical reaction pathways is a significant computational challenge, particularly in the case where a given chemical system can exhibit multiple reactants and products, as well as multiple pathways connecting these. Here, we outline a computational approach to allow automated sampling of chemical reaction pathways, including sampling of di↵erent chemical species at the reaction end-points. The key features of this scheme are (i) introduction of a Hamiltonian which describes a reaction "string" connecting reactant and products, (ii) definition of reactant and product species as chemical connectivity graphs, and (iii) development of a scheme for updating the chemical graphs associated with the reaction end-points. By performing molecular dynamics sampling of the Hamiltonian describing the complete reaction pathway, we are able to sample multiple di↵erent paths in configuration space between given chemical products; by periodically modifying the connectivity graphs describing the chemical identities of the end-points we are also able to sample the allowed chemical space of the system. Overall, this scheme therefore provides a route to automated generation of a "roadmap" describing chemical reactivity. This approach is first applied to model dissociation pathways in formaldehyde, H 2 CO, as described by a parameterised potential energy surface (PES). A second application to the HCo(CO) 3 catalyzed hydroformylation of ethene (oxo process), using density functional tight-binding to model the PES, demonstrates that our graph-based approach is capable of sampling the intermediate paths in the commonly accepted catalytic mechanism, as well as several secondary reactions. Further algorithmic improvements are suggested which will pave the way for treating complex multi-step reaction processes in a more e cient manner. C 2015 AIP Publishing LLC. [http://dx

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“…The high computational cost largely originates from evaluating committor or steps equivalent to it. For instance, estimating the committor of a single configuration with the standard shooting procedure 30 requires up to 100 short shooting trajectories, each of which is of the average length of reactive trajectories. This computational cost is intimidatingly high for large biomolecular systems even when it can be significantly reduced by a newly developed fitting procedure.…”

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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Kinetic Pathways of Ion Pair Dissociation in Water

Cited by 328 publications

References 16 publications

Solvent Reorganization Entropy of Electron Transfer in Polar Solvents

Solvent Reorganization Entropy of Electron Transfer in Polar Solvents

Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis

A benchmark for reaction coordinates in the transition path ensemble

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