Konrad Wilke,Shuxia Tao,Sofia Calero,Anders Lervik,Titus S van Erp
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引用次数: 0
Abstract
Utilizing the replica exchange transition interface sampling (RETIS) technique, we simulated the dynamics of sodium chloride dissociation in water. Subsequently, the resulting trajectories were analyzed using predictive power analysis (PPA), enabling the identification and quantification of collective variables (CVs) capable of forecasting the reaction occurrence. We improved the robustness of the PPA method by incorporating the Savitzky-Golay (SG) filter on integrated histograms, effectively avoiding the limitations associated with binning. Applying this adapted PPA method, the previously designed solvent parameters and distances from the index invariant distance matrix were assessed. This revealed that the sixth closest oxygen to sodium serves as an equally effective predictor as the best complex solvent parameter. The latter, however, required more knowledge and human intuition as an input for its design, while the former provided such intuition purely as an output. Through a comparable analysis, the chloride solvation shell appears to contain less predictive information. Employing a linear combination of several CVs can further enhance predictability, albeit at the expense of a reduced human interpretability.
期刊介绍:
The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.