A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development

Komissarov, Leonid; Krep, Lukas; Schmalz, Felix; Kopp, Wassja A.; Leonhard, Kai; Verstraelen, Toon

doi:10.1002/cphc.202200786

Cited by 2 publications

(10 citation statements)

References 78 publications

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“…The rMD simulations were performed using the ReaxFF parameters developed in part I of our series. [61] Some reactions discussed below were obtained using a preliminary version of the force field parameters. The preliminary version differs from the published parameters only by the parameters for Cl-Cl interactions, meaning that only the systems containing multiple chlorine atoms are affected.…”

Section: Simulation Setupmentioning

confidence: 99%

“…This combination of maximum batch length and simulation temperature is expected to result in the majority of observed reactions having a reaction barrier below 210 kJ mol À 1 , as previously discussed. [70] Due to the uncertainty in ReaxFF energies of � 125kJ mol À 1 , [61] higher reaction barriers can be found after recomputing them with higher-level methods.…”

Section: Simulation Setupmentioning

confidence: 99%

“…We ran one replica for each system with both the old and the final force field parameters, the latter of which are reported in the first part of our paper series. [61] Only for the phenoxy radical plus 1,3,5-trichlorobenzene system and the final force field parameters, we increased the number of replica to five, to expand the number of observed reactions. As we have discussed in a previous study, [70] it is generally advisable to run multiple replica of CTY-TAD simulations to obtain more complete reaction networks.…”

Section: Simulation Setupmentioning

confidence: 99%

“…Therefore, we have developed a new ReaxFF force field parametrization for the study of the formation and decomposition processes of COCs in the first part of our paper series. [61] In this second part, we first introduce four conceptual updates to the CTY rMD-QM coupling scheme in the Methodology section, among them a self-learning method for the recovery of failed transition state (TS) searches. The conceptual updates address known shortcomings of our coupling scheme, [30] enhancing its computational resource efficiency and TS search success rate.…”

Section: Introductionmentioning

confidence: 99%

“…The reactions derived in this study by the updated CTY scheme are used as validation data for the force field parameters described in part I of our series. [61] The chemical structure of dibenzofuran is given in Figure 1. We present reaction pathways for (i) the formation of CDFs from the precursors phenoxy radical plus 1,3,5trichlorobenzene, (ii) the pyrolysis of singly-chlorinated and unchlorinated CDFs, and (iii) the oxidation processes of singlychlorinated and unchlorinated 1-peroxy-dibenzofuranyl radicals.…”

Section: Introductionmentioning

confidence: 99%

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A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

et al. 2023

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In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics -Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.

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Section: Simulation Setupmentioning

confidence: 99%

Section: Simulation Setupmentioning

confidence: 99%

Section: Simulation Setupmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

et al. 2023

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Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina

Dumortier,

Chizallet,

Creton

et al. 2024

J. Chem. Theory Comput.

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ReaxFF is a computationally efficient model for reactive molecular dynamics simulations that has been applied to a wide variety of chemical systems. When ReaxFF parameters are not yet available for a chemistry of interest, they must be (re)optimized, for which one defines a set of training data that the new ReaxFF parameters should reproduce. ReaxFF training sets typically contain diverse properties with different units, some of which are more abundant (by orders of magnitude) than others. To find the best parameters, one conventionally minimizes a weighted sum of squared errors over all of the data in the training set. One of the challenges in such numerical optimizations is to assign weights so that the optimized parameters represent a good compromise among all the requirements defined in the training set. This work introduces a new loss function, called Balanced Loss, and a workflow that replaces weight assignment with a more manageable procedure. The training data are divided into categories with corresponding "tolerances", i.e., acceptable root-mean-square errors for the categories, which define the expectations for the optimized ReaxFF parameters. Through the Log-Sum-Exp form of Balanced Loss, the parameter optimization is also a validation of one's expectations, providing meaningful feedback that can be used to reconfigure the tolerances if needed. The new methodology is demonstrated with a nontrivial parametrization of ReaxFF for water adsorption on alumina. This results in a new force field that reproduces both the rare and frequent properties of a validation set not used for training. We also demonstrate the robustness of the new force field with a molecular dynamics simulation of water desorption from a γ-Al 2 O 3 slab model.

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A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development

Cited by 2 publications

References 78 publications

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina

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