Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces

Zádor, Judit; Martí, Carles; Vijver, Ruben Van de; Johansen, Sommer; Yang, Yoona; Michelsen, Hope A.; Najm, Habib N.

doi:10.1021/acs.jpca.2c06558

Cited by 32 publications

(30 citation statements)

References 128 publications

(253 reference statements)

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“…The C 7 H 7 PES was explored automatically using KinBot . A detailed description of the code is provided elsewhere; , therefore, only a brief description is given here. KinBot is an automated gas-phase kinetics workflow code that drives electronic structure calculations on a PES, starting from a single approximate structure.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

“…In this article, the goal is to study the reactions on the C 7 H 7 PES through a systematic approach that is less biased by human intuitions, using KinBot, − and to unravel the chemistry more globally and comprehensively across the PES than was possible in previous studies. KinBot has previously provided an automated, systematic, and comprehensive approach to studying important gas-phase chemical systems, including C 5 H 5 and C 6 H 6 , which are very similar to the C 7 H 7 PES. In both cases, we found most of the previously explored channels, and we found many new routes.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the traditional PES representation of wells and barriers becomes visually so crowded that it prevents interpretation. We have recently implemented an interactive graph-based depiction 64 in the PESViewer code 68 to create a cleaner view of such complicated reactive landscapes (for a static example, see Figures 6 and 7). Each species is represented as a node that contains the 2D chemical structure of a well generated with RDKit 69 and is connected to other species if there is a first-order saddle point or a barrierless pathway between them.…”

Section: ■ Introductionmentioning

confidence: 99%

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Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions

et al. 2023

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The automated kinetics workflow code, KinBot, was used to explore and characterize the regions of the C 7 H 7 potential energy surface that are relevant to combustion environments and especially soot inception. We first explored the lowest-energy region, which includes the benzyl, fulvenallene + H, and cyclopentadienyl + acetylene entry points. We then expanded the model to include two higher-energy entry points, vinylpropargyl + acetylene and vinylacetylene + propargyl. The automated search was able to uncover the pathways from the literature. In addition, three important new routes were discovered: a lower-energy pathway connecting benzyl with vinylcyclopentadienyl, a decomposition mechanism from benzyl that results in side-chain hydrogen atom loss to produce fulvenallene + H, and shorter and lower energy routes to the dimethylene-cyclopentenyl intermediates. We systematically reduced the extended model to a chemically relevant domain composed of 63 wells, 10 bimolecular products, 87 barriers, and 1 barrierless channel and constructed a master equation using the CCSD(T)-F12a/cc-pVTZ//ωB97X-D/6-311++G(d,p) level of theory to provide rate coefficients for chemical modeling. Our calculated rate coefficients show excellent agreement with measured ones. We also simulated concentration profiles and calculated branching fractions from the important entry points to provide an interpretation of this important chemical landscape.

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Section: Methods and Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions

et al. 2023

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“…Potential energy surfaces for each of the five DMO radicals shown in Figure were explored automatically with the open-source kinetics workflow code, KinBot. − The initial saddle point guess is constructed by a series of constrained optimization steps at the L0 = AM1 level of theory. The initial guess is refined to a true first-order saddle-point (FOSP) at the L1 = B3LYP/6-31+G level of theory and confirmed by intrinsic reaction coordinate (IRC) calculations at the same level.…”

Section: Computational Methodsmentioning

confidence: 99%

Unimolecular Reactions of 2,4-Dimethyloxetanyl Radicals

Doner¹,

Zádor

Rotavera³

2023

J. Phys. Chem. A

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Alkyl-substituted oxetanes are cyclic ethers formed via unimolecular reactions of QOOH radicals produced via a six-membered transition state in the preceding isomerization step of organic peroxy radicals, ROO. Owing to radical isomer-specific formation pathways, cyclic ethers are unambiguous proxies for inferring QOOH reaction rates. Therefore, accounting for subsequent oxidation of cyclic ethers is important in order to accurately determine rates for QOOH → products. Cyclic ethers can react via unimolecular reaction (ring-opening) or via bimolecular reaction with O 2 to form cyclic ether-peroxy adducts. The computations herein provide reaction mechanisms and theoretical rate coefficients for the former type in order to determine competing pathways for the cyclic ether radicals. Rate coefficients of unimolecular reactions of 2,4-dimethyloxetanyl radicals were computed using master equation modeling from 0.01 to 100 atm and from 300 to 1000 K. Coupled-cluster methods were utilized for stationary-point energy calculations, and uncertainties in the computed rate coefficients were accounted for using variation in barrier heights and in well depths. The potential energy surfaces reveal accessible channels to several species via crossover reactions, such as 2-methyltetrahydrofuran-5-yl and pentanonyl isomers. For the range of temperature over which 2,4-dimethyloxetane forms during n-pentane oxidation, the following are the major channels: 2,4dimethyloxetan-1-yl → acetaldehyde + allyl, 2,4-dimethyloxetan-2-yl → propene + acetyl, and 2,4-dimethyloxetan-3-yl → 3-butenal + methyl, or, 1-penten-3-yl-4-ol. Well-skipping reactions were significant in a number of channels and also exhibited a markedly different pressure dependence. The calculations show that rate coefficients for ring-opening are approximately an order of magnitude lower for the tertiary 2,4-dimethyloxetanyl radicals than for the primary and secondary 2,4-dimethyloxetanyl radicals. Unlike for reactions of the corresponding ROO radicals, however, unimolecular rate coefficients are independent of the stereochemistry. Moreover, rate coefficients of cyclic ether radical ring-opening are of the same order of magnitude as O 2 addition, underscoring the point that a competing network of reactions is necessary to include for accurate chemical kinetics modeling of species profiles for cyclic ethers.

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“…Specifically, we use a simple reaction step, a H-migration reaction, as a basis of generating data, which consists of pairs of molecular geometries and corresponding potential energies. We used our automated PES explorer code, KinBot [69][70][71], to generate the reactant (Well1), the product (Well2) and the transition state (TS) structures. The latter is a first-order saddle point, from which descent leads to the two wells.…”

Section: The Chemical System 21 Selection Of Anchor Points and Datase...mentioning

confidence: 99%

Multifidelity neural network formulations for prediction of reactive molecular potential energy surfaces

Yang

Eldred

Zádor

et al. 2023

Preprint

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This paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules, and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems, and then deployed for potential energy prediction for C5H5 using B2PLYPD3 6-311++G(d,p) for high fidelity simulation data and Hartree Fock 6-31G for low fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.

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Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces

Cited by 32 publications

References 128 publications

Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions

Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions

Unimolecular Reactions of 2,4-Dimethyloxetanyl Radicals

Multifidelity neural network formulations for prediction of reactive molecular potential energy surfaces

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Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces

Cited by 32 publications

References 128 publications

Comprehensive Kinetics on the C7H7 Potential Energy Surface under Combustion Conditions

Comprehensive Kinetics on the C7H7 Potential Energy Surface under Combustion Conditions

Unimolecular Reactions of 2,4-Dimethyloxetanyl Radicals

Multifidelity neural network formulations for prediction of reactive molecular potential energy surfaces

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Product

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Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions

Comprehensive Kinetics on the C₇H₇ Potential Energy Surface under Combustion Conditions