Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics

Intramolecular Catalytic Hydrogen Atom Transfer (CHAT)

Intramolecular catalysis (IntraCat) is the acceleration of a process at one site of a molecule catalyzed by a functional group in the same molecule; an external agent such as a solvent typically facilitates it. Here, we report a general first-principles-based IntraCat mechanism, which strictly occurs within a single molecule with no coreagent being involved─we call it intramolecular catalytic transfer of hydrogen atoms (CHAT). A reactive part of a molecule (chat catalyst moiety or chat agent, represented by -OOH, -COOH, -SH, -CH2OH, -HPO4, or another bifunctional H-donor/acceptor group) catalyzes an interconversion process, such as keto-enol or amino-imino tautomerization, and cyclization in the same molecule, while being regenerated in the process. It can thus be regarded as an intramolecular version of the intermolecular H atom transfer processes mediated by an external molecular catalyst, e.g., dihydrogen, water, or a carboxylic acid. Earlier, we proposed a general mechanistic systematization of intermolecular processes, illustrated in the simplest case of the H2-mediated reactions classified as dihydrogen catalysis [Asatryan, R.; et al. Catal. Rev.: Sci. Eng., 2014, 56, 403-475]. Following this systematization, the CHAT catalysis belongs to the category of relay transfer of H atoms, albeit in an intramolecular manner. A broader class of intramolecular processes includes all types of H-transfer reactions stimulated by an H-migration, which we call self-catalyzed H atom transfer (SC-HAT). The CHAT mechanism comprises a subset of SC-HAT in which the catalytic moiety is regenerated (i.e., acts as a true catalyst and not a reagent). We provide several characteristic examples of CHAT mechanism based on detailed analysis of the corresponding potential energy surfaces. All such cases showed a dramatically reduced activation barrier relative to the corresponding uncatalyzed H-transfer reactions. For example, we show that CHAT can facilitate long-range H-migration in larger molecules and can occur multiple times in one molecule with multiple interconverting groups. It also facilitates amino-imino tautomerization of unsaturated GABA-analogues and peptides, as well as intramolecular cyclization processes to form heterocycles, e.g., oxygenated rings. CHAT pathways may also explain the pH-dependent increase of mutarotation rate of glucose-6-phosphate demonstrated in pioneering experiments that introduced the classical IntraCat concept. In addition, we identify a ground electronic state CHAT pathway as an alternative to the UV-promoted long-range molecular crane keto-enol conversion with a remarkably low activation energy. To initially assess the possible impact of the new keto-enol conversion pathway on combustion of n-alkanes, we present a detailed kinetic analysis of isomerization and decomposition of pentane-2,4-ketohydroperoxide (2,4-KHP). The results are compared with key alternative reactions, including direct dissociation and Korcek channels (for which a new alkyl group migration channel is also identified), revealing the competitiveness of the CHAT pathway across a range of conditions. Taken together, this work provides insight into a general class of reaction pathways that has not previously being systematically considered and that may occur in a broad range of contexts from combustion to atmospheric chemistry to biochemistry.

Automated Generation of a Compact Chemical Kinetic Model for n-Pentane Combustion

We have employed automated mechanism generation tools to construct a detailed chemical kinetic model for combustion of n-pentane, as a step toward the generation of compact kinetic models for larger alkanes. Pentane is of particular interest as a prototype for combustion of alkanes and as the smallest paraffin employed as a hybrid rocket fuel, albeit at cryogenic conditions. A reaction mechanism for pentane combustion thus provides a foundation for modeling combustion of extra-large alkanes (paraffins) that are of more practical interest as hybrid rocket fuels, for which manual construction becomes infeasible. Here, an n-pentane combustion kinetic model is developed using the open-source software package Reaction Mechanism Generator (RMG). The model was generated and tested across a range of temperatures (650 to 1350 K) and equivalence ratios (0.5, 1.0, 2.0) at pressures of 1 and 10 atm. Available thermodynamic and kinetic databases were incorporated wherever possible. Predictions using the mechanism were validated against the published laminar burning velocities (Su) and ignition delay times (IDT) of n-pentane. To improve the model performance, a comprehensive analysis, including reaction path and sensitivity analyses of n-pentane oxidation, was performed, leading us to modify the thermochemistry and rate parameters for a few key species and reactions. These were combined as a separate data set, an RMG library, that was then used during mechanism generation. The resulting model predicted IDTs as accurately as the best manually constructed mechanisms, while remaining much more compact. It predicted flame speeds to within 10% of published experimental results. The degree of success of automated mechanism generation for this case suggests that it can be extended to construct reliable and compact models for combustion of larger n-alkanes, particularly when using this mechanism as a seed submodel.

Automatic Potential Energy Surface Exploration by Accelerated Reactive Molecular Dynamics Simulations: From Pyrolysis to Oxidation Chemistry

Automatic potential energy surface (PES) exploration is important to a better understanding of reaction mechanisms. Existing automatic PES mapping tools usually rely on predefined knowledge or computationally expensive on-the-fly quantum-chemical calculations. In this work, we have developed the PESmapping algorithm for discovering novel reaction pathways and automatically mapping out the PES using merely one starting species is present. The algorithm explores the unknown PES by iteratively spawning new reactive molecular dynamics (RMD) simulations for species that it has detected within previous RMD simulations. We have therefore extended the RMD simulation tool ChemTraYzer2.1 (Chemical Trajectory Analyzer, CTY) for this PESmapping algorithm. It can generate new seed species, automatically start replica simulations for new pathways, and stop the simulation when a reaction is found, reducing the computational cost of the algorithm. To explore PESs with low-temperature reactions, we applied the acceleration method collective variable (CV)-driven hyperdynamics. This involved the development of tailored CV templates, which are discussed in this study. We validate our approach for known pathways in various pyrolysis and oxidation systems: hydrocarbon isomerization and dissociation (C4H7 and C8H7 PES), mostly dominant at high temperatures and low-temperature oxidation of n-butane (C4H9O2 PES) and cyclohexane (C6H11O2 PES). As a result, in addition to new pathways showing up in the simulations, common isomerization and dissociation pathways were found very fast: for example, 44 reactions of butenyl radicals including major isomerizations and decompositions within about 30 min wall time and low-temperature chemistry such as the internal H-shift of RO2 → QO2H within 1 day wall time. Last, we applied PESmapping to the oxidation of the recently proposed biohybrid fuel 1,3-dioxane and validated that the tool could be used to discover new reaction pathways of larger molecules that are of practical use.

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

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.

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

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.

Efficient Reaction Space Exploration with ChemTraYzer-TAD

The development of a reaction model is often a time-consuming process, especially if unknown reactions have to be found and quantified. To alleviate the reaction modeling process, automated procedures for reaction space exploration are highly desired. We present ChemTraYzer-TAD, a new reactive molecular dynamics acceleration technique aimed at efficient reaction space exploration. The new method is based on the basin confinement strategy known from the temperature-accelerated dynamics (TAD) acceleration method. Our method features integrated ChemTraYzer bond-order processing steps for the automatic and on-the-fly determination of the positions of virtual walls in configuration space that confine the system in a potential energy basin. We use the example of 1,3-dioxolane-4-hydroperoxide-2-yl radical oxidation to show that ChemTraYzer-TAD finds more than 100 different parallel reactions for the given set of reactants in less than 2 ns of simulation time. Among the many observed reactions, ChemTraYzer-TAD finds the expected typical low-temperature reactions despite the use of extremely high simulation temperatures up to 5000 K. Our method also finds a new concerted β-scission plus O₂ addition with a lower reaction barrier than the literature-known and so-far dominant β-scission.

ReaxFF Force Field Development for Gas-Phase hBN Nanostructure Synthesis

Two-dimensional (2D) hexagonal boron nitride materials are isomorphs of carbon nanomaterials and hold promise for electronics applications owing to their unique properties. Despite the recent advances in synthesis, the current production capacity for boron nitride (BN) nanostructures is far behind that for carbon-based nanostructures. Understanding the growth mechanism of BN nanostructures through modeling and experiments is key to improving this situation. In the current work, we present the development of a ReaxFF-based force field capable of modeling the gas-phase chemistry important for the chemical vapor deposition (CVD) synthesis process. This force field is parameterized to model the boron nitride nanostructure (BNNS) formation in the gas phase using BN and HBNH as precursors. Our ReaxFF simulations show that BN is the best of these two precursors in terms of quality and the size of BNNSs. The BN precursors lead to the formation of closed BNNSs. However, BNNSs are replaced with complex polymeric structures at temperatures of 2500 K and higher due to entropic effects. Compared to the BN precursors, the HBNH precursors form relatively small, flat, and low-quality BNNSs, but this structure is less affected by temperature. Additives like H₂ significantly affect the BNNS formation by preventing closed BNNS formation. Our results show the ReaxFF capability in predicting the BN gas-phase chemistry and BNNS formation, thus providing key insights for experimental synthesis.