Multi-path variational transition state theory for chiral molecules: the site-dependent kinetics for abstraction of hydrogen from 2-butanol by hydroperoxyl radical, analysis of hydrogen bonding in the transition state, and dramatic temperature dependence of the activation energy

Theoretical kinetic studies on intramolecular H-migration reactions of peroxy radicals of diethoxymethane

Diethoxymethane (DEM), a promising carbon-neutral fuel, has high reactivity at low temperatures. The intramolecular hydrogen migration reaction of the DEM peroxy radicals can be viewed as a critical step in the low temperature oxidation mechanism of DEM. In this work, multistructural transition state theory (MS-TST) was utilized to calculate the high-pressure limit rate constants of 1,5, 1,6 and 1,7 H-migration reactions for DEM peroxy radicals. In addition to the tunneling effects and anharmonic effects, the intramolecular effects, including steric hindrance, intramolecular hydrogen bonding and conformational changes in reactants and transition states, are also considered in the rate constant calculations. The calculated energy barriers and rate constants demonstrated the substantial impact of intramolecular effects on the kinetics of H-migration reactions in DEM peroxy radicals. Specifically, the distinct configurations of transition states could potentially influence the reaction kinetics. The pressure-dependent rate constants are computed using system-specific quantum RRK theory. The calculated results show that the falloff effect of 1,5 and 1,6 H-migration reactions is more pronounced than that of the 1,7 H-migration reaction. The thermodynamics and kinetics presented in this study could be instrumental in understanding the low-temperature oxidation mechanism of DEM and might prove crucial for future research on comprehensively analyzing the autoignition behavior.

Reactions with Criegee intermediates are the dominant gas-phase sink for formyl fluoride in the atmosphere

Atmospheric oxidation processes are of central importance in atmospheric climate models. It is often considered that volatile organic molecules are mainly removed by hydroxyl radical; however, the kinetics of some reactions of hydroxyl radical with volatile organic molecules are slow. Here we report rate constants for rapid reactions of formyl fluoride with Criegee intermediates. These rate constants are calculated by dual-level multistructural canonical variational transition state theory with small-curvature tunneling (DL-MS-CVT/SCT). The treatment contains beyond-CCSD(T) electronic structure calculations for transition state theory, and it employs validated density functional input for multistructural canonical variational transition state theory with small-curvature tunneling and for variable-reaction-coordinate variational transition state theory. We find that the M11-L density functional has higher accuracy than CCSD(T)/CBS for the HC(O)F + CH2OO and HC(O)F + anti-CH3CHOO reactions. We find significant negative temperature dependence in the ratios of the rate constants for HC(O)F + CH2OO/anti-CH3CHOO to the rate constant for HC(O)F + OH. We also find that different Criegee intermediates have different rate-determining-steps in their reactions with formyl fluoride, and we find that the dominant gas-phase removal mechanism for HC(O)F in the atmosphere is the reaction with CH2OO and/or anti-CH3CHOO Criegee intermediates.

Insights into the role of the H-abstraction reaction kinetics of amines in understanding their degeneration fates under atmospheric and combustion conditions

Amines, a class of prototypical volatile organic compounds, have garnered considerable interest within the context of atmospheric and combustion chemistry due to their substantial contributions to the formation of hazardous pollutants in the atmosphere. In the current energy landscape, the implementation of carbon-neutral energy and strategic initiatives leads to generation of new amine sources that cannot be overlooked in terms of the emission scale. To reduce the emission level of amines from their sources and mitigate their impact on the formation of harmful substances, a comprehensive understanding of the fundamental reaction kinetics during the degeneration process of amines is imperative. This perspective article first presents an overview of both traditional amine sources and emerging amine sources within the context of carbon peaking and carbon neutrality and then highlights the importance of H-abstraction reactions in understanding the atmospheric and combustion chemistry of amines from the perspective of reaction kinetics. Subsequently, the current experimental and theoretical techniques for investigating the H-abstraction reactions of amines are introduced, and a concise summary of research endeavors made in this field over the past few decades is provided. In order to provide accurate kinetic parameters of the H-abstraction reactions of amines, advanced kinetic calculations are performed using the multi-path canonical variational theory combined with the small-curvature tunneling and specific-reaction parameter methods. By comparing with the literature data, current kinetic calculations are comprehensively evaluated, and these validated data are valuable for the development of the reaction mechanism of amines.

Comprehensive Multipath Variational Kinetics Study on Hydrogen Abstraction Reactions from Three Typical Dimethylcyclohexane Isomers by Hydroxyl Radicals: from the Electronic Structure to Model Applications

Cycloalkanes serve as an important class of chemical components in both fossil and alternative transportation fuels and have attracted considerable attention from the combustion community. Hydrogen abstractions from cycloalkanes by hydroxyl radicals initiate the fuel decomposition process and trigger off the subsequent chain reactions and thus play an important role in both combustion and atmospheric chemistry. The target of this study is to fill the vacancy in kinetics data toward the H-abstraction reactions by hydroxyl radical from three typical dimethylcyclohexane isomers through first-principles and direct dynamics. The rate constants involving 18 elementary reactions in total were accurately determined by the multipath canonical variational transition state theory with the multidimensional small-curvature correction for tunneling (MP-CVT/SCT), over a broad temperature range of 200-2000 K. The significant roles of multistructural torsional anharmonicity and recrossing effects were stressed per abstraction site, while the quantum tunneling effect was found to be slight at temperatures of interest in combustion. The discrepancies observed among different reaction systems at a similar abstraction site highlight the fuel molecular effects on site-specific rate constants. The comparison results of total rate constants given by different dynamics approaches prove the importance of considering the torsional anharmonicity, recrossing, and tunneling effects, and the robust feature of the simplified MS-CVT/SCT. The calculated total constants for dimethylcyclohexane isomers by OH are consistent with those measured for methylcyclohexane and 1,4-dimethylcyclohexane at low temperatures. The branching ratio analysis confirms the predominant role of the tertiary abstraction at low-to-intermediate temperatures and its growing competition with distinct secondary abstractions as temperature increases. The calculated rate constants were eventually fitted into the analytical expressions and incorporated into the kinetic models to learn about the influences on modeling performance.

Quantitative kinetics reveal that reactions of HO2 are a significant sink for aldehydes in the atmosphere and may initiate the formation of highly oxygenated molecules via autoxidation

Large aldehydes are widespread in the atmosphere and their oxidation leads to secondary organic aerosols. The current understanding of their chemical transformation processes is limited to hydroxyl radical (OH) oxidation during daytime and nitrate radical (NO3) oxidation during nighttime. Here, we report quantitative kinetics calculations of the reactions of hexanal (C5H11CHO), pentanal (C4H9CHO), and butanal (C3H7CHO) with hydroperoxyl radical (HO2) at atmospheric temperatures and pressures. We find that neither tunneling nor multistructural torsion anharmonicity should be neglected in computing these rate constants; strong anharmonicity at the transition states is also important. We find rate constants for the three reactions in the range 3.2-7.7 × 10-14 cm3 molecule-1 s-1 at 298 K and 1 atm, showing that the HO2 reactions can be competitive with OH and NO3 oxidation under some conditions relevant to the atmosphere. Our findings reveal that HO2-initiated oxidation of large aldehydes may be responsible for the formation of highly oxygenated molecules via autoxidation. We augment the theoretic studies with laboratory flow-tube experiments using an iodide-adduct time-of-flight chemical ionization mass spectrometer to confirm the theoretical predictions of peroxy radicals and the autoxidation pathway. We find that the adduct from HO2 + C5H11CHO undergoes a fast unimolecular 1,7-hydrogen shift with a rate constant of 0.45 s-1. We suggest that the HO2 reactions make significant contributions to the sink of aldehydes.

Quantum Tunneling Instability in Pericyclic Reactions

Several cycloreversion reactions of the retro-Diels-Alder type were computationally assessed to understand their quantum tunneling (QT) reactivity. N2, CO, and other leaving groups were considered based on their strong exothermicity, as it reduces their thermodynamic and kinetic stabilities. Our results indicate that for many of these reactions, it is essential to take into account their QT decomposition rate, which can massively weaken their molecular stability and shorten their half-lives even at deep cryogenic temperatures. In practical terms, this indicates that many supposedly stable molecules will actually be unsynthesizable or unisolable, and therefore trying to prepare or detect them would be a futile attempt. In addition, we discuss the importance of tunneling to correctly understand the enthalpy of activation and the collective atomic effect on the tunneling kinetic isotope effects to test if third-row atoms can tunnel in a chemical reaction. This project raises the question of the importance of in silico chemistry to guide in vitro chemistry, especially in cases where the latter cannot solve its own uncertainties.

New insights into the mechanism and kinetics of the addition reaction of unsaturated Criegee intermediates to CF3COOH and tropospheric implications

In this work, we have investigated the mechanism, thermochemistry and kinetics of the reaction of syn-cis-CH2RzCRyCO+O- (where Rz, Ry = H, CH3-) unsaturated Criegee intermediates (CIs) with CF3COOH using quantum chemical methods. The rate coefficients for the barrierless reactions were calculated using variable reaction coordinate variational transition state theory (VRC-VTST). For the syn-cis-CH2RzCRyCO+O- conformation in which conjugated CC and CO double bonds are aligned with each other, we propose a new pathway for the unidirectional addition of an OC-OH molecule (CF3COOH) to the CC double bond of syn-cis-CH2RzCRyCO+O-. The rate coefficient for the 1,4-CC addition reaction at 298 K is ∼10-10 to 10-11 cm3 s-1, resulting in the formation of CF3C(O)OCH2CRzRyCOOH trifluoroacetate alkyl allyl hydroperoxide (TFAAAH) as a new transitory adduct. It can act as a precursor for the formation of secondary organic aerosols (SOAs). This novel TFAAAH hydroperoxide was identified through a detailed quantum chemical study of the 1,4-addition mechanism and will provide new insights into the significance of the 1,4-addition reaction of unsaturated Cls with trace tropospheric gases on -CRzCH2 vinyl carbon atoms.

Rapid Atmospheric Reactions between Criegee Intermediates and Hypochlorous Acid

Hypochlorous acid (HOCl) is a paramount compound in the atmosphere due to its significant contribution to both tropospheric oxidation capacity and ozone depletion. The main removal routes for HOCl are photolysis and the reaction with OH during the daytime, while these processes are unimportant during the nighttime. Here, we report the rapid reactions of Criegee intermediates (CH2OO and anti/syn-CH3CHOO) with HOCl by using high-level quantum chemical methods as the benchmark; their accuracy is close to coupled cluster theory with single, double, and triple excitations and quasiperturbative connected quadruple excitations with a complete basis limit by extrapolation [CCSDT(Q)/CBS]. Their rate constants have been calculated by using a dual-level strategy; this combines conventional transition state theory calculated at the benchmark level with variational transition state theory with small-curvature tunneling by a validated density functional method. We find that the introduction of the methyl group into Criegee intermediates not only affects their reactivities but also exerts a remarkable influence on anharmonicity. The calculated results uncover that anharmonicity increases the rate constants of CH2OO + HOCl by a factor of 18-5, while it is of minor importance in the anti/syn-CH3CHOO + HOCl reaction at 190-350 K. The present findings reveal that the loose transition state for anti-CH3CHOO and HOCl is a rate-determining step at 190-350 K. We also find that the reaction of Criegee intermediates with HOCl contributes significantly to the sink of HOCl during the nighttime in the atmosphere.

Robust fragment-based method of calculating hydrogen atom transfer activation barrier in complex molecules

Dynamic processes driven by non-covalent interactions (NCI), such as conformational exchange, molecular binding, and solvation, can strongly influence the rate constants of reactions with low activation barriers, especially at low temperatures. Examples of this may include hydrogen-atom-transfer (HAT) reactions involved in the oxidative stress of an active pharmaceutical ingredient (API). Here, we develop an automated workflow to generate HAT transition-state (TS) geometries for complex and flexible APIs and then systematically evaluate the influences of NCI on the free activation energies, based on the multi-conformational transition-state theory (MC-TST) within the framework of a multi-step reaction path. The two APIs studied: fesoterodine and imipramine, display considerable conformational complexity and have multiple ways of forming hydrogen bonds with the abstracting radical-a hydroxymethyl peroxyl radical. Our results underscore the significance of considering conformational exchange and multiple activation pathways in activation calculations. We also show that structural elements and NCIs outside the reaction site minimally influence TS core geometry and covalent activation barrier, although they more strongly affect reactant binding and consequently the overall activation barrier. We further propose a robust and economical fragment-based method to obtain overall activation barriers, by combining the covalent activation barrier calculated for a small molecular fragment with the binding free energy calculated for the whole molecule.

Diffusion-based generative AI for exploring transition states from 2D molecular graphs

The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modeling their kinetics. Recently, machine learning (ML) models have shown remarkable performance for prediction of TS geometries. However, they require 3D conformations of reactants and products often with their appropriate orientations as input, which demands substantial efforts and computational cost. Here, we propose a generative approach based on the stochastic diffusion method, namely TSDiff, for prediction of TS geometries just from 2D molecular graphs. TSDiff outperforms the existing ML models with 3D geometries in terms of both accuracy and efficiency. Moreover, it enables to sample various TS conformations, because it learns the distribution of TS geometries for diverse reactions in training. Thus, TSDiff finds more favorable reaction pathways with lower barrier heights than those in the reference database. These results demonstrate that TSDiff shows promising potential for an efficient and reliable TS exploration.

Quantitative kinetics of the atmospheric reaction between isocyanic acid and hydroxyl radicals: post-CCSD(T) contribution, anharmonicity, recrossing effects, torsional anharmonicity, and tunneling

Hydroxyl radicals (OH) are the most important atmospheric oxidant, initiating atmospheric reactions for the chemical transformation of volatile organic compounds. Here, we choose the HNCO + OH reaction as a prototype reaction because it contains the fundamental reaction processes for OH radicals: H-abstraction reaction by OH and OH addition reaction. However, its kinetics are unknown under atmospheric conditions. We investigate the reaction of HNCO with OH by using the GMM(P).L method close to the accuracy of single, double, triple, and quadruple excitations and noniterative quintuple excitations with a complete basis set (CCSDTQ(P)/CBS) as benchmark results and a dual-level strategy for kinetics calculations. The calculated rate constant of HNCO + OH is in good agreement with the experimental data available at the temperatures between 620 and 2500 K. We find that the rate constant cannot be correctly obtained by using experimental data to extrapolate the atmospheric temperature ranges. We find that the post-CCSD(T) contribution is very large for the barrier height with the value of -0.85 kcal mol-1 for the H-abstraction reaction, while the previous investigations were done up to the CCSD(T) level. Moreover, we also find that recrossing effects, tunneling, torsional anharmonicity, and anharmonicity are important for obtaining quantitative kinetics in the OH + HNCO reaction.

Kinetics of Sulfur Trioxide Reaction with Water Vapor to Form Atmospheric Sulfuric Acid

Although experimental methods can be used to obtain the quantitative kinetics of atmospheric reactions, experimental data are often limited to a narrow temperature range. The reaction of SO3 with water vapor is important for elucidating the formation of sulfuric acid in the atmosphere; however, the kinetics is uncertain at low temperatures. Here, we calculate rate constants for reactions of sulfur trioxide with two water molecules. We consider two mechanisms: the SO3···H2O + H2O reaction and the SO3 + (H2O)2 reaction. We find that beyond-CCSD(T) contributions to the barrier heights are very large, and multidimensional tunneling, unusually large anharmonicity of high-frequency modes, and torsional anharmonicity are important for obtaining quantitative kinetics. We find that at lower temperatures, the formation of the termolecular precursor complexes, which is often neglected, is rate-limiting compared to passage through the tight transition states. Our calculations show that the SO3···H2O + H2O mechanism is more important than the SO3 + (H2O)2 mechanism at 5-50 km altitudes. We find that the rate ratio between SO3···H2O + H2O and SO3 + (H2O)2 is greater than 20 at altitudes between 10 and 35 km, where the concentration of SO3 is very high.

Quantitative Kinetics of HO2 Reactions with Aldehydes in the Atmosphere: High-Order Dynamic Correlation, Anharmonicity, and Falloff Effects Are All Important

Kinetics provides the fundamental parameters for elucidating sources and sinks of key atmospheric species and for atmospheric modeling more generally. Obtaining quantitative kinetics in the laboratory for the full range of atmospheric temperatures and pressures is quite difficult. Here, we use computational chemistry to obtain quantitative rate constants for the reactions of HO₂ with HCHO, CH₃CHO, and CF₃CHO. First, we calculate the high-pressure-limit rate constants by using a dual-level strategy that combines conventional transition state theory using a high level of electronic structure wave function theory with canonical variational transition state theory including small-curvature tunneling using density functional theory. The wave-function level is beyond-CCSD(T) for HCHO and CCSD(T)-F12a (Level-A) for XCHO (X = CH₃, CF₃), and the density functional (Level-B) is specifically validated for these reactions. Then, we calculate the pressure-dependent rate constants by using system-specific quantum RRK theory (SS-QRRK) and also by an energy-grained master equation. The two treatments of the pressure dependence agree well. We find that the Level-A//Level-B method gives good agreement with CCSDTQ(P)/CBS. We also find that anharmonicity is an important factor that increases the rate constants of all three reactions. We find that the HO₂ + HCHO reaction has a significant dependence on pressure, but the HO₂ + CF₃CHO reaction is almost independent of pressure. Our findings show that the HO₂ + HCHO reaction makes important contribution to the sink for HCHO, and the HO₂ + CF₃CHO reaction is the dominant sink for CF₃CHO in the atmosphere.

MISPR: an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure-Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure-property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

Large Pressure Effects Caused by Internal Rotation in the s-cis-syn-Acrolein Stabilized Criegee Intermediate at Tropospheric Temperature and Pressure

Criegee intermediates are important atmospheric oxidants, and quantitative kinetics for stabilized Criegee intermediates are key parameters for atmospheric modeling but are still limited. Here we report barriers and rate constants for unimolecular reactions of s-cis-syn-acrolein oxide (scsAO), in which the vinyl group makes it a prototype for Criegee intermediates produced in the ozonolysis of isoprene. We find that the MN15-L and M06-2X density functionals have CCSD(T)/CBS accuracy for the unimolecular cyclization and stereoisomerization of scsAO. We calculated high-pressure-limit rate constants by the dual-level strategy that combines (a) high-level wave function-based conventional transition-state theory (which includes coupled-cluster calculations with quasiperturbative inclusion of quadruple excitations because of the strongly multiconfigurational character of the electronic wave function) and (b) canonical variational transition-state theory with small-curvature tunneling based on a validated density functional. We calculated pressure-dependent rate constants both by system-specific quantum Rice-Ramsperger-Kassel theory and by solving the master equation. We report rate constants for unimolecular reactions of scsAO over the full range of atmospheric temperature and pressure. We found that the unimolecular reaction rates of this larger-than-previously studied Criegee intermediate depend significantly on pressure. Particularly, we found that falloff effects decrease the effective unimolecular cyclization rate constant of scsAO by about a factor of 3, but the unimolecular reaction is still the dominant atmospheric sink for scsAO at low altitudes. The large falloff caused by the inclusion of the stereoisomerization channel in the master equation calculations has broad implications for mechanistic analysis of reactions with competitive internal rotations that can produce stable rotamers.

An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers

This work presents a protocol designed to study hydrogen abstraction reactions by atomic hydrogen in molecules with multiple conformations.

Differences in the torsional anharmonicity between reactant and transition state: the case of 3-butenal + H abstraction reactions

Thermal rate coefficients for the hydrogen-abstraction reactions of 3-butenal by a hydrogen atom were obtained applying multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). Torsional anharmonicity due to the hindered rotors was taken into account by calculating the rovibrational partition function using the extended two-dimensional torsional (E2DT) method. For comparison, rovibrational partition functions were also estimated using the multistructural method with torsional anharmonicity based on a coupled torsional potential (MS-T(C)). By contrast, with (E)-2-butenal reactions, the abstraction reactions of 3-butenal proceed via five reaction channels (R1)-(R5). In a conformational search, 45 distinguishable structures of transition states were found, including enantiomers, which were separated into six conformational reaction channels (CRCs). The individual reactive paths were constructed, the recrossing and semiclassical transmission coefficients estimated, and the multipath rate constants were obtained. High torsional barriers between the wells of CRC2/CRC6 indicate a harmonic behavior. Consequently, a difference between the torsional anharmonicity of 3-butenal and the transition states is responsible for the increase in the thermal rate constants for channel (R2). Analysis of the contributions of each conformer of the transition state shows an important contribution of the high-energy rotamers in the total flux of (R1)-(R5). After fitting the rate constants in a four-parameter equation, the activation energy estimation showed a strong temperature dependence.

Benchmark calculations for bond dissociation energies and enthalpy of formation of chlorinated and brominated polycyclic aromatic hydrocarbons

Thermodynamic properties, i.e., bond dissociation energies and enthalpy of formation, of chlorinated and brominated polycyclic aromatic hydrocarbons play a fundamental role in understanding their formation mechanisms and reactivity. Computational electronic structure calculations routinely used to predict thermodynamic properties of various species are limited for these compounds due to large computational cost to obtain accurate results by employing high-level wave function theory methods. In this work, a number of composite model chemistry methods (CBS-QB3, G3MP2, G3, and G4) are used to compute bond dissociation energies and enthalpies of formation of small to medium-size chlorinated and brominated polycyclic aromatic hydrocarbon compounds. The enthalpy of formation is derived via the atomization method and compared against the recommended values. Statistical analysis indicates that G4 is the best method. For comparison, three commonly used density functional theory (DFT) methods (M06-2X, ωB97X-D and B2PLYP-D3) with various basis sets including 6-311++G(d, p), cc-pVTZ, and cc-pVQZ in the prediction of bond dissociation energies and enthalpies of formation have been tested using the optimized geometries at the same M06-2X/6-311++G(d, p) level of theory. It is found that ωB97X-D/6-311++G(d, p) shows the best performance in computing the bond dissociation energies, while ωB97X-D/cc-pVTZ exhibits the best prediction in enthalpy of formation of the studied reaction systems. The structural effect on the bond dissociation energies and enthalpy of formation of chlorinated and brominated polycyclic aromatic hydrocarbons are then systematically analyzed. Based on comparisons of the various methods, reliable DFT methods are recommended for future theoretical studies on large chlorinated and brominated polycyclic aromatic hydrocarbons considering both accuracy and computational cost. This work, to the authors' knowledge, is the first to systematically benchmark theoretical methods for the accurate prediction of thermodynamic properties for chlorinated and brominated polycyclic aromatic hydrocarbons.

Benchmark calculations using state-of-the-art DFT functionals and composite methods for bond dissociation energy and enthalpy of formation of halogenated polycyclic aromatic hydrocarbons are performed.

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Chemical kinetics plays a fundamental role in the understanding and modeling of tropospheric chemical processes, one of the most important being the atmospheric degradation of volatile organic compounds. These potentially harmful molecules are emitted into the troposphere by natural and anthropogenic sources and are chemically removed by undergoing oxidation processes, most frequently initiated by reaction with OH radicals, the atmosphere's "detergent". Obtaining the respective rate constants is therefore of critical importance, with calculations based on transition state theory (TST) often being the preferred choice. However, for molecules with rich conformational variety, a single-conformer method such as lowest-conformer TST is unsuitable while state-of-the-art TST-based methodologies easily become unmanageable. In this Feature Article, the author reviews his own cost-effective protocol for the calculation of bimolecular rate constants of OH-initiated reactions in the high-pressure limit based on multiconformer transition state theory. The protocol, which is easily extendable to other oxidation reactions involving saturated organic molecules, is based on a variety of freeware and open-source software and tested against a series of oxidation reactions of hydrofluoropolyethers, computationally very challenging molecules with potential environmental relevance. The main features, advantages and disadvantages of the protocol are presented, along with an assessment of its predictive utility based on a comparison with experimental rate constants.

Kinetic Study of Gas-Phase Reactions of Pyruvic Acid with HO2

Gas-phase reactions between pyruvic acid (PA) and HO₂ radicals were examined using ab initio quantum chemistry and transition state theory. The rate coefficients were determined over a temperature range of 200-400 K including tunneling contributions. Six potential reaction pathways were identified. The two hydrogen abstraction reactions yielding the H₂O₂ product were found to have high barriers. The HO₂ radical was also found to have a catalytic effect on the intramolecular hydrogen transfer reactions occurring by three distinct routes. These hydrogen-shift reactions are very interesting mechanistically although they are highly endothermic. The only reaction that contributes significantly to the consumption of PA is a multistep pathway involving a peroxy-radical intermediate, PA + HO₂ → CH₃COOH + OH + CO₂. This exothermic process has potential atmospheric relevance because it produces an OH radical as a product. Atmospheric models currently have difficulty predicting accurate OH concentrations for certain atmospheric conditions, such as environments free of NOx and the nocturnal boundary layer. Reactions of this sort, although not necessary with PA, may account for a portion of this deficit. The present study helps settle the issue of the relative roles of reaction and photolysis in consumption of PA in the troposphere.

BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules

A broad collection of technologies, including e.g. drug metabolism, biofuel combustion, photochemical decontamination of water, and interfacial passivation in energy production/storage systems rely on chemical processes that involve bond-breaking molecular reactions. In this context, a fundamental thermodynamic property of interest is the bond dissociation energy (BDE) which measures the strength of a chemical bond. Fast and accurate prediction of BDEs for arbitrary molecules would lay the groundwork for data-driven projections of complex reaction cascades and hence a deeper understanding of these critical chemical processes and, ultimately, how to reverse design them. In this paper, we propose a chemically inspired graph neural network machine learning model, BonDNet, for the rapid and accurate prediction of BDEs. BonDNet maps the difference between the molecular representations of the reactants and products to the reaction BDE. Because of the use of this difference representation and the introduction of global features, including molecular charge, it is the first machine learning model capable of predicting both homolytic and heterolytic BDEs for molecules of any charge. To test the model, we have constructed a dataset of both homolytic and heterolytic BDEs for neutral and charged (-1 and +1) molecules. BonDNet achieves a mean absolute error (MAE) of 0.022 eV for unseen test data, significantly below chemical accuracy (0.043 eV). Besides the ability to handle complex bond dissociation reactions that no previous model could consider, BonDNet distinguishes itself even in only predicting homolytic BDEs for neutral molecules; it achieves an MAE of 0.020 eV on the PubChem BDE dataset, a 20% improvement over the previous best performing model. We gain additional insight into the model's predictions by analyzing the patterns in the features representing the molecules and the bond dissociation reactions, which are qualitatively consistent with chemical rules and intuition. BonDNet is just one application of our general approach to representing and learning chemical reactivity, and it could be easily extended to the prediction of other reaction properties in the future.

Rate coefficients and product branching ratios for (E)-2-butenal + H reactions

Thermal rate constants for the hydrogen abstraction reactions of (E)-2-butenal by hydrogen atoms were calculated, for the first time, using the multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). After a torsional potential energy surface exploration, ten conformations of the transition states (including the mirror images) were found and separated into four conformational reaction channels (CRCs). Individual energy paths of each CRC were built, recrossing and quantum tunneling effects estimated, and the thermal rate constants obtained. Due to the hindered rotors, the torsional anharmonicity was incorporated in the rate coefficient through the calculations of the rovibrational partition functions using the extended two-dimensional torsional method (E2DT). For comparison, the one-well (1W-CVT/SCT) and harmonic multipath (MP-CVT/SCT) thermal rate constants were also estimated. In addition, kinetic Monte Carlo (KMC) simulations were performed to predict the product branching ratios. For all kinetic approaches, the formation of products of (R1) is predominant. Compared to the harmonic multipath estimation, the percentage of reaction (R4) increases by approximately 9% when the torsional anharmonicity is taken into account. For the reactions (R2) and (R3), the product branching ratio is slightly decreased when compared with the harmonic simulation.

Anharmonic kinetics of the cyclopentane reaction with hydroxyl radical

Cyclopentane is one of the major constituents of transportation fuels, especially jet fuel and diesel, and also is a volatile organic compound with a significant presence in the atmosphere. Hydrogen abstraction from cyclopentane by hydroxyl radical plays a significant role in combustion and atmospheric chemistry. In this work we study the kinetics of this reaction at 200-2000 K using direct dynamics calculations in which the potential energy surface is obtained by quantum mechanical electronic structure calculations. The forward and reverse barrier heights and reaction energies obtained by the CCSD(T)-F12a/jun-cc-pVTZ coupled cluster calculations are used as a benchmark to select an accurate electronic structure method among 36 combinations of exchange-correlation functional and basis set. The selected M06-2X/MG3S method shows the best performance with a mean unsigned deviation from the benchmark of only 0.22 kcal mol-1 for reaction energies and barrier heights. A quadratic-quartic function is adopted to describe the ring bending potential of cyclopentane, and the quartic anharmonicity in the bending mode is treated by a one-dimensional Schrödinger equation using both Wentzel-Kramers-Brillouin (WKB) and Fourier Grid Hamiltonian (FGH) methods. The torsional anharmonicity in the transition state is treated in turn by the free rotor approximation, the one-dimensional hindered rotor approximation, and the multi-structural torsional anharmonicity method. Rate constants of the title reaction are computed by canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation (CVT/SCT). The final rate constants include the quasiharmonic, quadratic-quartic, and torsional anharmonicity. Our calculations are in excellent agreement with all the experimental data available at both combustion and atmospheric temperatures with a deviation of less than 30%.

New mechanistic pathways for the formation of organosulfates catalyzed by ammonia and carbinolamine formation catalyzed by sulfuric acid in the atmosphere

Sulfuric acid exerts a remarkable catalytic role in the H₂SO₄ + HCHO + NH₃ reaction that leads to the formation of carbinolamine.

Multistructural Anharmonicity Controls the Radical Generation Process in Biofuel Combustion

The OH radical plays an important role in combustion, and isopentanol (3-methylbutan-1-ol) is a promising sustainable fuel additive and second-generation biofuel. The abstractions of H atoms from fuel molecules are key initiation steps for chain branching in combustion chemistry. In comparison with the more frequently studied ethanol, isopentanol has a longer carbon chain that allows a greater number of products, and experimental work is unavailable for the branching fractions to the various products. However, the site-dependent kinetics of isopentanol with OH radicals are usually experimentally unavailable. Alcohol oxidation by OH is also important in the atmosphere, and in the present study we calculate the rate constants and branching fractions of the hydrogen abstraction reaction of isopentanol by OH radical in a broad temperature range of 298-2400 K, covering temperatures important for atmospheric chemistry and those important for combustion. The calculations are done by multipath variational transition state theory (MP-VTST). With a combination of electronic structure calculations, we determine previously missing thermochemical data. With MP-VTST, a multidimensional tunneling approximation, multiple-structure anharmonicity, and torsional potential anharmonicity, we carried out more realistic rate constant calculations than can be computed by conventional single-structure harmonic transition state theory or by the empirical relations that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated, and we show that recrossing, tunneling, and multiple structures are all essential for accurate work. We conclude that the multiple structure anharmonicity is the most important correction to conventional transition state theory for this reaction, although recrossing effects and tunneling are by no means insignificant and the tunneling depends significantly on the path. The thermodynamic and kinetics data determined in this work are indispensable for the gas-phase degradation of alcohols in the atmosphere and for the detailed understanding and prediction of ignition mechanisms of biofuels in combustion.

Rapid unimolecular reaction of stabilized Criegee intermediates and implications for atmospheric chemistry

Elucidating atmospheric oxidation mechanisms is necessary for estimating the lifetimes of atmospheric species and understanding secondary organic aerosol formation and atmospheric oxidation capacity. We report an unexpectedly fast mechanistic pathway for the unimolecular reactions of large stabilized Criegee intermediates, which involves the formation of bicyclic structures from large Criegee intermediates containing an aldehyde group. The barrier heights of the mechanistic pathways are unexpectedly low – about 2–3 kcal/mol – and are at least 10 kcal/mol lower than those of hydrogen shift processes in large syn Criegee intermediates; and the calculated rate constants show that the mechanistic pathways are 10⁵-10⁹ times faster than those of the corresponding hydrogen shift processes. The present findings indicate that analogous low-energy pathways can now also be expected in other large Criegee intermediates and that oxidative capacity of some Criegee intermediates is smaller than would be predicted by existing models.

Criegee intermediates have received much attention in atmospheric chemistry because of their importance in ozonolysis mechanisms. Here, using quantum mechanical kinetics, the authors reveal an unexpectedly fast mechanistic pathway for unimolecular reactions of large stabilized Criegee intermediates.

Kinetics of Hydrogen Abstraction Reactions of Methyl Palmitate and Octadecane by Hydrogen Atoms

Hydrogen abstractions play a crucial role in the consumption of fuel molecules during fuel pyrolysis and combustion processes. In this study, a generalized energy-based fragmentation approach was used to obtain CCSD(T)-F12a/cc-pVTZ energy barriers of hydrogen abstraction reactions by hydrogen atoms from methyl palmitate (C₁₅H₃₁COOCH₃), a key component of biodiesel. The accuracy of M06-2X/6-311++G(d,p) for obtaining the energy barriers was evaluated against the CCSD(T) results. Based on the quantum chemical results, the high-pressure-limit rate constants for C₁₅H₃₁COOCH₃ + H were calculated and compared with those of octadecane ( n-C₁₈H₃₈) reacting with H. The treatment of hindered internal rotations for such long-chain molecules was discussed and the rate rules for different abstraction sites were summarized. The results show that in the C₁₅H₃₁COOCH₃ + H system, the α hydrogen abstraction no longer plays a dominant role as in small methyl esters, and the hydrogen atoms of CH₂ groups far away from the ester group are more easily abstracted than those near the ester group.

Benchmarking dual-level MS-Tor and DLPNO-CCSD(T) methods for H-abstraction from methyl pentanoate by an OH radical

Methyl pentanoate (MP) was recently proposed as a potential biodiesel surrogate due to its negative temperature coefficient region.

Kinetics of the Toluene Reaction with OH Radical

We calculated the kinetics of chemical activation reactions of toluene with hydroxyl radical in the temperature range from 213 K to 2500 K and the pressure range from 10 Torr to the high-pressure limit by using multistructural variational transition state theory with the small-curvature tunneling approximation (MS-CVT/SCT) and using the system-specific quantum Rice-Ramsperger-Kassel method. The reactions of OH with toluene are important elementary steps in both combustion and atmospheric chemistry, and thus it is valuable to understand the rate constants both in the high-pressure, high-temperature regime and in the low-pressure, low-temperature regime. Under the experimental pressure conditions, the theoretically calculated total reaction rate constants agree well with the limited experimental data, including the negative temperature dependence at low temperature. We find that the effect of multistructural anharmonicity on the partition functions usually increases with temperature, and it can change the calculated reaction rates by factors as small as 0.2 and as large as 4.2. We also find a large effect of anharmonicity on the zero-point energies of the transition states for the abstraction reactions. We report that abstraction of H from methyl should not be neglected in atmospheric chemistry, even though the low-temperature results are dominated by addition. We calculated the product distribution, which is usually not accessible to experiments, as a function of temperature and pressure.

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Mechanism and rate constant of proline-catalysed asymmetric aldol reaction of acetone and p-nitrobenzaldehyde in solution medium: Density-functional theory computation

In search of new ways to improve catalyst design, the current research focused on using quantum mechanical descriptors to investigate the effect of proline as a catalyst for mechanism and rate of asymmetric aldol reaction. A plausible mechanism of reaction between acetone and 4-nitrobenzaldehyde in acetone medium was developed using highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies calculated via density functional theory (DFT) at the 6-31G∗/B3LYP level of theory. New mechanistic steps were proposed and found to follow, with expansion, the previously reported iminium-enamine route of typical class 1 aldolase enzymes. From the elementary steps, the first step which involves a bimolecular collision of acetone and proline was considered as the rate-determining step, having the highest activation energy of 59.07 kJ mol^-1. The mechanism was used to develop the rate law from which the overall rate constant was calculated and found to be 4.04×10-8dm3mol-1s-1 . The new mechanistic insights and the explicit computation of the rate constant further improve the kinetic knowledge of the reaction.

A novel assessment of the role of the methyl radical and water formation channel in the CH3OH + H reaction

A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K. Furthermore, the kinetic rate constant of all three channels was calculated using a high-level deformed-transition state theory (d-TST) at a benchmark electronic structure level. d-TST is shown to be suitable for describing the overall rate constant for the CH₃OH + H reaction (an archetype of the moderate tunnelling regime) with the precision required for practical applications. Considering the experimental ratios at 1000 K, k_R1/k_R2 ≈ 0.84 and k_R1/k_R3 ≈ 15-40, we provided a better estimate when compared with previous theoretical work: 7.47 and 637, respectively. The combination of these procedures explicitly demonstrates the role of the third channel in a significant range of temperatures and indicates its importance considering the thermodynamic control to estimate methyl radical and water formation. We expect that these results can help to shed new light on the fundamental kinetic rate equations for the CH₃OH + H reaction.

Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: a definitive test for fluoroform dissociation

Understanding the falloff in rate constants of gas-phase unimolecular reaction rate constants as the pressure is lowered is a fundamental problem in chemical kinetics, with practical importance for combustion, atmospheric chemistry, and essentially all gas-phase reaction mechanisms. In the present work, we use our recently developed system-specific quantum RRK theory, calibrated by canonical variational transition state theory with small-curvature tunneling, combined with the Lindemann-Hinshelwood mechanism, to model the dissociation reaction of fluoroform (CHF3), which provides a definitive test for falloff modeling. Our predicted pressure-dependent thermal rate constants are in excellent agreement with experimental values over a wide range of pressures and temperatures. The present validation of our methodology, which is able to include variational transition state effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and torsional and other vibrational anharmonicity, together with state-of-the-art reaction-path-based direct dynamics calculations, is important because the method is less empirical than models routinely used for generating full mechanisms, while also being simpler in key respects than full master equation treatments and the full reduced falloff curve and modified strong collision methods of Troe.

Atmospheric chemistry of CH3CHO: the hydrolysis of CH3CHO catalyzed by H2SO4

We found the catalytic effect of H₂SO₄ on the hydrolysis of CH₃CHO in the atmosphere.

DFT studies on quantum mechanical tunneling in tautomerization of three-membered rings

Amino–imino and keto–enol tautomerization processes in three-membered ring systems have been explored to examine the role of quantum mechanical tunneling along with aromaticity. The DFT calculations shed light on the role of aromaticity in tautomerization processes and as perceived this property may not contribute entirely to facilitate the formation of tautomeric forms.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500-600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound's molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

Degradation of Carbonyl Hydroperoxides in the Atmosphere and in Combustion

Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autoxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere, the degradation of carbonyl hydroperoxides leads to low-vapor-pressure polyfunctional species that may precipitate in clouds and fog droplets or to the formation of secondary organic aerosols (SOAs). In combustion, the fate of carbonyl hydroperoxides is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the carbonyl hydroperoxides is reaction with OH radicals, for which kinetics data are experimentally unavailable. Here, we study 4-hydroperoxy-2-pentanone (CH₃C(═O)CH₂CH(OOH)CH₃) as a model compound to clarify the kinetics of OH reactions with carbonyl hydroperoxides, in particular H atom abstraction and OH addition reactions. With a combination of electronic structure calculations, we determine previously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunneling (MT) approximation, multiple-structure anharmonicity, and torsional potential anharmonicity, we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for the addition reaction are computed using system-specific quantum RRK theory. The calculated temperature range is 298-2400 K, and the pressure range is 0.01-100 atm. The accurate thermodynamic and kinetics data determined in this work are indispensable in the global modeling of SOAs in atmospheric science and in the detailed understanding and prediction of ignition properties of hydrocarbons and alternative fuels.

Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms

We studied hydrogen abstraction reactions at various sites of unsaturated methyl esters by H atoms, including variational effects, tunneling and multi-structural torsional anharmonicity.

Variational transition state theory: theoretical framework and recent developments

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.

Reaction of SO2with OH in the atmosphere

We theoretically investigate the rate constantk(T,p) of the OH + SO₂reaction with experimental accuracy.

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C₂F₄), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.