Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates

Fast and accurate prediction of solvent effects on reaction rates are crucial for kinetic modeling, chemical process design, and high-throughput solvent screening. Despite the recent advance in machine learning, a scarcity of reliable data has hindered the development of predictive models that are generalizable for diverse reactions and solvents. In this work, we generate a large set of data with the COSMO-RS method for over 28 000 neutral reactions and 295 solvents and train a machine learning model to predict the solvation free energy and solvation enthalpy of activation (ΔΔG‡solv, ΔΔH‡solv) for a solution phase reaction. On unseen reactions, the model achieves mean absolute errors of 0.71 and 1.03 kcal mol-1 for ΔΔG‡solv and ΔΔH‡solv, respectively, relative to the COSMO-RS calculations. The model also provides reliable predictions of relative rate constants within a factor of 4 when tested on experimental data. The presented model can provide nearly instantaneous predictions of kinetic solvent effects or relative rate constants for a broad range of neutral closed-shell or free radical reactions and solvents only based on atom-mapped reaction SMILES and solvent SMILES strings.

The merit of pressure dependent kinetic modelling in steam cracking

Renewable cracking feedstocks from plastic waste and the need for novel reactor designs related to electrification of steam crackers drives the development of accurate and fundamental kinetic models for this process, despite its large scale implementation for more than half a century. Pressure dependent kinetics have mostly been omitted in fundamental steam cracking models, while they are crucial in combustion models. Therefore, we have assessed the importance of pressure dependent kinetics for steam cracking via in-depth modelling and experimental studies. In particular we have studied the influence of considering fall-off on the product yields for ethane and propane steam cracking. A high-pressure limit fundamental kinetic model is generated, based on quantum chemical data and group additive values, and supplemented with literature values for pressure dependent kinetic parameters for β-scission reactions and homolytic bond scissions of C₂ and C₃ species. Model simulations with high-pressure limit rate coefficients and pressure dependent kinetics are compared to new experimental measurements. Steam cracking experiments for pure ethane and propane feeds are performed on a tubular bench-scale reactor at 0.17 MPa and temperatures ranging from 1058 to 1178 K. All important product species are identified using a comprehensive GC × GC-FID/q-MS. For homolytic bond scissions, the inclusion of pressure dependent kinetics has a significant effect on the conversion profile for ethane steam cracking. On the other hand, pressure dependence of C₂ β-scissions significantly influences conversion and product species profiles for both ethane and propane steam cracking. The C₃ β-scissions pressure dependence has a negligible effect in ethane steam cracking, while for propane steam cracking the effect is non-negligible on the product species profiles.

Fast Predictions of Reaction Barrier Heights: Toward Coupled-Cluster Accuracy

Quantitative estimates of reaction barriers are essential for developing kinetic mechanisms and predicting reaction outcomes. However, the lack of experimental data and the steep scaling of accurate quantum calculations often hinder the ability to obtain reliable kinetic values. Here, we train a directed message passing neural network on nearly 24,000 diverse gas-phase reactions calculated at CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP. Our model uses 75% fewer parameters than previous studies, an improved reaction representation, and proper data splits to accurately estimate performance on unseen reactions. Using information from only the reactant and product, our model quickly predicts barrier heights with a testing MAE of 2.6 kcal mol^-1 relative to the coupled-cluster data, making it more accurate than a good density functional theory calculation. Furthermore, our results show that future modeling efforts to estimate reaction properties would significantly benefit from fine-tuning calibration using a transfer learning technique. We anticipate this model will accelerate and improve kinetic predictions for small molecule chemistry.

High-Pressure-Limit and Pressure-Dependent Rate Rules for Unimolecular Reactions Related to Hydroperoxy Alkyl Radicals in Normal Alkyl Cyclohexane Combustion. 1. Concerted HO2 Elimination Reaction Class and β-Scission Reaction Class

The reactions of the concerted HO₂ elimination from alkyl peroxy radicals and the β-scission of the C-OOH bond from hydroperoxy alkyl radicals, which lead to the formation of olefins and HO₂ radicals, are two important reaction classes that compete with the second O₂ addition step of hydroperoxy alkyl radicals, which are responsible for the chain branching in the low-temperature oxidation of normal alkyl cycloalkanes. These two reaction classes are also believed to be responsible for the negative temperature coefficient behavior due to the formation of the relatively unreactive HO₂ radical, which has the potential to inhibit ignition of normal alkyl cycloalkanes. In this work, the kinetics of the above two reaction classes in normal alkyl cycloalkanes are studied, where reactions in the concerted elimination class are divided into subclasses depending upon the types of carbons from which the H atom is eliminated and the positions of the reaction center (on the alkyl side chain or on the cycle), and the reactions in the β-scission reaction class are divided into subclasses depending upon the types of the carbons on which the radical is located and the positions of the reaction center. Energy barriers by using quantum chemical methods at the CBS-QB3 level, high-pressure-limit rate constants by using canonical transition state theory, and pressure-dependent rate constants at pressures from 0.01 to 100 atm by using Rice-Ramsberger-Kassel-Marcus/Master Equation theory are calculated for a representative set of reactions from methyl cyclohexane to n-butyl cyclohexane in each subclass, from which high-pressure-limit rate rules and pressure-dependent rate rules for each subclass are derived from the average rate constants of reactions within each subclass. A comparison of the rate constants for the reactions in the two reaction classes calculated in this work is made with the rate constants of the same reactions from available mechanisms published in the literature, where most of the rate constants are approximately estimated from analogous reactions in alkanes or small alkyl cyclohexanes, and it is found that a large difference may exist between them, indicating that the present work, which provides more accurate kinetic parameters and reasonable rate rules for these reaction classes, can be helpful to construct higher-accuracy mechanism models for normal alkyl cyclohexane combustion.

Electronic structure-based rate rules for ipso addition-elimination reactions on mono-aromatic hydrocarbons with single and double OH/CH3/OCH3/CHO/C2H5 substituents: a systematic theoretical investigation

The recent interest in bio-oils combustion and the key role of mono-aromatic hydrocarbons (MAHs) in existing kinetic frameworks, both in terms of poly-aromatic hydrocarbons growth and surrogate fuels formulation, motivates the current systematic theoretical investigation of one of the relevant reaction classes in MAHs pyrolysis and oxidation: ipso substitution by hydrogen. State-of-the-art theoretical methods and protocols implemented in automatized computational routines allowed to investigate 14 different potential energy surfaces involving MAHs with hydroxy and methyl single (phenol and toluene) and double (o-,m-,p-C6H4(OH)2, o-,m-,p-CH3C6H4OH, and o-,m-,p-C6H4(CH3)2) substituents, providing rate constants for direct implementation in existing kinetic models. The accuracy of the adopted theoretical method was validated by comparison of the computed rate constants with the available literature data. Systematic trends in energy barriers, pre-exponential factors, and temperature dependence of the Arrhenius parameters were found, encouraging the formulation of rate rules for ipso substitutions on MAHs. The rules here proposed allow to extrapolate from a reference system the necessary activation energy and pre-exponential factor corrections for a large number of reactions from a limited set of electronic structure calculations. We were able to estimate rate constants for other 63 ipso addition-elimination reactions on di-substituted MAHs, reporting in total 75 rate constants for ipso substitution reactions o-,m-,p-R'C6H4R + → C6H5R + ', with R,R' = OH/CH3/OCH3/CHO/C2H5, in the 300-2000 K range. Additional calculations performed for validation showed that the proposed rate rules are in excellent agreement with the rate constants calculated using the full computational protocol in the 500-2000 K range, generally with errors below 20%, increasing up to 40% in a few cases. The main results of this work are the successful application of automatized electronic structure calculations for the derivation of accurate rate constants for ipso substitution reactions on MAHs, and an efficient and innovative approach for rate rules formulation for this reaction class.

An ab Initio/Transition State Theory Study of the Reactions of Ċ5H9 Species of Relevance to 1,3-Pentadiene, Part II: Pressure Dependent Rate Constants and Implications for Combustion Modeling

The temperature- and pressure-dependence of rate constants for several radicals and unsaturated hydrocarbons reactions (1,3-C₅H₈/1,4-C₅H₈/cyC₅H₈ + Ḣ, C₂H₄ + Ċ₃H₅-a, C₃H₆ + Ċ₂H₃) are analyzed in this paper. The abstraction reactions of these systems are also calculated and compared with available literature data. Ċ₅H₉ radicals can be produced via Ḣ atom addition reactions to the pentadiene isomers and cyclopentene, and also by H-atom abstraction reactions from 1- and 2-pentene and cyclopentane. Comprehensive Ċ₅H₉ potential energy surface (PES) analyses and high-pressure limiting rate constants for related reactions have been explored in part I of this work ( J. Phys. Chem. A 2019, 123 (22), 9019-9052). In this work, a chemical kinetic model is constructed based on the computed thermochemistry and high-pressure limiting rate constants from part I, to further understand the chemistry of different C₅H₈ molecules. The most important channels for these addition reactions are discussed in the present work based on reaction pathway analyses. The dominant reaction pathways for these five systems are combined together to generate a simplified Ċ₅H₉ PES including nine reactants, 25 transition states (TSs), and nine products. Spin-restricted single point energies are calculated for radicals and TSs on the simplified PES at the ROCCSD(T)/aug-cc-pVTZ level of theory with basis set corrections from MP2/aug-cc-pVXZ (where X = T and Q). Temperature- and pressure-dependent rate constants are calculated using RRKM theory with a Master Equation analysis, with restricted energies used for minima on the simplified Ċ₅H₉ PES and unrestricted energies for other species, over a temperature range of 300-2000 K and in the pressure range 0.01-100 atm. The rate constants calculated are in good agreement with those in the literature. The chemical kinetic model is updated with pressure-dependent rate constants and is used to simulate the species concentration profiles for Ḣ atom addition to cyclopentane and cyclopentene. Through detailed analyses and comparisons, this model can reproduce the experimental measurements of species qualitatively and quantitatively with reasonably good agreement.

Deep Learning of Activation Energies

Quantitative predictions of reaction properties, such as activation energy, have been limited due to a lack of available training data. Such predictions would be useful for computer-assisted reaction mechanism generation and organic synthesis planning. We develop a template-free deep learning model to predict the activation energy given reactant and product graphs and train the model on a new, diverse data set of gas-phase quantum chemistry reactions. We demonstrate that our model achieves accurate predictions and agrees with an intuitive understanding of chemical reactivity. With the continued generation of quantitative chemical reaction data and the development of methods that leverage such data, we expect many more methods for reactivity prediction to become available in the near future.

A combined experimental and computational study on the reaction dynamics of the 1-propynyl radical (CH3CC; X2A1) with ethylene (H2CCH2; X1A1g) and the formation of 1-penten-3-yne (CH2CHCCCH3; X1A')

The crossed molecular beam reactions of the 1-propynyl radical (CH₃CC; X²A₁) with ethylene (H₂CCH₂; X¹A_1g) and ethylene-d₄ (D₂CCD₂; X¹A_1g) were performed at collision energies of 31 kJ mol^-1 under single collision conditions. Combining our laboratory data with ab initio electronic structure and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) calculations, we reveal that the reaction is initiated by the barrierless addition of the 1-propynyl radical to the π-electron density of the unsaturated hydrocarbon of ethylene leading to a doublet C₅H₇ intermediate(s) with a life time(s) longer than the rotation period(s). The reaction eventually produces 1-penten-3-yne (p1) plus a hydrogen atom with an overall reaction exoergicity of 111 ± 16 kJ mol^-1. About 35% of p1 originates from the initial collision complex followed by C-H bond rupture via a tight exit transition state located 22 kJ mol^-1 above the separated products. The collision complex (i1) can also undergo a [1,2] hydrogen atom shift to the CH₃CHCCCH₃ intermediate (i2) prior to a hydrogen atom release; RRKM calculations suggest that this pathway contributes to about 65% of p1. In higher density environments such as in combustion flames and circumstellar envelopes of carbon stars close to the central star, 1-penten-3-yne (p1) may eventually form the cyclopentadiene (c-C₅H₆) isomer via hydrogen atom assisted isomerization followed by hydrogen abstraction to the cyclopentadienyl radical (c-C₅H₅) as an important pathway to key precursors to polycyclic aromatic hydrocarbons (PAHs) and to carbonaceous nanoparticles.

Theoretical, Experimental, and Modeling Study of the Reaction of Hydrogen Atoms with 1- and 2-Pentene

Alkyl radicals are prominent in combustion chemistry as they are formed by hydrocarbon decomposition or from a radical attack on hydrocarbons. Accurate determinations of the thermochemistry and kinetics of their unimolecular isomerization and decomposition reactions and related addition reactions of alkenes are therefore important in simulating the combustion chemistry of virtually all hydrocarbon fuels. In this work, a comprehensive potential energy surface (PES) for Ḣ-atom addition to and abstraction from 1- and 2-pentene, and the subsequent C-C and C-H β-scission reactions, and H-atom transfer reactions has been considered. Thermochemical values for the species on the Ċ₅H₁₁ PES were calculated as a function of temperature (298-2000 K), with enthalpies of formation determined using a network of isodesmic reactions. High-pressure limiting and pressure-dependent rate constants were calculated using the Rice-Ramsperger-Kassel-Marcus theory coupled with a one-dimensional master equation. As a validation of our theoretical results, hydrogen atomic resonance absorption spectrometry experiments were performed on the Ḣ-atom addition and abstraction reactions of 1- and 2-pentene. By incorporating our calculations into a detailed chemical kinetic model (AramcoMech 3.0), excellent agreement with these experiments is observed. The theoretical results are further validated via a comprehensive series of simulations of literature data. Our a priori model is found to reproduce important absolute species concentrations and product ratios reported therein.

Pressure-dependent rate rules for cycloaddition, intramolecular H-shift, and concerted elimination reactions of alkenyl peroxy radicals at low temperature

The reactions of cycloaddition, intramolecular H-shift and concerted elimination of alkenyl peroxy radicals are three kinds of important reactions in the low temperature combustion of alkenes. In this study, the cycloaddition reactions are divided into classes considering endo-cycloaddition, exo-cycloaddition and the size of the transition states; the intramolecular H-shift reactions are divided into classes depending upon the ring size of the transition states and the type of C-H bonds from which the hydrogen atom is transferred; the concerted elimination reactions are divided into classes according to the type of H-C_βC_αOO bond that is broken. All geometry optimizations are performed at the B3LYP/6-31G(2df,p) level. With the electronic structure calculations being performed using the composite Gaussian-4 (G4) method, high pressure limit rate constants and pressure-dependent rate constants at pressures varying from 0.01 to 100 atm are calculated by using canonical transition state theory and the Rice-Ramsberger-Kassel-Marcus/master equation method, respectively. All rate constants are given in the form of the modified Arrhenius expression. The high pressure limit rate rules and the pressure-dependent rate rules are derived by averaging the rate constants of a representative set of reactions in each class. The results show that the rate rules for these three classes of reactions have a large uncertainty and the impact of the pressure on the rate constants increases as temperature increases.

Ab initio derived group additivity model for intramolecular hydrogen abstraction reactions

A set of group additivity values for intramolecular hydrogen abstraction reactions of alkanes, alkenes and alkynes is reported. Calculating 448 reaction rate coefficients at the CBS-QB3 level of theory for 1-2 up to 1-7 hydrogen shift reactions allowed the estimation of ΔGAV° values for 270 groups. The influence of substituents on (1) the attacking radical, (2) the attacked carbon atom, and (3) the carbon chain between the attacking and attacked reactive atom has been systematically studied. Substituents have been varied between hydrogen atoms and sp3, sp2 and sp hybridized carbon atoms. It has been assumed that substituents further away from the reactive atoms or their connecting carbon chain have negligible influences on the kinetics. This group additivity model is applicable to a wide variety of reactions in the 300-1800 K temperature range. Correlations for tunneling coefficients have been generated which are complementary to the ΔGAV°'s to obtain accurate rate coefficients without the need for imaginary frequencies or electronic energies of activation. These correlations depend on the temperature and activation energy of the exothermic step. The group additivity model has been successfully applied to a test set of reactions also calculated at the CBS-QB3 level of theory. A mean absolute deviation of 1.18 to 1.71 has been achieved showing a good overall accuracy of the model.

Automated Transition State Theory Calculations for High-Throughput Kinetics

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

Ab initio study of the influence of resonance stabilization on intramolecular ring closure reactions of hydrocarbon radicals

The cyclization reactions of dieneyl radicals provide a low energy route to the formation of molecular weight growth products.

Reactions of allylic radicals that impact molecular weight growth kinetics

The reactions of allylic radicals have the potential to play a critical role in molecular weight growth (MWG) kinetics during hydrocarbon oxidation and/or pyrolysis.

Transition state geometry prediction using molecular group contributions

Geometries of reaction transition states can be predicted accurately using group-contribution scheme with data arranged in a hierarchical tree database.

Pressure dependence and branching ratios in the decomposition of 1-pentyl radicals: shock tube experiments and master equation modeling

The decomposition and intramolecular H-transfer isomerization reactions of the 1-pentyl radical have been studied at temperatures of 880 to 1055 K and pressures of 80 to 680 kPa using the single pulse shock tube technique and additionally investigated with quantum chemical methods. The 1-pentyl radical was generated by shock heating dilute mixtures of 1-iodopentane and the stable products of its decomposition have been observed by postshock gas chromatographic analysis. Ethene and propene are the main olefin products and account for >97% of the carbon balance from 1-pentyl. Also produced are very small amounts of (E)-2-pentene, (Z)-2-pentene, and 1-butene. The ethene/propene product ratio is pressure dependent and varies from about 3 to 5 over the range of temperatures and pressures studied. Formation of ethene and propene can be related to the concentrations of 1-pentyl and 2-pentyl radicals in the system and the relative rates of five-center intramolecular H-transfer reactions and β C-C bond scissions. The 3-pentyl radical, formed via a four-center intramolecular H transfer, leads to 1-butene and plays only a very minor role in the system. The observed (E/Z)-2-pentenes can arise from a small amount of beta C-H bond scission in the 2-pentyl radical. The current experimental and computational results are considered in conjunction with relevant literature data from lower temperatures to develop a consistent kinetics model that reproduces the observed branching ratios and pressure effects. The present experimental results provide the first available data on the pressure dependence of the olefin product branching ratio for alkyl radical decomposition at high temperatures and require a value of <ΔE(down)(1000 K)> = (675 ± 100) cm(-1) for the average energy transferred in deactivating collisions in an argon bath gas when an exponential-down model is employed. High pressure rate expressions for the relevant H-transfer reactions and β bond scissions are derived and a Rice Ramsberger Kassel Marcus/Master Equation (RRKM/ME) analysis has been performed and used to extrapolate the data to temperatures between 700 and 1900 K and pressures of 10 to 1 × 10(5) kPa.