Reaction Rate Predictions Via Group Additivity. Part 3: Effect of Substituents with CH2 as the Mediator

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.

Machine Learning Applications for Chemical Reactions

Machine learning (ML) approaches have enabled rapid and efficient molecular property predictions as well as the design of new novel materials. In addition to great success for molecular problems, ML techniques are applied to various chemical reaction problems that require huge costs to solve with the existing experimental and simulation methods. In this review, starting with basic representations of chemical reactions, we summarized recent achievements of ML studies on two different problems; predicting reaction properties and synthetic routes. The various ML models are used to predict physical properties related to chemical reaction properties (e. g. thermodynamic changes, activation barriers, and reaction rates). Furthermore, the predictions of reactivity, self-optimization of reaction, and designing retrosynthetic reaction paths are also tackled by ML approaches. Herein we illustrate various ML strategies utilized in the various context of chemical reaction studies.

Ab initio rate coefficients for reactions of 2,5-dimethylhexyl isomers with O2: temperature- and pressure-dependent branching ratios

Chemical kinetics of O2-addition to alkyl radicals (R), termed first O2-addition in the oxidation mechanism of alkanes, are of central importance to next-generation combustion strategies designed for operations in the low- to intermediate-temperature region (<1000 K). In the present work, stationary points on potential energy surfaces (PES), temperature- and pressure-dependent rate coefficients, and branching fractions of product formation from R + O2 reactions initiated by the addition of molecular oxygen (3O2) to the three alkyl radicals of a branched alkane, 2,5-dimethylhexane, are reported. The stationary points were determined utilizing ab initio/DFT methods and the reaction energies were computed using the composite CBS-QB3 method. Rice-Ramsperger-Kassel-Marcus (RRKM)/master equation (ME) calculations were employed to compute rate coefficients, from which branching fractions were determined over the pressure range of 10-3-20 atm and the temperature range of 400-900 K on three different surfaces. The quantum chemistry results reveal several distinct features. For the addition of O2 to the tertiary alkyl radical 2,5-dimethylhex-2-yl, the most energetically favorable channel leads to the formation of 2,2,5,5,-tetramethyl-tetrahydrofuran, a cyclic ether intermediate formed coincident with OH in a chain-propagating step from the decomposition of tertiary-tertiary hydroperoxyalkyl (QOOH). On the R + O2 surface of the secondary radical, 2,5-dimethylhex-3-yl, the pathways for the formation of methyl-propanal + iso-butene + OH via concerted C-C and O-O bond scission of tertiary QOOH and that of cyclic ether + OH are the most energetically favorable pathways. The R + O2 surface for the reaction of the primary radical, 2,5-dimethylhex-1-yl, reveals two competitive chain-propagation channels, leading to 2-iso-propyl-4-methyl-tetrahydrofuran + OH and 2,2,5-trimethyltetrahydropyran + OH. Below 100 Torr, the formation of the aforementioned species dominates the respective total R + O2 rate coefficient, while at pressures above 1 atm collisionally stabilized alkylperoxy (ROO) dominates at the temperatures considered here. The results of this study are in very good agreement with the experimentally measured intermediates and products of the 2,5-dimethylhexyl radical + O2 reaction.

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.

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.

Feasibility of Activation Energy Prediction of Gas-Phase Reactions by Machine Learning

Machine learning based on big data has emerged as a powerful solution in various chemical problems. We investigated the feasibility of machine learning models for the prediction of activation energies of gas-phase reactions. Six different models with three different types, including the artificial neural network, the support vector regression, and the tree boosting methods, were tested. We used the structural and thermodynamic properties of molecules and their differences as input features without resorting to specific reaction types so as to maintain the most general input form for broad applicability. The tree boosting method showed the best performance among others in terms of the coefficient of determination, mean absolute error, and root mean square error, the values of which were 0.89, 1.95, and 4.49 kcal mol^-1 , respectively. Computation time for the prediction of activation energies for 2541 test reactions was about one second on a single computing node without using accelerators.

Thermochemistry of gas-phase and surface species via LASSO-assisted subgraph selection

Graph theory-based regression techniques, such as group additivity, have widely been implemented for fast estimation of thermochemistry of large molecules.

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.

Performance of First-Principles-Based Reaction Class Transition State Theory

Performance of the Reaction Class Transition State Theory (RC-TST) for prediction of rates constants of elementary reactions is examined using data from its previous applications to a number of different reaction classes. The RC-TST theory is taking advantage of the common structure denominator of all reactions in a given family combined with structure activity relationships to provide a rigorous theoretical framework to obtain rate expression of any reaction within a reaction class in a simple and cost-effective manner. This opens the possibility for integrating this methodology with an automated mechanism generator for "on-the-fly" generation of accurate kinetic models of complex reacting systems.

Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation

The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.

Contra-thermodynamic Behavior in Intermolecular Hydrogen Transfer of Alkylperoxy Radicals

Quantum chemical investigation of bimolecular hydrogen transfer involving alkylperoxy radicals, a key reaction family in the free-radical oxidation of hydrocarbons, was performed to establish structure-reactivity relationships. Eight different reactions were investigated featuring four different alkane substrates (methane, ethane, propane and isobutane) and two different alkylperoxy radicals (methylperoxy and iso-propylperoxy). Including forward and reverse pairs, sixteen different activation energies and enthalpies of reaction were used to formulate structure-reactivity relationships to describe this chemistry. We observed that the enthalpy of formation of loosely bound intermediate states has a strong inverse correlation with the overall heat of reaction and that this results in unique contra-thermodynamic behavior such that more exothermic reactions have higher activation barriers. A new structure-reactivity relationship was proposed that fits the calculated data extremely well: E(A)=E(o)+alphaDeltaH(rxn) where alpha=-0.10 for DeltaH(rxn)<0, and alpha=1.10 for DeltaH(rxn)>0 and E(o)=3.05 kcal mol(-1).

Measurements and Automated Mechanism Generation Modeling of OH Production in Photolytically Initiated Oxidation of the Neopentyl Radical

Production of OH in the reaction of the neopentyl radical with O2 has been measured by a laser photolysis/cw absorption method for various pressures and oxygen concentrations at 673, 700, and 725 K. The MIT Reaction Mechanism Generator (RMG) was used to automatically generate a model for this system, and the predicted OH concentration profiles are compared to present and literature experimental results. Several reactions significantly affect the OH profile. The experimental data provide useful constraints on the rate coefficient for the formally direct chemical activation reaction of neopentyl radical with O2 to form OH (CH3)3CCH2 + O2 --> OH + 3,3-dimethyloxetane (Rxn 1) At 673 K and 60 Torr, log k(1) (cm(3) molecule(-1) s(-1)) = -13.7 +/- 0.5. Absolute absorbance measurements on OH and I indicate that the branching ratio for R + O2 to OH is about 0.03 under these conditions. The data suggest that the ab initio neopentyl + O2 potential energy surface of Sun and Bozzelli is accurate to within 2 kcal mol(-1).

Rate coefficients of H-atom abstraction from ethers and isomerization of alkoxyalkylperoxy radicals

Group rate expressions for the hydrogen(H)-atom abstraction reactions from ethers by hydrogen atoms and hydroxyl(OH) radicals and the intramolecular hydrogen-transfer isomerization reactions of alkoxyalkylperoxy radicals, which result from the H-abstraction from ethers followed by the addition of O(2), have been evaluated based on the quantum chemical calculations and experimental data. With the relative method proposed in the present study, it was shown that the rate coefficients of the reactions, for which only poor experimental information is available, can be reliably evaluated by calculating and extracting the difference from the well-established reactions of alkane hydrocarbons. The major features on the H-abstraction reactions from O-adjacent sites of ethers compared to those from alkanes were the suppression of the activation energy due to the decrease of the C-H bond dissociation energy and non-next neighbor substituent effect from the alkyl group on the counter side of -O-. For the hydrogen transfer isomerization reactions, similar suppression of the activation energy as well as the change in the ring strain energy was found as a major feature.

Uncovering the Fundamental Chemistry of Alkyl + O2Reactions via Measurements of Product Formation

The reactions of alkyl radicals (R) with molecular oxygen (O(2)) are critical components in chemical models of tropospheric chemistry, hydrocarbon flames, and autoignition phenomena. The fundamental kinetics of the R + O(2) reactions is governed by a rich interplay of elementary physical chemistry processes. At low temperatures and moderate pressures, the reactions form stabilized alkylperoxy radicals (RO(2)), which are key chain carriers in the atmospheric oxidation of hydrocarbons. At higher temperatures, thermal dissociation of the alkylperoxy radicals becomes more rapid and the formation of hydroperoxyl radicals (HO(2)) and the conjugate alkenes begins to dominate the reaction. Internal isomerization of the RO(2) radicals to produce hydroperoxyalkyl radicals, often denoted by QOOH, leads to the production of OH and cyclic ether products. More crucially for combustion chemistry, reactions of the ephemeral QOOH species are also thought to be the key to chain branching in autoignition chemistry. Over the past decade, the understanding of these important reactions has changed greatly. A recognition, arising from classical kinetics experiments but firmly established by recent high-level theoretical studies, that HO(2) elimination occurs directly from an alkylperoxy radical without intervening isomerization has helped resolve tenacious controversies regarding HO(2) formation in these reactions. Second, the importance of including formally direct chemical activation pathways, especially for the formation of products but also for the formation of the QOOH species, in kinetic modeling of R + O(2) chemistry has been demonstrated. In addition, it appears that the crucial rate coefficient for the isomerization of RO(2) radicals to QOOH may be significantly larger than previously thought. These reinterpretations of this class of reactions have been supported by comparison of detailed theoretical calculations to new experimental results that monitor the formation of products of hydrocarbon radical oxidation following a pulsed-photolytic initiation. In this article, these recent experiments are discussed and their contributions to improving general models of alkyl + O(2) reactions are highlighted. Finally, several prospects are discussed for extending the experimental investigations to the pivotal questions of QOOH radical chemistry.

Ab Initio Group Contribution Method for Activation Energies of Hydrogen Abstraction Reactions

The group contribution method for activation energies is applied to hydrogen abstraction reactions. To this end an ab initio database was constructed, which consisted of activation energies calculated with the ab initio CBS-QB3 method for a limited set of well-chosen homologous reactions. CBS-QB3 is shown to predict reaction rate coefficients within a factor of 2-4 and Arrhenius activation energies within 3-5 kJ mol(-1) of experimental data. Activation energies in the set of homologous reactions vary over 156 kJ mol(-1) with the structure of the abstracting radical and over 94 kJ mol(-1) with the structure of the abstracted hydrocarbon. The parameters required for the group contribution method, the so-called standard activation group additivity values, were determined from this database. To test the accuracy of the group contribution method, a large set of 88 additional activation energies were calculated from first principles and compared with the predictions from the group contribution method. It was found that the group contribution method yields accurate activation energies for hydrogen-transfer reactions between hydrogen molecules, alkylic hydrocarbons, and vinylic hydrocarbons, with the largest deviations being less than 6 kJ mol(-1). For reactions between allylic and propargylic hydrocarbons, the transition state is believed to be stabilized by resonance effects, thus requiring the introduction of an appropriate correction term to obtain a reliable prediction of the activation energy for this subclass of hydrogen abstraction reactions.