Modeling the kinetics of bimolecular reactions

New theoretical insights into the reaction kinetics of toluene and hydroxyl radicals

This work provides theoretical insights into the kinetics of toluene + OH, focusing on the anharmonic effect and the accuracy of barrier heights.

The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy

While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.

Modeling Ionic Reactions at Interstellar Temperatures: The Case of NH2- + H2 ⇔ NH3 + H. J Phys Chem A 2019;123:9905-9918. [PMID: 31633351 DOI: 10.1021/acs.jpca.9b07317]

Structural features and enthalpy details are presented for the title reactions, both for the exothermic (forward) path to NH₃ formation and for the endothermic (reverse) reaction to NH₂^- formation. Both pathways have relevance for the nitrogen chemistry in the interstellar medium (ISM). They are also helpful to document the possible role of H^- in molecular clouds at temperatures well below room temperature. The structural calculations are carried out using different ab initio methods and are further employed to obtain the reaction rates down to the interstellar temperatures detected in earlier experiments. The reaction rates are obtained from the computed minimum energy path (MEP) using the variational transition-state theory (VTST) approach. The results indicate very good accord with experiment results at room temperature, while measured low temperature data down to 8 K are well described using an appropriately modified VTST approach. This is done by employing a temperature-dependent scaling, from room temperature conditions down to the lower ISM temperatures, which acknowledges the noncanonical behavior of the fast, barrierless exothermic reaction. The reasons for this behavior and the need for improving on the VTST method when used away from room temperatures are discussed.

Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals

The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO^.+ and Mg₂ O₂ ^.+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO^.+ with CH₄ , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg₂ O₂ ^.+ /CH₄ couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. Part 5: Computational Study of Ethane Dissociation and Recombination Reactions C2H6 ⇌ CH3 + CH3

Fossil fuel oxy-combustion is an emerging technology where the habitual nitrogen diluent is replaced by high-pressure supercritical CO₂ (sCO₂), which increases the efficiency of energy conversion. In this study, the chemical kinetics of the combustion reaction C₂H₆ ⇌ CH₃ + CH₃ in the sCO₂ environment is predicted at 30-1000 atm and 1000-2000 K. We adopt a multiscale approach, where the reactive complex is treated quantum mechanically in rigid rotor/harmonic oscillator approximation, while environment effects at different densities are taken into account by the potential of mean force, produced with classical molecular dynamics (MD). Here, we used boxed MD, where enhanced sampling of infrequent events of barrier crossing is accomplished without application of the bias potential. The multistate empirical valence bond model is applied to describe free radical formation accurately at the cost of the classical force field. Predicted rates at low densities agree well with the literature data. Rate constants at 300 atm are 2.41 × 10¹⁴ T^-0.20 exp(-77.03 kcal/mol/ RT) 1/s for ethane dissociation and 8.44 × 10^-19 T^1.42 exp(19.89 kcal/mol/ RT) cm³/molecule/s for methyl-methyl recombination.

Mechanism and rate constants of the CH2 + CH2 CO reactions in triplet and singlet states: A theoretical study

Ab initio and density functional CCSD(T)-F12/cc-pVQZ-f12//B2PLYPD3/6-311G** calculations have been performed to unravel the reaction mechanism of triplet and singlet methylene CH₂ with ketene CH₂ CO. The computed potential energy diagrams and molecular properties have been then utilized in Rice-Ramsperger-Kassel-Marcus-Master Equation (RRKM-ME) calculations of the reaction rate constants and product branching ratios combined with the use of nonadiabatic transition state theory for spin-forbidden triplet-singlet isomerization. The results indicate that the most important channels of the reaction of ketene with triplet methylene lead to the formation of the HCCO + CH₃ and C₂ H₄ + CO products, where the former channel is preferable at higher temperatures from 1000 K and above. In the C₂ H₄ + CO product pair, the ethylene molecule can be formed either adiabatically in the triplet electronic state or via triplet-singlet intersystem crossing in the singlet electronic state occurring in the vicinity of the CH₂ COCH₂ intermediate or along the pathway of CO elimination from the initial CH₂ CH₂ CO complex. The predominant products of the reaction of ketene with singlet methylene have been shown to be C₂ H₄ + CO. The formation of these products mostly proceeds via a well-skipping mechanism but at high pressures may to some extent involve collisional stabilization of the CH₃ CHCO and cyclic CH₂ COCH₂ intermediates followed by their thermal unimolecular decomposition. The calculated rate constants at different pressures from 0.01 to 100 atm have been fitted by the modified Arrhenius expressions in the temperature range of 300-3000 K, which are proposed for kinetic modeling of ketene reactions in combustion. © 2018 Wiley Periodicals, Inc.

Comparing the performances of various density functionals for modelling the mechanisms and kinetics of bimolecular free radical reactions in aqueous solution

We systematically tested the performances of 18 density functionals for the mechanisms and kinetics of reactions of the α-hydroxyisopropyl radical with 9 organic substrates.

Anomalous kinetics of the reaction between OH and HO2on an accurate triplet state potential energy surface

The quasi-classical trajectory predicts the rate coefficient of the OH + HO₂→ H₂O + O₂reaction based on a full dimensional accurate PIP-NN PES, which is fit to 108 000 points calculated at the CCSD(T)-F12a/AVTZ level.

Designing the Backbone of Hexasilabenzene Derivatives with a High Unimolecular Kinetic Stability

It is an important subject to theoretically predict the kinetic stability of transient species. In this study, we have studied the kinetic stability of hexasilabenzene Si₆ H₆ and its derivatives, that is, decasilanaphthalene Si₁₀ H₈ and Li-substituted hexasilabenzene Si₆ Li₆ , theoretically by the artificial force induced reaction (AFIR) method combined with the rate constant matrix contraction (RCMC) method. Molecular design was further conducted to extend the unimolecular lifetime of hexasilabenzene derivatives. Although both Si₁₀ H₈ and Si₆ Li₆ were shown to possess shorter lifetimes than Si₆ H₆ , we found that the lifetimes of Si₆ Li₆ changed depending on arrangements of Li atoms around the monocyclic Si₆ backbone. Based on this knowledge, we found that a compound of an atomic composition Si₆ H₄ Li₂ with a planar, monocyclic Si₆ backbone has a relatively long unimolecular lifetime. Moreover, substitution of the two Li atoms by Na atoms further increased the lifetime.

Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling

Isomerization kinetics of molecules in the gas phase naturally falls on the microcanonical ensemble of statistical mechanics, which for small systems might significantly differ from the more traditional canonical ensemble. In this work, we explore the examples of cis-trans isomerization in butane and bibenzyl and to what extent the fully atomistic rate constants in isolated molecules can be reproduced by coarse-graining the system into a lower dimensional potential of mean force (PMF) along a reaction coordinate of interest, the orthogonal degrees of freedom acting as a canonical bath in a Langevin description. Time independent microcanonical rate constants can be properly defined from appropriate state residence time correlation functions; however, the resulting rate constants acquire some time dependence upon canonical averaging of initial conditions. Stationary rate constants are recovered once the molecule is placed into a real condensed environment pertaining to the canonical ensemble. The effective one-dimensional kinetics along the PMF, based on appropriately chosen inertia and damping parameters, quantitatively reproduces the atomistic rate constants at short times but deviates systematically over long times owing to the neglect of some couplings between the system and the bath that are all intrinsically present in the atomistic treatment. In bibenzyl, where stronger temperature effects are noted than in butane, the effective Langevin dynamics along the PMF still performs well at short times, indicating the potential interest of this extremely simplified approach for sampling high-dimensional energy surfaces and evaluating reaction rate constants.

Effects of multidimensional tunneling in the kinetics of hydrogen abstraction reactions of O (3 P) with CH3 OCHO

Quantum tunneling paths are important in reactions when there is a significant component of hydrogenic motion along the potential energy surface. In this study, variational transition state with multidimensional tunneling corrections are employed in the calculations of the thermal rate constants for hydrogen abstraction from the cis-CH₃ OCHO by O (³ P) giving CH₃ OCO + OH (R1) and CH₂ OCHO + OH (R2). The structures and electronic energies are computed with the M06-2X method. Benchmark calculations with the CBS_D-T approach give an enthalpy of reaction at 0 K for R1 (-2.8 kcal/mol) and R2 (-2.5 kcal/mol) which are in good agreement with the experiment, i.e. -2.61 and -1.81 kcal/mol. At the low and intermediate values of temperatures, small- and large-curvature tunneling dominate the kinetics of R1, which is the dominant path over the range of temperature from 250 to 1200 K. This study shows the importance of multidimensional tunneling corrections for both R1 and R2, for which the total rate constant at 298 K calculated with the CVT/μOMT method is 8.2 × 10^-15 cm³ molecule^-1 s^-1 which agrees well with experiment value of 9.3 × 10^-15 cm³ molecule^-1 s^-1 (Mori, Bull. Inst. Chem. Res. 1981, 59, 116). © 2018 Wiley Periodicals, Inc.

Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable, and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready to use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodological advancement of chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Atom tunnelling in the reaction NH3+ + H2 → NH4+ + H and its astrochemical relevance

The title reaction is involved in the formation of ammonia in the interstellar medium. We have calculated thermal rates including atom tunnelling using different rate theories. Canonical variational theory with microcanonically optimised multidimensional tunnelling was used for bimolecular rates, modelling the gas-phase reaction and also a surface-catalysed reaction of the Eley-Rideal type. Instanton theory provided unimolecular rates, which model the Langmuir-Hinshelwood type surface reaction. The potential energy was calculated on the CCSD(T)-F12 level of theory on the fly. We report thermal rates and H/D kinetic isotope effects. The latter have implications for observed H/D fractionation in molecular clouds. Tunnelling causes rate constants to be sufficient for the reaction to play a role in interstellar chemistry even at cryogenic temperature. We also discuss intricacies and limitations of the different tunnelling approximations to treat this reaction, including its pre-reactive minimum.

Potential Energy Surface for Large Barrierless Reaction Systems: Application to the Kinetic Calculations of the Dissociation of Alkanes and the Reverse Recombination Reactions

The isodesmic reaction method is applied to calculate the potential energy surface (PES) along the reaction coordinates and the rate constants of the barrierless reactions for unimolecular dissociation reactions of alkanes to form two alkyl radicals and their reverse recombination reactions. The reaction class is divided into 10 subclasses depending upon the type of carbon atoms in the reaction centers. A correction scheme based on isodesmic reaction theory is proposed to correct the PESs at UB3LYP/6-31+G(d,p) level. To validate the accuracy of this scheme, a comparison of the PESs at B3LYP level and the corrected PESs with the PESs at CASPT2/aug-cc-pVTZ level is performed for 13 representative reactions, and it is found that the deviations of the PESs at B3LYP level are up to 35.18 kcal/mol and are reduced to within 2 kcal/mol after correction, indicating that the PESs for barrierless reactions in a subclass can be calculated meaningfully accurately at a low level of ab initio method using our correction scheme. High-pressure limit rate constants and pressure dependent rate constants of these reactions are calculated based on their corrected PESs and the results show the pressure dependence of the rate constants cannot be ignored, especially at high temperatures. Furthermore, the impact of molecular size on the pressure-dependent rate constants of decomposition reactions of alkanes and their reverse reactions has been studied. The present work provides an effective method to generate meaningfully accurate PESs for large molecular system.

Advances in fixed-bed reactor modeling using particle-resolved computational fluid dynamics (CFD)

In 2006, Dixon et al. published the comprehensive review article entitled “Packed tubular reactor modeling and catalyst design using computational fluid dynamics.” More than one decade later, many researchers have contributed to novel insights, as well as a deeper understanding of the topic. Likewise, complexity has grown and new issues have arisen, for example, by coupling microkinetics with computational fluid dynamics (CFD). In this review article, the latest advances are summarized in the field of modeling fixed-bed reactors with particle-resolved CFD, i.e. a geometric resolution of every pellet in the bed. The current challenges of the detailed modeling are described, i.e. packing generation, meshing, and solving with an emphasis on coupling microkinetics with CFD. Applications of this detailed approach are discussed, i.e. fluid dynamics and pressure drop, dispersion, heat and mass transfer, as well as heterogeneous catalytic systems. Finally, conclusions and future prospects are presented.

Prediction of rate constants of important chemical reactions in water radiation chemistry in sub and supercritical water – non-equilibrium reactions

The rate constants for reactions involved in the radiolysis of water under relevant thermodynamic conditions in supercritical water-cooled reactors are estimated for inputs in simulations of the radiation chemistry in Generation IV nuclear reactors. We have discussed the mechanism of each chemical reaction with a focus on non-equilibrium reactions. We found most of the reactions are activation controlled above the critical point and that the rate constants are not significantly pressure dependent below 300 °C. This work will aid industry with developing chemical control strategies to suppress the concentration of eroding species.

Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature

The kinetics of the reaction of methanol with hydroxyl radicals is revisited in light of the reported new kinetic data, measured in cold expansion beams. The rate constants exhibit an approximately 10(2)-fold increase when the temperature decreases from 200 to 50 K, a result that cannot be fully explained by tunneling, as we confirm by new calculations. These calculations also show that methanol dimers are much more reactive to hydroxyl than monomers and imply that a dimer concentration of about 30% of the equilibrium concentration can account quantitatively for the observed rates. The assumed presence of dimers is supported by the observation of cluster formation in these and other cold beams of molecules subject to hydrogen bonding. The calculations imply an important caveat with respect to the use of cold expansion beams for the study of interstellar chemistry.

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.

Assessing the Molecular Basis of the Fuel Octane Scale: A Detailed Investigation on the Rate Controlling Steps of the Autoignition of Heptane and Isooctane

N-Heptane and 2,2,4-trimethylpentane (isooctane) are the key species in the modeling of ignition of hydrocarbon-based fuel formulations. Isooctane is knock-resistant whereas n-heptane is a very knock-prone hydrocarbon. It has been suggested that interconversion of their associated alkylperoxy and hydroperoxyalkyl species via hydrogen-transfer isomerization reaction is the key step to understand their different knocking behavior. In this work, the kinetics of unimolecular hydrogen-transfer reactions of n-heptylperoxy and isooctylperoxy are determined using canonical variational transition-state theory and multidimensional small curvature tunneling. Internal rotation of involved molecules is taken explicitly into account in the molecular partition function. The rate coefficients are calculated in the temperature range 300-900 K, relevant to low-temperature autoignition. The concerted HO₂ elimination is an important reaction that competes with some H-transfer and is associated with chain termination. Thus, the branching ratio between these reaction channels is analyzed. We show that variational and multidimensional tunneling effects cannot be neglected for the H-transfer reaction. In particular, the pre-exponential Arrhenius fitting parameter derived from our rate constants shows a strong dependence on the temperature, because tunneling increases quickly at temperatures below 500 K. On the basis of our results, the existing qualitative model for the reasons for different knock behavior observed for n-heptane and isooctane is quantitatively validated at the molecular level.

Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences

Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (³ H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.

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.

Direct measurements of DOCO isomers in the kinetics of OD + CO

Quantitative and mechanistically detailed kinetics of the reaction of hydroxyl radical (OH) with carbon monoxide (CO) have been a longstanding goal of contemporary chemical kinetics. This fundamental prototype reaction plays an important role in atmospheric and combustion chemistry, motivating studies for accurate determination of the reaction rate coefficient and its pressure and temperature dependence at thermal reaction conditions. This intricate dependence can be traced directly to details of the underlying dynamics (formation, isomerization, and dissociation) involving the reactive intermediates cis- and trans-HOCO, which can only be observed transiently. Using time-resolved frequency comb spectroscopy, comprehensive mechanistic elucidation of the kinetics of the isotopic analog deuteroxyl radical (OD) with CO has been realized. By monitoring the concentrations of reactants, intermediates, and products in real time, the branching and isomerization kinetics and absolute yields of all species in the OD + CO reaction are quantified as a function of pressure and collision partner.

Accurate Determination of Tunneling-Affected Rate Coefficients: Theory Assessing Experiment

The thermal rate coefficients of a prototypical bimolecular reaction are determined on an accurate ab initio potential energy surface (PES) using ring polymer molecular dynamics (RPMD). It is shown that quantum effects such as tunneling and zero-point energy (ZPE) are of critical importance for the HCl + OH reaction at low temperatures, while the heavier deuterium substitution renders tunneling less facile in the DCl + OH reaction. The calculated RPMD rate coefficients are in excellent agreement with experimental data for the HCl + OH reaction in the entire temperature range of 200-1000 K, confirming the accuracy of the PES. On the other hand, the RPMD rate coefficients for the DCl + OH reaction agree with some, but not all, experimental values. The self-consistency of the theoretical results thus allows a quality assessment of the experimental data.