Intramolecular effects on the kinetics of unimolecular reactions of ß-HOROO˙ and HOQ˙OOH radicals.

A theoretical study describing the influence of intramolecular effects on the energy barriers and rate constants of unimolecular reactions involving ß-HOROO˙ and HOQ˙OOH radicals is proposed. The reactions considered are HO2˙ elimination, the Waddington mechanism, H-shift, cyclic ether formation and ß-scission. All the calculations are performed at the CBS-QB3 level of theory along with canonical transition state theory and statistical thermodynamics, including a specific treatment of hindered rotors. Several structural parameters are investigated, such as the location of the hydroxyl function in the cyclic transition states or the substitution of H atoms by alkyl groups on carbon atoms involved in the reaction coordinate. It is shown that these molecular systems involve numerous transition states, especially for reactions such as 1,5 or 1,6 H-shift, and that, a priori simplification is not possible. It is also shown that the position of the -OH group in the transition state can largely modify both the barrier heights and the rate constants. However, opposite trends can be observed depending on the competition between energetic and entropic effects. Similar observations are made when H atoms are replaced by methyl or alkyl groups. These results can largely be explained by intramolecular effects such as hydrogen bonds, stabilization effects (from -OH or -CH3 groups), steric influences and by the coupling between them. The last point renders the classic establishment of the structure-reactivity relationship challenging.

JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.

JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML.

Development of a Detailed Kinetic Model for the Oxidation of n-Butane in the Liquid Phase.

The chemistry underlying liquid-phase oxidation of organic compounds, the main cause of their aging, is characterized by a free-radical chain reaction mechanism. The rigorous simulation of these phenomena requires the use of detailed kinetic models that contain thousands of species and reactions. The development of such models for the liquid phase remains a challenge as solvent-dependent thermokinetic parameters have to be provided for all the species and reactions of the model. Therefore, accurate and high-throughput methods to generate these data are required. In this work, we propose new methods to generate these data, and we apply them for the development of a detailed chemical kinetic model for n-butane autoxidation, which is then validated against literature data. Our approach for model development is based on the work of Jalan et al. [J. Phys. Chem. B 2013, 117, 2955-2970] who used Gibbs free energies of solvation [ΔsolvG(T)] to correct the data of the gas-phase kinetic model. In our approach, an equation of state (EoS) is used to compute ΔsolvG as a function of temperature for all the chemical species in the mechanism. Currently, ΔsolvG(T) of free radicals cannot be computed with an EoS and it was calculated for their parent molecule (H-atom added on the radical site). Theoretical calculations with the implicit solvent model were performed to quantify the impact of this assumption and showed that it is acceptable for radicals in n-butane and probably in all n-alkanes. New rate rules were proposed for the most important reactions of the model, based on theoretical calculations and the literature data. The developed detailed kinetic model for n-butane autoxidation is the first proposed model in the literature and was validated against the experimental data from the literature. Simulations showed that the main autoxidation products, sec-butyl hydroperoxides and 2-butanol, are produced from H-abstractions from n-butane by sec-C4H9OO radicals and the C4H9OO + C4H9OO reaction, respectively. The uncertainty of the product ratio ("butanone + 2-butanol"/"2-butoxy + 2-butoxy") of the latter reaction remains high in the literature, and our simulations suggest a 1:1 ratio in n-butane solvent.