Implementation of Stereochemistry in Automatic Kinetic Model Generation

Abstract

The kinetic model generation code Genesys is extended by the addition of algorithms for the detection of stereocenters and for the detection of stereoisomers. To make this possible, a so‐called 2.5D representation of molecules that accounts for the presence of stereocenters and that keeps track of the associated stereoconfiguration of the stereocenters is introduced. A novel algorithm for the detection of steric relations between substituents allows the automated assignment of rate coefficients to stereoselective reactions. The functionality of the algorithms is illustrated for the thermal rearrangement of the monoterpenoid 2‐pinanol, an intermediate in the fragrance industry. Accounting for stereochemistry proves to be essential in explaining the reactive behavior of 2‐pinanol and the selectivity to its products. Good agreement with experimental data from the literature was obtained. CBS‐QB3 calculations for (R)‐cis‐ and (R)‐trans‐2‐pinanol support the experimentally observed differences for the suggested stereoselective and stereospecific reactions.

Stereoisomerism in Lanthanide Complexes: Enumeration, Chirality, Identification, Random Coordination Ratios

“…Rotational symmetry numbers, σ, the number of equivalent rotational orientations of a molecule, among several uses, are employed in kinetic models, in transition-state theory, and on the low-temperature autoignition chemistry …”

“…Rotational Symmetry Numbers. Rotational symmetry numbers, 15 σ, the number of equivalent rotational orientations of a molecule, among several uses, are employed in kinetic models, 16 in transition-state theory, 17 and on the lowtemperature autoignition chemistry. 18 We observed that random coordination weights are related to rotations around the central metal ion, in such a manner that the group with the smallest random coordination weight will always be the one with the highest number of rotations (symmetry number).…”

Multi-Scale Modeling of Plastic Waste Gasification: Opportunities and Challenges

“…Figure 11 illustrates the flow diagram that is used in an automatic reaction network generation (Genesys), proposed by Vandewiele et al [135]. Many challenges in automated network generation have been successfully tackled over the years-including symmetry detection of molecules [147], taking stereochemistry into account [148,149], and predicting molecular properties [150,151]. However, one challenge still remains: kinetic model generators all rely on pre-defined reaction templates, which limit the reactions in the model to those anticipated by the user or developer.…”

Diastereomers and Low-Temperature Oxidation

“…In contrast to the prevalence of chirality in these areas, gas-phase chemical kinetics research tends to neglect the importance of chirality. For example, in published combustion mechanisms the distinction between stereochemically related species seems to be limited to cis/trans isomers and simple, enantiomeric pairs . Some discussion of chirality in the form of diastereomers can be found in recent atmospheric chemistry studies (see refs and ) and in a recent combustion chemistry paper of Mohamed et al As part of their work, Mohamed et al provided high-pressure-limit (HPL) rate constants for isomerizations of O 2 QOOH diastereomers in a set of C 2 –C 8 alkane systems using energies obtained from an average of CBS-QB3, G3, and G4 ab initio methods.…”

“…For example, in published combustion mechanisms the distinction between stereochemically related species seems to be limited to cis/trans isomers and simple, enantiomeric pairs. 4 Some discussion of chirality in the form of diastereomers can be found in recent atmospheric chemistry studies (see refs 5 and 6) and in a recent combustion chemistry paper of Mohamed et al 7 As part of their work, Mohamed et al provided high-pressure-limit (HPL) rate constants for isomerizations of O 2 QOOH diastereomers in a set of C 2 −C 8 alkane systems using energies obtained from an average of CBS-QB3, G3, and G4 ab initio methods. At this level of theory, their HPL rate constants differed by at most a factor of ∼3−4 between the (S,R)-and (R,R)-O 2 QOOH diastereomers (see Figure 7 of ref 7).…”