Learning Molecular Representations for Thermochemistry Prediction of Cyclic Hydrocarbons and Oxygenates

Accurate thermochemistry estimation of polycyclic molecules is crucial for kinetic modeling of chemical processes that use renewable and alternative feedstocks. In kinetic model generators, molecular properties are estimated rapidly with group additivity, but this method is known to have limitations for polycyclic structures. This issue has been resolved in our work by combining a geometry-based molecular representation with a deep neural network trained on ab initio data. Each molecule is transformed into a probabilistic vector from its interatomic distances, bond angles, and dihedral angles. The model is tested on a small experimental dataset (200 molecules) from the literature, a new medium-sized set (4000 molecules) with both open-shell and closed-shell species, calculated at the CBS-QB3 level with empirical corrections, and a large G4MP2-level QM9-based dataset (40 000 molecules). Heat capacities between 298.15 and 2500 K are calculated in the medium set with an average deviation of about 1.5 J mol^-1 K^-1 and the standard entropy at 298.15 K is predicted with an average error below 4 J mol^-1 K^-1. The standard enthalpy of formation at 298.15 K has an average out-of-sample error below 4 kJ mol^-1 on a QM9 training set size of around 15 000 molecules. By fitting NASA polynomials, the enthalpy of formation at higher temperatures can be calculated with the same accuracy as the standard enthalpy of formation. Uncertainty quantification by means of the ensemble standard deviation is included to indicate when molecules that are on the edge or outside of the application range of the model are evaluated.