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Site-specific graph neural network for predicting protonation energy of oxygenate molecules

Bio-oil molecule assessment is essential for the sustainable development of chemicals and transportation fuels. These oxygenated molecules have adequate carbon, hydrogen, and oxygen atoms that can be used for developing new value-added molecules (chemicals or transportation fuels). One motivation for our study stems from the fact that a liquid phase upgrading using mineral acid is a cost-effective chemical transformation. In this chemical upgrading process, adding a proton (positively charged atomic hydrogen) to an oxygen atom is a central step. The protonation energies of oxygen atoms in a molecule determine the thermodynamic feasibility of the reaction and likely chemical reaction pathway. A quantum chemical model based on coupled cluster theory is used to compute accurate thermochemical properties such as the protonation energies of oxygen atoms and the feasibility of protonation-based chemical transformations. However, this method is too computationally expensive to explore a large space of chemical transformations. We develop a graph neural network approach for predicting protonation energies of oxygen atoms of hundreds of bioxygenate molecules to predict the feasibility of aqueous acidic reactions. Our approach relies on an iterative local nonlinear embedding that gradually leads to global influence of distant atoms and a output layer that predicts the protonation energy. Our approach is geared to site-specific predictions for individual oxygen atoms of a molecule in comparison with commonly used graph convolutional networks that focus on a singular molecular property prediction. We demonstrate that our approach is effective in learning the location and magnitudes of protonation energies of oxygenated molecules.