Neural Message Passing for NMR Chemical Shift Prediction

Fast and accurate prediction of NMR spectra enables automatic structure validation and elucidation of molecules on a large scale. In this Article, we propose an improved method of learning from an NMR database to predict the chemical shifts of NMR-active atoms of a new molecule. For this purpose, we use a message passing neural network that operates on the graph representation of a molecule. The compactness and informativeness of the graph representation are enhanced by treating hydrogen atoms implicitly and incorporating various node and edge features. Experimental investigation demonstrates that the proposed method achieves higher prediction performance for the chemical shifts in the ¹H NMR and ¹³C NMR spectra of small molecules. We apply this method to determine the correct molecular structure for a new NMR spectrum by searching from a set of candidate molecules.