Inverse-IMPRESSION: A Graph-based Platform for Molecular Structure Elucidation from Experimental NMR Spectroscopic Properties

Zheqi Jin, Grace Armitage, Richard Cox, Ben Honoré, Mohammad Golbabaee, Craig Butts

Here, we present a platform built on our inverted Graph Transformer Network, IMPRESSION-G2, which can accurately and rapidly reconstruct molecular bonding directly from experimental nuclear magnetic resonance (NMR) spectroscopic information. It comprises three interconnected stages: a one-shot model that predicts bond connectivity between atoms; a structure-correction stage that corrects the predicted structures by removing uncertain bonds and iteratively reassigning them; noise-augmented multi-shot prediction, generating an ensemble of candidate structures, which are ranked to identify the best-fit structure. By integrating a range of $^{1}$H and $^{13}$C NMR data, including two-dimensional (2D) experiments such as COSY, HSQC, and HMBC, the inverse-IMPRESSION platform correctly identifies the structures of 77.8% of molecules with up to 30 heavy atoms (H, C, N, O and F) using simulated NMR data, and 10 of 19 (53%) molecules using experimental NMR data. The experimental structures solved have molecular weights of up to 480 Da and are representative of the complex structures in synthetic and natural products that routinely challenge chemists. The inverse-IMPRESSION framework thus provides the first effective approach for automated molecular structure elucidation using graph-based machine learning on experimental data.