SolvBERT for solvation free energy and solubility prediction: a demonstration of an NLP model for predicting the properties of molecular complexes

Abstract

Deep learning models based on NLP, mainly the Transformer family, have been successfully applied to solve many chemistry-related problems, but their applications are mostly limited to chemical reactions. Meanwhile, solvation is an important concept in physical and organic chemistry, describing the interaction of solutes and solvents. In this study, we introduced the SolvBERT model, which reads the solute and solvent through the SMILES representation of their combination. SolvBERT was pre-trained in an unsupervised learning fashion using a large database of computational solvation free energies. The pre-trained model could be used to predict the experimental solvation free energy or solubility, depending on the fine-tuning database. To the best of our knowledge, this multi-task prediction capability has not been observed in previously developed graph-based models for predicting the properties of molecular complexes. Furthermore, the performance of our SolvBERT in predicting solvation free energy was comparable to the state-of-the-art graph-based model DMPNN, mainly due to the clustering feature of the pre-training phase of the model, as demonstrated using the TMAP visualization algorithm. Last but not least, our SolvBERT outperformed the recently-developed GNN–Transformer hybrid model, GROVER, in predicting a set of experimentally evaluated solubility data with out-of-sample solute–solvent combinations.