Determining the aqueous solubility of molecules is a vital step in many pharmaceutical, environmental, and energy storage applications. Despite efforts made over decades, there are still challenges associated with developing a solubility prediction model with satisfactory accuracy for many of these applications. The goals of this study are to assess current deep learning methods for solubility prediction, develop a general model capable of predicting the solubility of a broad range of organic molecules, and to understand the impact of data properties, molecular representation, and modeling architecture on predictive performance. Using the largest currently available solubility data set, we implement deep learning-based models to predict solubility from the molecular structure and explore several different molecular representations including molecular descriptors, simplified molecular-input line-entry system strings, molecular graphs, and three-dimensional atomic coordinates using four different neural network architectures—fully connected neural networks, recurrent neural networks, graph neural networks (GNNs), and SchNet. We find that models using molecular descriptors achieve the best performance, with GNN models also achieving good performance. We perform extensive error analysis to understand the molecular properties that influence model performance, perform feature analysis to understand which information about the molecular structure is most valuable for prediction, and perform a transfer learning and data size study to understand the impact of data availability on model performance.
Aqueous organic redox flow batteries offer an environmentally benign, tunable, and safe route to large-scale energy storage. The energy density is one of the key performance parameters of organic redox flow batteries, which critically depends on the solubility of the redox-active molecule in water. Prediction of aqueous solubility remains a challenge in chemistry. Recently, machine learning models have been developed for molecular properties prediction in chemistry and material science. The fidelity of a machine learning model critically depends on the diversity, accuracy, and abundancy of the training datasets. We build a comprehensive open access organic molecular database “Solubility of Organic Molecules in Aqueous Solution” (SOMAS) containing about 12,000 molecules that covers wider chemical and solubility regimes suitable for aqueous organic redox flow battery development efforts. In addition to experimental solubility, we also provide eight distinctive quantum descriptors including optimized geometry derived from high-throughput density functional theory calculations along with six molecular descriptors for each molecule. SOMAS builds a critical foundation for future efforts in artificial intelligence-based solubility prediction models.
Machine learning-based prediction of material properties is often hampered by the lack of sufficiently large training datasets. The majority of such measurement data is embedded in scientific literature and the ability to automatically extract these data is essential to support the development of reliable property prediction methods. In this work, we describe a methodology for an automatic property extraction framework using material solubility as the target property. We create an annotated dataset containing tags for solubility-related entities using a combination of regular expressions and manual tagging. We then compare five entity recognition models leveraging both token-level and span-level architectures on the task of classifying solute names, solubility values, and solubility units. Additionally, we explore a novel pretraining approach that leverages automated chemical name and quantity extraction tools to generate large datasets that do not rely on intensive manual effort. Finally, we perform an analysis to identify the causes of classification errors.
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