Predicting Molecular Self-Assembly on Metal Surfaces Using Graph Neural Networks Based on Experimental Data Sets

The application of supramolecular chemistry on solid surfaces has received extensive attention in the past few decades. To date, combining experiments with quantum mechanical or molecular dynamic methods represents the key strategy to explore the molecular self-assembled structures, which is, however, often laborious. Recently, machine learning (ML) has become one of the most exciting tools in material research, allowing for both efficiency and accuracy in predicting molecular properties. In this work, we constructed a graph neural network to predict the self-assembly of functional polycyclic aromatic hydrocarbons (PAHs) on metal surfaces. Using scanning tunneling microscopy (STM), we characterized the self-assembled nanostructures of a homologous series of PAH molecules on different metal surfaces to construct an experimental data set for model training. Compared with traditional ML algorithms, our model exhibits better predictive performance. Finally, the generalization of the model is further verified by comparing the ML predictions and experimental results of different functionalized molecule. Our results demonstrate training experimental data sets to produce a predictive ML model of molecular self-assembly with generalization performance, which allows for the predictive design of nanostructures with functional molecules.