TERS-ABNet: A Deep Learning Approach for Automated Single-Molecule Structure Reconstruction with Atomic Precision from TERS Mapping

Abstract

Determining the chemical structure for a single molecule on surface from spectroscopic data represents a challenging high-dimensional inverse problem. Tip-enhanced Raman spectroscopy (TERS) enables chemically specific imaging of single molecules with sub-nanometer spatial resolution, yet reconstructing complete molecular structures from TERS maps remains difficult owing to the ambiguous vibrational signatures and reliance on expert interpretation. Here, we introduce TERS-ABNet, a deep-learning framework that formulates single-molecule structure determination from spectroscopic images as an image-to-graph inference task. Using a "two-track" architecture, the model jointly predicts probabilistic atom and bond maps, enabling direct construction of explicit atom-bond graphs without relying on predefined chemical rules. Trained on simulated datasets, TERS-ABNet achieves about 94% atom-type classification accuracy (with a mean coordinate error of about 0.23 \AA), enabling to reliably recovering molecular connectivity and fully reconstruct single-molecule structure from its TERS maps. The framework generalizes across varying spatial resolutions and structural complexity through transfer learning, and successfully reconstructs the atomic structure of a single porphyrin molecule from experimental TERS data. This work establishes a general deep-learning strategy for inferring explicit atom-bond graph representations from high-dimensional spectroscopic imaging data, providing a new pathway towards automated molecular structure determination in nanoscale characterization.