physics.chem-phApr 27, 2026

Enhancing molecular dynamics with equivariant machine-learned densities

Authors: Mihail BogojeskiMuhammad R. HasyimLeslie Vogt-MarantoKlaus-Robert MüllerKieron BurkeMark E. Tuckerman

Organizations: BIFOLD and Machine Learning Group, Technische Universität Berlin, Franklinstr. 28/29, 10587 Berlin, Germany · Department of Chemistry, New York University, New York, NY 10003, USA · Department of Artificial Intelligence, Korea University, Seoul 02841, Korea · Max-Planck-Institut für Informatik, 66123 Saarbrücken, Germany · Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA · Department of Chemistry, University of California, Irvine, CA 92697, USA · Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA · NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China

Abstract

Machine-learning interatomic potentials (MLIPs) have enabled molecular dynamics at near ab initio accuracy, yet remain limited to energies and forces by construction, leaving electronic observables such as dipole moments and polarizabilities inaccessible. We introduce DenSNet, a density-first approach to machine-learned electronic structure that learns the Hohenberg--Kohn map from nuclear configurations to the ground-state electron density. Our approach employs an SE(3)-equivariant neural network to predict density coefficients of a flexible atom-centered Gaussian basis, combined with a ΔΔ-learning strategy that uses superposed atomic densities as a prior to accelerate training. A second equivariant network then maps the predicted density to the total energy, providing a unified framework for molecular dynamics and electronic structure. We validate DenSNet on ethanol, ethanethiol, and resorcinol, where infrared spectra from machine-learned trajectories show excellent agreement with experimental gas-phase measurements. To test scalability, we train on polythiophene oligomers with 1--6 monomers and extrapolate to chains of up to 12 monomers, generating stable long-time trajectories whose infrared spectra agree with reference density functional theory calculations. Here, we show that reinstating the electron density as the central learned quantity opens a practical route to transferable prediction of spectroscopic and electronic observables in large-scale molecular simulations.

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