Helium nanodroplet force field for advancing single-molecule serial electron diffraction imaging

Single-molecule serial electron diffraction imaging (SS-EDI) is a promising methodology to determine biomolecular structures that employs helium nanodroplets (HNDs) as the sample delivery system. Until now, structural determination methods have used liquid helium only as a coolant, but SS-EDI offers a novel application for HNDs as an embedding matrix to isolate single molecules in an ultracold and weakly interacting fluid environment with minimal scattering. SS-EDI is still under active development, and to advance it, researchers require an understanding of the interactions within HNDs at the nanoscale level. To support ongoing experimental efforts, we present a molecular dynamics (MD) force field for HNDs at 0.38 K, enabling direct calculation of electron diffraction patterns from atomic configurations. Our force field combines a Morse potential for van der Waals interactions with a Drude oscillator to capture polarization effects induced by charged dopants, and its parameters were validated against four key quantities of interest: bulk density, an upper bound for viscosity, droplet stability, and the radial profile of the average electron diffraction signal. During validation, we identified instabilities associated with the polarizable model at ultralow temperatures and mitigated them by reducing the effective polarizability, introducing an ultracold Drude particle, and employing canonical ensembles. Finally, we applied the force field to simulate HNDs doped with a tri-atom argon ion, and the changes in electron diffraction profiles were compared with experimental measurements of HNDs of similar size. Despite significant statistical fluctuations in both simulations and experiments, the simulations reproduce the key peak positions observed experimentally, demonstrating qualitative agreement between them. These results establish MD simulations as a valuable tool to advance the application of liquid helium as a new embedding matrix for structural determination.