DOE OSTI · 3020780
Generative modeling enables molecular structure retrieval from Coulomb explosion imaging
Abstract
Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.
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Li, Xiang [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)] (ORCID:0000000183384123), Jahnke, Till [European XFEL, Schenefeld (Germany); Max Planck Inst. fuer Kernphysik, Heidelberg (Germany)] (ORCID:0000000313585629), Boll, Rebecca [European XFEL, Schenefeld (Germany)] (ORCID:0000000162864064), Han, Jiaqi [Stanford Univ., CA (United States)], Xu, Minkai [Stanford Univ., CA (United States)], Meyer, Michael [European XFEL, Schenefeld (Germany)] (ORCID:0000000214446770), Piancastelli, Maria Novella [Sorbonne Univ., Paris (France); Centre National de la Recherche Scientifique (CNRS), Paris (France). Laboratoire de Chimie Physique-Matière et Rayonnement (LCPMR)], Rolles, Daniel [Kansas State Univ., Manhattan, KS (United States)], Rudenko, Artem [Kansas State Univ., Manhattan, KS (United States)] (ORCID:0000000291548463), Trinter, Florian [Fritz Haber Institute of the Max Planck Society, Berlin (Germany)] (ORCID:0000000208919180), Wolf, Thomas J. A. [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)] (ORCID:0000000206411279), Thayer, Jana B. [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)], Cryan, James P. [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)] (ORCID:0000000277760919), Ermon, Stefano [Stanford Univ., CA (United States)] (ORCID:0000000300392887), Ho, Phay J. [Argonne National Laboratory (ANL), Argonne, IL (United States)] (ORCID:0000000152142180). 2026-03-03. Generative modeling enables molecular structure retrieval from Coulomb explosion imaging. https://doi.org/10.1038/s41467-026-70160-5
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