Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance
Dec 15, 2023
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Austin Cheng
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Santiago Miret
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Brooks Pate
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Alan Aspuru-Guzik
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About
Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Kraitchman analysis uses these moments to determine isotopic substitution coordinates, which are the unsigned |x|,|y|,|z| coordinates of all atoms with natural isotopic abundance, including carbon, nitrogen, and oxygen. While unsigned substitution coordinates can verify guesses of structures, the missing +/- signs make it a hard computational problem to determine the actual structure from just the substitution coordinates. To tackle this inverse problem, we develop KREED (Kraitchman REflection-Equivariant Diffusion), a diffusion generative model which infers a molecule's all-atom 3D structure conditioned on the molecular formula, moments of inertia, and unsigned substitution coordinates of carbon and other heavy atoms. KREED's top-1 predictions identify the correct 3D structure with >98Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Kraitchman analysis uses these moments to determine isotopic substitution coordinates, which are the unsigned |x|,|y|,|z| coordinates of all atoms with natural isotop…
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NeurIPS 2023
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