Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM

A Ambarneil Saha (National Center for Electron Microscopy, Molecular Foundry) A Alexander J. Pattison (National Center for Electron Microscopy, Molecular Foundry) K Karen C. Bustillo (National Center for Electron Microscopy, Molecular Foundry) D David W. Mittan-Moreau (Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States) A Aaron S. Brewster (Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States) J Jian Zhang P Peter Ercius (Molecular Foundry)

Abstract

Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.

Article Details

Volume / Issue Vol. 122, Issue 42
Published October 21, 2025
ISSN 0027-8424
Publisher National Academy of Sciences

Authors (7)

A

Ambarneil Saha

National Center for Electron Microscopy, Molecular Foundry

A

Alexander J. Pattison

National Center for Electron Microscopy, Molecular Foundry

K

Karen C. Bustillo

National Center for Electron Microscopy, Molecular Foundry

D

David W. Mittan-Moreau

Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States

A

Aaron S. Brewster

Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States

J

Jian Zhang

P

Peter Ercius

Molecular Foundry