skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination
High-energy electrons induce sample damage and motion at the nanoscale to fundamentally limit the determination of molecular structures by electron diffraction. Using a fast event-based electron counting (EBEC) detector, we characterize beam-induced, dynamic, molecular crystal lattice reorientations (BIRs). These changes are sufficiently large to bring reciprocal lattice points entirely in or out of intersection with the sphere of reflection, occur as early events in the decay of diffracted signal due to radiolytic damage, and coincide with beam-induced migrations of crystal bend contours within the same fluence regime and at the same illuminated location on a crystal. These effects are observed in crystals of biotin, a series of amino acid metal chelates, and a six-residue peptide, suggesting that incident electrons inevitably warp molecular lattices. The precise orientation changes experienced by a given microcrystal are unpredictable but are measurable by indexing individual diffraction patterns during beam-induced decay. Reorientations can often tilt a crystal lattice several degrees away from its initial position before irradiation, and for an especially beam-sensitive Zn(II)-methionine chelate, are associated with dramatic crystal quakes prior to 1 e− Å−2electron beam fluence accumulates. Since BIR coincides with the early stages of beam-induced damage, it echoes the beam-induced motion observed in single-particle cryoEM. As with motion correction for cryoEM imaging experiments, accounting for BIR-induced errors during data processing could improve the accuracy of MicroED data.  more » « less
Award ID(s):
1933487
PAR ID:
10592888
Author(s) / Creator(s):
; ;
Publisher / Repository:
University of Oxford
Date Published:
Journal Name:
IUCrJ
Volume:
12
Issue:
2
ISSN:
2052-2525
Page Range / eLocation ID:
223 to 238
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Nature Communications)
    Abstract Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. 
    more » « less
  2. ; ; ; (, Nano Letters)
    We report a systematic analysis of electron beam damage of the zeolitic imidazolate framework (ZIF-8) during liquid cell transmission electron microscopy (LCTEM). Our analysis reveals ZIF-8 morphology is strongly affected by solvent used (water vs dimethylformamide), electron flux applied, and imaging mode (i.e., TEM vs STEM), while ZIF-8 crystallinity is primarily affected by accumulated electron fluence. Our observations indicate that the stability of ZIF-8 morphology is higher in dimethylformamide (DMF) than in water. However, in situ electron diffraction indicates that ZIF-8 nanocrystals lose crystallinity at critical fluence of ∼80 e−Å−2 independent of the presence of solvent. Furthermore, 4D-STEM analysis as a postmortem method reveals the extent of electron beam damage beyond the imaging area and indicates that radiolytic reactions are more pronounced in TEM mode than in STEM mode. These results illustrate the significance of radiolysis occurring while imaging ZIF-8 and present a workflow for assessing damage in LCTEM experiments. 
    more » « less
  3. ; (, Nature Communications)
    null (Ed.)
    Abstract High-resolution transmission electron microscopy (HRTEM) has been transformative to the field of polymer science, enabling the direct imaging of molecular structures. Although some materials have remarkable stability under electron beams, most HRTEM studies are limited by the electron dose the sample can handle. Beam damage of conjugated polymers is not yet fully understood, but it has been suggested that the diffusion of secondary reacting species may play a role. As such, we examine the effect of the addition of antioxidants to a series of solution-processable conjugated polymers as an approach to mitigating beam damage. Characterizing the effects of beam damage by calculating critical dose D C values from the decay of electron diffraction peaks shows that beam damage of conjugated polymers in the TEM can be minimized by using antioxidants at room temperature, even if the antioxidant does not alter or incorporate into polymer crystals. As a consequence, the addition of antioxidants pushes the resolution limit of polymer microscopy, enabling imaging of a 3.6 Å lattice spacing in poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3″′-di(2-octyldodecyl)-2,2′;5′,2″;5″,2″′-quaterthiophene-5,5″′-diyl)] (PffBT4T-2OD). 
    more » « less
  4. ; ; ; ; (, Scientific Reports)
    Abstract A BiFeO3film is grown epitaxially on a PrScO3single crystal substrate which imparts ~ 1.45% of biaxial tensile strain to BiFeO3resulting from lattice misfit. The biaxial tensile strain effect on BiFeO3is investigated in terms of crystal structure, Poisson ratio, and ferroelectric domain structure. Lattice resolution scanning transmission electron microscopy, precession electron diffraction, and X-ray diffraction results clearly show that in-plane interplanar distance of BiFeO3is the same as that of PrScO3with no sign of misfit dislocations, indicating that the biaxial tensile strain caused by lattice mismatch between BiFeO3and PrScO3are stored as elastic energy within BiFeO3film. Nano-beam electron diffraction patterns compared with structure factor calculation found that the BiFeO3maintains rhombohedral symmetry, i.e., space group ofR3c. The pattern analysis also revealed two crystallographically distinguishable domains. Their relations with ferroelectric domain structures in terms of size and spontaneous polarization orientations within the domains are further understood using four-dimensional scanning transmission electron microscopy technique. 
    more » « less
  5. ; ; ; ; ; ; ; ; (, Advanced Science)
    Abstract Thermally activated annealing in semiconductors faces inherent limitations, such as dopant diffusion. Here, a nonthermal pathway is demonstrated for a complete structural restoration in predamaged germanium via ionization‐induced recovery. By combining experiments and modeling, this study reveals that the energy transfer of only 2.4 keV nm−1from incident ions to target electrons can effectively annihilate pre‐existing defects and restore the original crystalline structure at room temperature. Moreover, it is revealed that the irradiation‐induced crystalline‐to‐amorphous (c/a) transformation in Ge is reversible, a phenomenon previously considered unattainable without additional thermal energy imposed during irradiation. For partially damaged Ge, the overall damage fraction decreases exponentially with increasing fluence. Surprisingly, the recovery process in preamorphized Ge starts with defect recovery outside the amorphous layer and a shrinkage of the amorphous thickness. After this initial stage, the remaining damage decreases slowly with increasing fluence, but full restoration of the pristine state is not achieved. These differences in recovery are interpreted in the framework of structural differences in the initial defective layers that affect recovery kinetics. This study provides new insights on reversing the c/a transformation in Ge using highly‐ionizing irradiation and has broad implications across materials science, radiation damage mitigation, and fabrication of Ge‐based devices. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email