Atomic-Resolution Imaging of Small Organic Molecules on Graphene

Priti Kharel, Blanka E. Janicek, Sang Hyun Bae, Amanda L. Loutris, Patrick T. Carmichael, Pinshane Y. Huang

Research output: Contribution to journalArticlepeer-review


Here, we demonstrate atomic-resolution scanning transmission electron microscopy (STEM) imaging of light elements in small organic molecules on graphene. We use low-dose, room-temperature, aberration-corrected STEM to image 2D monolayer and bilayer molecular crystals, followed by advanced image processing methods to create high-quality composite images from 102-104 individual molecules. In metalated porphyrin and phthalocyanine derivatives, these images contain an elementally sensitive contrast with up to 1.3 resolution?sufficient to distinguish individual carbon and nitrogen atoms. Importantly, our methods can be applied to molecules with low masses (0.6 kDa) and nanocrystalline domains containing just a few hundred molecules, making it possible to study systems for which large crystals cannot easily be grown. Our approach is enabled by low-background graphene substrates, which we show increase the molecules' critical dose by 2-7×. These results indicate a new route for low-dose, atomic-resolution electron microscopy imaging to solve the structures of small organic molecules.

Original languageEnglish (US)
Pages (from-to)3628–3635
JournalNano letters
Issue number9
Early online dateApr 12 2022
StatePublished - May 11 2022
Externally publishedYes


  • atomic resolution
  • graphene support
  • scanning transmission electron microscopy
  • small organic molecules
  • structure determination

ASJC Scopus subject areas

  • General Chemistry
  • Condensed Matter Physics
  • Mechanical Engineering
  • Bioengineering
  • General Materials Science


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