Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Atomic mechanism of metal crystal nucleus formation in a single-walled carbon nanotube


Knowing how crystals nucleate at the atomic scale is crucial for understanding, and in turn controlling, the structure and properties of a wide variety of materials. However, because of the scale and highly dynamic nature of nuclei, the formation and early growth of nuclei are very difficult to observe. Here, we have employed single-walled carbon nanotubes as test tubes, and an ‘atomic injector’ coupled with aberration-corrected transmission electron microscopy, to enable in situ imaging of the initial steps of nucleation at the atomic scale. With three different metals we observed three main processes prior to heterogeneous nucleation: formation of crystal nuclei directly from an atomic seed (Fe), from a pre-existing amorphous nanocluster (Au) or by coalescence of two separate amorphous sub-nanometre clusters (Re). We demonstrate the roles of the amorphous precursors and the existence of an energy barrier before nuclei formation. In all three cases, crystal nucleus formation occurred through a two-step nucleation mechanism.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Structure of Fe@SWNT and time-series AC-HRTEM images of an atomic injector.
Fig. 2: Sequential AC-HRTEM images and corresponding simulations showing the first and second stages of γ-Fe crystallite nucleation.
Fig. 3: Sequential AC-HRTEM images and corresponding image simulations showing the third and fourth stages of γ-Fe crystallite nucleation.
Fig. 4: Electron-beam-stimulated nucleation of Au crystallite from the amorphous state.
Fig. 5: Electron-beam-stimulated nucleation of Re crystallite by coalescing two amorphous sub-nanometre Re clusters.

Similar content being viewed by others

Data availability

All data supporting the findings of this study are available in the manuscript or the Supplementary Information. The data for the electron elastic scattering cross-section that support the findings of this study are publicly available online at


  1. Myerson, A. S. & Trout, B. L. Nucleation from solution. Science 341, 855–856 (2013).

    Article  CAS  Google Scholar 

  2. Kashchiev, D. Thermodynamically consistent description of the work to form a nucleus of any size. J. Chem. Phys. 118, 1837–1851 (2003).

    Article  CAS  Google Scholar 

  3. Sleutel, M., Lutsko, J., Driessche, A. E. S. V. A. N., Durán-Olivencia, M. A. & Maes, D. Observing classical nucleation theory at work by monitoring phase transitions with molecular precision. Nat. Commun. 5, 5598 (2014).

    Article  CAS  Google Scholar 

  4. Habraken, W. J. E. M. et al. Ion-association complexes unite classical and non-classical theories for the biomimetic nucleation of calcium phosphate. Nat. Commun. 4, 1507 (2013).

    Article  Google Scholar 

  5. Dey, A. et al. The role of prenucleation clusters in surface-induced calcium phosphate crystallization. Nat. Mater. 9, 1010–1014 (2010).

    Article  CAS  Google Scholar 

  6. Erdemir, D., Lee, A. Y. & Myerson, A. S. Nucleation of crystals from solution: classical and two-step models. Acc. Chem. Res. 42, 621–629 (2009).

    Article  CAS  Google Scholar 

  7. De, Y. et al. Crystallization by particle attachment in synthetic, biogenic and geologic environments. Science 349, aaa6760 (2015).

    Article  Google Scholar 

  8. Gebauer, D. & Cölfen, H. Prenucleation clusters and non-classical nucleation. Nano Today 65, 564–584 (2011).

    Article  Google Scholar 

  9. Vekilov, P. G. The two-step mechanism of nucleation of crystals in solution. Nanoscale 2, 2346–2357 (2010).

    Article  CAS  Google Scholar 

  10. Lutsko, J. F. & Nicolis, G. Theoretical evidence for a dense fluid precursor to crystallization. Phys. Rev. Lett. 6, 0461024 (2006).

    Google Scholar 

  11. Loh, N. D. et al. Multistep nucleation of nanocrystals in aqueous solution. Nat. Chem. 9, 77–82 (2017).

    Article  CAS  Google Scholar 

  12. Nielsen, M. H., Aloni, S. & De Yoreo, J. J. In situ TEM imaging of CaCO3 nucleation reveals coexistence of direct and indirect pathways. Science 345, 1158–1162 (2014).

    Article  CAS  Google Scholar 

  13. Gal, A. et al. Calcite crystal growth by a solid-state transformation of stabilized amorphous calcium carbonate nanospheres in a hydrogel. Angew. Chem. Int. Ed. 52, 4867–4870 (2013).

    Article  CAS  Google Scholar 

  14. Navrotsky, A. Energetic clues to pathways to biomineralization: precursors, clusters and nanoparticles. Proc. Natl Acad. Sci. USA 101, 12096–12101 (2004).

    Article  CAS  Google Scholar 

  15. Baumgartner, J. et al. Nucleation and growth of magnetite from solution. Nat. Mater. 12, 310–314 (2013).

    Article  CAS  Google Scholar 

  16. Galkin, O., Chen, K., Nagel, R. L., Hirsch, R. E. & Vekilov, P. G. Liquid–liquid separation in solutions of normal and sickle cell hemoglobin. Proc. Natl Acad. Sci. USA 99, 8479–8483 (2002).

    Article  CAS  Google Scholar 

  17. Wolf, S. E., Leiterer, J., Kappl, M., Emmerling, F. & Tremel, W. Early homogenous amorphous precursor stages of calcium carbonate and subsequent crystal growth in levitated droplets. J. Am. Chem. Soc. 130, 12342–12347 (2008).

    Article  CAS  Google Scholar 

  18. Gebauer, D., Völkel, A. & Cölfen, H. Stable prenucleation calcium carbonate clusters. Science 322, 1819–1822 (2008).

    Article  CAS  Google Scholar 

  19. Sellberg, J. A. et al. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature. Nature 510, 381–384 (2014).

    Article  CAS  Google Scholar 

  20. Bera, M. K. & Antonio, M. R. Crystallization of Keggin heteropolyanions via a two-step process in aqueous solutions. J. Am. Chem. Soc. 138, 7282–7288 (2016).

    Article  CAS  Google Scholar 

  21. Yau, S.-T. & Vekilov, P. G. Direct observation of nucleus structure and nucleation pathways in apoferritin crystallization. J. Am. Chem. Soc. 123, 1080–1089 (2001).

    Article  CAS  Google Scholar 

  22. Lupulescu, A. I. & Rimer, J. D. In situ imaging of silicalite-1 surface growth reveals the mechanism of crystallization. Science 344, 729–732 (2014).

    Article  CAS  Google Scholar 

  23. Pusey, P. N. & van Megen, W. Phase behaviour of concentrated suspensions of nearly hard colloidal spheres. Nature 320, 340–342 (1986).

    Article  CAS  Google Scholar 

  24. Tsarfati, Y. et al. Crystallization of organic molecules: nonclassical mechanism revealed by direct imaging. ACS Cent. Sci. 4, 1031–1036 (2018).

    Article  CAS  Google Scholar 

  25. Zheng, H. et al. Observation of single colloidal platinum nanocrystal growth trajectories. Science 324, 1309–1312 (2009).

    Article  CAS  Google Scholar 

  26. Evans, J. E., Jungjohann, K. L., Browning, N. D. & Arslan, I. Controlled growth of nanoparticles from solution with in situ liquid transmission electron microscopy. Nano Lett. 11, 2809–2813 (2011).

    Article  CAS  Google Scholar 

  27. Sosso, G. C. et al. Crystal nucleation in liquids: open questions and future challenges in molecular dynamics simulations. Chem. Rev. 116, 7078–7116 (2016).

    Article  CAS  Google Scholar 

  28. Skowron, S. T. et al. Chemical reactions of molecules promoted and simultaneously imaged by the electron beam in transmission electron microscopy. Acc. Chem. Res. 50, 1797–1807 (2017).

    Article  CAS  Google Scholar 

  29. Cao, K. et al. Comparison of atomic scale dynamics for the middle and late transition metal nanocatalysts. Nat. Commun. 9, 3382 (2018).

    Article  Google Scholar 

  30. Khlobystov, A. N. Carbon nanotubes: from nano test tube to nano-reactor. ACS Nano 5, 9306–9312 (2011).

    Article  CAS  Google Scholar 

  31. Zoberbier, T. et al. Interactions and reactions of transition metal clusters with the interior of single-walled carbon nanotubes imaged at the atomic scale. J. Am. Chem. Soc. 134, 3073–3079 (2012).

    Article  CAS  Google Scholar 

  32. Somada, H., Hirahara, K., Akita, S. & Nakayama, Y. A molecular linear motor consisting of carbon nanotubes. Nano Lett. 9, 62–65 (2009).

    Article  CAS  Google Scholar 

  33. Warner, J. H. et al. Capturing the motion of molecular nanomaterials encapsulated within carbon nanotubes with ultrahigh temporal resolution. ACS Nano 3, 3037–3044 (2010).

    Article  Google Scholar 

  34. Ran, K., Zuo, J. –M., Chen, Q. & Shi, Z. Electron beam stimulated molecular motions. ACS Nano 5, 3367–3372 (2011).

    Article  CAS  Google Scholar 

Download references


K.C. acknowledges financial support from the China Scholarship Council (CSC). J.B. and U.K. acknowledge support from the ‘Graphene Flagship’ and DFG within the project KA 1295-33 as well as the DFG and the Ministry of Science, Research and the Arts (MWK) of Baden-Wuerttemberg within the frame of the SALVE (Sub Angstrom Low-Voltage Electron microscopy) project. T.W.C. and A.N.K. acknowledge EPSRC for financial support and the Nanoscale & Microscale Research Centre (nmRC) and the Centre for Sustainable Chemistry, University of Nottingham, for access to instrumentation. E.B. acknowledges a Royal Society Wolfson Fellowship for financial support. Calculations were performed using the High Performance Computing facility at the University of Nottingham. Z.L. and K.S. acknowledge support from a JST Research Acceleration Program and the Japan Society for the Promotion of Science KAKENHI Grant JP 25107003.

Author information

Authors and Affiliations



R.L.M. prepared the samples. C.T.S. carried out initial analysis of the samples. T.W.C. developed the methodology of filling nanotubes with metal precursors. Z.L., J.B. and K.S. performed the EELS mapping of the sample. K.C. and J.B. investigated of the sample by AC-HRTEM and recorded the videos of nucleation. K.C., J.B., A.N.K. and U.K. discussed the results and analysed the data. E.B. and S.T.S. carried out theoretical modelling. K.C., J.B., A.N.K. and U.K. drafted the manuscript. All the authors have revised the manuscript. U.K. and A.N.K. supervised the research.

Corresponding authors

Correspondence to Andrei N. Khlobystov or Ute Kaiser.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Section 1–8, Figs. 1–17 and references 1–25.

Supplementary Video 1

Fe crystal nuclei formed from atomic seed.

Supplementary Video 2

Au crystal nuclei formed from amorphous nanocluster.

Supplementary Video 3

Re crystal nuclei formed by coalescence.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cao, K., Biskupek, J., Stoppiello, C.T. et al. Atomic mechanism of metal crystal nucleus formation in a single-walled carbon nanotube. Nat. Chem. 12, 921–928 (2020).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing