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.

  • Letter
  • Published:

Visualizing single-molecule diffusion in mesoporous materials


Periodic mesoporous materials formed through the cooperative self-assembly of surfactants and framework building blocks can assume a variety of structures1,2,3, and their widely tuneable properties make them attractive hosts for numerous applications4,5,6,7. Because the molecular movement in the pore system is the most important and defining characteristic of porous materials8, it is of interest to learn about this behaviour as a function of local structure. Generally, individual fluorescent dye molecules can be used as molecular beacons with which to explore the structure of—and the dynamics within—these porous hosts9,10,11,12,13, and single-molecule fluorescence techniques provide detailed insights into the dynamics of various processes, ranging from biology14,15 to heterogeneous catalysis16. However, optical microscopy methods cannot directly image the mesoporous structure of the host system accommodating the diffusing molecules, whereas transmission electron microscopy provides detailed images of the porous structure17, but no dynamic information. It has therefore not been possible to ‘see’ how molecules diffuse in a real nanoscale pore structure. Here we present a combination of electron microscopic mapping and optical single-molecule tracking experiments to reveal how a single luminescent dye molecule travels through linear or strongly curved sections of a mesoporous channel system. In our approach we directly correlate porous structures detected by transmission electron microscopy with the diffusion dynamics of single molecules detected by optical microscopy. This opens up new ways of understanding the interactions of host and guest.

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

Figure 1: Sample systems.
Figure 2: Merging of the single-molecule trajectories and the TEM micrographs.
Figure 3: Structural elements found in real two-dimensional hexagonal mesoporous silica film.
Figure 4: Structural elements and molecular trajectories found in real two-dimensional hexagonal mesoporous silica film.

Similar content being viewed by others


  1. Beck, J. S. et al. A new family of mesoporous molecular sieves prepared with liquid-crystal templates. J. Am. Chem. Soc. 114, 10834–10843 (1992)

    Article  CAS  Google Scholar 

  2. Sen, T., Tiddy, G. J. T., Casci, J. L. & Anderson, M. W. Synthesis and characterization of hierarchically ordered porous silica materials. Chem. Mater. 16, 2044–2054 (2004)

    Article  CAS  Google Scholar 

  3. Zhao, D. et al. Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 angstrom pores. Science 279, 548–552 (1998)

    Article  ADS  CAS  Google Scholar 

  4. Dag, Ö., Ozin, G. A., Yang, H., Reber, C. & Bussière, G. Photoluminescent silicon clusters in oriented hexagonal mesoporous silica film. Adv. Mater. 11, 474–480 (1999)

    Article  CAS  Google Scholar 

  5. Davis, M. E. Ordered porous materials for emerging applications. Nature 417, 813–821 (2002)

    Article  ADS  CAS  Google Scholar 

  6. Shen, J. L. et al. Photoluminescence sites on MCM-48. Micropor. Mesopor. Mater. 64, 135–143 (2003)

    Article  CAS  Google Scholar 

  7. Yang, C.-M., Cho, A.-T., Pan, F.-M., Tsai, T.-G. & Chao, K.-J. Spin-on mesoporous silica films with ultralow dielectric constants, ordered pore structures, and hydrophobic surfaces. Adv. Mater. 13, 1099–1102 (2001)

    Article  CAS  Google Scholar 

  8. Kukla, V. et al. NMR studies of single-file diffusion in unidimensional channel zeolites. Science 272, 702–704 (1996)

    Article  ADS  CAS  Google Scholar 

  9. Hellriegel, C., Kirstein, J. & Bräuchle, C. Tracking of single molecules as a powerful method to characterize diffusivity of organic species in mesoporous materials. New J. Phys. 7, 23 (2005)

    Article  Google Scholar 

  10. Jung, C., Hellriegel, C., Michaelis, J. & Bräuchle, C. Single-molecule traffic in mesoporous materials: translational, orientational, and spectral dynamics. Adv. Mater. 19, 956–960 (2007)

    Article  CAS  Google Scholar 

  11. Kirstein, J. et al. Exploration of nanostructured channel systems with single-molecule probes. Nature Mater. 6, 303–310 (2007)

    Article  ADS  CAS  Google Scholar 

  12. McCain, K. S., Hanley, D. C. & Harris, J. M. Single-molecule fluorescence trajectories for investigating molecular transport in thin silica sol-gel films. Anal. Chem. 75, 4351–4359 (2003)

    Article  CAS  Google Scholar 

  13. Werley, C. A. & Moerner, W. E. Single-molecule nanoprobes explore defects in spin-grown crystals. J. Phys. Chem. B 110, 18939–18944 (2006)

    Article  CAS  Google Scholar 

  14. Schmidt, T., Schütz, G. J., Baumgartner, W., Gruber, H. J. & Schindler, H. Imaging of single molecule diffusion. Proc. Natl Acad. Sci. USA 93, 2926–2929 (1996)

    Article  ADS  CAS  Google Scholar 

  15. Seisenberger, G. et al. Real-time single-molecule imaging of the infection pathway of an adeno-associated virus. Science 294, 1929–1932 (2001)

    Article  ADS  CAS  Google Scholar 

  16. Roeffaers, M. B. J. et al. Spatially resolved observation of crystal-face-dependent catalysis by single turnover counting. Nature 439, 572–575 (2006)

    Article  ADS  CAS  Google Scholar 

  17. Sakamoto, Y. et al. Direct imaging of the pores and cages of three-dimensional mesoporous materials. Nature 408, 449–453 (2000)

    Article  ADS  CAS  Google Scholar 

  18. Holtrup, F. O. et al. Terrylenimides: new NIR fluorescent dyes. Chem. Eur. J. 3, 219–225 (1997)

    Article  CAS  Google Scholar 

  19. Jung, C. et al. A new photostable terrylene diimide dye for applications in single molecule studies and membrane labeling. J. Am. Chem. Soc. 128, 5283–5291 (2006)

    Article  CAS  Google Scholar 

  20. Brinker, C. J., Lu, Y., Sellinger, A. & Fan, H. Evaporation-induced self-assembly: nanostructures made easy. Adv. Mater. 11, 579–585 (1999)

    Article  CAS  Google Scholar 

  21. Saxton, M. J. & Jacobson, K. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26, 373–399 (1997)

    Article  CAS  Google Scholar 

Download references


We thank K. Müllen for providing the TDI dye; Siltronic AG for the silicon wafers; the group of P. Müller-Buschbaum for the 2D-GISAXS measurements; and S. Schmidt and B. Platschek for assistance with electron microscopy. This work was funded by two Collaborative Research Centres (‘Manipulation of matter at the nanometer length scale’ and ‘Dynamics and intermediates of molecular transformations’) of the German Research Foundation (DFG) and by the Nanosystems Initiative Munich (NIM), as well as the Center for Integrated Protein Science Munich (CiPSM).

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Christoph Bräuchle or Thomas Bein.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-2 with Legends, Supplementary Table 1 and Legends for Supplementary Movies 1-3. (PDF 2427 kb)

Supplementary Movie 1

This file contains Supplementary Movie 1 which is a wide-field movie of fluorescent dye molecules diffusing through the porous system. Temporal resolution: 200 ms per frame. Animation with 5x real time. (MOV 6699 kb)

Supplementary Movie 2

This file contains Supplementary Movie 2 which shows the animation of the single particle trajectory superimposed with the porous structure from TEM (see Fig. 4a). The molecule clearly diffuses along the porous structure. Animation with 2x real time. (MOV 2655 kb)

Supplementary Movie 3

This file contains Supplementary Movie 3 which shows the animation of the single particle trajectory superimposed with the porous structure from TEM (see Fig. 4c). The molecule clearly diffuses along the porous structure and bounces back at domain boundaries. Animation with 2x real time. (MOV 4607 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zürner, A., Kirstein, J., Döblinger, M. et al. Visualizing single-molecule diffusion in mesoporous materials. Nature 450, 705–708 (2007).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


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