Structure and catalytic properties of the most complex intergrown zeolite ITQ-39 determined by electron crystallography

Journal name:
Nature Chemistry
Year published:
Published online


Porous materials such as zeolites contain well-defined pores in molecular dimensions and have important industrial applications in catalysis, sorption and separation. Aluminosilicates with intersecting 10- and 12-ring channels are particularly interesting as selective catalysts. Many porous materials, especially zeolites, form only nanosized powders and some are intergrowths of different structures, making structure determination very challenging. Here, we report the atomic structures of an aluminosilicate zeolite family, ITQ-39, solved from nanocrystals only a few unit cells in size by electron crystallography. ITQ-39 is an intergrowth of three different polymorphs, built from the same layer but with different stacking sequences. ITQ-39 contains stacking faults and twinning with nano-sized domains, being the most complex zeolite ever solved. The unique structure of ITQ-39, with a three-dimensional intersecting pairwise 12-ring and 10-ring pore system, makes it a promising catalyst for converting naphtha into diesel fuel, a process of emerging interest for the petrochemical industry.

At a glance


  1. Reconstructed electron diffraction patterns and HRTEM images of ITQ-39.
    Figure 1: Reconstructed electron diffraction patterns and HRTEM images of ITQ-39.

    a,b, Two perpendicular cuts of the reconstructed three-dimensional reciprocal lattice giving the h0l slice (a) and the 0kl slice (b). The h0l pattern in a can be indexed using two oblique reciprocal lattices that are related by a 180° rotation along c*; one of them is indicated. The 0kl pattern in b can be indexed using two different lattices; a rectangular one (marked b*Ac*) and an oblique one (marked b*Bc*), corresponding to two different polymorphs ITQ-39A and ITQ-39B, respectively. c,d, Structure projection reconstructed from 20 HRTEM images along b (c) and a (d), respectively. Inserts are the corresponding selected-area electron diffraction patterns. Pairwise channels are seen as ‘8’ in the thin crystal area in c. Twins can be identified from the orientation of the pairwise channels. 10-ring channels are observed in d and the channel stacking is traced by a line in d. The different stacking leads to three polymorphs A, B and C, also marked in d. The domains used for structure factor determination are outlined by rectangles.

  2. Three-dimensional electron potential map and atomic structure model of the stacking disorder in ITQ-39.
    Figure 2: Three-dimensional electron potential map and atomic structure model of the stacking disorder in ITQ-39.

    a, Three-dimensional electrostatic potential map of the building layer of ITQ-39 reconstructed from the structure factor amplitudes and phases extracted from the marked nano-domains in Fig. 1c,d. The 28 symmetry-independent silicon atoms could be located directly from the three-dimensional map and placed based on chemical knowledge. The refined structure model of ITQ-39 is superimposed and only the silicon–silicon connections are shown. b, Atomic structure model of the three polymorphs viewed along a. The building layers (highlighted) are stacked along c* either without any shift (ITQ-39C) or with a shift of −1/3b (ITQ-39B) or ±1/3b (ITQ-39A). c, Projection along b showing the unique pairwise 12-ring channels. The different polymorphs are not distinguishable from this projection because the relative layer shifts are along b.

  3. Comparison of simulated and experimental powder X-ray diffraction patterns.
    Figure 3: Comparison of simulated and experimental powder X-ray diffraction patterns.

    The experimental powder X-ray diffraction pattern was obtained from a calcined pure-silica ITQ-39 sample. The simulated powder X-ray diffraction pattern was calculated using DIFFaX34 from a model containing both the intergrowth of ITQ-39A (45%), ITQ-39B (45%) and ITQ-39C (10%) and twinning with twin domains 6 nm in thickness along c*, as estimated from HRTEM images. Translational disorder within the building layer was not included in the simulation.

  4. Three-dimensional channel system in ITQ-39A with its structure model superimposed.
    Figure 4: Three-dimensional channel system in ITQ-39A with its structure model superimposed.

    a, Projection along b showing that the 12-ring channels intersect with 10-ring channels running along three directions (indicated by arrows). b, Different view of the channel system with a cross-section of the intersecting channels, illustrating channel connectivity. The 12-ring channels along b are straight, and the 10-ring channels along a, c and a + c zig-zag. The channel systems in ITQ-39B and ITQ-39C are similar to those in ITQ-39A, except for the relative heights of the 10-ring channels.

  5. Channel system in ITQ-39A represented using a rod model.
    Figure 5: Channel system in ITQ-39A represented using a rod model.

    a, Viewed along the pairwise 12-ring channels. b, Viewed perpendicular to the pairwise 12-ring channels. The straight pairwise 12-ring channels and their connection with the zig-zag 10-ring channels are clearly shown.

  6. Comparison of the catalytic results of ITQ-39, beta and MWW for alkylation of naphtha with olefins.
    Figure 6: Comparison of the catalytic results of ITQ-39, beta and MWW for alkylation of naphtha with olefins.

    A mixture of 70 wt% heavy and 30 wt% light naphtha was used. Catalysis was performed at 230 °C and 3.5 MPa with 1.7 h contact time with respect to the olefins. TOS, time on stream.


  1. Lobo, R. F. et al. SSZ-26 and SSZ-33—2 molecular-sieves with intersecting 10-ring and 12-ring pores. Science 262, 15431546 (1993).
  2. Dorset, D. L., Weston, S. C. & Dhingra, S. S. Crystal structure of zeolite MCM-68: a new three-dimensional framework with large pores. J. Phys. Chem. B 110, 20452050 (2006).
  3. Simancas, R. et al. Modular organic structure-directing agents for the synthesis of zeolites. Science 330, 12191222 (2010).
  4. Leonowicz, M. E., Lawton, J. A., Lawton, S. L. & Rubin, M. K. MCM-22—a molecular-sieve with 2 independent multidimensional channel systems. Science 264, 19101913 (1994).
  5. Lobo, R. F. & Davis, M. E. CIT-1—a new molecular-sieve with intersecting pores bounded by 10-rings and 12-rings. J. Am. Chem. Soc. 117, 37643779 (1995).
  6. Corma, A., Rey, F., Valencia, S., Jorda, J. L. & Rius, J. A zeolite with interconnected 8-, 10- and 12-ring pores and its unique catalytic selectivity. Nature Mater. 2, 493497 (2003).
  7. Paillaud, J. L., Harbuzaru, B., Patarin, J. & Bats, N. Extra-large-pore zeolites with two-dimensional channels formed by 14 and 12 rings. Science 304, 990992 (2004).
  8. Corma, A., Diaz-Cabanas, M. J., Rey, F., Nicolooulas, S. & Boulahya, K. ITQ-15: the first ultralarge pore zeolite with a bi-directional pore system formed by intersecting 14- and 12-ring channels, and its catalytic implications. Chem. Commun. 13561357 (2004).
  9. Corma, A., Diaz-Cabanas, M. J., Jorda, J. L., Martinez, C. & Moliner, M. High-throughput synthesis and catalytic properties of a molecular sieve with 18- and 10-member rings. Nature 443, 842845 (2006).
  10. Treacy, M. M. J. & Newsam, J. M. Two new three-dimensional twelve-ring zeolite frameworks of which zeolite beta is a disordered intergrowth. Nature 332, 249251 (1988).
  11. Kokotailo, G. T., Lawton, S. L., Olson D. H. & Meier W. M. Structure of synthetic zeolite ZSM-5. Nature 272, 437438 (1978).
  12. Castaneda, R., Corma, A., Fornes, V., Rey, F. & Rius, J. Synthesis of a new zeolite structure ITQ-24, with intersecting 10- and 12-membered ring pores. J. Am. Chem. Soc. 125, 78207821 (2003).
  13. Cantin, A. et al. Synthesis and structure of the bidimensional zeolite ITQ-32 with small and large pores. J. Am. Chem. Soc. 127, 1156011561 (2005).
  14. Moliner, M. et al. A new aluminosilicate molecular sieve with a system of pores between those of ZSM-5 and beta zeolite. J. Am. Chem. Soc. 133, 94979505 (2011).
  15. Baerlocher, Ch., Weber, T., McCusker, L. B., Palatinus, L. & Zones, S. T. Unraveling the perplexing structure of the zeolite SSZ-57. Science 333, 13341337 (2011).
  16. DeRosier, D. J. & Klug, A. Reconstruction of three dimensional structures from electron micrographs. Nature 217, 130134 (1968).
  17. Henderson, R. & Unwin, P. N. T. Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257, 2832 (1975).
  18. Hovmöller, S., Sjögren, A., Farrants, G., Sundberg, M. & Marinder, B-O. Accurate atomic positions from electron microscopy. Nature 311, 238241 (1984).
  19. Gramm, F. et al. Complex zeolite structure solved by combining powder diffraction and electron microscopy. Nature 444, 7981 (2006).
  20. Baerlocher, Ch. et al. Structure of the polycrystalline zeolite catalyst IM-5 solved by enhanced charge flipping. Science 315, 11131116 (2007).
  21. Baerlocher, Ch. et al. Ordered silicon vacancies in the framework structure of the zeolite catalyst SSZ-74. Nature Mater. 7, 631635 (2008).
  22. Sun, J. L. et al. The ITQ-37 mesoporous chiral zeolite. Nature 458, 11541157 (2009).
  23. Jiang, J-X. et al. Synthesis and structure determination of the hierarchical meso-microporous zeolite ITQ-43, Science 333, 13311334 (2011).
  24. Sun, J. L. et al. Structure determination of the zeolite IM-5 using electron crystallography. Z. Kristallogr. 225, 7785 (2010).
  25. Zhang, D., Oleynikov, P., Hovmöller, S. & Zou, X. D. Collecting 3D electron diffraction data by the rotation method. Z. Kristallogr. 225, 94102 (2010).
  26. Wan, W., Hovmöller, S. & Zou, X. D. Structure projection reconstruction from through-focus series of high-resolution transmission electron microscopy images. Ultramicroscopy (revision submitted).
  27. Zou, X. D., Sundberg, M., Larine, M. & Hovmöller, S. Structure projection retrieval by image processing of HRTEM images taken under non-optimal defocus conditions. Ultramicroscopy 62, 103121 (1996).
  28. Weirich, T. E., Ramlau, R., Simon, A., Hovmöller, S. & Zou, X. D. A crystal structure determined to 0.02 Å accuracy by electron microscopy. Nature 382, 144146 (1996).
  29. Oleynikov, P., Hovmöller, S. & Zou, X. D. ED-Tomo; available at
  30. Zou, X. D., Hovmöller, S. & Oleynikov, P. Electron Crystallography: Electron Microscopy and Electron Diffraction, IUCr Texts on Crystallography (Oxford Univ. Press, 2011).
  31. Wan, W., Hovmöller, S. & Zou, X. D. QFocus; available at
  32. Hovmöller, S. CRISP: crystallographic image processing on a personal computer. Ultramicroscopy 41, 121135 (1992).
  33. Oleynikov, P. eMap and eSlice: a software package for crystallographic computing. Cryst. Res. Technol. 46, 569579 (2011).
  34. Baerlocher, Ch., Hepp, A. & Meier W. M. DLS-76. Distance Least Squares Refinement Program (Institut für Kristallographie, ETH Zurich, 1977).
  35. Gale, J. D. GULP: a computer program for the symmetry-adapted simulation of solids. J. Chem. Soc. Faraday Trans. 93, 629637 (1997).
  36. Gale, J. D. & Rohl, A. L. The general utility lattice program (GULP). Mol. Simul. 29, 291341 (2003).
  37. Braunbarth, C. et al. Structure of strontium ion-exchanged ETS-4 microporous molecular sieves. Chem. Mater. 12, 18571865 (2000).
  38. Treacy, M. M. J., Newsam, J. M. & Deem, M. W. A general recursion method for calculating diffracted intensities from crystals containing planar faults. Proc. R. Soc. Lond. A 433, 499520 (1991).
  39. Baerlocher, Ch. & McCusker, L. B. Database of zeolite structures; available at
  40. Perego, C. & Ingallina, P. Recent advances in the industrial alkylation of aromatics: new catalysts and new processes. Catal. Today 73, 322 (2002).
  41. Collins, N. A., Landis, M. E., Timken, H. K. C. & Trewella, J. C. Cetane upgrading via aromatic alkylation. WO patent 00/39253 (2000).
  42. Corma, A., Corell, C. & Perez-Pariente, J. Synthesis and characterization of the MCM-22 zeolite. Zeolites 15, 28 (1995).
  43. Catlow, C. R. A. & Cormack, A. N. Computer modeling of silicates. Int. Rev. Phys. Chem. 6, 227250 (1987).
  44. Schröder, K. P., Sauer, J., Leslie, M., Catlow, C. R. A. & Thomas, J. M. Bridging hydroxyl-groups in zeolitic catalysts—a computer-simulation of their structure, vibrational properties and acidity in protonated faujasites (H-Y zeolites). Chem. Phys. Lett. 188, 320325 (1992).

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Author information


  1. Berzelii Centre EXSELENT on Porous Materials, and Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden

    • Tom Willhammar,
    • Junliang Sun,
    • Wei Wan,
    • Peter Oleynikov,
    • Daliang Zhang &
    • Xiaodong Zou
  2. Instituto de Tecnología Química (UPV-CSIC), Universidad Politécnica de Valencia, Consejo Superior de Investigaciones Científicas, E-46022 Valencia, Spain

    • Manuel Moliner,
    • Jorge Gonzalez,
    • Cristina Martínez,
    • Fernando Rey &
    • Avelino Corma
  3. Escuela de Ciencias Químicas, Universidad de Colima, Colima, 28040, Mexico

    • Jorge Gonzalez
  4. State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China

    • Daliang Zhang


T.W., W.W., P.O and D.L.Z. carried out the TEM work. T.W and J.L.S. executed the structure solution and verification. M.M., J.G. and F.R. carried out the OSDA and zeolite syntheses work. C.M. performed the catalytic experiments. X.D.Z, T.W., J.L.S., M.M. and A.C. were responsible for completing the manuscript.

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The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary information (1,616 KB)

    Supplementary information


  1. Supplementary information (5,881 KB)

    Supplementary Video 1 showing part of 3D electron diffraction data collection

  2. Supplementary information (6,538 KB)

    Supplementary Video 2 displaying the reconstructed 3D reciprocal lattice from 880 ED frames

  3. Supplementary information (10,702 KB)

    Supplementary Video 3 showing the 3D intersecting channel system in ITQ-39A

Crystallographic information files

  1. Supplementary information (6 KB)

    Crystallographic data for zeolite ITQ-39A

  2. Supplementary information (5 KB)

    Crystallographic data for zeolite ITQ-39B

  3. Supplementary information (4 KB)

    Crystallographic data for zeolite ITQ-39C

Additional data