Detailed Structural Survey of the Zeolite ITQ-39 by Electron

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A detailed structural survey of the zeolite ITQ-39 by electron crystallography Elina Kapaca, Xiaodong Zou, and Tom Willhammar Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.6b01874 • Publication Date (Web): 06 Mar 2017 Downloaded from http://pubs.acs.org on March 9, 2017

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Crystal Growth & Design

A detailed structural survey of the zeolite ITQ-39 by electron crystallography Elina Kapaca†, Xiaodong Zou†,* ,Tom Willhammar†,* † Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden KEYWORDS Zeolite, electron crystallography, structural disorders

ABSTRACT The structure of the highly faulted zeolite ITQ-39 was previously determined by electron crystallography, revealing the presence of stacking disorders and twinning. Structural models of three polytypes were proposed, providing a basic description of the ITQ-39 material. Here a more comprehensive description of the complex structure of the ITQ-39 zeolite is presented, based on a 1D periodic building unit. The study includes a detailed description of the structural defects in the material based on the analysis of high resolution transmission electron microscopy (HRTEM) images and information on how the defects influence the pore system. A new structure arrangement with alternating twinning was found in the material, and structural models of three twinned end-members are presented. The geometry of the different structural models is evaluated in order to understand the formation of the crystals.

1 Environment ACS Paragon Plus


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1. INTRODUCTION Zeolites are built from corner sharing tetrahedra with oxygen atoms in the corner and T-atoms (T=Si, Al, B…) in the centers, which define the crystalline atomic structure of the zeolitic materials. The unique properties of zeolites exploit for different applications, including gas separation, catalysis and ion exchange, can be mostly explained by the presence of micropores with well-defined sizes and shapes.1 Structure determination of zeolites is often challenging by the following reasons: 1) zeolite crystals frequently grow with sizes too small for structure determination using single crystal X-ray diffraction; 2) zeolite structures are often complex with large unit cells and many unique atoms per unit cell; and 3) zeolitic materials often appear as disordered solids. The use of electron crystallography has provided powerful tools to overcome these difficulties2 allowing successful structure determination of several complex zeolites based on three dimensional (3D) electron diffraction3–5 or electron diffraction combined with high resolution transmission electron microscopy (HRTEM)6–8. The zeolite ITQ-39 is an outstanding example of structure determination by electron crystallography because of its extreme framework complexity and high structural disorder. The crystals of ITQ-39 have a needle like morphology with a length of 1-2 µm and a cross-section of approx. 30 nm, and these needles appear forming bundles, see Figs. 1a and 1b. In addition, the material contains severe structural disorders, which in combination with its small crystal sizes, results in severely broadened peaks in the powder X-ray diffraction (PXRD) pattern, see Fig. 1c.


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Figure 1. (a) SEM image of ITQ-39 reveals the needle-like morphology with the longest dimension of 1-2 µm. The needles always grow together in bundles. (b) A view of the crosssection shows that the crystal agglomerates are 100-200 nm in diameter, while individual crystals are ~30 nm in diameter. (c) The PXRD pattern of ITQ-39 shows rather few and broad peaks. The synthesis of zeolite ITQ-39 was first reported by Moliner et. al.9,10 and later a material exhibiting a similar PXRD pattern, SSZ-83, was reported by Zones et.al.11. Due to the severe disorder a structural elucidation of ITQ-39 was only possible by combining rotation electron diffraction (RED)12 and HRTEM as shown by Willhammar et.al.1312. Firstly, 3D RED data was used to determine the unit cell parameters, and to obtain information about the presence of stacking disorders and twinning. The RED data was further used to identify the two main projections [010] and [100] from which HRTEM images were acquired. Based on the through-



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focus series of HRTEM images, structure projection images were reconstructed using the structure projection reconstruction software QFOCUS.14 Stacking disorder could be observed from the structure projection image along [100] and three polytypes, named A, B, C, could be identified,, two of them are among the crystallographically most complex zeolite structures determined by then. The images were used for reconstruction of a 3D electrostatic potential map from which the coordinates of silicon atoms for polytype B of ITQ-39 could be obtained. The structure was completed with oxygen atoms and later geometrically refined using a distance least square refinement. Finally, the structural model was further verified by different methods including simulations of PXRD and electron diffraction patterns, solid state NMR among others. The three polytypes defining the ITQ-39 material present interconnected large (12-ring) and medium (10-ring) pores, creating an attractive multipore zeolitic structure for several catalytic applications. Indeed, the ITQ-39 material has been described as an efficient catalyst for alkylation of aromatics with olefins,9 conversion of low value naphtha fractions into diesel fuel,13 selective epoxidation of olefins,16 and oligomerization of alkenes.17 The ITQ-39 family has been assigned with the framework code *-ITN in the Database of Zeolite Structures of the International Zeolite Association.18 The structure description of ITQ-39 as it is presented till now 13 provides a good general understanding of the zeolite material. But in order to have a complete overview of the complex crystalline structure of ITQ-39 we have further studied the material by electron microscopy. Here we provide a more comprehensive description of the structure of the ITQ-39 material. 2. EXPERIMENTAL METHODS


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The ITQ-39 sample for electron microscopy studies was prepared by crushing the powder in an agate mortar, followed by adding ethanol, sonicating the dispersion and placing a droplet on a copper grid covered by a holey carbon film. In order to facilitate the imaging along the long needle direction of the crystals, the crystals were sectioned by ultramicrotomy as the following; the powder was first dried at 80 ˚C to remove additional humidity, then embedded into a resin (SPURR), and hardened at 70 ˚C for 16 h. The resin with embedded ITQ-39 crystals was cut into thin sections of 50-70 nm in thickness. Electron diffraction patterns and HRTEM images were collected under weak beam conditions using a JEOL JEM2100F TEM (point resolution 1.9 Å, Gatan Ultrascan 1000 2048 × 2048 CCD) operated at an acceleration voltage of 200 kV. The electron beam dose was approximately 100 e-/Å2 for each of the HRTEM images acquired in the through-focus series. In order to minimize the electron beam damage of the samples a script was used to control the brightness of the beam. Scanning electron microscopy (SEM) images were acquired using a JEOL JSM7401F microscope with a secondary electron detector (LEI) operated at an accelerating voltage of 2 kV and a working distance of 8 mm. The cross-sectioning for SEM was prepared by first embedding the powder into a resin followed by sectioning for 12 hours by a cross section polisher, JEOL SM-09010, using Argon beam milling. In order to facilitate the acquisition and interpretation of the HRTEM images, through-focus series were collected. The through-focus series contained 20 images acquired with a constant defocus step. Each series passed through the Scherzer defocus condition and hence contained at least one image close to the Scherzer defocus. From the through-focus series a structure projection image was reconstructed by a contrast transfer function (CTF) correction algorithm using the software QFocus.14 Structure projection reconstruction is based on the weak-phase-



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object approximation. Defocus values and two-fold astigmatism is determined from throughfocus series and the effect of the CTF is corrected followed by image combination. For geometrical optimization of the structural models obtained from HRTEM images and model building, distance least squares refinements were performed using the software DLS76.19 DLS76 is a software for geometry optimization of framework type structures with very well defined interatomic distances and bond angles. The nearest Si-O, O-O and Si-Si distances were refined, the Si-O distances (1.61 Å) refined with a stronger weighting (2.000), the O-O distances (2.63 Å) with a weaker weighting (0.4058), and the Si-Si distances (3.14 Å) with the weakest weighting (0.2288). The geometrical refinement will provide an R value that represents how well the structure model agrees with desired distances and bond angles. 3. RESULTS AND DISCUSSION The basic structure of ITQ-39 is a random intergrowth between three structures consisting of the same building layer but with different layer stacking sequences showing a polytypic behavior. The building layer of ITQ-39 allows connectivity with three different lateral translations along the b-axis, see Fig. 2a. The adjacent layers are translated by +1/3b, -1/3b, or 0*b. These translations can give rise to three different basic stacking sequences, resulting in three polytypes, which are denoted polytypes A, B and C. By strictly alternating the translations in the sequence +1/3b, -1/3b, +1/3b… (or -1/3b, +1/3b, -1/3b…) the monoclinic polytype A is formed. By consecutive translations of +1/3b, +1/3b … (or -1/3b, -1/3b …) the triclinic polytype B is formed. The third possibility is repetitive stacking without any translation which generates the monoclinic polytype C. In addition to stacking disorder, twinning is observed in the material. The twinning can be obtained by a mirror operation of the aforementioned building layer in the


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plane perpendicular to the c*-axis followed by a translation of 1/2a, see Fig. 2b. The intergrowth between the three polytypes maintains the 3D pore system with intersecting 12 × 10 × 10-ring channels. The 3D framework stays intact, with only terminals from the bridging Si-site in the center of the pairwise 12-ring channels running along the b-axis. The above description of the stacking disorder and twinning allows a basic understanding of the structure of ITQ-39. However, in order to fully understand the growth of this material a more comprehensive description of the structure will be presented below.

Figure 2. Structure of ITQ-39 viewed along (a) [100] and (b) [010]. Three different stacking sequences are shown in (a) A stacking of ABA… character results in polytype A, ABC… stacking in polytype B and CC… type stacking in polytype C. (b) The twinning can be described as a mirror operation perpendicular to c* (plane indicated by a black line) followed by a translation of 1/2a.

3.1 Stacking disorder



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In this section a more comprehensive description of the stacking disorder within the ITQ-39 crystals will be given. In the structure projection images along [100], the presence of the three basic polytypes A, B and C can be observed (see A, B and C in Fig. 3a). While the 10-ring channels can be clearly seen in some regions (surrounded by smaller 5- and 6-rings) as indicated by a white arrow in Fig. 3a, they are interrupted in other regions, as indicated by a black arrow in Fig. 3a. This structural feature cannot be explained by the original description of the structure, which was based on a stacking of the same 2D building layer, presented in Fig. 2a. However, it can be described using a basic 1D building rod instead of the previous 2D building layer, as shown in Figs. 4a and b. The BU can be connected with neighboring BUs along the b-axis to

a

b

form a 1D rod with 10-ring channels running along the [100] direction, see Fig. 4c. This 1D rod-

a like unit can be considered to be the periodic building unit (PBU) from which the entire structure of ITQ-39 can be constructed.

Figure 3. (a) Structure projection image of ITQ-39 along [100] with selected area electron diffraction pattern inset. The stacking disorder can be observed, marked by a white guide line. Domains with straight 10-ring channels can be clearly seen, as indicated by a white arrow. In


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other regions the 10-ring channels are no longer obvious, as indicated by a black arrow. The contrast can be explained by zig-zag 10-ring channels. (b) Structure projection image along [010] showing straight pair-wise 12-ring channels and the presence of SiO4 columns shared by the pairwise 12-ring channels, marked by an arrow.

Figure 4. The basic building unit (BU) of the ITQ-39 structure viewed along (a) [100] and (b) [010] directions. The BU contains 52 Si atoms. (c) The BUs in (a) are connected along the b-axis to form a 1D periodic building unit (PBU) from which the structure of ITQ-39 can be built, here viewed along [100] with one BU highlighted. The PBUs can be connected along the c*-axis with three possible translations, +1/3b, -1/3b or 0b. As the PBUs are connected along the c*- axis they will in addition bridge neighboring PBUs along the a-axis to form an extended 3D framework, see Fig. 5a. Each PBU has the freedom to attain a separate translation along the b-axis, in multiples of 1/3b. If consecutive PBUs along the [100] direction have the same translational position along the b-axis, the 10-ring channels along



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[100] will be straight, whereas in other cases, the 10-ring channel will be zig-zag in the ab-plane, see Fig 5b. In the case where consecutive PBUs in the ab-plane have identical translational shifts, the three basic structural models described as polytype A, B and C will be formed (see Table 1). The straight pairwise 12-ring channels running along the b-axis as well as the 10-ring channels running along [100] will not be interrupted by this disorder. Two neighboring PBUs along the a-axis with the same translational shift along the b-direction allows for a bridging Si-site, linking the two PBUs together, see Fig. 5a. The bridging T-site can be clearly seen in the structure projection images along [010], as indicated by an arrow in Fig. 3b.

Figure 5. The 3D structure of ITQ-39 resulting from the combination of PBUs viewed along (a) [010] and (b) [100]. The two PBUs in the middle layer (highlighted in a) are at different heights (differ by 1/3b and hence the 10-ring channels running along [100] become zig-zag as shown in b). Bridging Si atoms between two PBUs are marked by a red arrow.

3.2 Twinning


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It is evident from selected area electron diffraction (SAED) patterns as well as structure projection images that ITQ-39 contains twinning when viewed along the [010] direction, see Fig. 6. From the structure projection images it can also be observed that the twinning is present at two different length scales: i.

The twinning exists at the local level, within a crystallite, where each layer of PBUs in the ab-plane can undergo a mirror operation in the (001) plane followed by a translation of 1/2a. The structure of ITQ-39 allows for connectivity between ab-layers after the twin operation with the geometry reasonably preserved, see Fig. 7a and b. In order to preserve a geometrically feasible structure, all PBUs within the same ab-layer must belong to the same twin component, otherwise the crystal growth will be disturbed.

ii.

The twinning also appears at a longer range, between neighboring needle-shaped crystallites within the same bundle of crystals. The crystallites are related by the same twin operation as the local twinning mentioned above as is evident from structure projection images, see Fig. 6.



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Figure 6. (a) HRTEM image of ITQ-39 viewed along [010] with the corresponding SAED pattern (e). Fourier transforms (FT) calculated from two neighboring crystallites (b and c), showing that the orientations of the crystallites are related by a mirror operation in the plane perpendicular to the c*-axis. (d) FT from the region marked with yellow color presents an overlap of (b) and (c) from several smaller crystallites, with red color showing diffraction spots from region (b) and with green color showing diffraction spots from region (c).


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Figure 7. Structure projection images acquired along [010] reveals large domains of (a) the same twin component and (b) a small domain of strictly alternating twinning. The ab-layer is horizontal (marked by a rectangle in panel b) and one pair-wise channel in each layer is marked in red or green in order to guide the twinning. In some structure projection images acquired along [010], larger domains without twinning can be observed (Fig. 7a), whereas in other crystallites the twinning occurs more frequently. In rare cases, strictly alternating twinning can be observed, as seen in Fig. 7b. This alternating twinning generates new polytypes in the ITQ-39 family. Twinned crystal structures of the three polytypes were constructed based on their respective original structures and the models were geometrically refined. See Table 1 for a comparison between the unit cells and space groups of the structures with and without alternating twinning, the structures of all three polytypes and their corresponding twin structures are presented in Figure S1. A geometrical refinement based on a least squares refinement of the nearest neighbor Si-O, OO and Si-Si distances, was performed for each of the six structural models. In the refinement,



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the weighted residuals are minimized and their sum represents an overall agreement factor for the geometry, called Rdls. The geometric refinement of polytype A without twinning results in a Rdls of 0.237 % and for the model with alternating twinning the corresponding residual is 0.225 %. The overall geometric feasibility for polytypes B and C is not hampered by the introduction of twinning, see Figure S1. For polytype A the average deviation from the ideal Si-O distances for the original model is 0.0004 Å with a maximum of 0.0020 Å. For the model with alternating twinning the average is 0.0005 Å with a maximum of 0.0019 Å, see Table S1 for further details. However, it can be observed that the Rdls for polytype C is significantly higher than those for polytype A and B. This is a natural consequence of the strained geometry introduced by the double 4-rings present in the polytype C structure. A detailed overview of the results from the refinements for all three polytypes can be found in Table S1. Furthermore, the models with alternating twinning have an equally good geometry as their respective structures without twinning, see Table 1. This explains the high degree of both stacking disorder and twinning found in the structure projection images. The geometrical refinements show that all six structural models are geometrically reasonable.

Table 1. Structural characteristics for the three structures without twinning (Polytype A, B and C) as well as the three structures with alternating twinning (Polytype A Tw, B Tw and C Tw). Polytype

A

B

C

A Tw

B Tw

C Tw

Space group

P2/c

P-1

P2/m

P21221

P21/c

Pcma

Unique atoms Si | O

28 | 56

28 | 56

16 | 34

28 | 56

28 | 56

16 | 34

a (Å)

24.42

24.50

24.38

24.53

12.61

24.60

b (Å)

12.61

12.61

12.71

12.60

24.46

12.69

c (Å)

27.42

14.42

13.70

22.54

28.11

22.53

Unit cell


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α (ᵒ)

90

73.01

90

90

90

90

β (ᵒ)

124.6

123.1

124.6

90

126.7

90

γ (ᵒ)

90

90.01

90

90

90

90

16

16

16

16

16

16

Volume (Å )

6949

3439

3493

6967

6952

7033s

Channel system

3D

3D

3D

3D

3D

3D

Rdls (%)

0.237

0.228

0.360

0.225

0.231

0.344

FDSi (T/1000Å) 3

All six presented zeolite structures have 3D channel systems with straight pairwise 12-ring channels and one straight and one zig-zag 10-ring channels. The intergrowth between the three polytypes A, B and C, including their twinned versions, will maintain a 3D channels system with straight 12- and 10-ring channels. Just the shape of the 10-ring channels extending along the c*axis will be affected. All structures have very similar framework densities, (FDSi), 16 T/1000Å (Table 1). The stacking disorder and the twinning can occur completely independent of each other. Viewed along the [010] direction, it is not possible to distinguish between the polytypes A, B or C, whereas viewed along the [100] direction, it is not possible to determine whether the crystal contains twinning. 3.3 Simulation of diffraction patterns An important part of verifying the structure includes simulations of both PXRD and electron diffraction patterns. As stated above the PXRD pattern of the ITQ-39 zeolite shows few and broad peaks, see Fig. 1c. The peak broadening is a combined effect of the stacking disorder, the small domains of the twinning and the small and non-isotropically shaped crystals. Due to the severe disorder in the structure, the program DIFFaX20 was used to simulate diffraction patterns. A simulation model was constructed in order to obtain a model that best describes the real



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material. The model takes into account the random intergrowth between the three polytypes (A, B and C) as well as the twinning. Based on the model diffraction from a random intergrowth of polytypes A, B and C with a probability of 45:45:10 respectively, and an average size of the twin domain of 4 layers was simulated. The simulated PXRD pattern is given in Fig. S2, which matches well with the experimental PXRD pattern. The simulated diffraction pattern is in agreement with the experimental SAED pattern, where reflections with index (0 3n l)A/B (n is integer number) are sharp while the others are shown as streaks, see Fig 8. In order to understand the X-ray diffraction behavior as a function of the stacking disorder a series of simulations were performed. For these simulations a hypothetical model only containing an intergrowth between the two major phases, polytype A and B, was constructed. Simulations were performed for eleven models ranging from pure polytype A to pure polytype B, using a sharp peak shape function to enhance the characteristic features in the patterns. The result is shown in Fig. 9. A large number of the peaks are common between the structures of the two pure polytypes A and B, but some of them are characteristic for the two structures. The (010) peak of polytype A, denoted (010)A, at 7.08° and the (012)A peak 10.58° are unique for the polytype A structure. Polytype B has an exclusive peak at 12.61°, (01-1)B. In the experimental PXRD data a large broad peak is dominating the region between 7° - 9° as several peaks are overlapping in this region. The region contains two high intensity peaks which are common between the two structures, the (20-2)A/(20-1)B peak at 7.84° and the (200)A/B peak at 8.88°. In addition, polytype A has a high intensity peak at 8.08° (011)A whereas polytype B has a strong peak at 7.54°, indexed as (010)B. This knowledge about the X-ray diffraction behavior of the intergrown structures can help in understanding the material and for potentially facilitating discoveries of enriched forms.


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c*

c*

Figure 8. Comparison of experimental (a) and simulated (b) SAED patterns along the [100] direction. The simulation was based on the random intergrowth of 45% polytype A, 45% polytype B and 10% polytype C. The simulation was performed using the program DIFFaX20.



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Figure 9. Simulated PXRD patterns using DIFFaX from the disordered model with different ratios of polytypes A and B ranging from pure polytype A (purple, bottom) to pure polytype B (red, top). In order to emphasize the details of the patterns, the simulations have a sharp peak shape function and only include the intergrowth of polytype A and B.


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4. CONCLUSIONS ITQ-39 grows as very small needle-like crystals with a large amount of disorders. A new comprehensive description of the structure based on a 1D periodic building unit (PBU) has been presented. This model provides a more complete description of the three main types of disorders present in the material; stacking disorder, twinning as well as faulting within the ab-plane. Using the new PBU, structure models of the three basic polytypes of the ITQ-39 family and their corresponding twin structures were built. The structures of polytypes A and B have a slightly more favorable geometry compared to that of polytype C. This is in a good agreement with the HRTEM observations where polytype C is less abundant. Twinning does not create any additional geometrical strain to the structure as long as each layer in the ab-plane belongs to the same twin-component. The structure description using the 1D periodic building unit (PBU) is consistent with the needlelike morphology of the ITQ-39 crystals. The 1D PBU is aligned with the longest dimension (the b-axis) of the ITQ-39 crystals. While the crystals can grow undisturbed along the b-axis, the stacking disorder and twinning hamper the crystal growth along the a and c-axes. A better understanding of the structural disorders and crystal growth would be desired in order to tailor the synthesis and take full advantages of the unique pore structures of ITQ-39 for desired applications.



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ASSOCIATED CONTENT The Supporting Information is available free of charge on the ACS Publications website at DOI:

AUTHOR INFORMATION Corresponding Authors * E-mail: [email protected], [email protected] Author Contributions E.K. and T.W. have acquired the electron microscopy data as well as performed the analysis of the structure and the geometric refinements. T.W has performed the simulations of diffraction. All authors were involved in planning the work, writing the paper and have given approval to the final version of the manuscript. Notes The authors declare no competing financial interest.

ACKNOWLEDGMENT This work was supported by the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (VINNOVA), and the Knut & Alice Wallenberg Foundation through a grant for purchasing the TEM and the project grant 3DEM-NATUR. T.W. acknowledges a postdoc grant from the Swedish Research Council. The authors thank Manuel Moliner and Avelino Corma for the ITQ-39 sample and valuable comments on the manuscript.


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9. Moliner, M., González, J., Portilla, M. T., Willhammar, T., Rey, F., Llopis, F. J., Zou, X., Corma, A. A new aluminosilicate molecular sieve with a system of pores between those of ZSM-5 and beta zeolite. J. Am. Chem. Soc. 133, 9497–9505 (2011). 10. Corma, C., Moliner, M., Rey, G. & Gonzalez, G. Microporous Crystalline Material of Zeolitic Nature, Zeolite Itq-39, Method of Preparation and Uses, WO2008092984 (A1). (2008). 11. Burton, J. & Zones, S. I. METHOD FOR MAKING MOLECULAR SIEVE SSZ-83, US 20090104112 (A1). (2009). 12. Zhang, D., Oleynikov, P., Hovmöller, S. & Zou, X. Collecting 3D electron diffraction data by the rotation method. Z. Für Krist. Int. J. Struct. Phys. Chem. Asp. Cryst. Mater. 225, 94– 102 (2010). 13. Willhammar, T., Sun, J., Wan, W., Oleynikov, P., Zhang, D., Zou, X., Moliner, M., Gonzalez, J., Martínez, C., Rey, F., Corma, A. Structure and catalytic properties of the most complex intergrown zeolite ITQ-39 determined by electron crystallography. Nat. Chem. 4, 188–194 (2012). 14. Wan, W., Hovmöller, S. & Zou, X. Structure projection reconstruction from through-focus series of high-resolution transmission electron microscopy images. Ultramicroscopy 115, 50–60 (2012). 15. Martínez-Armero, M. E., Moliner, M., Sastre, G., Rey, F., Martínez, C., Corma, A. ITQ-39 zeolite, an efficient catalyst for the conversion of low value naphtha fractions into diesel fuel: The role of pore size on molecular diffusion and reactivity. J. Catal. 333, 127–138 (2016).


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A detailed structural survey of the zeolite ITQ-39 by electron crystallography Elina Kapaca, Xiaodong Zou, Tom Willhammar

Synopsis: High resolution transmission electron microscopy has been applied to study the complex structural disorders in the zeolite ITQ-39. The ITQ-39 crystals can be described using a basic building unit with 52 T-atoms. The basic building units are connected in different manners to form three polytypes and their corresponding twin structures.


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Detailed Structural Survey of the Zeolite ITQ-39 by Electron

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