Supporting Information for: Locating organic guests in inorganic host materials from X-ray powder diffraction data

Transcription

1 Supporting Information for: Locating organic guests in inorganic host materials from X-ray powder diffraction data Stef Smeets, Lynne B. McCusker, Christian Baerlocher, Saleh Elomari, Dan Xie, Stacey I. Zones Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich CH-8093, Switzerland Chevron Energy Technology Company, Richmond, California 94802, United States S1

2 Detailed method Once the framework structure of a zeolite has been solved, an optimization of the framework geometry should be performed. With TOPAS, 1 the simplest way to do this is to perform a geometrical refinement against the angle and distance restraints using the penalties_only instruction. Another option is to use use the distance-least-squares algorithm in the program DLS At this point, the background of the diffraction pattern should be removed. Manual background removal is preferred, because of the added control it gives over the sometimes erratic and unreliable nature of fitting a polynomial, especially when the structural model is incomplete. To help with this, the program Lines was developed ( Most of the information about the residual electron density in the channel system is in the low-angle portion of the powder diffraction pattern. A reasonable estimate of the scale factor can be made by performing a few cycles of refinement with all other parameters fixed using only the high angle data. If the profile fit at the higher 2θ angles is not good, the background should probably be adjusted. Calculating a difference map with the scale factor obtained with the high-angle data and using the complete 2θ range should show the residual electron density. For this purpose, we use the tool topasdiff ( which generates a map in xplor format. If an SDA and/or other extra-framework species are present, their approximate locations should be revealed (e.g. Figure 2). Difference maps can be visualized using the programs VESTA 3 or Chimera. 4 There are several ways of introducing the SDA molecule into the structural model. If the structure of the SDA has been determined before, online databases such as the Cambridge structural database 5 can be consulted to get a starting model. An approximate model for the molecule can also be generated from scratch, and optimized using molecular modeling. This works best for bulky, rigid molecules. Chemical editors, such as JSME 6 or MarvinSketch, allow chemical drawings to be exported to the SMILES syntax. 7. A SMILES string is a convenient way of describing the connectivity of a molecule as a short string that can be read by many different programs. The program Jmol 8 can be used to load the SMILES string (e.g. to load the SDA used for SSZ-56: load the SMILES string $CC[N+]2(CC)C(C)CCC1CCCCC12), optimize the geometry of the model using a force-field minimization (minimize), and to export the molecule in.xyz format (write template.xyz). Alternatively, the program Avogadro 9 can be used for this purpose. The latter also allows the user to construct the molecule in three dimensions directly. It is useful to know that for a rigid body in TOPAS, the first atom in the list is taken as the center of the molecule. The second atom defines the z-axis, and the third atom the xz-plane. The x-axis is in the same direction as the a lattice vector, and y is in the ab-plane. By choosing the first three atoms carefully, the placement of the molecule can sometimes be directed by aligning it with a symmetry element. The multiplatform program OpenBabel 10 can then be used to convert the.xyz file into a Fenske-Hall z-matrix. Unfortunately, the TOPAS z-matrix syntax is slightly different from the Fenske-Hall one, so for the conversion, we have developed the script fh2topas ( It should be mentioned that it also possible to use the Rigid-body Editor in TOPAS to generate the correct rigid-body syntax (from a TOPAS.str file with the SDA in the center of a P1 unit cell), but we usually prefer to use the alternative approach described above, because it gives the user additional control. Once the molecule has been added to the TOPAS input file as a rigid body, the keyword Auto_T(10) tells TOPAS to run the simulated annealing routine using it s default temperature regime and continue_after_convergence to ensure that TOPAS repeats the simulated annealing routine until in- S2

3 terrupted. We have not found it necessary to deviate from the default settings TOPAS uses. All parameters, except the six parameters describing the location and orientation of the SDA, should remain fixed during the global optimization. The occupancy of the SDA can usually be estimated from the location of the electron density cloud in the difference map, but sometimes allowing the global optimization to find a good value is helpful. Sometimes it is worthwhile to allow the scale factor to refine as well, because it can influence the fitting of the SDA, and is difficult to determine otherwise. The peak shape, unit cell, and instrument parameters should be determined beforehand with a Pawley fit and kept fixed during the global optimization, because they will cause it to slow down significantly. In some cases, the AI_Anti_Bump macro can be helpful to push the SDA in the right direction. Usually, the simulated annealing procedure takes no longer than a few minutes to determine a reliable starting position. H atoms can be modeled by scaling the occupancy of the parent atom accordingly to account for the additional electron density. Once a suitable location for the SDA has been found, the rigid body parameters can also be refined as one would normally during a Rietveld refinement. Usually we keep the rigidy-body model to refine the position of the SDA for a couple of cycles, and only after the refinement has sufficiently converged, do we exchange the rigid-body model for a restrained one. S3

4 Contents of.xyz file for the SDA used in SSZ-56: 15 C C N C C C C C C C C C C C Contents of the.fh file corresponding to the SDA used for SSZ-56: 15 C 1 C N C C C C C C C C C C C C S4

5 Code added to TOPAS input file to introduce the the SDA in the model for SSZ-56: rigid z_matrix C1 z_matrix C2 C z_matrix N3 C C z_matrix C4 N C C z_matrix C5 C N C z_matrix C6 N C C z_matrix C7 C N C z_matrix C8 C N C z_matrix C9 C C N z_matrix C10 C C C z_matrix C11 C C C z_matrix C12 C C C z_matrix C13 C C C z_matrix C14 C C C z_matrix C15 N C C randomize_on_errors) randomize_on_errors) prm!occ1 0.5 min 0.0 max 1.0 prm!beq1 3.0 min 1.0 max 10.0 site C1 site C2 site N3 site C4 site C5 site C6 site C7 site C8 site C9 site C10 site C11 site C12 site C13 site C14 site C15 x 0.0 y 0.0 z 0.0 occ N =occ1; beq =beq1; S5

6 Table S1. Crystallographic details for the structure refinements of the 5 zeolite samples. Sample SSZ-53 SSZ-55 SSZ-56 SSZ-58 SSZ-59 Space group C2/c C222 1 P2 1/m Pmma P-1 a (Å) (3) (7) (16) (2) (3) b (Å) (3) (3) (17) (13) (14) c (Å) (2) (4) (11) (13) (18) ( ) (10) ( ) (9) (4) (19) ( ) (8) V (Å 3 ) (5) (2) (6) (7) (15) Z (g/cm 3 ) (5) (9) (4) (6) (6) (Å) (1) (1) (1) (1) (1) 2 range ( ) R I R wp R exp GoF Observations Reflections Parameters Restraints Chemical compositions: SSZ-53: (C 15N 1) 2.67 [Si 61.8B 2.1O 128]; SSZ-55: (C 15N 1F 1) 1.04 [Si 22.9B 1.1O 48]; SSZ-56: (C 14N 1) 1.67 [Si 55.1B 0.9O 112]; SSZ-58: (C 16N 1) 2O 2 [Si 72.1B 1.9O 140]; SSZ-59: (C 17N 1) 0.54 [Si 15.6B 0.4O 32] S6

7 Table S2. Selected bond lengths and angles (Å, ). T O T O T O T O SSZ-53 min max avg SSZ-55 min max avg SSZ-56 min max avg SSZ-58 min max avg SSZ-59 min max avg SSZ min max avg SSZ min max avg SSZ min max avg Restraints used: T O T: ; O T O: ; T O: Å; w=1/ 2 Table S3. Comparison of intermolecular distances between SDA and framework O atoms Shortest distances (Å) SSZ (6), 3.061(5), 3.080(7), and 3.085(5) SSZ (3), 2.974(3), 2.975(4), 2.979(4), and 2.995(3) SSZ-56 > 3.4 SSZ (6) SSZ (4), 3.076(3), 3.077(2), and 3.079(3) All other intermolecular distances are over 3.1 Å S7

8 Figure S1. Observed (blue), calculated (red), and difference (black) plot for the Rietveld refinement of as-synthesized SSZ-53. Figure S2. Observed (blue), calculated (red), and difference (black) plot for the Rietveld refinement of as-synthesized SSZ-55. S8

9 Figure S3. Observed (blue), calculated (red), and difference (black) plot for the Rietveld refinement of as-synthesized SSZ-56. Figure S4. Observed (blue), calculated (red), and difference (black) plot for the Rietveld refinement of as-synthesized SSZ-58. S9

10 Figure S5. Observed (blue), calculated (red), and difference (black) plot for the Rietveld refinement of as-synthesized SSZ q ( ) Figure S6. Observed (blue) plot for as-synthesized SSZ-60, compared to the calculated (red) plot of the framework only. S10

11 Figure S7. Comparison of SDA location obtained in (a, b) this study with those from (c, d) molecular modeling for SSZ-56, showing a view along the (a, c) 10-ring and (b, d) 12-ring channels. (c) and (d) reprinted from reference 14 with permission of Elsevier. Figure S8. Comparison of the SDA location obtained from molecular modeling (a,d) with those in this study (b, c, e, f) for SSZ- 58. The SDA was found to be disordered in this study, so two representative orientations are shown. Additional water molecules are shown as red balls. (a) and (d) reprinted (adapted) with permission from reference 15. Copyright 2016 American Chemical Society. S11

12 Figure S9. Comparison of the SDA locations obtained in (a, c, e) this study with those from (b, d, f) molecular modeling for (a, b) SSZ-53, (c, d) SSZ-55, and (e, f) SSZ-59, showing a view perpendicular to the channel direction. (b) and (f) reprinted from reference 16 with permission of John Wiley and Sons. (d) Reprinted (adapted) with permission reference 17. Copyright 2016 American Chemical Society. S12

13 References (1) Coelho, A. A. TOPAS-ACADEMIC v5.0; (2) Baerlocher, C.; Hepp, A.; Meier, W. M. DLS-76; (3) Momma, K.; Izumi, F. J. Appl. Crystallogr. 2011, 44 (6), (4) Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. J. Comput. Chem. 2004, 25 (13), (5) Allen, F. H. Acta Cryst. B 2002, 58, (6) Bienfait, B.; Ertl, P. J. Cheminform. 2013, 5:24. (7) Weininger, D. J. Chem. Inf. Comput. Sci. 1988, 28 (1), (8) Hanson, R. M. J. Appl. Crystallogr. 2010, 43, (9) Hanwell, M. D.; Curtis, D. E.; Lonie, D. C.; Vandermeersch, T.; Zurek, E.; Hutchison, G. R. J. Cheminform. 2012, 4, (10) O Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. J. Cheminform. 2011, 3:33. (11) Smeets, S.; Xie, D.; McCusker, L. B.; Baerlocher, C.; Zones, S. I.; Thompson, J. A.; Lacheen, H. S.; Huang, H.-M. Chem. Mater. 2014, 26 (13), (12) Smeets, S.; Xie, D.; Baerlocher, C.; McCusker, L. B.; Wan, W.; Zou, X.; Zones, S. I. Angew. Chem. 2014, 126, (13) Smeets, S.; McCusker, L. B.; Baerlocher, C.; Xie, D.; Chen, C.-Y.; Zones, S. I. J. Am. Chem. Soc. 2015, 137, (14) Elomari, S.; Burton, A.; Medrud, R. C.; Grosse-Kunstleve, R. Micropor. Mesopor. Mat. 2009, 118 (1-3), (15) Burton, A.; Elomari, S.; Medrud, R. C.; Chan, I. Y.; Chen, C.-Y.; Bull, L. M.; Vittoratos, E. S. J. Am. Chem. Soc. 2003, 125 (6), (16) Burton, A.; Elomari, S.; Chen, C.-Y.; Medrud, R. C.; Chan, I. Y.; Bull, L. M.; Kibby, C.; Harris, T. V.; Zones, S. I.; Vittoratos, E. S. Chem.-Eur. J. 2003, 9 (23), (17) Burton, A.; Darton, R. J.; Davis, M. E.; Hwang, S.-J.; Morris, R. E.; Ogino, I.; Zones, S. I. J. Phys. Chem. B 2006, 110 (11), S13