Home The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
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The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers

  • Bernd Marler ORCID logo EMAIL logo , Antje Gruenewald-Lueke , Hermann Gies and Trees de Baerdemaeker
Published/Copyright: April 5, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 3

Abstract

C48H200N8O104Si32, monoclinic, C2/m (no. 12), a = 16.2532(14) Å, b = 13.3020(7) Å, c = 16.7771(14) Å, β = 96.476(10)°, V = 3604.07(3) Å3, Z = 1, R(F) = 0.031, χ 2 = 2.44, Rgt (F) = , wRref (F 2) = , T = 293 K.

CCDC no.: 2341037

Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colorless grains
Size: 1 × 1 × 0.05 μm
Wavelength: Cu Kα radiation (1.54059 Å)
μ: not determined
Diffractometer, scan mode: Siemens D5000, Debye–Scherrer
2θ range used: 2.96°–89.77°
N(hkl)measured 1822
N(param)refined: 78
Programs: Fullprof 2K [1], VESTA [2]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso */U eq
Si1 −0.0848 (2) 0.7313 (3) 0.0322 (2) 0.0162 (6)*
Si2 0.8537 (2) 0.8814 (3) 0.1592 (2) 0.0162 (6)*
Si3 0.4920 (2) 0.8827 (3) 0.1872 (2) 0.0162 (6)*
Si4 0.1630 (2) 0.6159 (3) 0.1206 (2) 0.0162 (6)*
O1 −0.1270 (7) 0.8248 (6) 0.0763 (4) 0.021 (3)*
O2 −0.0602 (7) 0.6489 (6) 0.1025 (4) 0.021 (3)*
OH3 0.9106 (7) 0.8530 (8) 0.2419 (5) 0.021 (3)*
O4 0.8708 (10) 0.00000 0.1449 (10) 0.021 (3)*
O5 0.00000 0.7743 (8) 0.00000 0.021 (3)*
OH6 0.4697 (8) 0.8107 (7) 0.2598 (5) 0.021 (3)*
O10 0.3556 (6) 0.8127 (8) −0.0425 (5) 0.021 (3)*
O12 0.2544 (2) 0.6365 (8) 0.1672 (5) 0.021 (3)*
O13 0.9689 (10) 0.50000 0.2023 (10) 0.021 (3)*
O15 1.0909 (3) 0.6330 (9) 0.1782 (6) 0.021 (3)*
O16 0.3453 (12) 0.00000 −0.0918 (8) 0.021 (3)*
N1 0.1769 (5) 0.00000 0.1364 (6) 0.411 (6)*
C1 0.2189 (15) 0.9090 (11) 0.1758 (6) 0.411 (6)*
C2 0.2047 (18) 0.00000 0.0546 (9) 0.411 (6)*
C3 0.0837 (6) 0.00000 0.1243 (17) 0.411 (6)*
C4 0.2335 (14) 0.1119 (15) 0.2668 (5) 0.411 (6)*
N2 0.2418 (5) 0.50000 0.4157 (6) 0.411 (6)*
C5 0.1509 (6) 0.50000 0.3899 (16) 0.411 (6)*
C6 0.2669 (19) 0.50000 0.5045 (6) 0.411 (6)*
C7 0.2874 (12) 0.5873 (9) 0.3851 (7) 0.411 (6)*
C8 0.3201 (16) 0.6596 (13) 0.4549 (10) 0.411 (6)*
O17(water) 0.4985 (13) 0.50000 0.6430 (12) 0.098 (3)*
O18(water) −0.0780 (9) 0.7807 (8) 0.6470 (9) 0.098 (3)*
O19(water) 0.50000 0.7838 (12) 0.50000 0.098 (3)*
O20(water) 0.0803 (7) 0.5964 (8) 0.6004 (7) 0.098 (3)*

1 Source of material

RUB-56 samples were hydrothermally synthesized in Teflon-lined autoclaves at 140 °C for 2–7 days using diethyldimethylammonium hydroxide (Sigma-Aldrich, 20 % in water) as the structure directing agent (SDA). Reaction mixtures of composition 0.9–1 SiO2 : 0.5 SDA : 6–10 H2O were used. Lab-made silica gel (11 wt% H2O) served as the silica source. A more detailed view on the synthesis of RUB-56 is presented in a patent application [3]. The sample of highest crystallinity with respect to purity and (small) halfwidths of the reflections was used for the structure analysis.

2 Experimental details

Powder diffraction data were collected using a Siemens D5000 diffractometer equipped with a Braun linear position-sensitive detector (2θ coverage = 6°) and a curved germanium (111) primary monochromator. The powder was kept in a sealed glass capillary (0.3 mm in diameter) to avoid preferred orientation of the crystals. No absorption correction was necessary. The powder pattern contains a weak additional peak at 5.75°. Since no other reflections could be detected that do not belong to the pattern of RUB-56, this peak was not assigned to an impurity phase. Instead, the peak at 5.75° was included in the background. Soft distance restraints were applied to d(Si–O) = 1.620(5) Å, d(Si⋯Si) = 3.08(4) Å, d(O⋯O) = 2.63(3) Å, d(C–C) = 1.54(1) Å, d(C–N) = 1.48(1) Å, d(N⋯C, next–next neighbour) = 2.45(4) Å and d(C⋯C, next–next neighbour) = 2.50(4) Å. Common isotropic displacement parameters B (iso) were refined for all Si, all O (layer), all O (water molecules) and all C and N atoms. The occupancy factors of carbon atoms and those oxygen atoms representing water molecules were increased to include the scattering power of the hydrogen atoms which could not be located. This procedure was chosen because the highly diffuse electron density at the position of the carbon and (water) oxygen atoms includes also the electrons of the hydrogen atoms.

3 Comment

Hydrous layer silicates (HLSs) – sometimes also called 2-dimensional zeolites (2D-zeolites) – are materials consisting of (i) pure silica layers (seldom traces of other elements are present such as Al, B, Ga, Fe), (ii) intercalated cations of low charge density like [Na(H2O)6] complexes or organic cations such as tetramethylammonium, and (iii) in most cases water molecules. Overviews on HLSs have for example been published by Marler et al. [4], Ramos et al. [5] and Roth et al. [6]. HLSs are mainly used as precursors to form expanded silica frameworks by techniques of pillaring, mesoporous silicas by delamination of the structures, and high silica zeolites by topotactic condensation of the layers.

RUB-56 forms very small and thin, quadrangular, plate-like crystals (approx. size: 1 × 1 × 0.05 μm3). Because of the small size of the crystals only powder data were available for structure analysis. The powder XRD pattern of RUB-56 was indexed in the monoclinic system with approx. lattice parameters a = 16.22 Å, b = 13.28 Å, c = 16.76 Å and β = 96.45°. The analysis of systematically extincted reflections led to possible space group symmetries C2, Cm or C2/m. In addition, RUB-56 had been characterized by thermal analysis, SEM, FTIR spectroscopy as well as 29Si MAS and 1H–29Si CP MAS NMR spectroscopy [7].

The structure was solved by model building taking into account the close correspondence of the structures of RUB-56 and ITQ-8 [8, 9] which became obvious from the comparison of lattice parameters, FTIR and NMR spectra. Based on the known structure of ITQ-8 [9] a rough model of the structure of RUB-56 was built to start the Rietveld refinement. While the atoms of the silicate layer were, at the very beginning of the refinement, already close to the finally refined positions, the sites of the water molecules and the coordinates of the carbon and nitrogen atoms were derived from successively calculated difference Fourier maps. All atomic coordinates (ignoring protons) were subsequently refined by the Rietveld method using FullProf [1] in space group no. 12 (C2/m). The structure refinement of the title compound gave T–O, T–T and O–O distances in the range of 1.606–1.652 Å, 3.072–3.163 Å, and 2.385–2.802 Å, respectively, which are typical values for layer silicates possessing only Si at T sites of the [TO4]-tetrahedra.

RUB-56 contains levyne-type silicate layers (lev layer) as the main structural constituents. In contrast to most HLSs [10], which possess dense silicate layers with 6-rings as largest pores (free diameter ca. 2.5 Å), the lev layer of RUB-56 contains slightly elliptical 8-rings pores with free diameters of 4.0 Å × 3.3 Å (see Figure 1). These pores are large enough to let small organic molecules pass, rendering the lev layer a microporous silicate layer. The lev layers in the structure of RUB-56, are interconnected to neighboring ones by bands of water molecules being hydrogen bonded to each other and to the terminal Si–OH-/Si–O- groups of the layers (see Figure 2). The diethyldimethylammonium cations which are intercalated between water bands and lev layers compensate their negative charge. Like ITQ-8, RUB-56 is also an interesting material to act as a precursor for the synthesis of microporous framework silicates by interlayer expansion reactions. Intercalating suitable metal-linker units like Si(CH3)2Cl2, Fe(III)Cl3 or Fe(III) acetylacetonate and docking these linkers to two neighboring lev layers would lead to framework structures with three-dimensional pore systems.

Figure 1: The lev layer projected on (010) to show the 8-ring pores. Si: purple, O: red, O–/OH groups: blue.
Figure 1:

The lev layer projected on (010) to show the 8-ring pores. Si: purple, O: red, O–/OH groups: blue.

Figure 2: The structure of RUB-56 constructed from silicate layers ([SiO4] = blue tetrahedra with terminal O–/OH groups as blue spheres), bands of hydrogen bonded water molecules (light blue) and diethyldimethylammonium cations (C: brown, N: green).
Figure 2:

The structure of RUB-56 constructed from silicate layers ([SiO4] = blue tetrahedra with terminal O–/OH groups as blue spheres), bands of hydrogen bonded water molecules (light blue) and diethyldimethylammonium cations (C: brown, N: green).

Corresponding author: Bernd Marler, Institute of Geology, Mineralogy und Geophysics, Ruhr-University Bochum, Universitaetsstrasse 150, 44801 Bochum, Germany, E-mail:

Funding source: International Network of Centers of Excellence (INCOE) project coordinated by BASF SE, Germany

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: International Network of Centers of Excellence (INCOE) project coordinated by BASF SE, Germany.

  3. Conflict of interest: The authors declare no conflicts of interest regarding this article.

References

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Received: 2024-02-16
Accepted: 2024-03-20
Published Online: 2024-04-05
Published in Print: 2024-06-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/ncrs-2024-0067
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of tris((Z)-2-hydroxy-N-((E)-pyridin-2-ylmethylene)benzohydrazonato-k2O,N)europium(III), C39H30N9O6Eu
  4. Crystal structure of (E)-3-(benzylideneamino)-2-phenylthiazolidin-4-one, C16H14N2OS
  5. The crystal structure of (E)-4-fluoro-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H15FN2O
  6. Crystal structure of (6-chloropyridin-3-yl)methyl 2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  7. Crystal structure of methyl 3-methoxy-4-(2-methoxy-2-oxoethoxy)benzoate, C12H14O6
  8. The crystal structure of bis[(4-methoxyphenyl)(picolinoyl)amido-κ2 N:N′]copper(II), C26H22CuN4O4
  9. The crystal structure of poly[di(μ2-aqua)-diaqua-bis(3-aminopyridine-4-carboxylate-κ2 O: O′)-tetra(μ2-3-aminopyridine-4-carboxylate-κ2 O: O′)-dineodymium(III), [Nd2(C6H5N2O2)6(H2O)4] n
  10. The crystal structure of t-butyl 7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoate, C28H34FNO4
  11. Crystal structure of catena-poly[(benzylamine-κ1 N)-(sorbato-κ1 O)-(μ2-sorbato-κ2 O,O′)-copper(II), C19H23CuNO4
  12. Crystal structure of (4-(2-chlorophenyl)-1H-pyrrol-3-yl)(ferrocenyl) methanone, C21H16ClFeNO
  13. The crystal structure of N-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-3-(2-methylphenyl)-2-sulfanylprop-2-enamide hydrate, C19H17BrN2O2S2
  14. The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate
  15. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C26H24O3
  16. Crystal structure of naphthalen-1-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C25H22O3
  17. Crystal structure of poly[diaqua- (μ4-5-(1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ5N:O,O’:O’’:O’’’)calcium(II), C10H9CaN3O6
  18. Crystal structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-dimethylformimidamide, C14H19N3O2
  19. Crystal structure of (E)-3-(dimethylamino)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one, C13H17NO4
  20. Crystal structure of (2-chloropyridin-3-yl)methyl-2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  21. The crystal structure of diethyl 4-(3,4-dimethylphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, C21H27NO4
  22. Crystal structure of (8R,9S,10R,13S,14S,17S)-17-hydroxy-10,13-dimethyl-17-((4-(2-phenylpropyl)phenyl)ethynyl)-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H42O2
  23. Synthesis and crystal structure of 4-(4-cyclopropylnaphthalen-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C15H13N3S
  24. Crystal structure of catena-poly[aqua-(2,6-di-(2-pyridyl)-pyridine-κ3 N,N′, N″)(μ2-1,4-naphthalene dicarboxylato-κ2 O,O′)nickel(II)], C27H19NiN3O5
  25. Crystal structure of 3-(diphenylphosphoryl)-3-hydroxy-1-phenylpropan-1-one, C21H19O3P
  26. The crystal structure of R,S-{N-[(2-oxidonaphthalen-1-yl)methylidene]phenylglycinato}divinylsilicon, C23H19NO3Si
  27. The crystal structure of 1,2,4-tris(bromomethyl)benzene, C9H9Br3
  28. Crystal structure of chlorido-[4-(pyridin-2-yl)benzaldehyde-κ2 N,C]-(diethylamine-κ1 N)platinum(II), C16H18ClN2OPt
  29. Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
  30. The crystal structure of 1-(2-chlorobenzyl)-3-(3-chlorophenyl)urea, C14H12Cl2N2O
  31. Hydrothermal synthesis and crystal structure of aqua-tris(4-acetamidobenzoato-κ2 O,O′)-(1,10-phenanthroline-κ2 N,N′)terbium(III) hydrate C39H36N5O11Tb
  32. The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2
  33. The crystal structure of bis{[monoaqua-μ2-4-[(pyridine-4-carbonyl)-amino]-phthalato-κ3 N:O,O′-(2,2′-bipyridine κ2 N,N′)copper(II)]}decahydrate, C48H56N8O22Cu2
  34. Crystal structure of poly[μ10-4,4′-methylene-bis(oxy)benzoatodipotassium], C15H10K2O6
  35. The crystal structure of catena-poly[[tetraaqua[(μ2-1,4-di(4-methyl-1-imidazolyl)benzene] cobalt(II)]bis(formate)], C16H24CoN4O8
  36. The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
  37. The crystal structure of (E)-1-(((2-amino-4,5-dimethylphenyl)iminio)methyl)naphthalen-2-olate, C19H18N2O
  38. Crystal structure of N-(acridin-9-yl)-2-(4-methylpiperidin-1-yl) acetamide monohydrate, C21H25N3O2
  39. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2 O,O′)-zinc(II), C14H20Cl2N4O4Zn
  40. The crystal structure of 2,8-diethyl-1,3,7,9-tetramethyl-4λ4,5λ4-spiro[dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine-5,2′-naphtho[1,8-de][1,3,2]dioxaborinine], C25H29BN2O2
  41. The crystal structure of 5-tert-butyl-2-(5-tert-butyl-3-iodo-benzofuran-2-yl)-3-iodobenzofuran, C24H24I2O2
  42. Synthesis and crystal structure of methyl 2-{[4-(4-cyclopropyl-1-naphthyl)-4H-1,2,4-triazole-3-yl]thio} acetate, C18H17N3O2S
  43. The crystal structure of n-propylammonium bis(2,3-dimethylbutane-2,3-diolato)borate-boric acid (1/1), [C3H10N][C12H24BO4]·B(OH)3
  44. Crystal structure of methyl 1-(2-bromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C19H17BrN2O2
  45. Crystal structure of (4-bromobenzyl)triphenylphosphonium bromide ethanol solvate, C52H48Br4OP2
  46. The crystal structure of unsymmetrical BOPHY C26H27BN4
  47. The crystal structure of Tb3B5O11(OH)2
  48. The crystal structure of (Z)-4-ethyl-2-((4-ethyl-3,5-dimethyl-1H-pyrrol-2-yl)methylene)-3,5-dimethyl-2H-pyrrol-1-ium 2,2'-spirobi[naphtho[1,8-de][1,3,2]dioxaborinin]-2-uide, C37H37BN2O4
  49. Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16
  50. The crystal structure of (2-diphenylphosphanylphenyl) 2-[7-(dimethylamino)-2-oxochromen-4-yl]acetate, C31H26NO4P
  51. Crystal structure of (E)-6-(4-ethylpiperazin-1-yl)-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C23H25FN2O
  52. The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
  53. Crystal structure of 4-amino-3,5-dibromobenzonitrile, C7H4Br2N2
  54. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-acetoxybenzoate, C21H18O4
  55. Single-crystal structure determination of Tm3B12O19(OH)7
  56. Crystal structure determination of NdB3.6O7
  57. The crystal structure of NdB6O8(OH)5·H3BO3
  58. Crystal structure of 2-(5-ethylpyridin-2-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H25NO3
  59. Crystal structure of N-(1-(3,4-dimethoxyphenyl)-2-methylpropyl)aniline, C18H23NO2
  60. Crystal structure of Ba6Cd12Mn4SiF48
  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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