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  • 1
    ISSN: 0948-5023
    Keywords: Keywords: Molecular mechanics ; Intercalated clays ; Keggin cation.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulation using Cerius2 modeling environment have been used to investigate the structure of montmorillonite, intercalated with Keggin-like cation7+. Present work is focused to the strategy of modelling in case of intercalated layered structures and to investigation of structure parameters characterizing the interlayer porosity, that means: the interlayer distance, the position, orientation and distribution of Keggin cations in the interlayer space and the stacking of layers. Molecular simulations revealed the structure of the interlayer and led to the following conclusions: In the most stable configuration the 3-fold axis of Keggin cation is perpendicular to the silicate layer. This orientation of Keggin cations leads to the basal spacing 19.51 (10-10 m). Energy minimization during the translation of Keggin cation along the silicate layer gives only small fluctuations of basal spacing and no correlation has been found between the shift of cation along the layers and the value of basal spacing. No systematic relationship has been found between the shift of cation and crystal energy and no systematic relationship exists between the mutual shift of two successive layers and the values of basal spacing and crystal energy. Consequently, no two-dimensional ordering of Keggin cations in the interlayer and no regular stacking of layers can be expected. X-ray diffraction diagrams obtained for montmorillonites, intercalated with Keggin cation, confirm present conclusions.
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  • 2
    ISSN: 0948-5023
    Keywords: Molecular mechanics ; Structure of intercalates ; Vanadyl phosphate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulations using Cerius2 combined with X-ray diffraction and supported with vibrational spectroscopy have been used to investigate the layered structure of vanadyl phosphate VOPO4 intercalated with ethanol. This intercalated structure exhibits certain degree of disorder, which affects the diffraction diagram and obstructs the conventional structure analysis based on diffraction methods only. Present structure analysis is focused to the crystal packing in the interlayer space and layer stacking in the intercalate. The bilayer arrangement of ethanol molecules in the interlayer has been found, giving the basal spacing d = 13.21 Å, experimental d-value obtained from X-ray diffraction is 13.17 Å. One half from the total number of CH3CH2OH molecules is anchored with their oxygens to VOPO4 layers to complete vanadium octahedra and their orientation is not very strictly defined. The second half of ethanoles is linked with hydrogen bridges to the anchored etahanoles and sometimes also to the layer oxygens. Positions and orientations of these unachored ethanoles with respect to VOPO4 layers exhibit certain degree of disorder, resulting in the disorder in layer stacking. Molecular mechanics simulations revealed the character of this displacement disorder in layer stacking and enabled to determine the components of the displacement vector.
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  • 3
    ISSN: 0948-5023
    Keywords: Keywords Vanadyl phosphate ; Zirconium phosphate ; Molecular mechanics ; Vibrational spectroscopy ; Host-guest interaction ; Intercalates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulations using Cerius2 modelling environment combined with vibrational spectroscopy (IR and Raman) have been used to study the host-guest interactions in zirconium and vanadyl phosphate intercalated with ethanole. The strategy of investigation is based on the comparison of vibrational spectra for the host compound, intercalate and guest species. This comparison confirmed the rigidity of VOPO4- and Zr(HPO4)2-layers during the intercalation and provided us with the basis for the strategy of modelling. Molecular mechanics simulations revealed the structure of intercalates and enabled to analyse the host-guest interaction energy and bonding geometry. The bilayer arrangement of ethanole molecules in the interlayer space with two differently bonded ethanole molecules has been found in both intercalates. The average interaction energy ethanole-layer for two differently bonded ethanole molecules is : 127.5 and 135.7 kcal·mol-1 in Zr(HPO4)2·2C2H5OH, respectively 94.0 and 104.4 kcal·mol-1 in VOPO4·2C2H5OH. The Coulombic contribution to the ethanole-layer interaction energy is predominant in all cases, but the hydrogen bonding contribution is much higher in Zr(HPO4)2·2C2H5OH than in VOPO4·2C2H5OH. Present results of modelling enabled the interpretation of vibrational spectra and explanation of small changes in positions and shapes of spectral bands, in infrared and Raman spectra, proceeding from the host structure to intercalates.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 6 (2000), S. 9-15 
    ISSN: 0948-5023
    Keywords: Keywords Vanadyl phosphate-alkanol intercalates, Molecular mechanics, Structure analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulations supported by X-ray powder diffraction measurements have been used to investigate the structure of vanadyl phosphate intercalated with 1-alkanols CnH2n+1OH for n = 2, 3, 4. Modeling revealed the specific features and differences in arrangement of alkanol molecules with different chain length, depending on the relation between the parameters of active sites network and size of guest molecules. This result enabled us to explain the irregularities in dependence of basal spacing on the chain length. The comparison of experimental dexp and calculated dcalc values of basal spacing showed the good agreement of modeling with x-ray powder diffraction. While we obtained dcalc(Univ) = 13.05 Å for vanadyl phosphate-ethanol using the Universal force field (dexp=13.17 Å), for vanadyl phosphate-propanol and vanadyl phosphate-butanol better agreement with experiment was obtained using the Tripos force field. In the case of vanadyl phosphate-propanol the calculated basal spacing dcalc(Tripos) = 14.49 Å, compared with an experimental value of dexp=14.36 Å. For vanadyl phosphate-butanol dcalc(Tripos) = 17.71 Å and dexp=17.90 Å.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 4 (1998), S. 176-182 
    ISSN: 0948-5023
    Keywords: Intercalation ; Montmorillonite ; Tetramethylammonium ; Trimethylphenylammonium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The intercalation of organoammonium cations into smectite structure is the important step in the technology of non-linear optical materials. In this study we investigated the structure of montmorillonite (MMT), intercalated with two organoammonium cations : tetramethylammonium (TMA) and trimethylphenylammonium (TMPA) using molecular mechanics simulations. The studies were focused to following aspects: arrangement of organoammonium cations in the interlayer, their positions and orientation with respect to silicate layers and their anchoring to the layers. The calculated (basal) d-spacings for MMT with TMA 14.29 Å and 15.36 Å for MMT with TMPA are in good agreement with X-ray diffraction data.
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  • 6
    ISSN: 0948-5023
    Keywords: Keywords Vermiculite ; Intercalate ; Aniline ; Tetramethylammonium ; Molecular mechanics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulations in Cerius2 have been used for modelling vermiculite intercalated with tetramethylammonium and aniline cations. The published structure data obtained for these intercalated structures from X-ray single crystal diffraction have been used to test the force fields and modelling strategy for organo-clays. The strategy of modelling was based on the nonbond host-guest interactions and on rigid silicate layers and rigid guest species. The rigidity of silicate layers requires that the cell parameters a, b andγare kept fixed during the energy minimisation. The energy term was set up using the nonbond interaction terms only and the Crystal Packer module in Cerius2 has been used for the energy minimisation. In Crystal Packer the rigid units, i.e. the silicate layers and guest species can be translated and rotated during energy minimisation and the cell parameters c, α, and β have been varied. Three sets of Van derWaals (VDW) parameters available in Crystal Packer: Tripos, Universal and Dreiding have been used in present molecular simulations. Ab initio MP2 calculations were performed to justify the application of the force field. The best agreement of molecular mechanics simulations with both: experimental and ab initio data was obtained with the Tripos VDW parameters for both intercalates. The results of modelling are in good agreement with the experimental data as to the cell parameters and the interlayer packing. The cell parameters reported by Vahedi-Faridi and Guggenheim (1997) for tetramethylammonium-vermiculite are: c = 13.616 Å, α = 90°, β = 97.68° ; from the present modelling we obtained: c = 13.609 Å, α = 90.19°, β = 97.56°. Tetramethylammonium-cations are arranged in one layer in the interlayer space. One C-C edge of NC4 tetrahedra is perpendicular to the silicate layers. The deep immersion of the methyl groups into the ditrigonal cavities suggested by Vahedi-Faridi and Guggenheim was not confirmed by modelling. Slade and Stone (1984) presented the measured cell parameters for aniline vermiculite: c = 14.89 Å, α = 90°, β = 97°; present result is: c = 14.81 Å, α = 90.72°, β = 96.70° for partially exchanged vermiculite and c = 14.84 Å, α = 90.53°, β = 97.17° for fully exchanged vermiculite. The aniline cations are positioned over the ditrigonal cavities alternating in their anchoring to lower and upper silicate layer. The C-N bonds are perpendicular to layers.
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  • 7
    ISSN: 0948-5023
    Keywords: Intercalated clays ; Tetramethylammonium-clays ; Modeling ; Molecular mechanics ; Montmorillonite ; Beidellite
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular mechanics simulations, combined with X-ray powder diffraction and infrared spectroscopy, have been used in structure analysis of montmorillonite and beidellite intercalated with tetramethylammonium cations. A complex structure analysis provided us with the detailed structure model, including characterization of the disorder, the total sublimation energy and a charge distribution in the structure of intercalates. The calculated basal spacings (14.36 Å for TMA-montmorillonite and 14.12 Å for TMA-beidellite) are in good agreement with the experimental values (14.31 Å for TMA-montmorillonite and 14.147 Å for TMA-beidellite). Both intercalated structures exhibit positional and orientational disorder in the arrangement of TMA cations, and consequently disorder in layer-stacking. In the present work we analyse the effect of octahedral and tetrahedral substitutions in a 2:1 silicate layer on the arrangement of tetramethylammonium (TMA) cations in the interlayer space of montmorillonite and beidellite. The most significant difference between TMA-montmorillonite and TMA-beidellite is in the charge distribution on the TMA cations and silicate layer. The TMA-beidellite structure is highly polarized, the total charge on one TMA cation is +0.167 e−, while the total charge on the TMA cation in montmorillonite is +0.050 e−.
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  • 8
    ISSN: 1600-5775
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Synchrotron and standard X-ray powder diffraction (XRD) combined with IR spectroscopy and molecular simulations have been used to investigate the crystal structure of two crystalline mesogenic diols: 4,4′-bis(6-hydroxy-1-hexyloxy)biphenyl (D-I) and 4,4′-bis(11-hydroxy-1-undecyloxy)biphenyl (D-II). The crystal structure of D-I has been determined from high-resolution synchrotron powder-diffraction data collected at BM16 of the ESRF. The methods of grid search and Rietveld refinement have been used to determine this structure. The space group is Cc, with unit-cell parameters a = 44.392 (3), b = 7.221 (1), c = 6.631 (1) Å and β = 91.09 (1)°. The structure of D-II has a small degree of disorder. This structure was analyzed with a combination of experimental methods, conventional XRD, IR spectroscopy and molecular mechanics simulations, revealing the character of the structural disorder. Both the structures of D-I and D-II are lamellar-packed and layered. The hydrogen-bonding system between two adjacent layers in the structure of D-II is distorted.
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  • 9
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 31 (1998), S. 845-850 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Molecular simulation supported by X-ray diffraction and IR spectroscopy has been used to analyse the structure of α-zirconium phosphate intercalated by ethanol, Zr(HPO4)2.2C2H5OH. Molecular-mechanics simulations using the Crystal Packer module in the Cerius2 modelling environment revealed the crystal packing in the interlayer, i.e. the positions of ethanol with respect to the Zr(HPO4)2 layers and the layer stacking in the intercalated structure. The average interlayer distance d\,=\,14.03 (13) Å obtained by modelling is in agreement with the experimental d value of 14.05 (4) Å obtained from the X-ray diffraction analysis. The disorder in the Zr(HPO4)2.2C2H5OH structure found by molecular simulation has been confirmed by the character of the X-ray diffraction pattern.
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  • 10
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of two intercalated compounds have been determined using a combination of synchrotron powder diffraction and molecular mechanics simulations: (1) vanadyl phosphate intercalated with tetrahydrofuran, VOPO4·(CH2)4O, and (2) vanadyl phosphate intercalated with diethylene glycol, VOPO4·HO(CH2)2O(CH2)2OH. Both intercalates preserve the tetragonal space group P4/n, as found in the host structure VOPO4·2H2O. (1): a = 6.208, c = 8.930 Å, Z = 2, Dx = 2.51 g cm−3; (2): a = 6.223, c = 11.417 Å, Z = 2, Dx = 2.66 g cm−3. Both intercalates exhibit the same type of orientational disorder in the arrangement of guest molecules, as observed in the same host compound intercalated with water. These two intercalates also exhibit, rather surprisingly, perfect ordering in layer stacking without the displacement disorder, characteristic of many intercalated layered structures. Thanks to this regularity in the arrangement of guests and layers, synchrotron powder diffraction could be used in the present structure determination. The present results also enabled the analysis of the effect of geometrical parameters characterizing the mutual host–guest complementarity and the effect of host–guest and guest–guest interaction on the crystal packing of intercalates.
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