Elucidation of the Structure of Solanoeclepin A, a Natural Hatching Factor of Potato and Tomato Cyst Nematodes, by Single-crystal X-ray Diffraction

Potato crops can be severely damaged by potato cyst nematodes Globodera rostochiensis and Globodera pallida, nematodes highly specific to potatoes and some other Solanaceae. Hatching of juveniles is controlled by agents excreted by the roots of some Solanaceae species. Over seventy years much effort has been expended by many groups to isolate these agents and to determine their structures. However, all attempts have failed. We report here the structure determination of a hatching factor excreted from potato and tomato roots. The hatching factor bears some resemblance to Glycinoeclepins as found by Masamune et al.2-5 and is hence designated as Solanoeclepin A.1 C27H30O9.3H2O, Mr = 498.5, monoclinic, P21, a = 11.289(2), b = 20.644(4), c = 11.632(12) Å, β = 90.81(4), V = 2711(3) Å3, Z = 4, Dx = 1.35 g cm–3, λ(Cu-K&alpha ) = 1.5418 Å, μ(Cu-Kα ) = 9.0 cm–1, F(000) = 1176, –60 °C. Final R = 0.117 for 3721 observed reflections

Characterization of intercalated smectites using XRD profile analysis in the low-angle region

X-ray diffraction (XRD) characterization of natural and intercalated smectites is usually limited to the apparent d-value estimated from the peak maxima in the raw data. This can lead to the misinterpretation of the measured data. In the case of XRD, the interference function is modulated by instrumental factors (Lorentz-polarization factor, diffraction geometry) and physical factors (structure factor, surface roughness effect). These effects lead to diffraction profile distortions, depending on the diffraction angle and peak full width at half maximum (FWHM). As a result, the diffraction profiles for structures with large line broadening (FWHM > 1°)exhibit a significant peak shift (Delta d similar to 1.5 Å), especially at low angles (2 theta less than or equal to 10 degrees). The present work deals with the detailed analysis of all these effects, their corrections and their consequences for the interpretation of diffraction patterns (including possible errors in determining lattice parameters or the structure model). The investigated materials were montmorillonites (MMT) intercalated with hydroxy-A1 polymers. Diffraction profile analysis revealed the corrected d-values and showed that the intercalated sample is not a mixed-layered structure. As a result a structural model of the interlayer is presented

XRD profile analysis of clay minerals

XRD profile analysis of smectites is usually limited to the apparent d-spacing estimated from the peak maxima from the raw data. This can lead to the wrong d-spacing and consequently to the wrong conclusions about mixed layering (interstratification) and wrong structural model of interlayer. The interference function is modulated by the angle dependent instrumental factors (Lorentz-polarization, diffraction geometry) and physical factors (structural factor, volume absorption, surface roughness absorption) which lead to profile distortions and to the shift of the peak maxima. This effect is especially significant at low diffraction angles and for broadened diffraction lines (FWHM>1 degrees). Present work deals with detailed analysis of these effects, their corrections and their consequences for the interpretation of diffraction patterns. The proposed methodology and effect of all corrections is shown on the example of montmorillonite intercalated with Al-hydroxy complexes

Interlayer Porosity in Montmorillonite Intercalated with Keggin-like Cation Studied by Molecular Mechanics Simulation

Molecular mechanics simulation using Cerius(2) modeling environment have been used to investigate the structure of montmorillonite, intercalated with Keggin-like cation(7+). 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

Modelling of Aniline-Vermiculite and Tetramethylammonium-Vermiculite; Test of Force Fields

Molecular mechanics simulations in Cerius(2) 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 and gamma are kept fixed during the energy minimisation. The energy term was set up using the nonbond interaction terms only and the Crystal Packer module in Cerius(2) 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, alpha, and beta 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, alpha = 90°, beta = 97.68° ; from the present modelling we obtained: c = 13.609 Å, alpha = 90.19°, beta = 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, alpha = 90°, beta = 97°; present result is: c = 14.81 Å, alpha = 90.72°, beta = 96.70° for partially exchanged vermiculite and c = 14.84 Å, alpha = 90.53°, beta = 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