Solanoeclepin A

Potato crops can be severely damaged by potato cyst nematodes. Hatching of juveniles is controlled by agents excreted by the roots of potatoes. Over seventy years much effort has been expended by many groups to isolate these agents and to determine their structures.

After extensive research, 200 micrograms of pure compound was purified from crude biological material obtained from potato culivation. When this small amount was subjected to NMR experiments, the compound crystallised overnight into 10 crystals of approximately equal size and generally suitable for single-crystal X-ray diffraction. The first two crystals tried were unstable and a twin, respectively. The third one, an irregularly shaped crystal with approximate dimensions 0.5 x 0.6 x 0.8 mm, was used for data collection. All attempts to solve the structure by all conventional Direct Methods packages failed, also due to the fact that there was no knowledge on the nature of the compound. The structure was finally solved by the program package CRUNCH (de Gelder et al., 1993), a method based on new mathematical procedures.

This is an example of Method Development in Chemical Crystallography.
See also research in Chemical Crystallography.

References

  1. Elucidation of the Structure of Solanoeclepin A, a Natural Hatching Factor of Potato and Tomato Cyst Nematodes by Single-crystal X-ray Diffraction.
     H. Schenk, R.A.J. Driessen, R. de Gelder, K. Goubitz, H. Nieboer, I.E.M. Brüggemann-Rotgans, and P. Diepenhorst.
    Croatica Chemica Acta (1999) Vol. 72, No. 2-3, 593-606.

  2. Automatic Determination of Crystal Structures using Karle-Hauptman Matrices.
     R. de Gelder, R.A.G. de Graaff, and H. Schenk.
    Acta Crystallografica A49 (1993), 287-293.

Other references to Method Development in Structure Determination

  1. On the Construction of Karle-Hauptman Matrices.
    R. de Gelder, R.A.G. de Graaff, and H. Schenk.
    Acta Crystallografica A46 (1990), 688-692.

  2. Karle-Hauptman Matrices and the Phase Problem in Single-Crystal X-ray Diffraction.
    R. de Gelder.
    Thesis (1992). University of Leyden. The Netherlands.

  3. Automatic Determination of Crystal Structures using Karle-Hauptman Matrices.
     R. de Gelder, R.A.G. de Graaff, and H. Schenk.
    Acta Crystallografica A49 (1993), 287-293.

  4. Symmetry and the Generalized Maximum Determinant Rule.
     R. de Gelder, M.O. Elout, R.A.G. de Graaff, and H. Schenk.
    Zeitschrift für Kristallografie 207 (1993), 237-243.

  5. The Vitamin D2 story.
    I. Leban, R.A.G. de Graaff, R. de Gelder, J. Turkenburg, K.S. Wilson, and Z. Dauter.
    In: The Collected Works of Dorothy Crowfoot Hodgkin. Volume-III. General Crystallography and Essays. Editors: G.G. Dodson, J.P. Glusker, S. Ramaseshan, K. Venkatesan. 1994 Interline Publishing Pvt. Ltd., Bangalore.

  6. The Cochran Distribution for Incommensurately Modulated Structures.
    R. de Gelder, E.J.W. Lam, R. Israël, P.T. Beurskens, and S. van Smaalen.
    Proceedings of the International Conference on Aperiodic Crystals, p. 414-418. Aperiodic '94. Les Diablerets, Switzerland 18-22 september 1994. Editors: Gervais Chapuis and Wlodzimierz Paciorek. Published by: World Scientific Publishing Co. Pte. Ltd. PO Box 125, Farrer Road, Singapore 9128.

  7. The DIRDIF scaling procedures; rescaling for structures showing superstructure effects.
     R. Israël, C. Smykalla, R. de Gelder, and P.T. Beurskens.
    Zeitschrift für Kristallografie 210 (1995), 909-919.

  8. Direct Methods for Incommensurately Modulated Structures.
    On the Applicability of Normalized Structure Factors.
     R. de Gelder, R. Israël, E.J.W. Lam, P.T. Beurskens, S. van Smaalen, Fu Zheng-Qing, and Fan Hai-Fu.
    Acta Crystallographica A52 (1996), 947-954.

  9. CRUNCH : solving structures using Karle-Hauptman matrices.
    R.A.G. de Graaff and R. de Gelder.
    Acta Crystallographica A46 (1996), C-53.

  10. DIRDIF-96 : Patterson methods, direct methods on difference structures, and completion of the structure by automatic recycling.
    P.T. Beurskens, R. Israël, G. Beurskens, R. de Gelder, W.P. Bosman and J.M.M. Smits.
    Acta Crystallographica A46 (1996), C-72.

  11. CRUNCH: Getting the Maximum Out of Determinants.
    R. de Gelder and R.A.G. de Graaff.
    IUCr XVIII Congress and General Assembly, Collected Abstracts, C.C. Wilson, K. Shankland and T. Csoka, Eds., (1999), 92.

  12. The R2-Criterion as a Figure of Merit in Patterson Applications.
    P.T. Beurskens, G. Beurskens, R. Israël and R. de Gelder.
    IUCr XVIII Congress and General Assembly, Collected Abstracts, C.C. Wilson, K. Shankland and T. Csoka, Eds., (1999), 245.


  13. Development and Applicability of Advanced Methods for Solving 'Difficult' Structures by X-ray Analysis.
    R. Israël.
    Thesis (2000). University of Nijmegen. The Netherlands.

  14. The reliability index R2 as a versatile tool in the structure analysis of difficult inorganic and small molecular compounds.
     P.T. Beurskens, R. Israël, R. de Gelder, G. Beurskens, and R.A.G. de Graaff.
    Journal of Applied Crystallography (2001), 34, 178-186.