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Knowledge Acquisition from Crystallographic Databases: Applications in Molecular Modelling, Crystal Engineering and Structural Chemistry

  • Chapter
Fundamental Principles of Molecular Modeling

Abstract

The interplay between theory and experiment has always been crucial to the development of structural chemistry. This interplay has become more sharply focused in recent decades, as increasingly detailed calculations and increasingly precise experimental structure determinations are facilitated by rapid technological advances. It is these advances, particularly in raw computing power and in graphics capabilities, that now bring the most sophisticated computational methods to the chemists desk, and underpin the branch of chemistry that forms the subject of this book: molecular modelling. So persuasive are these models, however, that there is a tendency to imbue each graphic, each energy value, each atomic partial charge, with a veracity that is neither warranted, nor claimed by the originators of the software. There are many computational techniques, and many different levels of sophistication. Each technique makes different assumptions and approximations, and each must be understood and assessed in deciding its suitability in a given problem domain.

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References

  1. F.H. Allen, G. Bergerhoff and R. Sievers, eds., “Crystallographic Databases.” International Union of Crystallography, Chester, UK (1987).

    Google Scholar 

  2. F.H. Allen, J.E. Davies, J.J. Galloy, O. Johnson, O. Kennard, CF. Macrae, E.M. Mitchell, G.F. Mitchell, J.M. Smith and D.G. Watson, J. Chem. Inf. Comput. Sci. 31:187 (1991).

    Article  CAS  Google Scholar 

  3. F.H. Allen, O. Kennard and D.G. Watson, in: “Structure Correlation”, H.-B. Biirgi and J.D. Dunitz, eds., Chapter 3. VCH Publishers, Weinheim (1994).

    Google Scholar 

  4. R. Taylor and F.H. Allen, in: “Structure Correlation”, H.-B. Biirgi and J.D. Dunitz, eds., Chapter 3. VCH Publishers, Weinheim (1994).

    Google Scholar 

  5. Cambridge Structural Database System User’s Manual: Getting Started with the CSD System. CCDC, ambridge, England (1994).

    Google Scholar 

  6. EH. Allen, O. Kennard, D.G. Watson, L. Brammer, A.G. Orpen and R. Taylor, J. Chem. Soc, Perkin Trans. 2:S1 (1987).

    Google Scholar 

  7. A.G. Orpen, L. Brammer, F.H. Allen, O. Kennard, D.G. Watson and R. Taylor, J. Chem. Soc., Dallon Trans., page S1 (1989).

    Google Scholar 

  8. See many of the individual chapters in “Structure Correlation” H.-B. Biirgi and J.D. Dunitz, eds., VCH Publishers, Weinheim, Germany (1994).

    Google Scholar 

  9. H.-B. Bürgi and J.D. Dunitz, Acta Crystallogr. B44:445 (1988).

    Google Scholar 

  10. F.H. Allen, Acta Crystallogr. B36:81 (1980).

    Google Scholar 

  11. R. Hoffmann, Tetrahedron Lett. 2907 (1970).

    Google Scholar 

  12. R. Hoffmann and R.B. Davidson, J. Amer. Chem. Soc. 93:5699 (1971)

    Article  CAS  Google Scholar 

  13. D. Cremer and J.A. Pople, J. Amer. Chem. Soc. 97:1354 (1975)

    Article  CAS  Google Scholar 

  14. R. Taylor, J. Mol. Graphics 3: 106 (1986).

    Google Scholar 

  15. F.H. Allen, M.J. Doyle and T.P.E. Auf der Heyde, Acta Crystallogr. B47:412 (1991).

    CAS  Google Scholar 

  16. F.H. Allen, J.A.K. Howard and N.A. Pitchford, Acta Crystallogr. B49:910 (1993).

    CAS  Google Scholar 

  17. T.P.E. Auf der Heyde and H.-B. Bürgi, Inorg.Chem. 28:3960 (1989).

    Article  CAS  Google Scholar 

  18. F.H. Allen, M.J. Doyle and R. Taylor, Acta Crystallogr. B47:51 (1991).

    Google Scholar 

  19. EH. Allen, S.E. Harris and R. Taylor, J. Comp.-Aided Mol. Design, Submitted.

    Google Scholar 

  20. M.F. Guest, J.H. van Lenthe, J. Kendrick, K. Schoeffel, P. Sherwood and R.J. Harrison, “GAMESS-UK User’s Guide and Reference Manual.” Computing for Science Ltd., Daresbury Laboratory, Warrington (1993).

    Google Scholar 

  21. J.-M. Lehn, Angew. Chem. (Int. Ed. Engl.) 27:89 (1988).

    Article  Google Scholar 

  22. G.R. Desiraju, “Crystal Engineering: The Design of Organic Solids.” Elsevier, Amsterdam (1989).

    Google Scholar 

  23. I.C. Hayes and AJ. Stone, Mol. Phys. 53:83 (1984)

    Article  CAS  Google Scholar 

  24. J.P.M. Lommerse, AJ. Stone, R. Taylor and EH. Allen, J. Amer. Chem. Soc., Submitted.

    Google Scholar 

  25. E.H. Allen, C.M. Bird and R.S. Rowland, Acta Crystallogr., Submitted.

    Google Scholar 

  26. G. Gilli, F. Bellucci, V. Ferretti and V. Bertolasi, J. Amer. Chem. Soc. 111:1023 (1989).

    Article  CAS  Google Scholar 

  27. G.A. Jeffrey and W. Saenger, “Hydrogen Bonding in Biological Structures.” Springer-Verlag, Berlin (1991).

    Book  Google Scholar 

  28. D.J. Sutor, Nature 195:68 (1962)

    Article  CAS  Google Scholar 

  29. J. Donohue in:, “Structural Chemistry and Molecular Biology,” A. Rich and N. Davidson, eds., W.H. Freeman, San Francisco (1968).

    Google Scholar 

  30. R. Taylor and O. Kennard, J. Amer. Chem. Soc. 104:5063 (1982).

    Article  CAS  Google Scholar 

  31. G.R. Desiraju, Acc. Chem. Res. 24:290 (1991).

    Article  CAS  Google Scholar 

  32. G.R. Desiraju and J. Murty, Chem. Phys. Lett. 139:360 (1987).

    Article  CAS  Google Scholar 

  33. V.R. Pedireddi and G.R. Desiraju, J. Chem. Soc., Chem. Commun. 988 (1992).

    Google Scholar 

  34. M.A. Viswamitra, G. Bandekhar, R. Radhakrishnan and G.R. Desiraju, J. Amer. Chem. Soc. 115:4868 (1993).

    Article  CAS  Google Scholar 

  35. EH. Allen, J.P.M. Lommerse, J.A.K. Howard, V.J. Hoy and G.R. Desiraju, Acta Crystallogr., Submitted.

    Google Scholar 

  36. L. Joris, P. von R. Schleyer and R. Gleiter, J. Amer. Chem. Soc. 90:327 (1968).

    Article  CAS  Google Scholar 

  37. T. Steiner, J. Chem. Soc., Chem. Commun. 95 (1995).

    Google Scholar 

  38. T. Steiner, E.B. Starikov, A.M. Amado and J.J.C. Teixeira-Dias, J. Chem. Soc, Perkin Trans. 2:1321 (1995).

    Google Scholar 

  39. The early history of structure correlation is expertly summarised in: J.D. Dunitz, “X-Ray Analysis and the Structure of Organic Molecules.” Cornell Univ. Press, Ithaca (1979).

    Google Scholar 

  40. R. Taylor, A. Mullaley and G.W. Mullier, Pestic. Sci. 29:197 (1990).

    Article  CAS  Google Scholar 

  41. EH. Allen, S.B. Goud, V.J. Hoy, J.A.K. Howard and G.R. Desiraju, J. Chem. Soc., Chem. Commun. 2729 (1994).

    Google Scholar 

  42. G.R. Desiraju, Angew. Chem. (Int. Ed. Engl.), In Press for November 1995.

    Google Scholar 

  43. EH. Allen, CM. Bird and R.S. Rowland, Acta Crystallogr., Submitted.

    Google Scholar 

  44. EH. Allen, R.S. Rowland, S. Fortier and J.I. Glasgow, Tetrahedron Computer Methodology 3:757 (1990).

    Article  CAS  Google Scholar 

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Allen, F.H. (1996). Knowledge Acquisition from Crystallographic Databases: Applications in Molecular Modelling, Crystal Engineering and Structural Chemistry. In: Gans, W., Amann, A., Boeyens, J.C.A. (eds) Fundamental Principles of Molecular Modeling. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-0212-2_6

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  • DOI: https://doi.org/10.1007/978-1-4899-0212-2_6

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