How to derive force field parameters by genetic algorithms: Modelling tripod-Mo(CO)3 compounds as an example

European Journal of Inorganic Chemistry

Volumn , Issue 6, 1998, Pages 693-702

  Hunger, Johannes ^a   Beyreuther, Stefan ^a   Huttner, Gottfried ^a   Allinger, Kurt ^a   Radelof, Uwe ^a   Zsolnai, Laszlo ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Conformational analysis; Force field calculations; Genetic Algorithms; Refinement of force field parameters; Tripod metal compounds

Indexed keywords

CONFORMATIONS; CRYSTAL STRUCTURE; MOLECULES; MOLYBDENUM COMPOUNDS; PARAMETER ESTIMATION; TRANSITION METALS;

ALGORITHM MODEL; CONFORMATIONAL ANALYSIS; CONFORMATIONAL SPACE; COORDINATION COMPOUNDS; DATA BASE; FORCE FIELD CALCULATIONS; FORCE FIELD PARAMETERS; REFINEMENT OF FORCE FIELD PARAMETER; RMS DEVIATIONS; TRIPOD METAL COMPOUND;

GENETIC ALGORITHMS;

EID: 0001387834     PISSN: 14341948     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1099-0682(199806)1998:6<693::AID-EJIC693>3.0.CO;2-M     Document Type: Article

References (40)

1. See for example: [1a] H. Brintzinger, D. Fischer, R. Muhlhaupt, B. Rieger, R. M. Waymouth, Angew. Chem. Int. Ed. Engl. 1995, 34(11), 1143-1170. [1b] C. R. Landis, C. R. Halpern, J. Am. Chem. Soc. 1987, 109, 1746-1754. [1c] G. Helmchen, S. Kudis, P. Sennhenn, H. Steinhagen, Pure Appl. Chem. 1997, 69, 513-518.
2. See for example: [1a] H. Brintzinger, D. Fischer, R. Muhlhaupt, B. Rieger, R. M. Waymouth, Angew. Chem. Int. Ed. Engl. 1995, 34(11), 1143-1170. [1b] C. R. Landis, C. R. Halpern, J. Am. Chem. Soc. 1987, 109, 1746-1754. [1c] G. Helmchen, S. Kudis, P. Sennhenn, H. Steinhagen, Pure Appl. Chem. 1997, 69, 513-518.
3. See for example: [1a] H. Brintzinger, D. Fischer, R. Muhlhaupt, B. Rieger, R. M. Waymouth, Angew. Chem. Int. Ed. Engl. 1995, 34(11), 1143-1170. [1b] C. R. Landis, C. R. Halpern, J. Am. Chem. Soc. 1987, 109, 1746-1754. [1c] G. Helmchen, S. Kudis, P. Sennhenn, H. Steinhagen, Pure Appl. Chem. 1997, 69, 513-518.
4. G. Frenking, I. Antes, M. Boehme, S. Dapprich, A. W. Ehlers, V. Jonas, A. Neuhaus, M. Otto, R. Stegmann, A. Veldkamp, S. F. Vyboishchikov, in Reviews in Computational Chemistry, Vol. 8 (Eds.: K. B. Lipkowitz, D. B. Boyd). VCH Publishers, Inc., New York, 1996, p. 63-130
5. L. J. Bartolotti, K. Flurchick, in Reviews in Computational Chemistry, Vol 7 (Eds.: K. B. Lipkowitz, D. B. Boyd), VCH Publishers. Inc., New York, 1996, p. 187-259.
6. N. L. Allinger, J. Am. Chem. Soc. 1977, 99, 8127-8134.
7. U. Burkert, N. L. Allinger, Molecular Mechanics, ACS monograph, Washington, 1992.
8. P. Comba, T. W. Hambley, Molecular Modelling of Inorganic Compunds, VCH, Weinheim, 1995.
9. B. J. Hay, Coord. Chem. Rev. 1993, 126, 177-236.
10. C. R. Landis, D. M. Root, T. Cleveland, in Reviews in Computational Chemistry, Vol. 6 (Eds.: K. B. Lipkowitz, D. B. Boyd), VCH Publishers, Inc., New York, 1995, 73-148.
11. S. Beyreuther, J. Hunger, G. Huttner, S. Mann, L. Zsolnai, Chem. Ber. 1996, 129, 745-757.
12. G. Huttner, S. Beyreuther, J. Hunger, in Software-Entwicklung in der Chemie 10 (Ed.: J. Gasteiger), GDCH, Frankfurt am Main, 1996, 201-207.
13. W. H. Press, Numerical Recipes: The Art of Scientific Computation, Cambridge University Press, Cambridge, 1986.
14. P. E. Gill, W. Murray, M H. Wright, Practical Optimization, Wiley, New York, 1988.
15. O. Walter, Th. Klein, G. Huttner, L. Zsolnai, J. Organomet. Chem. 1993, 458, 636-640.
16. A. Muth, O. Walter, G. Huttner, A. Asam, L. Zsolnai, J Organomet. Chem. 1994, 468, 149-163.
17. Th. Seitz, A. Muth, G. Huttner, Th. Klein, O. Walter, M. Fritz, L. Zsolnai, J. Organomet. Chem. 1994, 469, 155-162.
18. Th. Seitz, A. Asam, G. Huttner, O. Walter, L. Zsolnai, Z. Naturforsch. 1995, 50b, 1287-1306.
19. The structures 3, 8 and 10 (see Tablel) have not yet been published, but have now been submitted. Details of the crystal structure investigations may be obtained from the Fachmformationszentrum Karlsruhe, D-76344 Eggenstein-Leopoldshafen (Germany), on quoting the depository numbers CSD-406278 (3), CSD-406277 (8) and CSD-406275 (10).
20. The mm2 force field as implemented in Macromodel 5.0 (mm2*) has been used throughout (see F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C Caufield, G. Chang, T. Hendrickson, W. C. Still, J. Comp. Chem. 1990, 11, 440-467).
21. J. Devillers (Ed.), Genetic Algorithms in Molecular Modelling, Academic Press, San Diego, 1996.
22. R. Judson, in Reviews in Computational Chemistry, Vol. 10 (Eds.: K. B. Lipkowitz, D. B. Boyd), VCH Publishers, Inc., New York, 1997, 1-73.
23. The idea of applying global minimizers to the inverse problem of finding optimized force field parameters has also been mentioned by van Gunsteren: - [21a] P. Ulrich, W. R. P. Scott, W. F. van Gunsteren, A. E. Torda, Protein Structure Prediction Force Fields: Parameterization With Quasi-Newtonian Dynamics; Proteins 1997, 27, 367-384. In contrast, local minimizers have routinely been used to locally improve parameters [21b] S. Lifson, A. Warshel, J. Chem. Phys. 1968, 49, 5116-5128.
24. The idea of applying global minimizers to the inverse problem of finding optimized force field parameters has also been mentioned by van Gunsteren: - [21a] P. Ulrich, W. R. P. Scott, W. F. van Gunsteren, A. E. Torda, Protein Structure Prediction Force Fields: Parameterization With Quasi-Newtonian Dynamics; Proteins 1997, 27, 367-384. In contrast, local minimizers have routinely been used to locally improve parameters [21b] S. Lifson, A. Warshel, J. Chem. Phys. 1968, 49, 5116-5128.
25. Cicero, De divinatione, II, 59, "If somebody shoots the whole day, shouldn't he occasionally hit?"
26. The problem is not drastically reduced when instead of the Alps, the Scottish Highlands or the Rocky Mountains are considered.
27. J. Holland, Adaption in Natural and Artificial Systems, MIT Press, Michigan, 1975.
28. D. E. Goldberg, Genetic Algorithms in Search, Research and Machine Learning, Addison-Wesley, New York, 1989.
29. The strategy of simulated annealing is yet another way of combining deterministically analytic and stochastic strategies. See for example: [26a] S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi, Science 1983, 220, 671-680. This methodology has been successfully applied to problems of conformational search, see for example [26b] S. R. Wilson, W. Cui, J. W. Moskowitz, K. E. Schmidt, Tetrahedron Lett. 1988, 29, 4373-4376.
30. The strategy of simulated annealing is yet another way of combining deterministically analytic and stochastic strategies. See for example: [26a] S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi, Science 1983, 220, 671-680. This methodology has been successfully applied to problems of conformational search, see for example [26b] S. R. Wilson, W. Cui, J. W. Moskowitz, K. E. Schmidt, Tetrahedron Lett. 1988, 29, 4373-4376.
31. E. B. Wilson, J. C. Decious, P. C. Cross, Molecular Vibrations - The Theory of Infrared and Roman Vibrational Spectroscopy, Maple Press Company, New York, 1955.
32. L. H. Jones, R. S. MacDowell, M. Goldblatt, Inorg. Chem. 1960, 8, 11, 2349-2363.
33. Since bending force constants derived from spcctroscopy may not be too accurate (see for instance ref. [5]), refinement was also performed including the Mo-C-O force constant in the subset of variable parameters. The force field parameters derived for this augmented set did not show an improvement over those with the bending force constants at the value given. It was observed, however, that the refined values of this force constant tended to be smaller than the value taken from the literature.
34. In the scattergraph published previously for the same data (ref.[9] ), a distortion by a partially incorrect treatment of symmetry had been introduced; this is now corrected in the diagram presented in Figure 7. We thank H. B. Bürgi for helpful discussions.
35. P. Schober, Ph.D thesis, Heidelberg 1997.
36. R. K. Z. Tan, S. C. Harvey, J. Comp. Chem. 1993, 14, 455-470.
37. D. Heisterberg, 1990, unpublished results; the program is available from the software archive of the Computational Chemistry List (CCL) at http://ccl.osc.edu/chemistry.html.
38. D. Levine, Argonne National Laboratory, 1995; the package is available at http://www.mcs.anl.gov/pgapack.html.
39. W Gropp, E. Lusk, Argonne National Laboratory, 1996 (available from http://www.mcs.anl.gov/mpi).
40. G. Syswerda, Proc. 3rd Int. Conference on Genetic Algorithms, Morgan Kaufman Publishing, 1989.