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A Method for Multiconformational Modeling of the Three‐Dimensional Shape of a Molecule

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Abstract

A method for multiconformational modeling of the three‐dimensional shape of a molecule is proposed that includes search for conformers, their optimum superposition, and analysis of spatial features of the resulting structure. The method allows one to determine features of various molecular conformations of compounds under study, to assess the contributions of conformers to particular properties of the substance, to evaluate the space occupied by the molecule, and to compare the average size of the multiconformational model of the molecule with the sizes of the most stable conformations. The potentials of the model are illustrated by density calculations for 137 organic liquids.

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REFERENCES

  1. A. I. Kitaigorodskii, Organic Crystal Chemistry [in Russian], Izd. Akad. Nauk SSSR, Moscow (1955).

    Google Scholar 

  2. A. I. Kitaigorodskii, Molecular Crystals [in Russian], Nauka, Moscow (1971).

    Google Scholar 

  3. Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 58, No. 5, 713-746 (1989).

    Google Scholar 

  4. Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 64, No. 5, 446-461 (1995).

    Google Scholar 

  5. M. L. Connolly, J. Amer. Chem. Soc., 107, 1118-1124 (1985).

    Google Scholar 

  6. J. A. Grant, M. A. Gallardo, and B. T. Pickup, J. Comput. Chem., 17, No. 14, 1653-1666 (1996).

    Google Scholar 

  7. Yu. I. Naberukhin, V. P. Voloshin, and N. N. Medvedev, Zh. Fiz. Khim., 66, No. 1, 155-162 (1992).

    Google Scholar 

  8. S. Srivastava and G. M. Grippen, J. Med. Chem., 36, No. 21, 3171-3177 (1993).

    Google Scholar 

  9. A. V. Belik, L. V. Ul'yanova, and N. S. Zefirov, Dokl. Akad. Nauk SSSR, 313, No. 3, 628-629 (1990).

    Google Scholar 

  10. A. V. Belik and V. A. Potemkin, Zh. Fiz. Khim., 66, No. 1, 140-142 (1992).

    Google Scholar 

  11. V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 72, No. 4, 650-656 (1998).

    Google Scholar 

  12. V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 70, No. 3, 448-452 (1996).

    Google Scholar 

  13. V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Izv. Akad. Nauk, Ser. Khim., No. 10, 1781-1784 (1997).

    Google Scholar 

  14. A. V. Belik, V. A. Potemkin, and D. V. Belousov, Izv. Vyssh. Uchebn. Zaved., Khim. Khim. Tekhnol., 35, No. 3, 49-52 (1992).

    Google Scholar 

  15. A. V. Belik, V. A. Potemkin, and Yu. N. Grevtseva, Zh. Fiz. Khim., 69, No. 1, 101-105 (1995).

    Google Scholar 

  16. A. I. Kitaigorodskii, P. M. Zorkii, and V. K. Bel'skii, Structure of Organic Matter. Structural Data of 1971-1973 [in Russian], Nauka, Moscow (1982).

    Google Scholar 

  17. M. A. Mazo, E. B. Gusarova, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1985-1989 (2000).

    Google Scholar 

  18. A. L. Rabinovich and P. O. Ripatti, Zh. Fiz. Khim., 72, No. 4, 590-594 (1998).

    Google Scholar 

  19. A. L. Rabinovich, P. O. Ripatti, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1990-1996 (2000).

    Google Scholar 

  20. L. Piela, J. Kostrowicki, and H. A. Scheraga, J. Phys. Chem., 93, 3339-3346 (1989).

    Google Scholar 

  21. R. V. Pappu, R. K. Hart, and J. W. Ponder, J. Phys. Chem. B, 102, 9725-9742 (1998).

    Google Scholar 

  22. A. O. Griewank, J. Opt. Theor. Appl., 34, 11-39 (1981).

    Google Scholar 

  23. A. R. Butler and E. E. Slaminka, J. Comput. Phys., 99, 28-32 (1993).

    Google Scholar 

  24. J. W. Rogers and R. A. Donnelly, SIAM J. Optim., 5, 871-891 (1995).

    Google Scholar 

  25. R. S. Dembo and T. Steihaug, Math. Prog., 26, 190-212 (1983).

    Google Scholar 

  26. P. Derreumaux, G. Zhang, T. Schlick, and B. R. Brooks, J. Comput. Chem., 15, 532-552 (1994).

    Google Scholar 

  27. S. J. Kearsley, J. Comput. Chem., 11, 1187-1192 (1990).

    Google Scholar 

  28. V. A. Potemkin, E. V. Bartashevich, M. A. Grishina, and S. Guccione, "Rational approaches to drug design," in: H. D. Holtje and W. Sippl (eds.), Proc. of the 13th Europ. Symp. on Quantitative Structure-Activity Relationships, QSAR 2000 (Heinrich-Heine-Universität, Dusseldorf, Germany, August 27-September 1, 2000), Prous Science Publishers, Dusseldorf (2001), pp. 349-353.

    Google Scholar 

  29. T. Noguti and N. Go, J. Phys. Soc. Jpn., 52, 3685-3690 (1983).

    Google Scholar 

  30. H. Abe, W. Braun, T. Noguti, and N. Go, Comput. Chem., 8, 239-247 (1984).

    Google Scholar 

  31. V. M. Tatevskii, Theory of Physicochemical Properties of Molecules and Substances [in Russian], Izd. Mosk. Univ., Moscow (1987).

    Google Scholar 

  32. V. M. Tatevskii, Zh. Fiz. Khim., 68, No. 7, 1157-1170 (1994).

    Google Scholar 

  33. N. L. Allinger, F. Li, and L. Yan, J. Comput. Chem., 11, 848-867 (1990).

    Google Scholar 

  34. N. L. Allinger, F. Li, L. Yan, and J. C. Tai, J. Comput. Chem., 11, 868-895 (1990).

    Google Scholar 

  35. J.-H. Lii and N. L. Allinger, J. Comput. Chem., 19, 1001-1016 (1998).

    Google Scholar 

  36. M. A. Porai-Koshits and V. S. Kuz'min, Dokl. Akad. Nauk SSSR, 317, No. 5, 1148-1149 (1991).

    Google Scholar 

  37. V. I. Shil'nikov, V. S. Kuz'min, and Yu. T. Struchkov, Zh. Strukt. Khim., 34, No. 4, 98-106 (1993).

    Google Scholar 

  38. B. P. Nikol'skii (ed.), Chemistry Handbook [in Russian], Vol. 2, Khimiya, Leningrad (1964), pp. 398-1153.

    Google Scholar 

  39. A. A. Potekhin (ed.), Properties of Organic Compounds [in Russian], Khimiya, Leningrad (1984).

    Google Scholar 

  40. V. A. Rabinovich and Z. Ya. Khavin, Brief Chemistry Handbook [in Russian], Khimiya, Leningrad (1978).

    Google Scholar 

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Bartashevich, E.V., Potemkin, V.A., Grishina, M.A. et al. A Method for Multiconformational Modeling of the Three‐Dimensional Shape of a Molecule. Journal of Structural Chemistry 43, 1033–1039 (2002). https://doi.org/10.1023/A:1023611131068

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