Journal of Structural Chemistry

, Volume 43, Issue 6, pp 1033–1039 | Cite as

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

  • E. V. Bartashevich
  • V. A. Potemkin
  • M. A. Grishina
  • A. V. Belik


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.


Physical Chemistry Inorganic Chemistry Spatial Feature Density Calculation Organic Liquid 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    A. I. Kitaigorodskii, Organic Crystal Chemistry [in Russian], Izd. Akad. Nauk SSSR, Moscow (1955).Google Scholar
  2. 2.
    A. I. Kitaigorodskii, Molecular Crystals [in Russian], Nauka, Moscow (1971).Google Scholar
  3. 3.
    Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 58, No. 5, 713-746 (1989).Google Scholar
  4. 4.
    Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 64, No. 5, 446-461 (1995).Google Scholar
  5. 5.
    M. L. Connolly, J. Amer. Chem. Soc., 107, 1118-1124 (1985).Google Scholar
  6. 6.
    J. A. Grant, M. A. Gallardo, and B. T. Pickup, J. Comput. Chem., 17, No. 14, 1653-1666 (1996).Google Scholar
  7. 7.
    Yu. I. Naberukhin, V. P. Voloshin, and N. N. Medvedev, Zh. Fiz. Khim., 66, No. 1, 155-162 (1992).Google Scholar
  8. 8.
    S. Srivastava and G. M. Grippen, J. Med. Chem., 36, No. 21, 3171-3177 (1993).Google Scholar
  9. 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. 10.
    A. V. Belik and V. A. Potemkin, Zh. Fiz. Khim., 66, No. 1, 140-142 (1992).Google Scholar
  11. 11.
    V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 72, No. 4, 650-656 (1998).Google Scholar
  12. 12.
    V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 70, No. 3, 448-452 (1996).Google Scholar
  13. 13.
    V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Izv. Akad. Nauk, Ser. Khim., No. 10, 1781-1784 (1997).Google Scholar
  14. 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. 15.
    A. V. Belik, V. A. Potemkin, and Yu. N. Grevtseva, Zh. Fiz. Khim., 69, No. 1, 101-105 (1995).Google Scholar
  16. 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. 17.
    M. A. Mazo, E. B. Gusarova, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1985-1989 (2000).Google Scholar
  18. 18.
    A. L. Rabinovich and P. O. Ripatti, Zh. Fiz. Khim., 72, No. 4, 590-594 (1998).Google Scholar
  19. 19.
    A. L. Rabinovich, P. O. Ripatti, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1990-1996 (2000).Google Scholar
  20. 20.
    L. Piela, J. Kostrowicki, and H. A. Scheraga, J. Phys. Chem., 93, 3339-3346 (1989).Google Scholar
  21. 21.
    R. V. Pappu, R. K. Hart, and J. W. Ponder, J. Phys. Chem. B, 102, 9725-9742 (1998).Google Scholar
  22. 22.
    A. O. Griewank, J. Opt. Theor. Appl., 34, 11-39 (1981).Google Scholar
  23. 23.
    A. R. Butler and E. E. Slaminka, J. Comput. Phys., 99, 28-32 (1993).Google Scholar
  24. 24.
    J. W. Rogers and R. A. Donnelly, SIAM J. Optim., 5, 871-891 (1995).Google Scholar
  25. 25.
    R. S. Dembo and T. Steihaug, Math. Prog., 26, 190-212 (1983).Google Scholar
  26. 26.
    P. Derreumaux, G. Zhang, T. Schlick, and B. R. Brooks, J. Comput. Chem., 15, 532-552 (1994).Google Scholar
  27. 27.
    S. J. Kearsley, J. Comput. Chem., 11, 1187-1192 (1990).Google Scholar
  28. 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. 29.
    T. Noguti and N. Go, J. Phys. Soc. Jpn., 52, 3685-3690 (1983).Google Scholar
  30. 30.
    H. Abe, W. Braun, T. Noguti, and N. Go, Comput. Chem., 8, 239-247 (1984).Google Scholar
  31. 31.
    V. M. Tatevskii, Theory of Physicochemical Properties of Molecules and Substances [in Russian], Izd. Mosk. Univ., Moscow (1987).Google Scholar
  32. 32.
    V. M. Tatevskii, Zh. Fiz. Khim., 68, No. 7, 1157-1170 (1994).Google Scholar
  33. 33.
    N. L. Allinger, F. Li, and L. Yan, J. Comput. Chem., 11, 848-867 (1990).Google Scholar
  34. 34.
    N. L. Allinger, F. Li, L. Yan, and J. C. Tai, J. Comput. Chem., 11, 868-895 (1990).Google Scholar
  35. 35.
    J.-H. Lii and N. L. Allinger, J. Comput. Chem., 19, 1001-1016 (1998).Google Scholar
  36. 36.
    M. A. Porai-Koshits and V. S. Kuz'min, Dokl. Akad. Nauk SSSR, 317, No. 5, 1148-1149 (1991).Google Scholar
  37. 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. 38.
    B. P. Nikol'skii (ed.), Chemistry Handbook [in Russian], Vol. 2, Khimiya, Leningrad (1964), pp. 398-1153.Google Scholar
  39. 39.
    A. A. Potekhin (ed.), Properties of Organic Compounds [in Russian], Khimiya, Leningrad (1984).Google Scholar
  40. 40.
    V. A. Rabinovich and Z. Ya. Khavin, Brief Chemistry Handbook [in Russian], Khimiya, Leningrad (1978).Google Scholar

Copyright information

© Plenum Publishing Corporation 2002

Authors and Affiliations

  • E. V. Bartashevich
    • 1
    • 2
  • V. A. Potemkin
    • 1
    • 2
  • M. A. Grishina
    • 1
    • 2
  • A. V. Belik
    • 1
    • 2
  1. 1.Chelyabinsk State UniversityChelyabinsk
  2. 2.Institute of Organic Synthesis, Ural BranchRussian Academy of SciencesEkaterinburg

Personalised recommendations