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.
Similar content being viewed by others
REFERENCES
A. I. Kitaigorodskii, Organic Crystal Chemistry [in Russian], Izd. Akad. Nauk SSSR, Moscow (1955).
A. I. Kitaigorodskii, Molecular Crystals [in Russian], Nauka, Moscow (1971).
Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 58, No. 5, 713-746 (1989).
Yu. V. Zefirov and P. M. Zorkii, Usp. Khim., 64, No. 5, 446-461 (1995).
M. L. Connolly, J. Amer. Chem. Soc., 107, 1118-1124 (1985).
J. A. Grant, M. A. Gallardo, and B. T. Pickup, J. Comput. Chem., 17, No. 14, 1653-1666 (1996).
Yu. I. Naberukhin, V. P. Voloshin, and N. N. Medvedev, Zh. Fiz. Khim., 66, No. 1, 155-162 (1992).
S. Srivastava and G. M. Grippen, J. Med. Chem., 36, No. 21, 3171-3177 (1993).
A. V. Belik, L. V. Ul'yanova, and N. S. Zefirov, Dokl. Akad. Nauk SSSR, 313, No. 3, 628-629 (1990).
A. V. Belik and V. A. Potemkin, Zh. Fiz. Khim., 66, No. 1, 140-142 (1992).
V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 72, No. 4, 650-656 (1998).
V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Zh. Fiz. Khim., 70, No. 3, 448-452 (1996).
V. A. Potemkin, E. V. Bartashevich, and A. V. Belik, Izv. Akad. Nauk, Ser. Khim., No. 10, 1781-1784 (1997).
A. V. Belik, V. A. Potemkin, and D. V. Belousov, Izv. Vyssh. Uchebn. Zaved., Khim. Khim. Tekhnol., 35, No. 3, 49-52 (1992).
A. V. Belik, V. A. Potemkin, and Yu. N. Grevtseva, Zh. Fiz. Khim., 69, No. 1, 101-105 (1995).
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).
M. A. Mazo, E. B. Gusarova, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1985-1989 (2000).
A. L. Rabinovich and P. O. Ripatti, Zh. Fiz. Khim., 72, No. 4, 590-594 (1998).
A. L. Rabinovich, P. O. Ripatti, and N. K. Balabaev, Zh. Fiz. Khim., 74, No. 11, 1990-1996 (2000).
L. Piela, J. Kostrowicki, and H. A. Scheraga, J. Phys. Chem., 93, 3339-3346 (1989).
R. V. Pappu, R. K. Hart, and J. W. Ponder, J. Phys. Chem. B, 102, 9725-9742 (1998).
A. O. Griewank, J. Opt. Theor. Appl., 34, 11-39 (1981).
A. R. Butler and E. E. Slaminka, J. Comput. Phys., 99, 28-32 (1993).
J. W. Rogers and R. A. Donnelly, SIAM J. Optim., 5, 871-891 (1995).
R. S. Dembo and T. Steihaug, Math. Prog., 26, 190-212 (1983).
P. Derreumaux, G. Zhang, T. Schlick, and B. R. Brooks, J. Comput. Chem., 15, 532-552 (1994).
S. J. Kearsley, J. Comput. Chem., 11, 1187-1192 (1990).
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.
T. Noguti and N. Go, J. Phys. Soc. Jpn., 52, 3685-3690 (1983).
H. Abe, W. Braun, T. Noguti, and N. Go, Comput. Chem., 8, 239-247 (1984).
V. M. Tatevskii, Theory of Physicochemical Properties of Molecules and Substances [in Russian], Izd. Mosk. Univ., Moscow (1987).
V. M. Tatevskii, Zh. Fiz. Khim., 68, No. 7, 1157-1170 (1994).
N. L. Allinger, F. Li, and L. Yan, J. Comput. Chem., 11, 848-867 (1990).
N. L. Allinger, F. Li, L. Yan, and J. C. Tai, J. Comput. Chem., 11, 868-895 (1990).
J.-H. Lii and N. L. Allinger, J. Comput. Chem., 19, 1001-1016 (1998).
M. A. Porai-Koshits and V. S. Kuz'min, Dokl. Akad. Nauk SSSR, 317, No. 5, 1148-1149 (1991).
V. I. Shil'nikov, V. S. Kuz'min, and Yu. T. Struchkov, Zh. Strukt. Khim., 34, No. 4, 98-106 (1993).
B. P. Nikol'skii (ed.), Chemistry Handbook [in Russian], Vol. 2, Khimiya, Leningrad (1964), pp. 398-1153.
A. A. Potekhin (ed.), Properties of Organic Compounds [in Russian], Khimiya, Leningrad (1984).
V. A. Rabinovich and Z. Ya. Khavin, Brief Chemistry Handbook [in Russian], Khimiya, Leningrad (1978).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
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
Issue Date:
DOI: https://doi.org/10.1023/A:1023611131068