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Quantum Molecular Similarity: Theory and Applications to the Evaluation of Molecular Properties, Biological Activities and Toxicity

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Part of the book series: Mathematical and Computational Chemistry ((MACC))

Abstract

In this chapter we present an updated revision of the mathematical interpretation leading to further development of the theory and practice associated with quantum similarity measures (QSM) [1–40]. The role of QSM can be resumed on their ability to be the vehicle producing discrete ndimensional mathematical representations of molecular structures. This property transforms QSM into a general source of unbiased molecular descriptors. QSM descriptors are general indeed, because of their quantum chemical origin: They can be computed, in principle, for any quantum system or any molecular structure possessing arbitrary geometrical conformation or state. Moreover, QSM descriptors are unbiased, because their values are not chosen by a priori designs: They are built up as a consequence of the theoretical quantum framework results and only depend on the nature and topological characteristics of the studied molecular set.

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References

  1. R. Carbó, M. Arnau, and L. Leyda, Int. J. Quantum Chem. 17, 1185 (1980).

    Article  Google Scholar 

  2. E. E. Hodgkin and W. G. Richards, Int. J. Quantum Chem. 14, 105 (1987).

    Article  CAS  Google Scholar 

  3. C. Burt, W. G. Richards, and P. Huxley, J. Comput. Chem. 11, 1139 (1990).

    Article  CAS  Google Scholar 

  4. A. C. Good, E. E. Hodgkin, and W. G. Richards, J. Chem. Inf. Comput. Sci. 32, 188 (1992).

    Article  CAS  Google Scholar 

  5. A. C. Good, S.-S. So, and W. G. Richards, J. Med. Chem. 36, 433 (1993).

    Article  CAS  Google Scholar 

  6. C. Good and W. G. Richards, J. Chem. Inf. Comput. Sci. 33, 112 (1993).

    Article  CAS  Google Scholar 

  7. D. L. Cooper and N. L. Allan, J. Comput.-Aided Mol. Des. 3, 253 (1989).

    Article  CAS  Google Scholar 

  8. D. L. Cooper and N. L. Allan, J. Am. Chem. Soc. 114, 4773 (1992).

    Article  CAS  Google Scholar 

  9. D. L. Cooper, K. A. Mort, N. L. Allan, D. Kinchington, and C. McGuidan, J. Am. Chem Soc. 115, 12615 (1993).

    Article  CAS  Google Scholar 

  10. N. L. Allan and D. L. Cooper, Top. Curr. Chem. 173, 85 (1995).

    Article  CAS  Google Scholar 

  11. J. Cioslowski and E. D. Fleishmann, J. Am. Chem. Soc. 113, 64 (1991).

    Article  CAS  Google Scholar 

  12. J. B. Ortiz and J. Cioslowski, Chem. Phys. Lett. 185, 270 (1991).

    Article  CAS  Google Scholar 

  13. J. Cioslowski and M. Challacombe, Int. J. Quantum Chem. S25, 81 (1991).

    Article  Google Scholar 

  14. J. Cioslowski and S. T. Mixon, Can. J. Chem. 70, 443 (1992).

    Article  CAS  Google Scholar 

  15. J. Cioslowski and A. Nanayakkara, J. Am. Chem. Soc. 115, 1213 (1993).

    Google Scholar 

  16. J. Cioslowski, B. B. Stefanov, and P. Constans, J. Comput. Chem. 17, 1352 (1996).

    Article  CAS  Google Scholar 

  17. R. Ponec and M. Strnad, Collect. Czech. Chem. Commun. 55, 896 (1990).

    Article  CAS  Google Scholar 

  18. R. Ponec and M. Strnad, Collect. Czech. Chem. Commun. 55, 2583 (1990).

    Article  CAS  Google Scholar 

  19. R. Ponec and M. Strnad, J. Phys. Org. Chem. 4, 701 (1991).

    Article  CAS  Google Scholar 

  20. R. Ponec and M. Strnad, J. Math. Chem. 8, 103 (1991).

    Article  CAS  Google Scholar 

  21. R. Ponec and M. Strnad, Int. J. Quantum Chem. 42, 501 (1992).

    Article  CAS  Google Scholar 

  22. R. Ponec, J. Chem. Inf. Comput. Sci. 33, 805 (1993).

    Article  CAS  Google Scholar 

  23. R. Ponec, Overlap Determinant Method in the Theory of Pericyclic Reactions, Lecture notes in Chemistry 65, Springer-Verlag, Berlin (1995).

    Book  Google Scholar 

  24. P. G. Mezey, Shape in Chemistry: An Introduction to Molecular Shape and Topology, VCH, New York (1993).

    Google Scholar 

  25. P. G. Mezey, Top. Curr. Chem. 173, 63 (1995).

    Article  CAS  Google Scholar 

  26. C. Lee and S. Smithline, J. Phys. Chem. 98, 1135 (1994).

    Article  CAS  Google Scholar 

  27. C. Amovilli and R. McWeeny, J. Mol. Struct. (Theochem) 227, 1 (1991).

    Article  Google Scholar 

  28. A. C. Good, J. Mol. Graph. 10, 144 (1992).

    Article  CAS  Google Scholar 

  29. R. Benigni, M. Cotta-Ramusino, F. Giorgi, and G. Gallo, J. Med. Chem. 38, 629 (1995)

    Article  CAS  Google Scholar 

  30. J. D. Petke, J. Comput. Chem. 14, 928 (1993).

    Article  CAS  Google Scholar 

  31. A. Riera, J. Mol. Struct. (Theochem) 259, 83 (1992).

    Article  Google Scholar 

  32. F. Fratev, O. E. Polansky, A. Mehlhorn, and V. Monev, J. Mol. Struct. 56, 245 (1979).

    Article  CAS  Google Scholar 

  33. F. Fratev, V. Monev, A. Mehlhorn, and O. E. Polansky, J. Mol. Struct. (Theochem) 56, 255 (1979).

    Article  CAS  Google Scholar 

  34. M. A. Johnson and G. Maggiora (eds.), Concepts and Applications of Molecular Similarity, John Wiley, New York (1990).

    Google Scholar 

  35. R. Carbó (ed.) Molecular Similarity and Reactivity: From Quantum Chemical to Phenomenological Approaches, Kluwer, Dordrecht (1995).

    Google Scholar 

  36. K. Sen (ed.), Molecular Similarity. Top. Curr. Chem. Vols. 173 and 174, SpringerVerlag, Berlin (1995).

    Google Scholar 

  37. P. M. Dean (ed.), Molecular Similarity in Drug Design, Blackie Academic & Professional, London (1995).

    Google Scholar 

  38. R. Carbó-Dorca and P. G. Mezey (eds.), Advances in Molecular Similarity, Vol. 1, JAI Press, Greenwich (1996).

    Google Scholar 

  39. R. Carbó-Dorca and P. G. Mezey (eds.), Advances in Molecular Similarity, Vol. 2, JAI Press, Greenwich (1998).

    Google Scholar 

  40. R. Carbó and L. Domingo, lnt. J. Quantum Chem. 23, 517 (1987).

    Article  Google Scholar 

  41. R. Carbó-Dorca, J. Math. Chem. 23, 353 (1998).

    Article  Google Scholar 

  42. R. Carbó-Dorca, J. Math. Chem. 23, 365 (1998).

    Article  Google Scholar 

  43. R. Carbó-Dorca, in Advances in Molecular Similarity, Vol. 2, R. Carbó-Dorca and P. G. Mezey (eds.), JAI Press, Greenwich (1998).

    Google Scholar 

  44. R. Carbó-Dorca and E. Besalú, J. Mol. Struct. (Theochem) 451, 11 (1998).

    Article  Google Scholar 

  45. R. Carbó and B. Calabuig, Comput. Phys. Commun. 55, 117 (1989).

    Article  Google Scholar 

  46. R. Carbó and B. Calabuig, J. Mol. Struct. (Theochem) 254, 517 (1992).

    Article  Google Scholar 

  47. R. Carbó and B. Calabuig, in Computational Chemistry: Structure, Interactions and Reactivity, Vol. A., S. Fraga (ed.) Elsevier, Amsterdam (1992).

    Google Scholar 

  48. R. Carbó, B. Calabuig, L. Vera, and E. Besalú, Adv. Quantum Chem. 25, 253 (1994).

    Article  Google Scholar 

  49. R. Carbó and B. Calabuig, Int. J. Quantum Chem. 42, 1681 (1992).

    Article  Google Scholar 

  50. R. Carbó and E. Besalú, in Molecular Similarity and Reactivity: From Quantum Chemistry to Phenomenological Approaches, R. Carbó (ed.) Kluwer, Dordrecht (1995).

    Chapter  Google Scholar 

  51. R. Carbó and B. Calabuig, J. Chem. lnf. Comput. Sci. 32, 600 (1992).

    Google Scholar 

  52. R. Carbó-Dorca, E. Besalú, L. Amat, and X. Fradera, in Advances in Molecular Similarity, Vol. 1, R. Carbó-Dorca and P. G. Mezey (eds.) JAI Press, Greenwich (1996).

    Google Scholar 

  53. D. Robert and R. Carbó-Dorca, J. Math. Chem. 23, 327 (1998).

    Article  CAS  Google Scholar 

  54. D. Robert and R. Carbó-Dorca, Nuovo Cimento A 111, 1311 (1998).

    Google Scholar 

  55. R. Carbó, E. Besalú, L. Amat, and X. Fradera, J. Math. Chem. 18, 237 (1995).

    Article  Google Scholar 

  56. X. Fradera, L. Amat, E. Besalú, and R. Carbó-Dorca, Quant. Struct. -Act. Relat. 16, 25 (1997).

    Article  CAS  Google Scholar 

  57. M. Lobato, L. Amat, E. Besalú, and R. Carbó-Dorca, Scientia Gerundensis 23, 17 (1998).

    Google Scholar 

  58. M. Lobato, L. Amat, E. Besalú, and R. Carbó-Dorca, Quant. Struct.-Act. Relat. 16, 465 (1997).

    Article  CAS  Google Scholar 

  59. D. Robert and R. Carbó-Dorca, J. Chem. Inf. Comput. Sci. 38, 620 (1998).

    Article  CAS  Google Scholar 

  60. L. Amat, D. Robert, E. Besalú, and R. Carbó-Dorca, J. Chem. Inf. Comput. Sci. 38, 624 (1998).

    Article  CAS  Google Scholar 

  61. D. Robert, L. Amat, and R. Carbó-Dorca, J. Chem. lnf. Comput. Sci. 39, 333 (1999).

    CAS  Google Scholar 

  62. R. Ponec, L. Amat, and R. Carbó-Dorca, J. Comput-Aided Mol. Des. 13, 259 (1999).

    Article  CAS  Google Scholar 

  63. L. Amat, R. Carbó-Dorca, and R. Ponec, J. Comput. Chem. 19, 1575 (1998).

    Article  CAS  Google Scholar 

  64. R. Ponec, L. Amat, and R. Carbó-Dorca, J. Phys. Org. Chem. 12, 447 (1999).

    Article  CAS  Google Scholar 

  65. P. G. Mezey, R. Ponec, L. Amat, and R. Carbó-Dorca, Enantiomer 4, 371 (1999).

    CAS  Google Scholar 

  66. L. Amat, R. Carbó-Dorca, and R. Ponec, J. Med. Chem. 42, 5169 (1999).

    Article  CAS  Google Scholar 

  67. D. Robert, X. Gironés, and R. Carbó-Dorca, J. Comput. -Aided Mol. Des. 13, 597 (1999).

    Article  CAS  Google Scholar 

  68. X. Gironés, L. Amat, and R. Carbó-Dorca, R., SAR QSAR Environ. Res. 10, 545 (1999).

    Google Scholar 

  69. D. Robert and R. Carbó-Dorca, SAR QSAR Environ. Res. 10, 401 (1999).

    Article  CAS  Google Scholar 

  70. C. Hansch, B. H. Venger, and A. Panthananickal, J. Med. Chem. 23, 459 (1980).

    Article  CAS  Google Scholar 

  71. S. E. Sherman and S. J. Lippard, Chem. Rev. 87, 1153 (1987).

    Article  CAS  Google Scholar 

  72. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, et al. Gaussian-94, (Revision E.2), Gaussian, Inc., Pittsburgh (1995).

    Google Scholar 

  73. E. Besalú, R. Carbó, J. Mestres, and M. Solà, Top. Curr. Chem. 173, 31 (1995).

    Google Scholar 

  74. R. Carbó and E. Besalú, J. Math. Chem. 20, 247 (1996).

    Article  Google Scholar 

  75. R. Carbó, E. Besalú, L. Amat, and X. Fradera, J. Math. Chem. 19, 47 (1996).

    Article  Google Scholar 

  76. D. Robert and R. Carbó-Dorca, J. Chem. Inf. Comput. Sci. 38, 469 (1998).

    Article  CAS  Google Scholar 

  77. P. Constans, L. Amat, and R. Carbó-Dorca, J. Comput. Chem. 18, 826 (1997).

    Article  CAS  Google Scholar 

  78. R. Carbó-Dorca, L. Amat, E. Besald, and M. Lobato, in Advances in Molecular Similarity, Vol. 2, R. Carbó-Dorca and P. G. Mezey (eds.), JAI Press, Greenwich (1998).

    Google Scholar 

  79. L. A. Zadeh, Inform. Control 8, 338 (1965).

    Article  Google Scholar 

  80. E. Trillas, C. Alsina, and J. M. Terricabras, Introducción a la Lógica Difusa, Ariel Matemática, Barcelona (1995).

    Google Scholar 

  81. R. Carbó-Dorca, J. Math. Chem. 22, 143 (1997).

    Article  Google Scholar 

  82. R. Carbó-Dorca, E. Besalú, and X. Gironés, Extended Density Functions and Quantum Chemistry, Technical Report: IT-IQC-99–02. Adv. Quantum Chem. in press.

    Google Scholar 

  83. J. S. Bell, Speakable and Unspeakable in Quantum Mechanics, Cambridge University Press, Cambridge (1993).

    Google Scholar 

  84. T. M. Vinigradov (ed.) Encyclopaedia of Mathematics, Vol. 8, Reidel-Kluwer, Dordrecht (1987).

    Google Scholar 

  85. J. von Neumann, Mathematical Foundations of Quantum Mechanics, Princeton University Press, Princeton (1955).

    Google Scholar 

  86. D. Bohm, Quantum Theory, Dover, New York (1989).

    Google Scholar 

  87. S. Goldstein, Physics Today, March, 42 (1988) and April, 38 (1988).

    Google Scholar 

  88. P. O. Löwdin, Phys. Rev. 97, 1474 (1955).

    Article  Google Scholar 

  89. R. McWeeny, Revs. Mod. Phys. 32, 335 (1960).

    Article  Google Scholar 

  90. R. McWeeny, Proc. Roy. Soc. A 253, 242 (1959).

    Article  CAS  Google Scholar 

  91. E. R. Davidson, Reduced Density Matrices in Quantum Chemistry, Academic Press, New York (1976).

    Google Scholar 

  92. J. Mestres, M. Solà, M. Duran, and R. Carbó, J. Comput. Chem. 15, 1113 (1994).

    Article  CAS  Google Scholar 

  93. P. Constans and R. Carbó, J. Chem. Inf. Comput. Sci. 35, 1046 (1995).

    Article  CAS  Google Scholar 

  94. P. Constans, L. Amat, X. Fradera, and R. Carbó-Dorca, in Advances in Molecular Similarity, Vol. 1, R. Carbó-Dorca and P. G. Mezey (eds.), JAI Press, Greenwich (1996).

    Google Scholar 

  95. L. Amat, X. Fradera, and R. Carbó, Scientia Gerundensis 22, 97 (1996).

    Google Scholar 

  96. L. Amat and R. Carbó-Dorca, J. Comput. Chem. 18, 2023 (1997).

    Article  CAS  Google Scholar 

  97. L. Amat and R. Carbó-Dorca, J. Comput. Chem. 20, 911 (1999).

    Article  CAS  Google Scholar 

  98. E. V. Ludeña, in Química Teórica, Nuevas Tendencias, Vol. 4, S. Fraga (ed.), CSIC, Madrid (1987).

    Google Scholar 

  99. I. Shavitt, in Methods of Electronic Structure Theory, Modern Theoretical Chemistry, Vol. 3, H. F. Schaefer III (ed.), Plenum Press, New York (1977).

    Google Scholar 

  100. A. Lichnerowicz, Algèbre et Analyse Linéaires, Masson & Cie. Éditeurs, Paris (1947).

    Google Scholar 

  101. C. G. J. Jacobi, J. Reine Angew. Math. 30, 51 (1846).

    Article  Google Scholar 

  102. R. Carbó and E. Besalú, in Strategies and Applications in Quantum Mechanics, Y. Ellinger and M. Defranceschi (eds.), Kluwer, Dordrecht (1996).

    Google Scholar 

  103. R. Carbb and E. Besalú, J. Math. Chem. 18, 37 (1995).

    Article  Google Scholar 

  104. R. Carbó and E. Besalú, Comput. Chem. 18, 117 (1994).

    Article  Google Scholar 

  105. R. Carbó and E. Besalú, J. Math. Chem. 13, 331 (1993).

    Article  Google Scholar 

  106. P. Hohenberg and W. Kohn, Phys. Rev. B136, 864 (1964).

    Article  Google Scholar 

  107. K. D. Sen, E. Besalú, and R. Carbó-Dorca, J. Math. Chem. 25, 253 (1999).

    Article  CAS  Google Scholar 

  108. P. G. Mezey, J. Math. Chem. 23, 65 (1998).

    Article  CAS  Google Scholar 

  109. S. K. Berberian, Introducción al Espacio de Hilbert, Teide, Barcelona (1970).

    Google Scholar 

  110. A. Jeffrey, Handbook of Mathematical Formulas and Integrals, Academic Press, New York (1995).

    Google Scholar 

  111. R. E. Moss, Advanced Molecular Quantum Mechanics, Chapman & Hall, London (1973).

    Book  Google Scholar 

  112. W. Greiner, Relativistic Quantum Mechanics, Springer-Verlag, Berlin (1997).

    Google Scholar 

  113. R. Dedekind, Essays on the Theory of Numbers, Dover, New York (1963).

    Google Scholar 

  114. R. Carbó, B. Calabuig, E. Besalú and A. Martínez, Molecular Engineering 2, 43 (1992).

    Article  Google Scholar 

  115. R. G. Parr, The Quantum Theory of Molecular Electronic Structure, W. A. Benjamin Inc., New York (1963).

    Google Scholar 

  116. R. Carbó and J. M. Riera, A general SCF Theory, Lecture Notes in Chemistry, Vol. 5, Springer-Verlag, Berlin (1978).

    Book  Google Scholar 

  117. T. Akutsu, IEICE Trans. Inf. Sys. E-75D, 95 (1992).

    Google Scholar 

  118. T. Akutsu, IEICE Trans. Fund. Elec. Com. Comput. Sci. E-76A, 9(1993).

    Google Scholar 

  119. T. Asano, Theo. Comput. Sci. 38, 249 (1985).

    Article  Google Scholar 

  120. D.J. Klein, J. Chem. Inf. Comput. Sci. 37, 656 (1997).

    Article  CAS  Google Scholar 

  121. I.T. Jolliffe, Principal Component Analysis, Springer, New York (1986).

    Book  Google Scholar 

  122. S. Wold, E. Johansson, and M. Cocchi, in 3D QSAR in Drug Design, H. Kubinyi (ed.), ESCOM, Leiden (1993).

    Google Scholar 

  123. S. Wold, in Chemometric Methods in Molecular Design, H. van de Waterbeemd (ed.), VCH, Weinheim (1995).

    Google Scholar 

  124. I. Borg and P. Groenen, Modern Multidimensional Scaling, Springer, New York (1997).

    Google Scholar 

  125. C.M. Cuadras and C. Arenas, Commun. Statist. Theor. Meth. 19, 2261 (1990).

    Article  Google Scholar 

  126. D.M. Allen, Technometrics 16, 125 (1974).

    Article  Google Scholar 

  127. S. Wold and L. Ericksson, in Chemometric Methods in Molecular Design, H. van de Waterbeemd (ed.), VCH, New York (1995).

    Google Scholar 

  128. L. Amnat, P. Constans, E. Besalú, and R. Carbó, MOLSIMIL 97, Institute of Computational Chemistry, University of Girona (1997).

    Google Scholar 

  129. L. Amat, D. Robert, and E. Besalú, TQSAR-SIM, Institute of Computational Chemistry, University of Girona (1997).

    Google Scholar 

  130. K. Yutani, K. Ogasahara, T. Tsujita, K. Kanemoto, et al.,J. Biol. Chem. 262, 13429 (1987).

    CAS  Google Scholar 

  131. K. Yutani, K. Ogasahara, K. Aoki, T. Kakuno, and Y. Sugino, J. Biol. Chem. 259, 14076 (1984).

    CAS  Google Scholar 

  132. K. Yutani, K. Ogasahara, and Y. Sugino, Adv. Biophys. 20, 13 (1985).

    Article  CAS  Google Scholar 

  133. K. Yutani, K. Ogasahara, T. Tsujita, and Y. Sugino, Proc. Natl. Acad. Sci. USA 84, 4441 (1987).

    Article  CAS  Google Scholar 

  134. J. Damborský, Prot. Eng. 11, 21 (1998).

    Article  Google Scholar 

  135. PC Spartan Plus, Wavefunction Inc., Irvine CA, 92612 USA.

    Google Scholar 

  136. O. Exner, Correlation Analysis of Chemical Data, Plenum Press, New York (1988).

    Google Scholar 

  137. Y. Nozaki and C. Tanford, J. Theor. Biol. 67, 567 (1971).

    Google Scholar 

  138. M. R. Sweet and D. Eisenberg, J. Mol. Biol. 171, 479 (1983).

    Article  CAS  Google Scholar 

  139. S. Rackovsky and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 74, 5248 (1977).

    Article  CAS  Google Scholar 

  140. R. D. Cramer III, D. E. Patterson, and J. D. Bunce, J. Am. Chem. Soc. 110, 5959 (1988).

    Article  CAS  Google Scholar 

  141. R. F. Rekker, in Pharmacochemistry Library, W. T. Nauta and R. F. Rekker (eds.), Elsevier, New York (1977).

    Google Scholar 

  142. E. Urrestarazu, W. H. J. Vaes, H. J. M. Verhaar, and J. L. M. Hermens, J. Chem. Inf. Comput. Sci. 38, 845 (1998).

    Article  Google Scholar 

  143. S. Karabunarliev, O. G. Mekenyan, W. Karcher, C. L. Russom, and S. P. Bradbury, Quant. Struct.-Act. Relat. 15, 311 (1996).

    Article  CAS  Google Scholar 

  144. L. H. Hall, L. B. Kier, and G. Phipps, Environ. Toxicol. Chem. 3, 355 (1984).

    Article  CAS  Google Scholar 

  145. B. D. Gute and S. C. Basak, SAR QSAR Environ. Res. 7, 117 (1997).

    Article  CAS  Google Scholar 

  146. D. L. Geiger, L. T. Brooke, and D. J. Call (eds.) Acute toxicities of Organic Chemicals to Fathead Minnows (Pimephales promelas), Vol. 5, Center for Lake Environmental Studies, University of Wisconsin-Superior, Superior (1990).

    Google Scholar 

  147. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).

    Article  CAS  Google Scholar 

  148. AMPAC 6.0, 1994 Semichem, 7128 Summit, Shawnee, KS 66216 D.A.

    Google Scholar 

  149. H.J. M. Verhaar, C. J. van Leeuwen, and J. L. M. Hermens, Chemosphere 25, 471 (1992).

    Article  CAS  Google Scholar 

  150. P.G. Mezey, Molec. Phys. 96, 169 (1999).

    Article  CAS  Google Scholar 

  151. N. S. E. Sargent, D. G. Upshall, and J. W. Bridges, Biochem. Pharmac. 31, 1309 (1982).

    Article  CAS  Google Scholar 

  152. R. W. Taft, J. Am. Chem. Soc. 86, 5175 (1968).

    Google Scholar 

  153. L. P. Hammett, J. Am. Chem. Soc. 59, 96 (1937).

    Article  CAS  Google Scholar 

  154. A. Streitweiser, Molecular Orbital Theory for Organic Chemists, Wiley, New York (1961).

    Google Scholar 

  155. A. K. Saxena, Quant. Struct. -Act. Relat. 14, 142 (1995).

    Article  CAS  Google Scholar 

  156. M. Randic, J. Am. Chem. Soc. 97, 6609 (1975).

    Article  CAS  Google Scholar 

  157. L. B. Kier, W. J. Murray, M. Randic, and L. M. Hall, J. Pharm. Sci. 65, 1226 (1976).

    Article  CAS  Google Scholar 

  158. C.K. Chu, R. F. Schinazi, M. K. Ahn, G. V. Ullas, and Z. P. Gu, J. Med Chem. 32, 612 (1989).

    Article  CAS  Google Scholar 

  159. A. T. Balaban, J. Chem. Inf. Comput. Sci. 35, 339 (1995).

    Article  CAS  Google Scholar 

  160. M. Randic, B. Jerman-Blacic, and N. Trinajstic, Comput. Chem. 14, 237 (1990).

    Article  CAS  Google Scholar 

  161. Z. Mihalic and N. Trinajstic, J. Chem. Educ. 69, 701 (1992).

    Article  CAS  Google Scholar 

  162. M. Wagener, J. Sadowski, and J. Gasteiger, J. Am. Chem. Soc. 117, 7769 (1995).

    Article  CAS  Google Scholar 

  163. http://iqc.udg.es/cat/similarity/QSAR/steroids.htm.

    Google Scholar 

  164. H. Hosoya, Bull. Chem. Soc. Jap. 45, 2332 (1971).

    Article  Google Scholar 

  165. H. Hosoya, Bull. Chem. Soc. Jap. 45, 3415 (1971).

    Article  Google Scholar 

  166. D. C. Montgomery and E. A. Peck, Introduction to Linear Regression Analysis, Wiley, New York (1992).

    Google Scholar 

  167. B.D. Silverman and D. E. Platt, J. Med. Chem. 39, 2130 (1996).

    Article  Google Scholar 

  168. D. A. Pierre, Optimization Theory with Applications, Wiley, New York (1969).

    Google Scholar 

  169. R. Carbó, L. Molino, and B. Calabuig, J. Comput. Chem. 13, 155 (1992).

    Article  Google Scholar 

  170. M. R. Spiegel, Mathematical Handbook, McGraw-Hill, New York (1968).

    Google Scholar 

  171. J.S. Binkley, J. A. Pople, and W. J. Hehre, J. Am. Chem. Soc. 102, 939 (1980).

    Article  CAS  Google Scholar 

  172. M. S. Gordon, J. S. Binkley, J. A. Pople, W. J. Pietro, and W. J. Hehre, J. Am. Chem. Soc. 104, 2797 (1982).

    Article  CAS  Google Scholar 

  173. R. Carbó-Dorca, ATOMIC Program 1995, based on: B. Roos, C. Salez, A. Veillard, and E. Clementi, A General Program for Calculation of SCF Orbitals by the Expansion Method, IBM Research/RJ518(#10901) (1968).

    Google Scholar 

  174. ASA coefficients and exponents can be downloaded from: http://iqc.udg.es/cat/similarity/ASA/func6–21.html

    Google Scholar 

  175. R. Bonaccorsi, E. Scrocco, and T. Tomasi, J. Chem. Phys. 52, 5270 (1970).

    Article  CAS  Google Scholar 

  176. H. E. Bethe and E. E. Salpeter, Quantum Mechanics of One- and Two-Electron Systems, Springer-Verlag, London (1957).

    Google Scholar 

  177. R. E. Moss, Advanced Molecular Quantum Mechanics, Chapman & Hall, London (1973).

    Book  Google Scholar 

  178. R. McWeeny, Methods of Molecular Quantum Mechanics, Academic Press, London (1978).

    Google Scholar 

  179. J. Almlöf and O. Gropen, Revs. Comput. Chem. 8, 203 (1996).

    Google Scholar 

  180. M. D. Miller, R. P. Sheridan, and S. K. Kearsley, J. Med. Chem. 42, 1505 (1999).

    Article  CAS  Google Scholar 

  181. G. Sello, J. Chem. Inf. Comput. Sci. 38, 691 (1998).

    Article  CAS  Google Scholar 

  182. D. D. Robinson, P. D. Lyne, and W. G. Richards, J. Chem. Inf. Comput. Sci. 39, 594 (1999).

    Article  CAS  Google Scholar 

  183. J. Mestres, D. C. Rohrer, and G. M. Maggiora, J. Comput. Chem. 18, 934 (1997).

    Article  CAS  Google Scholar 

  184. J. A. Grant, M. A. Gallardo, and B. T. Pickup, J. Comput. Chem. 17, 1653 (1996).

    Article  CAS  Google Scholar 

  185. M. J. Sippl and H. Stegbuchner, Comput. Chem. 15, 73 (1991).

    Article  CAS  Google Scholar 

  186. P. K. Redington, Comput. Chem. 16, 217 (1992).

    Article  CAS  Google Scholar 

  187. A. T. Brint and P. Willett, J. Chem. Inf. Comput. Sci. 27, 152 (1987).

    Article  CAS  Google Scholar 

  188. P. A. Bath, A. R. Poirrette, P. Willett, and F. H. Allen, J. Chem. Inf. Comput. Sci. 34, 141 (1994).

    Article  CAS  Google Scholar 

  189. D. J. Wild and P. Willett, J. Chem. Inf. Comput. Sci. 34, 224 (1994).

    Article  CAS  Google Scholar 

  190. D. A. Thorner, D. J. Wild, P. Willett, and P. M. Wright, J. Chem. Inf. Comput. Sci. 36, 900 (1996).

    Article  CAS  Google Scholar 

  191. S. Handschuh, J. Chem. Inf Comput. Sci. 38, 220 (1998).

    Article  CAS  Google Scholar 

  192. G. Bravi, E. Gancia, P. Mascagni, M. Pegna, R. Todeschini, and A. Zalianni, J. ComputAided Mol. Des. 11, 79 (1997).

    Article  CAS  Google Scholar 

  193. G. E. Kellogg, L. B. Kier, P. Gaillard, and L. H. Hall, J. Comput-Aided Mol. Des. 10, 513 (1996).

    Article  CAS  Google Scholar 

  194. F. H. Allen, S. Bellard, M. D. Brice, B. A. Cartwright, et al., Acta Cryst. B35, 2331 (1979).

    CAS  Google Scholar 

  195. P. J. Artymiuk, P. A. Bath, H. M. Grindley, C. A. Pepperrell, et al., J. Chem. Inf. Comput. Sci. 32, 617 (1992).

    Article  CAS  Google Scholar 

  196. R. Attias, J. Chem. Inf. Comput. Sci. 23, 102 (1983).

    Article  CAS  Google Scholar 

  197. C. W. Crandell and D. H. Smith, J. Chem. Inf. Comput. Sci. 23, 186 (1983).

    Article  CAS  Google Scholar 

  198. J. K. Cringean and M. F. Lynch, J. Inf. Sci. 15, 211 (1989).

    Article  Google Scholar 

  199. A. J. Gushurst, J. G. Nourse, W. D. Houndshell, B. A. Leland, and D. G. Raich, J. Chem. Inf. Comput. Sci. 31, 447 (1991).

    Article  CAS  Google Scholar 

  200. T. R. Hagadone, J. Chem. Inf. Comput. Sci. 32, 515 (1992).

    Article  CAS  Google Scholar 

  201. E. M. Rasmussen, G. M. Downs, and P. Willett, J. Comput. Chem. 9, 378 (1988).

    Article  CAS  Google Scholar 

  202. P. Willet, J. Chem. Inf. Comput. Sci. 25, 114 (1985).

    Article  Google Scholar 

  203. P. Willet, J. Inf. Sci. 15, 223 (1989).

    Article  Google Scholar 

  204. P. Willet, V. Winterman, and D. Bawden, J. Chem. Inf. Comput. Sci. 26, 36 (1983).

    Google Scholar 

  205. P. Willet, V. Winterman, and D. Bawden, J. Chem. Inf. Comput. Sci. 26, 109 (1983).

    Google Scholar 

  206. H. Zhang, M. Minoh, and K. Ikeda, J. Inf. Proc. 15, 108 (1992).

    Google Scholar 

  207. E. Garcia and L. M. Reyes, J. Mol. Struct. (Theochem) 101, 101 (1993).

    Google Scholar 

  208. P. Kuner and B. Ueberreiter, Int. J. Pat. Recog. Art. Intel. 2, 527 (1988).

    Article  Google Scholar 

  209. E. Bienenstock and C. von der Malsburg, Europhys. Lett. 4, 4 (1987).

    Article  Google Scholar 

  210. R. Sitaraman and A. Rosenfeld, Patt. Recog. 22, 331 (1989).

    Article  Google Scholar 

  211. A. Tomlin (ed.), The Pesticide Manual: a World Compendium:Incorporating the Agrochemicals Handbook, Royal Society of Chemistry, London (1995).

    Google Scholar 

  212. B. Böhm, J. Stürzbecher, and G. Klebe, J. Med. Chem. 42, 458 (1999).

    Google Scholar 

  213. W. E. Lorensen and H. E. Cline, Comput. Graphics 21, 163 (1987).

    Article  Google Scholar 

  214. A. Watt and M. Watt, Advanced Animation and Rendering Techniques, Addison-Wesley, Reading (1992).

    Google Scholar 

  215. Marching cubes algorithm Internet site: http://exaflop.org/docs/marchcubes

  216. Marching cubes algorithm Internet site: http://panda.uchc.edu/htbit/indiv/software_docs/marching_cubes.html

  217. A Fortran 90 procedure for the MCA can be downloaded from: http://iqc.udg.es/cat/similarity/ASA/mca.html

  218. GiD, Geometry and Data, a pre/post processor graphical interface. Internet site: http://gatxan.upc.es. International Center for Numerical Methods in Engineering (CIMNE), Barcelona (1999).

  219. X. Gironés, L. Amat, and R. Carbó-Dorca, J. Mol. Graph. Model. 16, 190 (1998).

    Google Scholar 

  220. I. M. Vinogradov (ed.) Encyclopaedia of Mathematics, Vol. 7, Reidel-Kluwer, Dordrecht (1987).

    Google Scholar 

  221. R. Carbó-Dorca and K. D. Sen, J. Mol. Struct. (Theochem), 501, 173 (2000).

    Article  Google Scholar 

  222. C. Roos, T. Terlaky, and J.-P. Vial, Theory and Algorithms for Linear Optimization, Wiley, New York (1997).

    Google Scholar 

  223. I. M. Vinogradov (ed.) Encyclopaedia of Mathematics, Vol. 4, Kluwer, Dordrecht (1989).

    Google Scholar 

  224. LF 95 Language Reference, Lahey Computer Systems, Incline Village NV (1998). For more details browse at: http://www.lahey.com.

    Google Scholar 

  225. R. Carbci-Dorca, J. Math. Chem. 23, 365 (1998).

    Article  Google Scholar 

  226. H. Eyring, J. Walter, and G. E. Kimball, Quantum Chemistry, Wiley, New York (1940).

    Google Scholar 

  227. L. Pauling and E. B. Wilson Jr., Introduction to Quantum Mechanics, Dover, New York (1985).

    Google Scholar 

  228. For a recent matrix formulation, see: E. Besalú and R. Carbó-Dorca, J. Math. Chem. 22, 85 (1997).

    Article  Google Scholar 

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Carbó-Dorca, R., Amat, L., Besalú, E., Gironés, X., Robert, D. (2001). Quantum Molecular Similarity: Theory and Applications to the Evaluation of Molecular Properties, Biological Activities and Toxicity. In: Carbó-Dorca, R., Gironés, X., Mezey, P.G. (eds) Fundamentals of Molecular Similarity. Mathematical and Computational Chemistry. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-3273-3_12

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