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Using molecular electrostatic potential maps for similarity studies

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Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 174))

Abstract

In this work the use of molecular electrostatic potential (MEP) maps for similarity studies is reviewed in light of the latest results. First, methods of obtaining MEP maps is overviewed. The methodology, reliability and the efficiency of calculations based on semi-empirical as well as ab initio methods are discussed in detail. Point-charge models and multipole expansion methods which provide MEP maps of satisfactory quality are evaluated critically. Later on, similarity indices of various kinds are analyzed, compared and examples of their use are shown. Finally, the last section lists and summarizes software packages capable of calculating MEP map based similarity indices.

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6 References

  1. Johnson MA, Maggiora GM (eds) (1990) Concepts and applications of molecular similarity. John Wiley and Sons, New York

    Google Scholar 

  2. Richards WG (1989) Computer-aided molecular design. IBC Technical Services, London

    Google Scholar 

  3. Náray-Szabó G (1989) J Mol Graphics 7: 76

    Google Scholar 

  4. Dean PM (1987) Molecular foundations of drug-receptor interaction. Cambridge University Press, Cambridge

    Google Scholar 

  5. Scrocco E, Tomasi J (1978) Adv Quantum Chem 11: 115

    Google Scholar 

  6. Westbrook JD, Levy RM, Krogh-Jespersen K (1992) J Comp Chem 13: 979

    Google Scholar 

  7. Weinstein H, Politzer P, Srebrenik S (1975) Theor Chim Acta 38: 159

    Google Scholar 

  8. Sen KD, Politzer P (1989) J Chem Phys 90: 4370

    Google Scholar 

  9. Pathak RK, Gadre SR (1990) J Chem Phys 93: 1770

    Google Scholar 

  10. Silberbach, H (1991) J Chem Phys 94: 8638

    Google Scholar 

  11. Shirsat RN, Bapat SV, Gadre SR (1992) Chem Phys Lett 200: 373

    Google Scholar 

  12. Scrocco E, Tomasi J (1973) Topics in Current Chemistry 42: 95

    Google Scholar 

  13. Politzer P, Daiker KC (1981) In: Deb BM (ed) The force concept in chemistry. Van Nostrand Reinhold Co., New York, p 294

    Google Scholar 

  14. Politzer P, Truhlar DG (eds) (1981) Chemical applications of atomic and molecular electrostatic potentials. Plenum Press, New York

    Google Scholar 

  15. Poltizer P, Murray JS (1991) In: Lipkowitz KB, Boyd DB (eds) Reviews in Computational Chemistry II. VCH, New York, p 273

    Google Scholar 

  16. Johnson BG, Gill PMW, Pople JA (1993) Chem Phys Lett 206: 239

    Google Scholar 

  17. Gadre SR, Bapat SV, Sundararajan K, Shrivastava IH (1990) Chem Phys Lett 175: 307

    Google Scholar 

  18. Gadre SR, Bapat S, Shrivastava I (1991) Comput Chem 15: 203

    Google Scholar 

  19. Frisch MJ, Trucks GW, Head-Gordon M, Gill PMW, Wong MW, Foresman JB, Johnson BG, Schlegel HB, Robb MA, Reploge ES, Gomperts R, Andres JL, Raghavachari K, Binkley JS, Gonzalez C, Martin RL, Fox DJ, DeFrees DJ, Baker J, Stewart JJP, Pople JA (1992) Gaussian 92, Gaussian, Inc., Pittsburg, PA

    Google Scholar 

  20. Pople JA, Santry DL, Segal GA (1965) J Chem Phys 43: S129; Pople JA, Segal GA (1965) J Chem Phys 43: S136; Pople JA, Segal GA (1966) J Chem Phys 44: 3289

    Google Scholar 

  21. Pople JA, Beveridge DL, Dobosh PA (1967) J Chem Phys 47: 2026

    Google Scholar 

  22. Giessner-Prettre C, Pullman A (1972) Theor Chim Acta 25: 83

    Google Scholar 

  23. Löwdin PO (1970) J Chem Phys 56: 365

    Google Scholar 

  24. Chung-Phillips A (1989) J Comp Chem 10: 17

    Google Scholar 

  25. Politzer P (1977) In: Rheingold AL (ed) Homoatomic rings, chains, and macromolecules of main-group elements, Elsevier, Amsterdam, p 95

    Google Scholar 

  26. Ridley JE, Zerner MC (1973) Theor Chim Acta 32: 111

    Google Scholar 

  27. Culberson JC, Zerner MC (1985) Chem Phys Lett 122: 436

    Google Scholar 

  28. Bonaccorsi R, Pullman A, Scrocco E, Tomasi J (1972) Theor Chim Acta 24: 51

    Google Scholar 

  29. Benoit RL, Fréchette M (1986) Can J Chem 64: 2348

    Google Scholar 

  30. Del Bene JE (1983) J Phys Chem 87: 367

    Google Scholar 

  31. Ford GP, Wang B (1993) J Comp Chem 14: 1101

    Google Scholar 

  32. Dewar MJS, Thiel W (1977) J Am Chem Soc 99: 4899

    Google Scholar 

  33. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107: 3902

    Google Scholar 

  34. Stewart JJP (1989) J Comp Chem 10: 209, 221

    Google Scholar 

  35. Pople JA, Beveridge DL (1970) Approximate molecular orbital theory, McGraw-Hill, New York

    Google Scholar 

  36. Hehre WJ, Radom L, Schleyer PR, Pople JA (1986) Ab initio molecular orbital theory, Wiley, New York

    Google Scholar 

  37. Luque FJ, Illas F, Orozco M (1990) J Comp Chem 11: 416

    Google Scholar 

  38. Luque FJ, Orozco M (1990) Chem Phys Lett 168: 269

    Google Scholar 

  39. Alemán C, Luque FJ, Orozco M (1993) J Comp Chem 14: 799

    Google Scholar 

  40. Ferenczy GG, Reynolds CA, Richards WG (1990) J Comp Chem 11: 159

    Google Scholar 

  41. Reynolds CA, Ferenczy GG, Richards WG (1992) J Mol Struct (Theochem) 256: 249

    Google Scholar 

  42. Tasi G, Kiricsi I, Förster H (1991) Magy Kém Foly 97: 441

    Google Scholar 

  43. Tasi G, Kiricsi I, Förster H (1992) J Comp Chem 13: 371

    Google Scholar 

  44. Tasi G, Pálinkó I, Nyerges L, Fejes P, Förster H (1993) J Chem Inf Comput Sci 33: 296

    Google Scholar 

  45. Bingham RC, Dewar MJS, Lo H (1975) J Am Chem Soc 97: 1285

    Google Scholar 

  46. Tasi G, Pálinkó I, Halász J Náray-Szabó G (1992) Semiempirical quantum chemical calculations on microcomputers. CheMicro Ltd, Budapest

    Google Scholar 

  47. Nelder JA, Mead R (1965) Comput J 7: 308

    Google Scholar 

  48. Cummins PL, Gready JE (1990) Chem Phys Lett 174: 355

    Google Scholar 

  49. Parr RG, Yang W (1989) Density functional theory of atoms and molecules. Oxford University Press, New York

    Google Scholar 

  50. Murray JS, Seminario JM, Concha MC, Politzer P (1992) Int J Qunatum Chem 44: 113

    Google Scholar 

  51. Fliszár S (1983) Charge distributions and chemical effects. Springer-Verlag, Berlin

    Google Scholar 

  52. Bowen JP, Allinger NL (1991) In: Lipkowitz KB, Boyd DB (eds) Reviews in Computational Chemistry II. VCH, New York, p 81

    Google Scholar 

  53. McCammon JA, Harvey SC (1987) Dynamics of proteins and nucleic acids. Cambridge University Press, Cambridge

    Google Scholar 

  54. Montagnani R, Tomasi J (1993) J Mol Struct (Theochem) 279: 131; Kozaki T, Morihashi K, Kikuchi O (1988) J Mol Struct 168: 265

    Google Scholar 

  55. Hall GG (1985) Adv Atomic Mol Phys 20: 41

    Google Scholar 

  56. Williams DE, Yan Y-M (1988) Adv Atomic Mol Phys 23: 87

    Google Scholar 

  57. Williams DE (1991) In: Lipkowitz KB, Boyd DB (eds) Reviews in Computational Chemistry II. VCH, New York, p 219

    Google Scholar 

  58. Momany FA (1978) J Phys Chem 83: 592

    Google Scholar 

  59. Cox SR, Williams DE (1981) J Comp Chem 2: 304

    Google Scholar 

  60. Singh UC, Kollman PA (1984) J Comp Chem 5: 129

    Google Scholar 

  61. Chirlian LE, Francl MM (1987) J Comp Chem 8: 894

    Google Scholar 

  62. Woods RJ, Khalil M, Pell W, Moffat SH, Smith VH, Jr. (1990) J Comp Chem 11: 297

    Google Scholar 

  63. Besler BH, Merz, KM, Jr., Kollman PA (1990) J Comp Chem 11: 431

    Google Scholar 

  64. Orozco M, Luque FJ (1990) J Comp Chem 11: 909

    Google Scholar 

  65. Chipot C, Maigret B, Rivail J-L, Scheraga HA (1992) J Phys Chem 96: 10276

    Google Scholar 

  66. Merz KM, Jr. (1992) J Comp Chem 13: 749

    Google Scholar 

  67. Bertsekas DP (1982) Constrained optimization and Lagrange multiplier methods. Academic Press, New York

    Google Scholar 

  68. Williams DE, Weller RR (1983) J Am Chem Soc 105: 4143

    Google Scholar 

  69. Breneman CM, Wiberg KB (1990) J Comp Chem 11: 361

    Google Scholar 

  70. Connolly M (1982) QCPE Program 429

    Google Scholar 

  71. Richard AM (1991) J Comp Chem 12: 959

    Google Scholar 

  72. Lee J-G. Friesner RA (1993) J Phys Chem 97: 3515

    Google Scholar 

  73. Orozco M, Luque FJ (1990) J Comput-Aided Mol Des 4: 441

    Google Scholar 

  74. Náray-Szabó G, Ferenczy GG (1992) J Mol Struct (Theochem) 261: 55; Ferenczy GG, Rivail J-L, Surján P, Náray-Szabó G (1992) J Comp Chem 13: 830

    Google Scholar 

  75. Su Z (1993) J Comp Chem 14: 1036

    Google Scholar 

  76. Coppens P (1992) Annu Rev Phys Chem 43: 663

    Google Scholar 

  77. RATTLER, Oxford Molecular Ltd, The Magdalen Centre, Oxford Science Park, Sandford-on-Thames, Oxford OX4 4GA, United Kingdom

    Google Scholar 

  78. Merz KM, Besler BH (1990) MOPAC-ESP, QCPE program 589

    Google Scholar 

  79. Mulliken RS (1955) J Chem Phys 23: 1833

    Google Scholar 

  80. Szabó A, Ostlung NS (1982) Modern quantum chemistry. Macmillan, New York

    Google Scholar 

  81. Huzinaga S, Sakai Y, Miyoshi E, Narita S (1990) J Chem Phys 93: 3319

    Google Scholar 

  82. Surján PR (1989) Second quantized approach to quantum chemistry. Springer-Verlag, Berlin

    Google Scholar 

  83. Mayer I (1983) Chem Phys Lett 97: 270

    Google Scholar 

  84. Rauhut G, Clark T (1993) J Comp Chem 14: 503

    Google Scholar 

  85. Foster JP, Weinhold F (1980) J Am Chem Soc 102: 7211

    Google Scholar 

  86. Ferenczy GG (1991) J Comp Chem 12: 913

    Google Scholar 

  87. Stone AJ (1981) Chem Phys Lett 83: 233; Stone AJ, Price SL (1988) J Phys Chem 92: 3325

    Google Scholar 

  88. Chipot C, Ángyán JG, Ferenczy GG, Scheraga HA (1993) J Phys Chem 97: 6628

    Google Scholar 

  89. Sawaryn A, Sokalski WA (1989) Comp Phys Comm 52: 397

    Google Scholar 

  90. Sokalski WA, Shibata M, Ornstein RL, Rein R (1993) Theor Chim Acta 85: 209

    Google Scholar 

  91. Sokalski WA, Hariharan PC, Kaufmann JJ (1987) Int J Quantum Chem, Quantum Biol Symp 14: 111

    Google Scholar 

  92. Sokalski WA, Maruszewski K, Hariharan PC, Kaufmann JJ (1989) Int J Quantum Chem, Quantum Biol Symp 16: 119

    Google Scholar 

  93. Sokalski WA, Poirier RA (1983) Chem Phys Lett 98: 86

    Google Scholar 

  94. Sokalski WA, Sawaryn A (1987) J Chem Phys 87: 526

    Google Scholar 

  95. Vigne-Maeder F, Claverie P (1988) J Chem Phys 88: 4934

    Google Scholar 

  96. Mezei M, Campbell ES (1977) Theor Chim Acta 43: 227

    Google Scholar 

  97. Spackman MA (1986) J Chem Phys 85: 6587

    Google Scholar 

  98. Sokalski WA, Sneddon SF (1991) J Mol Graphics 9: 74

    Google Scholar 

  99. Carbo R, Leyda L, Arnau M (1980) Int J Quantum Chem 17: 1185

    Google Scholar 

  100. Carbo R, Domingo L (1987) Int J Quantum Chem 32: 517

    Google Scholar 

  101. Carbo R, Calabuig B (1989) Comp Phys Comm 55: 117

    Google Scholar 

  102. Bowen-Jenkins PE, Cooper DL, Richards WG (1985) J Phys Chem 89: 2195

    Google Scholar 

  103. Hodgkin EE, Richards WG (1986) J Chem Soc, Chem Commun 1342

    Google Scholar 

  104. Hodgkin EE, Richards WG (1987) Int J Quantum Chem, Quantum Biol Symp 14: 105

    Google Scholar 

  105. Stewart JJP (1983) QCPE Bull 3: 43

    Google Scholar 

  106. Dewar MJS, McKee ML, Rzepa HS (1978) J Am Chem Soc 100: 3607

    Google Scholar 

  107. Dewar MJS, Reynolds CH (1986) J Comp Chem 7: 140

    Google Scholar 

  108. Burt C, Richards WG, Huxley P (1990) J Comp Chem 11: 1139

    Google Scholar 

  109. Burkert U, Allinger NL (1982) Molecular Mechanics. Am Chem Society, Washington, DC

    Google Scholar 

  110. Burt C, Richards WG (1990) J Comput-Aided Mol Des 4: 231

    Google Scholar 

  111. Reynolds CA, Essex JW, Richards WG (1992) J Am Chem Soc 114: 9075; Colonna F, Evleth EM (1993) Chem Phys Lett 212: 665

    Google Scholar 

  112. Sanz F, Manaut F, Sanchez JA, Lozoya E (1991) J Mol Struct. (Theochem) 230: 437

    Google Scholar 

  113. Good AC, Hodgkin EE, Richards WG (1992) J Chem Inf Comput Sci 32: 188

    Google Scholar 

  114. Namasivayam S, Dean PM (1986) J Mol Graphics 4: 46; Dean PM, Callow P, Chau P-L (1988) J Mol Graphics 6: 28

    Google Scholar 

  115. Manaut F, Sanz F, José J, Milesi M (1991) J Comput-Aided Mol Des 5: 371

    Google Scholar 

  116. Petke JD (1993) J Comp Chem 14: 928

    Google Scholar 

  117. Reynolds CA, Burt C, Richards WG (1992) Quant Struct-Activ Relat 11: 34

    Google Scholar 

  118. Good AC (1992) J Mol Graphics 10: 144

    Google Scholar 

  119. ASP (Automated Similarity Package), Oxford Molecular Ltd, The Magdalen Centre, Oxford Science, Park, Sandford-on-Thames, Oxford OX4 4GA, United Kingdom

    Google Scholar 

  120. Mezey PG (1986) Int J Quantum Chem, Quantum Biol Symp 12: 113

    Google Scholar 

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Kali Das Sen

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© 1995 Springer-Verlag

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Tasi, G., Pálinkó, I. (1995). Using molecular electrostatic potential maps for similarity studies. In: Sen, K.D. (eds) Molecular Similarity II. Topics in Current Chemistry, vol 174. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-58672-5_23

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  • DOI: https://doi.org/10.1007/3-540-58672-5_23

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