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Mixed QM/MM molecular electrostatic potentials

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Abstract

A new method is presented for the calculation of the Molecular Electrostatic Potential (MEP) in large systems. Based on the mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach, the method assumes both a quantum and classical description for the molecule, and the calculation of the MEP in the space surrounding the molecule is made using this dual treatment. The MEP at points close to the molecule is computed using a full QM formalism, while a pure classical evaluation of the MEP is used for points located at large distances from the molecule. The algorithm allows the user to select the desired level of accuracy in the MEP, so that the definition of the regions where the MEP is computed at the classical or QM levels is adjusted automatically. The potential use of this QM/MM MEP in molecular modeling studies is discussed.

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References

  1. Bonaccorsi, R., Petrongolo, C., Scrocco, E. and Orozco, M., Theoret. Chim. Acta, 20 (1971) 331.

    Google Scholar 

  2. Bonaccorsi, R., Pullman, A., Scrocco, E. and Tomasi, J., Theoret. Chim. Acta, 24 (1972) 51.

    Google Scholar 

  3. Berthier, G., Bonaccorsi, R., Scrocco, E. and Tomasi, J., Theoret. Chim. Acta, 26 (1972) 101.

    Google Scholar 

  4. Scrocco, E. and Tomasi, J., Top. Curr. Chem., 42 (1973) 95.

    Google Scholar 

  5. Giessner-Prettre, C. and Pullman, A., Theoret. Chim. Acta, 25 (1972) 83.

    Google Scholar 

  6. Srebrenik, A., Weinstein, H. and Pauncz, R., Chem. Phys. Lett., 20 (1973) 419.

    Google Scholar 

  7. Politzer, P., J. Am. Chem. Soc., 207 (1980) 3027.

    Google Scholar 

  8. Ritchie, J.P., J. Am. Chem. Soc., 107 (1985) 1829.

    Google Scholar 

  9. Politzer, P. and Murray, J.S., In Murray, J.S. and Sen, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 649-660.

    Google Scholar 

  10. Oliveira Neto, M., J. Comput. Chem., 7 (1986) 617.

    Google Scholar 

  11. Gilson, M.K. and Honig, B., Proteins, 4 (1988) 7.

    Google Scholar 

  12. Murray, J.S. and Politzer, P., J. Org. Chem., 56 (1991) 6715.

    Google Scholar 

  13. Tomasi, J., Mennucci, B. and Cammi, R., In Murray, J.S. and Ken, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 1-85.

    Google Scholar 

  14. Luque, F.J., Barril, X. and Orozco, M., J. Comput.-Aided Mol. Design, 13 (1999) 139.

    Google Scholar 

  15. Spackman, M.A. and Stewart, R.F., In Politzer, P. and Truhlar, D.G. (Eds) Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum, New York, NY, 1981, pp. 407-415.

    Google Scholar 

  16. Weber, H.P. and Craven, B.M., Acta Crystallogr., B46 (1990) 532.

    Google Scholar 

  17. White, J.C. and Hess, A.C., J. Phys. Chem., 97 (1993) 6398.

    Google Scholar 

  18. Gadre, S.R., Bhadane, P.K., Pundlik, S.S. and Pingale, S.S., In Murray, J.S. and Ken, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 219-256.

    Google Scholar 

  19. Mishra, P.C. and Kumar, A., In Murray, J.S. and Sen, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 257-296.

    Google Scholar 

  20. Náray-Szabó, G. and Surjan, P.R., In Náray-Szabó, G. (Ed.) Theoretical Chemistry of Biological Systems, Elsevier, Amsterdam, 1986, pp. 1-30.

    Google Scholar 

  21. March, N.H., In Murray, J.S. and Sen, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 619-648.

    Google Scholar 

  22. Baeten, A., In Murray, J.S. and Sen, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 587-618.

    Google Scholar 

  23. Loew, G.H. and Berkowitz, D.S., J. Med. Chem., 18 (1975) 656.

    Google Scholar 

  24. Hayes, D.M. and Kollman, P.A., J. Am. Chem. Soc., 98 (1976) 335.

    Google Scholar 

  25. Hayes, D.M. and Kollman, P.A., J. Am. Chem. Soc., 98 (1976) 7861.

    Google Scholar 

  26. Weinstein, H., Osman, R., Topiol, S. and Green, J.P., Ann. N.Y. Acad. Sci., 367 (1981) 434.

    Google Scholar 

  27. Lavery, R. and Pullman, B., Int. J. Quantum Chem., 20 (1981) 259.

    Google Scholar 

  28. Kollman, P.A., McKelvey, J., Johansson, A. and Rothenberg, S., J. Am. Chem. Soc., 97 (1975) 955.

    Google Scholar 

  29. Scrocco, E. and Tomasi, J., Adv. Quant. Chem., 11 (1978) 115.

    Google Scholar 

  30. Tomasi, J., In Ratajczak, H. and Orville-Thomas, W.T. (Eds) Molecular Interactions, Vol. 3, Wiley, New York, NY, 1982, pp. 119-166.

    Google Scholar 

  31. Momany, F.A., J. Phys. Chem., 82 (1978) 592.

    Google Scholar 

  32. Williams, D.E., J. Comput. Chem., 9 (1988) 745.

    Google Scholar 

  33. Ferenzcy, G.G., Reynolds, C.A. and Richards, W.G., J. Comput. Chem., 11 (1990) 159.

    Google Scholar 

  34. Besler, B.H., Merz, K.M. and Kollman, P.A., J. Comput. Chem., 11 (1990) 431.

    Google Scholar 

  35. Cornell, W.D., Cieplak, P., Bayly, C.I. and Kollman, P.A., J. Am. Chem. Soc., 115 (1993) 9620.

    Google Scholar 

  36. Bonaccorsi, R., Scrocco, E., Petrongolo, C. and Tomasi, J., Theor. Chim. Acta., 20 (1984) 331.

    Google Scholar 

  37. Petrongolo, C. and Tomasi, J., Int. J. Quantum Chem., Quantum Biol. Symp., 2 (1975) 181.

    Google Scholar 

  38. Orozco, M., Canela, E.I. and Franco, R., Mol. Pharmacol., 35 (1989) 257.

    Google Scholar 

  39. Orozco, M., Canela, E.I. and Franco, R., Eur. J. Biochem., 188 (1990) 155.

    Google Scholar 

  40. Warshel, A. and Åqvist, J., Annu. Rev. Biophys. Biophys. Chem., 20 (1991) 267.

    Google Scholar 

  41. Náray-Szabó, G. and Nagy, P., Int. J. Quantum Chem., 35 (1989) 215.

    Google Scholar 

  42. Breneman, C.M. and Martinov, M., In Murray, J.S. and Sen, K. (Eds)Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 143-180.

    Google Scholar 

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

    Google Scholar 

  44. BesalÚ, E., Carbó, R., Mestres, J. and Solà, M., In Sen, K. (Ed.), Topics in Current Chemistry: Molecular Similarity I, Vol. 173, Springer-Verlag, Berlin, 1995, p. 31.

    Google Scholar 

  45. Rogríguez, J., Manault, F. and Sanz, F., J. Comput. Chem., 14 (1993) 922.

    Google Scholar 

  46. Sanz, F., López, E., Rodríguez, J. and Manault, F., Quant. Struct.-Act. Relat., 13 (1994) 281.

    Google Scholar 

  47. Sanz, F., Manaut, F., Rodríguez, J., Lozoya, E. and López, J., J. Comput.-Aided Mol. Design, 7 (1993) 337.

    Google Scholar 

  48. Charlton, M.K. and Thomson, C., J. Chem. Soc., Faraday Trans., 90 (1994) 3533.

    Google Scholar 

  49. Orozco, M. and Luque, F.J., J. Comput. Chem., 14 (1993) 587.

    Google Scholar 

  50. Orozco, M. and Luque, F.J., Biopolymers, 33 (1993) 1851.

    Google Scholar 

  51. Alhambra, C., Luque, F.J. and Orozco, M., J. Phys. Chem., 99 (1995) 3084.

    Google Scholar 

  52. Orozco, M. and Luque, F.J., In Murray, J.S. and Sen, K. (Eds) Molecular Electrostatic Potentials. Concepts and Applications, Elsevier, Amsterdam, 1996, pp. 181-218.

    Google Scholar 

  53. Francl, M.M., J. Phys. Chem., 89 (1985) 428.

    Google Scholar 

  54. Luque, F.J. and Orozco, M., J. Comput. Chem., 19 (1998) 866.

    Google Scholar 

  55. Cubero, E., Luque, F.J. and Orozco, M., Proc. Natl. Acad. Sci. USA, 95 (1998) 5976.

    Google Scholar 

  56. Colominas, C., Orozco, M., Luque, F.J., Borrell, J.I. and Teixidó, J., J. Org. Chem., 63 (1998) 4947.

    Google Scholar 

  57. Gao, J., Luque, F.J. and Orozco, M., to be published.

  58. Luque, F.J., Illas, F. and Orozco, M., J. Comput. Chem., 11 (1990) 446.

    Google Scholar 

  59. Ferenczy, G.G., Reynolds, C.A. and Richards, W.G., J. Comput. Chem., 11 (1990) 159.

    Google Scholar 

  60. Besler, B.H., Merz, K.M. and Kollman, P.A., J. Comput. Chem. 11, (1990) 431.

    Google Scholar 

  61. Wang, B. and Ford, G.P., J. Comput. Chem., 12 (1994) 200.

    Google Scholar 

  62. Alhambra, C., Luque, F.J. and Orozco, M., J. Comput. Chem., 15 (1994) 12.

    Google Scholar 

  63. Soliva, R., Orozco, M. and Luque, F.J., J. Comput. Chem., 18 (1997) 980.

    Google Scholar 

  64. Soliva, R., Luque, F.J. and Orozco, M., Theor. Chem. Acc., 98 (1997) 42.

    Google Scholar 

  65. Luque, F.J., Orozco, M., Illas, F. and Rubio, J., J. Am. Chem. Soc., 113 (1991) 5203.

    Google Scholar 

  66. Williams, D.E., J. Comput. Chem., 9 (1988) 745.

    Google Scholar 

  67. Williams, D.E., Biopolymers, 29 (1990) 1367.

    Google Scholar 

  68. Gadre, S.R. and Shrivastava, I.H., Chem. Phys. Lett., 204 (1993) 350.

    Google Scholar 

  69. Singh, U.C. and Kollman, P.A., J. Comput. Chem., 5 (1984) 129.

    Google Scholar 

  70. Chipot, C., Angyán, J.G., Ferenczy, G.G. and Scheraga, H.A., J. Phys. Chem., 97 (1993) 6628.

    Google Scholar 

  71. Williams, D.E., J. Comput. Chem., 15 (1994) 719.

    Google Scholar 

  72. Alemán, C., Orozco, M. and Luque, F.J., Chem. Phys., 189 (1994) 573.

    Google Scholar 

  73. Orozco, M. and Luque, F.J., J. Comput.-Aided Mol. Design, 4 (1990) 411.

    Google Scholar 

  74. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T.A., Petersson, G.A., Montgomery, J.A., Raghavachari, K., Al-Laham, M.A., Zakrzewski, V.G., Ortiz, J.V., Foresman, J.B., Cioslowski, J., Stefanov, B.B., Nanayakkara, A., Challacombe, M., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Anfres, J.L., Replogle, E.S., Gomperts, R., Martin, R.L., Fox, D.J., Binkley, J.S., Defress, D.J., Baker, J., Stewart, J.J.P., Head-Gordon, M., Gonzalez, C. and Pople, J.A., GAUSSIAN 94 (Rev. A.1), GAUSSIAN Inc., Pittsburgh, PA, 1995.

    Google Scholar 

  75. Luque, F.J., Alhambra, C. and Orozco, M., MOPETE-99, Universitat de Barcelona, 1999.

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Authors and Affiliations

  1. Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, E-08028, Barcelona, Spain

    Begoña Hernández & Modesto Orozco

  2. Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, E-08028, Barcelona, Spain

    F. Javier Luque

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  1. Begoña Hernández
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  2. F. Javier Luque
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  3. Modesto Orozco
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Hernández, B., Luque, F.J. & Orozco, M. Mixed QM/MM molecular electrostatic potentials. J Comput Aided Mol Des 14, 329–339 (2000). https://doi.org/10.1023/A:1008111820916

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