Advertisement

Non-empirical Pair Potentials for the Interaction Between Amino Acids

  • J. A. Sordo
  • M. Probst
  • Steven Chin
  • G. Corongiu
  • Enrico Clementi

Abstract

A pair potential describing the potential hypersurface between interacting aliphatic amino acids (without sulphur) is presented. This pair potential has been derived entirely from ab initio calculations at the Hartree-Fock level. Almost two thousand SCF calculations have been performed and used as input for a nonlinear least-squares fitting in order to obtain the parameters for the atom-atom analytical pair potential.

Keywords

Interaction Energy Monte Carlo Carboxylic Group Carbonyl Oxygen Pair Potential 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    E. Clementi, “Lecture Notes in Chemistry” (and references therein), 19, Springer Verlag (1980).Google Scholar
  2. 2.
    A. Pullman, ed., “From Diatomics to Biopolymers,” John Wiley & Sons (1978).Google Scholar
  3. 3.
    A. Pullman, Fortschr. Chem. Forsch., 31, 45, (1972).CrossRefGoogle Scholar
  4. 4.
    B. Melly and A. Pullman, C.R. Acad. Sci., 274, 1371, (1972).Google Scholar
  5. 5.
    A. Momamy, R.F. McGuire, A.W. Burguess and H.A. Scheraga, J. Chem. Phys., 78, 1595 (1974); ibid., 79, 2361, (1975)CrossRefGoogle Scholar
  6. L.L. Shipman, A.W. Burgess and H.A. Scheraga, Proc. Natl. Acad. Sci. U.S.A., 72, 543, 854 (1975).PubMedCrossRefGoogle Scholar
  7. 6.
    W.L. Jorgensen and J. Gao, J. Am. Chem. Soc. (and references therein), 90, 2174, (1986).Google Scholar
  8. 7.
    E. Clementi, F. Cavallone and J. Scordamaglia, J. Am. Chem. Soc., 99, 5531 (1977); ibid. 99, 5545 (1977).PubMedCrossRefGoogle Scholar
  9. 8.
    G. Bolis and E. Clementi, J. Am. Chem. Soc., 99, 5550 (1977).PubMedCrossRefGoogle Scholar
  10. 9.
    S. Fraga, J. Comput. Chem., 3, 329 (1982); Comput. Phys. Commun., 29, 351 (1983).CrossRefGoogle Scholar
  11. 10.
    J.A. Sordo, M. Klobukowski and S. Fraga, J. Am. Chem. Soc., 107, 7569 (1985).CrossRefGoogle Scholar
  12. 11.
    Romano, S. and Clementi, E., Gazz. Chim. Ital., 108, 319, 1978.Google Scholar
  13. 12.
    S. Romano and E. Clementi, Int. J. Quantum Chem., 14, 839 (1978); ibid. 17, 1007 (1980).CrossRefGoogle Scholar
  14. 13.
    J. Snir, R.A. Nemenoff and H.A. Scheraga, J. Chem. Phys., 82, 2498 (1978).Google Scholar
  15. 14.
    O. Matsuoka, E. Clementi and M. Yoshimine, J. Chem. Phys., 64, 1351 (1976).CrossRefGoogle Scholar
  16. 15.
    E. Clementi and G. Corongiu, Int. J. Quantum Chem.: Quantum Biology Symposium, 10, 31 (1983).Google Scholar
  17. 16.
    J. Detrich, G. Corongiu and E. Clementi, Chem. Phys. Lett., 112, 426 (1984).CrossRefGoogle Scholar
  18. 17.
    G. Bolis, E. Clementi, H.A. Scheraga, H. Wertz and C. Tosi, J. Am. Chem. Soc., 105, 355 (1983).CrossRefGoogle Scholar
  19. 18.
    C.A. Venanzi, H. Weinstein, G. Corongiu and E. Clementi, Int. J. Quantum Chem., 9, 355 (1982).Google Scholar
  20. 19.
    E. Clementi, G. Corongiu, B. Jonsson and S. Romano, J. Chem. Phys., 72, 260 (1980).CrossRefGoogle Scholar
  21. 20.
    G. Corongiu, S.L. Fornili and E. Clementi, Int. J. Quantum Chem., 10, 277 (1983).Google Scholar
  22. 21.
    G. Ranghino, E. Clementi and S. Romano, Biopolymers, 22, 1449 (1983).CrossRefGoogle Scholar
  23. 22.
    M. Ragazzi, D.R. Ferro and E. Clementi, J. Chem. Phys., 70, 1040 (1979).CrossRefGoogle Scholar
  24. 23.
    G. Bolis and E. Clementi, Chem. Phys. Letters, 82, 147 (1981).CrossRefGoogle Scholar
  25. 24.
    G. Bolis, G. Corongiu and E. Clementi, Chem. Phys. Letters, 86, 299 (1982).CrossRefGoogle Scholar
  26. 25.
    S.L. Fornili, D.P. Vercauteren and E. Clementi, J. Biomolecular Struct. and Dynamics, 1, 1281 (1984).CrossRefGoogle Scholar
  27. 26.
    K.S. Kim, D.P. Vercauteren, M. Welti, S. Chin and E. Clementi, Biophysical J., 47, 327 (1985).CrossRefGoogle Scholar
  28. 27.
    L. Carozzo, G. Corongiu, C. Petrongolo, J. Chem. Phys., 68, 787 (1978).CrossRefGoogle Scholar
  29. 28.
    E. Clementi and G. Corongiu, J. Chem. Phys., 72, 3979 (1980).CrossRefGoogle Scholar
  30. 29.
    E. Clementi and G. Corongiu, Biopolymers, 18, 2431 (1979).PubMedCrossRefGoogle Scholar
  31. 30.
    E. Clementi and G. Corongiu, Int. J. Quantum Chem., 16, 897 (1979).CrossRefGoogle Scholar
  32. 31.
    E. Clementi and G. Corongiu, Chem. Phys. Letters, 60, 175 (1979).CrossRefGoogle Scholar
  33. 32.
    E. Clementi and G. Corongiu, Biopolymers, 21, 175 (1982).CrossRefGoogle Scholar
  34. 33.
    E. Clementi and G. Corongiu, Proceedings of the second SUNYA Conversation in the Discipline Biomolecular Stereodynamics, Vol. I, R.H. Sharma, ed., Adenine Press, NY (1982).Google Scholar
  35. 34.
    K.S. Kim and E. Clementi, J. Am. Chem. Soc., 102, 227 (1985).CrossRefGoogle Scholar
  36. 35.
    W.J. Hehre, R.F. Stewart and J.A. Pople, J. Chem. Phys., 51, 2657 (1969).CrossRefGoogle Scholar
  37. 36.
    L. Gianolio, R. Pavani and E. Clementi, Gazz. Chim. Ital., 108, 181 (1978).Google Scholar
  38. 37.
    M.J. Frisch, J.E. Del Bene, J.S. Binkley and HF Shaefer III, J. Chem. Phys., 84, 2279 (1986).CrossRefGoogle Scholar
  39. 38.
    D.W. Schwenke and D.G. Truhlar, J. Chem. Phys., 82, 2418 (1985).CrossRefGoogle Scholar
  40. 39.
    H.H. Greenwood and J.S. Plant, Int. J. Quantum Chem., 30, 127 (1986).CrossRefGoogle Scholar
  41. 40.
    M.M. Szczesniak and S. Scheiner, J. Chem. Phys., 84, 6328 (1986).CrossRefGoogle Scholar
  42. 41.
    R. Bonaccorsi, R. Cammi and J. Tornasi, Int. J. Quantum Chem., 29, 373 (1986).CrossRefGoogle Scholar
  43. 42.
    For an extended review on basis sets we refer to the very recent work by E.R. Davidson and D. Feller, Chem. Rev., 86., 681 (1986).CrossRefGoogle Scholar
  44. 43.
    W. Kolos, Theoret. Chim. Acta (Berl.), 51, 219 (1979).CrossRefGoogle Scholar
  45. 44.
    E. Clementi, J. Phys. Chem., 89, 4426 (1985).CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • J. A. Sordo
    • 1
    • 2
  • M. Probst
    • 1
    • 3
  • Steven Chin
    • 1
  • G. Corongiu
    • 1
  • Enrico Clementi
    • 1
  1. 1.Data Systems Division, Dept. 48B/MS 428IBM CorporationKingstonUSA
  2. 2.Departamento de Quimica FisicaUniversidad de OviedoOviedoSpain
  3. 3.Institute of Inorganic and Analytical ChemistryUniversity of InnsbruckInnsbruckAustria

Personalised recommendations