Advertisement

Theoretical Studies on the Conformation of Peptides in Solution

II: Conformations of N-Acetyl L-Alanine N-Methyl Amide in CC14and H20 and N-Acetyl Glycine N-Methyl Amide in CC14
  • V. Renugopalakrishnan
  • S. Nir
  • Robert Rein
Part of the The Jerusalem Symposia on Quantum Chemistry and Biochemistry book series (JSQC, volume 8)

Abstract

A procedure for a theoretical prediction of most preferred conformations of molecules in solutions is described and applied for N-acetyl L-alanine N-methyl amide in CCI4 and in water and for N-acetyl glycine N-methyl amide in CCI4. The calculation of intrinsic, or intramolecular energies, employs the method of partitioned energy potential, including electrostatic, nonbonded and torsional terms. The intramolecular electrostatic energies include terms up to segmental octopole moments. Convergence of the electrostatic series is always obtained when all distances between interacting groups are not appreciably less than the sum of corresponding van der Waals radii. The calculation of intermolecular interactions with the environment is based on the method of continuum reaction field, including electrostatic, dispersion and cavity terms, which depend on the conformations through molecular dipole moments, molecular volume, and molecular exposed surface area. The most stable conformations predicted and calculated dipole moment are in reasonable agreement with experimental findings. For the case of N-acetyl glycine N-methyl amide calculations of intramolecular energies with ab-initio (STO-3G) and IEHT/2 are also presented. It is concluded that in the cases treated in this study the partitioned potential method yields significantly better predictions for the stable conformations than the molecular orbital methods.

Keywords

Dipole Moment Solute Molecule Spherical Cavity Stable Conformation Molecular Dipole Moment 
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.
    Beveridge, D. L., Kelly, M. M., and Radna, R. J.: J. Am. Chem. Soc. 96, 3769 (1974).CrossRefGoogle Scholar
  2. 2.
    Sinanoglu, O.: in B. Pullman (ed.), Molecular Associations in Biology’, Academic Press, New York, 1968, pp. 427ff.Google Scholar
  3. 3.
    Rein, R., Renugopalakrishnan, V., Nir, S., and Swissler, T. J.: Int. J. Quantum Chem. (submitted).Google Scholar
  4. 4.
    Avignon, M., Huong, P. V., Lascombe, J., Marraud, M., and Neel, J.: Biopolymers 8, 69 (1969).CrossRefGoogle Scholar
  5. 5.
    Marraud, M., Neel, J., Avignon, M., and Huong, P. V.: J. Chim. Phys. 67, 959 (1970).Google Scholar
  6. 6.
    Thang, C. M., Canet, D., Granger, P., Marraud, M., and Neel, J.: Compt. Rend. Acad. Sci. (Paris) 269, 580 (1969).Google Scholar
  7. 7.
    Bystrov, V. F., Portnova, S. L., Tsetlin, V. I., Ivanov, V. T., and Ovchinnikov, V. A.: Tetrahedron 25, 493 (1969).CrossRefGoogle Scholar
  8. 8.
    Smolikova, J., Vitek, A., and Blaha, K.: Collection Czech. Chem. Comm. 36, 2474 (1971).Google Scholar
  9. 9.
    Ramachandran, G. N. and Sasisekharan, V.: in C. B. Anfinsen et al. (eds.), Adv. Protein Chemistry 23, Academic Press, New York, 1968, p. 283.Google Scholar
  10. 10.
    Scheraga, H. A.: Adv. in Physical Organic Chemistry 6, 103 (1968).CrossRefGoogle Scholar
  11. 11.
    Brant, D. A., Miller, W. G., and Flory, P. J.: J. Mol. Biol. 23, 47 (1967).CrossRefGoogle Scholar
  12. 12.
    DeSantis, P., Giglio, S., Liquori, A. M., and Ripamonti, A.: Nature 206, 456 (1965).CrossRefGoogle Scholar
  13. 13.
    Pullman, B. and Maigret, B.: in E. D. Bergmann and B. Pullman (eds.), Conformation of Biological Molecules and Polymers, The Israel Academy of Sciences and Humanities, Jerusalem, Israel 1973, p. 13.Google Scholar
  14. 14.
    Rein, R.: Adv. Quant. Chem. 2, 335 (1973).CrossRefGoogle Scholar
  15. 15.
    Rein, R., Swissler, T. J., Renugopalakrishnan, V., and Pack, G. R.: in E. D. Bergmann and B. Pullman (eds.), Conformation of Biological Molecules and Polymers, The Israel Acad. Sci. and Humanities, Jerusalem, Israel, 1973, p. 761.Google Scholar
  16. 16.
    Lassetre, E. and Dean, L.: J. Chem. Phys. 17, 317 (1949).CrossRefGoogle Scholar
  17. 17.
    Au-chin, Tang: Scientia Sinica III, 279 (1954); J. Chinese Chemical Soc. 18, 2 (1951).Google Scholar
  18. 18.
    Weiler-Fielchenfeld, H., Singerman, A., and Bergmann, E. D.: in E. D. Bergmann and B. Pullman (eds.), Conformation of Biological Molecules and Polymers, The Israel Academy of Sciences and Humanities, Jerusalem, Israel, 1973, p. 87.Google Scholar
  19. 19.
    Sinanoglu, O. and Abdulnur, S.: Photochem. Photobiol. 3, 333 (1964).CrossRefGoogle Scholar
  20. 20.
    Gibson, K. D. and Scheraga, H. A.: Proc. Nat. Acad. Sci. U.S. 58, 420 (1967).CrossRefGoogle Scholar
  21. 21.
    Hopfinger, A. J.: Macromolecules 4, 731 (1971).CrossRefGoogle Scholar
  22. 22.
    Venkatachalam, C. M. and Krimm, S.: in E. D. Bergmann and B. Pullman (eds.), Conformation of Biological Molecules and Polymers, The Israel Academy of Sciences and Humanities, Jerusalem, Israel, 1973, p. 141.Google Scholar
  23. 23.
    Alagona, G., Pullman, A., Scrocco, E., and Tomasi, J.: Int. J. Peptide and Protein Res. 5, 25 (1973).Google Scholar
  24. 24.
    Onsager, L.: J. Am. Chem. Soc. 58, 1486 (1936).CrossRefGoogle Scholar
  25. 25.
    Linder, B.: Adv. Chem. Phys. 12, 225 (1967).CrossRefGoogle Scholar
  26. 26.
    Nir, S.: Int. J. Quant. Chem., in press (1975).Google Scholar
  27. 27.
    Hermann, R. B.: J. Phys. Chem. 76, 2754 (1972).CrossRefGoogle Scholar
  28. 28.
    Marsh, R. E. and Donohue, J.: Adv. Protein Chem. 22, 235 (1967).CrossRefGoogle Scholar
  29. 29.
    Rein, R., Clarke, G. A., and Harris, F. E.: in E. D. Bergmann and B. Pullman (eds.), Quantum Aspects of Heterocyclic Compounds in Chemistry and Biochemistry, Israel Academy of Sciences and Humanities, Jerusalem, 1970, p. 86.Google Scholar
  30. 30.
    Nemethy, G. and Scheraga, H. A.: Biopolymers 3, 155 (1965).CrossRefGoogle Scholar
  31. 31.
    Kemp, J. D. and Pitzer, K. S.: J. Chem. Phys. 4, 749 (1936).CrossRefGoogle Scholar
  32. 32.
    Fowler, R. and Guggenheim, E. A.: Statistical Thermodynamics, Cambridge Univ. Press, London and New York, 1956.Google Scholar
  33. 33.
    Bondi, A.: J. Phys. Chem. 58, 929 (1954).CrossRefGoogle Scholar
  34. 34.
    Hill, T. L.: Statistical Mechanics, McGraw-Hill, New York and London, 1956.Google Scholar
  35. 35.
    Uhlig, H. H.: J. Phys. Chem. 41, 1215 (1937).CrossRefGoogle Scholar
  36. 36.
    Martin, A. R.: Phil. Mag. 8, 550 (1929); Trans Faraday Soc. 33, 191 (1937)Google Scholar
  37. 37.
    Bell, R. P.: Trans. Faraday Soc. 31, 1557 (1931).CrossRefGoogle Scholar
  38. 38.
    Kirkwood, J. G.: J. Chem. Phys. 2, 351 (1934).CrossRefGoogle Scholar
  39. 39.
    Bonnor, W. B.: Trans. Faraday Soc. 47, 1143 (1951).CrossRefGoogle Scholar
  40. 40.
    Bottcher, C. J. F.: Theory of Electric Polarization, Elsevier Publishing Co., Amsterdam, 1952.Google Scholar
  41. 41.
    Scholte, Th. Physica 15, 437 (1949).CrossRefGoogle Scholar
  42. 42.
    Scholte, Th. G.: Rec. Trav. Chim. 70, 50 (1951).CrossRefGoogle Scholar
  43. 43.
    Wada, A.: J. Chem. Phys. 22, 198 (1954).CrossRefGoogle Scholar
  44. 44.
    Stratton, J. A.: Electromagnetic Theory, McGraw-Hill, New York and London, 1940.Google Scholar
  45. 45.
    Shipman, L. L. and Scheraga, H. A.: J. Phys. Chem. 78, 909 (1974).CrossRefGoogle Scholar
  46. Nir, S.: Biophysical Society Abstracts 208a (1973).Google Scholar
  47. 47.
    Andersen, M., Painter, L. R., and Nir, S.: Biopolymers 13, 1261 (1974).CrossRefGoogle Scholar
  48. 48.
    Coumou, D. J.: Trans. Faraday Soc. 65, 2654 (1969).CrossRefGoogle Scholar
  49. 49.
    Nir, S., Adams, S., and Rein, R.: Int. J. Quant. Chem. 6, 295 (1972).CrossRefGoogle Scholar
  50. 50.
    Nir, S., Adams, S., and Rein, R.: J. Chem. Phys. 59, 3341 (1973).CrossRefGoogle Scholar
  51. 51.
    Denbigh, K. G.: Trans. Faraday Soc. 36, 936 (1940).CrossRefGoogle Scholar
  52. 52.
    LeFevre, R. J. W.: in V. Gold (ed.), Molecular Refractivity and Polarisability, in Adv. in Physical Organic Chem., Vol. 3, Academic Press, 1965.Google Scholar
  53. 53.
    Kihara, T.: Adv. Chem. Phys. 5, 147 (1963).CrossRefGoogle Scholar
  54. 54.
    Danon, F. and Pitzer, K. S.: J. Chem. Phys. 36, 425 (1962).CrossRefGoogle Scholar
  55. 55.
    Sinanoglu, O.: Adv. Chem. Phys. 12, 283 (1967).CrossRefGoogle Scholar
  56. 56.
    Linder, B.: J. Chem. Phys. 33, 668 (1960).CrossRefGoogle Scholar
  57. 57.
    Linder, B.: J. Chem. Phys. 35, 37 (1961).CrossRefGoogle Scholar
  58. 58.
    Pullman, A.: in R. Daudel and B. Pullman (eds.), (1974) The World of Quantum Chemistry, Reidel Publishing Co., Dordrecht-Holland, 1974, p. 239.CrossRefGoogle Scholar
  59. 59.
    Sinanoglu, O. and Abdulnur, S.: Fed. Proc, Fed. Am. Soc. Exp. Biol. 24, 5 (1965).Google Scholar
  60. 60.
    Sinanoglu, O.: Chem. Phys. Letters 1, 340 (1967).CrossRefGoogle Scholar
  61. 61.
    Linder, B.: J. Chem. Phys. 37, 963 (1962).CrossRefGoogle Scholar
  62. 62.
    Linder, B.: J. Chem. Phys. 40, 2003 (1964).CrossRefGoogle Scholar
  63. 63.
    Linder, B.: J. Chem. Phys. 44, 265 (1966).CrossRefGoogle Scholar
  64. 64.
    Callen, H. B. and Welton, T. A.: Phys. Rev. 83, 34 (1951).Google Scholar
  65. 65.
    Halicioglu, T. and Sinanoglu, O.: Ann. N.Y. Acad. Sci. 158, 308 (1969).CrossRefGoogle Scholar
  66. 66.
    Dewar, M. J. S.: Science 187, 1037 (1975).CrossRefGoogle Scholar
  67. 67.
    Hoffman, R. and Imamura, A.: Biopolymers 7, 207 (1969).CrossRefGoogle Scholar
  68. 68.
    Popov, E. M., Lipkind, G. M., Arkhipova, J. F., and Dashevskii, U. G.: Molecular Biol. 2, 622 (1968).Google Scholar
  69. 69.
    Neel, J.: Pure and Applied Chemistry 31, 201 (1972).CrossRefGoogle Scholar
  70. 70.
    Gibson, K. D. and Scheraga, H. A.: Biopolymers 3, 709 (1966).CrossRefGoogle Scholar
  71. 71.
    Momany, F. A., McGuire, R. F., Yan, J. F., and Scheraga, H. A.: J. Phys. Chem. 75, 2286 (1971).CrossRefGoogle Scholar
  72. 72.
    Maigret, B., Pullman, B., and Dreyfus, M.: J. Theor. Biol. 26, 321 (1970).CrossRefGoogle Scholar
  73. 73.
    Maigret, B., Pullman, B., and Perahia, D.: J. Theor. Biol. 31, 269 (1971).CrossRefGoogle Scholar
  74. 74.
    Iwasaki, F.: Acta Cryst. B30, 2503 (1974).Google Scholar

Copyright information

© D. Reidel Publishing Company, Dordrecht-Holland 1976

Authors and Affiliations

  • V. Renugopalakrishnan
    • 1
  • S. Nir
    • 2
  • Robert Rein
    • 3
  1. 1.Dept. of Chemistry, RutgersState University of New JerseyNewarkUSA
  2. 2.Roswell Park Memorial InstituteBuffaloUSA
  3. 3.Center for Theoretical BiologyState University of New York at BuffaloAmherstUSA

Personalised recommendations