PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid

Journal of Computer-Aided Molecular Design

Volumn 12, Issue 3, 1998, Pages 259-273

  Alemán, Carlos ^a   Casanovas, Jordi ^b   Galembeck, Sergio E ^c  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b UNIVERSITAT ROVIRA I VIRGILI   (Spain)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Homopeptides; MM and MD techniques; Parametrization

Indexed keywords

DENSITY FUNCTIONAL THEORY; HYDROGEN BONDS; QUANTUM THEORY;

1-AMINO-CYCLOPROPANE- 1-CARBOXYLIC ACIDS; AB INITIO; APPROXIMATE PARAMETRIZATION; CONFORMATIONAL STUDY; CYCLOPROPYL RING; HOMOPEPTIDES; MM AND MD TECHNIQUE; MOLECULAR SYSTEMS; PARAMETRIZATIONS; QUANTUM MECHANICAL;

CONFORMATIONS;

1 AMINOCYCLOPROPANECARBOXYLIC ACID; 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID; AMINO ACID; CYCLOPROPANE; CYCLOPROPANE DERIVATIVE; NEVIRAPINE; PEPTIDE;

ARTICLE; CHEMISTRY; PROTEIN CONFORMATION; QUANTUM THEORY;

AMINO ACIDS; AMINO ACIDS, CYCLIC; CYCLOPROPANES; NEVIRAPINE; PEPTIDES; PROTEIN CONFORMATION; QUANTUM THEORY;

EID: 0032060312     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1007908630431     Document Type: Article

References (85)

1. Karplus, M. and Petsko, G.A., Nature, 347 (1990) 631.
2. van Gunsteren, W.F. and Berendsen, H.J.C., Angew. Chem. Int. Ed. Engl., 29 (1990) 992.
3. Brooks, C.L. Karplus, M. and Pettit, B.M., Proteins: A theoretical Perspective of Dynamics, Structure and Thermodynamics, Wiley, New York, NY, 1988.
4. Allinger, N.L., J. Am. Chem. Soc., 99 (1977) 8127.
5. Lee, J.-H. and Allinger, N.L., J. Comput. Chem., 12 (1991) 186.
6. Weiner S.J., Kollman, P.A., Nguyen, D.T. and Case P.A., J. Comput. Chem., 7 (1986) 230.
7. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz Jr, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A., J. Am. Chem. Soc., 117 (1995) 5179.
8. Nilsson, L. and Karplus, M., J. Comput. Chem., 7 (1986) 591.
9. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.
10. Clark, M., Cramer III, R.D. and Opdenbosch, N., J. Comput. Chem., 10 (1989) 982.
11. Mommany, F.A., McGuire, R.F.M., Burgess, A.W. and Scheraga, H.A. J. Phys. Chem., 79 (1975) 2361.
12. Herman, J., .Berendsen, H.J.C., van Gunsteren, W.F. and Postma, J.P.M. Biopolymers, 23 (1984) 1513.
13. Hagler, A.T., Huler, E. and Lifson, S., J. Am. Chem. Soc., 96 (1974) 5319.
14. Hwang, M.J., Stockfisch, T.P. and Hagler, A.T., J. Am. Chem. Soc., 116 (1994) 2515.
15. For a recent review see: Orozco, M., Alemán, C. and Luque, F.J., Models Chem., 130 (1993) 695.
16. Dinur, U and Hagler, A.T., J. Am. Chem. Soc., 111 (1989) 5149.
17. Jorgensen, W.L., Brigs, J.M. and Contreras, M.L., J. Phys. Chem., 94 (1990) 1683.
18. Pranata, J., Wierschke, S.G. and Jorgensen, W.L., J. Am. Chem. Soc., 113 (1991) 2810.
19. Singh U.C. and Kollman P.A., J. Comput. Chem., 5 (1984) 191.
20. Cox, S.R. and Williams D.E., J. Comput. Chem., 5 (1984) 191.
21. Williams D.E., J. Comput. Chem., 7 (1988) 745.
22. Orozco, M. and Luque, F.J., J. Comput. Chem., 11 (1990) 909.
23. Alemán, C., Luque, F.J. and Orozco, M., J. Comput-Aided Mol. Design, 7 (1993) 721.
24. Bakowies, D. and Thiel W., J. Comput. Chem., 17 (1996) 87.
25. Park, J.E., Kwon, O.Y, No, K.T., Jhon, M.S. and Scheraga, H.A., J. Comput. Chem., 16 (1995) 1011.
26. Alhambra, C., Luque, F.J. and Orozco, M., J. Comput. Chem., 15 (1994) 12.
27. Fogarasi, G. and Pulay, P., Annu. Rev. Phys. Chem., 35 (1984) 191.
28. Maple, J.R., Dinur, U. and Hagler A.T., Proc. Natl. Acad. Sci. USA, 85 (1988) 5350.
29. Dinur, U. and Hagler, A.T., J. Comput. Chem., 11 (1990) 1234.
30. Leonard, J.M. and Ashman W.P., J. Comput. Chem., 11 (1990) 952.
31. Williams, R.W. and Lowreyl, A.H., J. Comput. Chem., 12 (1991) 761.
32. Challacombe, M. and Cioslowski, J., J. Chem. Phys., 95 (1991) 1064.
33. Hopfinger, A.J. and Pearlstein, R.A., J. Comput. Chem., 5 (1984) 486.
34. Alemán, C., Canela, E.I., Franco, R. and Orozco, M., J. Comput. Chem., 12 (1991) 664.
35. Alemán, C. and Orozco, M., J. Comput-Aided Mol. Design, 6 (1992) 331.
36. Allinger, N.L., Yuh, Y.H. and Lii, J.H., Am. Chem. Soc., 111 (1989) 8551.
37. DeClercq, E., J. Med. Chem., 38 (1995) 2491.
38. DeClercq, E., Med. Res. Rev., 13 (1993) 229.
39. Ren, J., Esnouf, R., Garman, E., Somers, D., Ross, C., Kirby, L, Keeling, J., Darby, G., Jones, Y., Stuart, D. and Stammers, D., Nat. Struct. Biol., 2 (1995) 293.
40. Toniolo, C. and Benedetti, E., Macromolecules, 24 (1991) 4004.
41. Benedetti, E., Di Blasio, B., Pavone, V., Pedone, C., Santini, A., Barone, V., Fraternali, F., Lelj, F., Bavoso, A., Crisma, M. and Toniolo, C., Int. J. Biol. Macromol., 11 (1989) 353.
42. Benedetti, E., Di Blasio, B., Pavone, V., Pedone, C., Santini, A., Crisma, M., Valle, G. and Toniolo, C., Biopolymers, 28 (1989) 175.
43. Alemán, C., J. Phys. Chem. B, 101 (1997) 5046.
44. Alemán, C., Subirana, J.A. and Pérez, J.J., Biopolymers, 32 (1992) 621.
45. Smythe, M.L, Huston, S.E. and Marshall, G.R., J. Am. Chem. Soc., 117 (1995) 5445.
46. Zhang, L. and Herman, J., J. Am. Chem. Soc., 116 (1994) 11915.
47. Alemán, C., Roca, R., Luque, F.J. and Orozco, M. Protein Struct. Funct. Genet., 28 (1997) 83.
48. Alemán, C., Protein Struct. Funct. Genet., 29 (1997) 575.
49. Balaram, P., Curr. Opini. Struct. Biol., 2 (1992) 1845.
50. Di Blasio, B., Pavone, V., Lombardi, A., Pedone, C. and Benedetti, E., Biopolymers 33 (1993) 1037.
51. Karle, I.L., Flippen-Andersen, J.L., Uma, K. and Balaram, P., Curr. Sci, 59 (1990) 875.
52. Orozco, M. and Luquel, F.J., Comput. Chem., 14 (1993) 881.
53. Luque, F.J., Orozco, M., Illas, F.J. and Rubio, J., J. Am. Chem. Soc., 113, (1991) 5203.
54. Buck, C.W., Pauchenko, Y.N. and Pupysev, V.I., J. Comput. Chem., 11, (1990) 623.
55. Bagus, P.S., Pacansky, J. and Wahlgren, U., J. Chem. Phys., 67 (1977) 618.
56. Yamaguchi, Y., Schaefer, H.F., III J. Chem. Phys, 73 (1980) 2310.
57. Alemán, C. and Orozco, M., Biopolymers, 34 (1994) 941.
58. Alemán, C. and Puiggalí, J., J. Org. Chem., 60 (1995) 910.
59. Alemán, C. and Muñoz-Guerra, J. Polym. Sci. Part B: Polym. Phys., 34 (1996) 963.
60. a. Hehre, W.J., Ditchfield, R. and Pople, J.A., J. Chem. Phys., 56 (1972) 2257.
61. b. Hariharan, C. and Pople, J.A., Mol. Phys., 27 (1974) 209.
62. Dewar, M.J.S., Zoebisch, E.S., Healy, E.E. and Stewart, J.J.P., J. Am. Chem. Soc., 107 (1985) 3902.
63. Beeke, A.D. Phys. Rev. A, 38 (1988) 3098.
64. Lee, C., Yang, W. and Parr, R.G., Phys. Rev. B, 37 (1993) 785.
65. Kottalan, J. and Case, D.A., Biopolymers, 29 (1990) 1409.
66. Alemán, C. and Pérez, J.J., Biopolymers, 33 (1993) 1811.
67. Alemán, C., Luque, F.J. and Orozco, M., J. Comput. Chem., 14 (1993) 799.
68. Ferenczy, G.G., Reynolds, C.A. and Richards, W.G., J. Comput. Chem., 11 (1990) 159.
69. Gaussian-94, revision B.3., Frisch, M.J., Trucks, H.B., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T., Petersson, G.A., Montgomery, J.A., Raghavachari, K., AI-Laham, M.A., Zakrzewski, V.G., Ortiz, V.G., Foresman, J.B., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Andres, J.L., Replogle, E.S., Gomperts, R., Martin, R.L., Fox, D.J., Binkley, J.S., Defrees, D.J., Baker, J. Stewart, J.J.P., Head-Gordon, M., Gonzalez, C. and Pople, J.A., Gaussian, Inc., Pittsburgh, PA, 1995.
70. Olivella, S., QCPE Bull., 4 (1984) 109. Extended by S. Olivella and J.M. Bofill in 1990.
71. Stewart, J.J.P., QCPE Bull., 3 (1983) 101.
72. Kollman, P., AMBER 3.0A. University of California, San Francisco, CA, 1990.
73. Stewart, J.J.P., J. Comput. Chem., 10 (1989) 221, and references therein.
74. Birngham, R.C., Dewar, M.J.S. and Lo, D.H., J. Am. Chem. Soc., 97 (1975) 1285.
75. Dewar, MJ.S. and Thiel, U., J. Am. Chem. Soc., 99 (1977) 4899.
76. Pulay, P., Meyer, W. and Boggs, J.E., J. Chem. Phys., 68 (1978) 5077.
77. Pulay, P., Lee, J.-G. and Boggs, J.E., J. Chem. Phys., 79 (1983) 3382.
78. Serrallach, A., Meyer, R. and Gunthard, H.H., J. Mol. Spectrosc, 52 (1974) 94.
79. Alemán, C., Luque, F.J. and Orozco, M., J. Comput. Chem, 7 (1993) 799.
80. Duncan, J.L. and Burns, G.R., J. Mol. Spectrosc, 30 (1969) 253.
81. Yamamoto, S., Nakata, M., Fukuyama, T. and Kuchitsu, K., J. Phys. Chem., 89 (1985) 3298.
82. Ferenczy, G.G., Reynolds, C.A. and Richards, W.G., J. Comput. Chem., 11 (1990) 159.
83. Reynolds, C.A., Essex, J.W. and Richards, W.G., J. Am. Chem. Soc., 114 (1992) 9075.
84. Alemán, C. and Casanovas, J., J. Chem. Soc. Perkin Trans II, (1994) 563.
85. Williams, D.E., Biopolymers, 29 (1990) 1397.