Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

Journal of Computational Chemistry

Volumn 24, Issue 9, 2003, Pages 1026-1042

  Perczel, András ^a   Farkas, Ödön ^a   Jákli, Imre ^a   Topol, Igor A ^b   Csizmadia, Imre G ^c  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b SAIC FREDERICK INC   (United States)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Ab inito and DFT computation; MP and CCSD(T); Peptides; Ramachandran surface; Structure and stability; X ray structure

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONFORMATIONS; DISCRETE FOURIER TRANSFORMS; MOLECULAR DYNAMICS; QUANTUM THEORY; X RAY ANALYSIS;

X-RAY STRUCTURE;

PROTEINS;

ALANINE; DIPEPTIDE; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; STEREOISOMERISM; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ALANINE; CRYSTALLOGRAPHY, X-RAY; DIPEPTIDES; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; STEREOISOMERISM; THERMODYNAMICS;

EID: 0037495961     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10267     Document Type: Article

References (43)

1. Perczel, A.; Csizmadia, I. G. In the Amide Linkage, Structrual Significance in Chemistry, Biochemistry and Materials Sciences; Greenberg, A., Breneman, C. M., Liebman, J. F., Eds.; Wiley-Interscience: New York, 2000, 409.
2. Berg, M. A., et al. J Mol Struct (Theochem) 2000, 500, 5.
3. Walker, P. D.; Mezey, P. G. J Am Chem Soc 1994, 116, 12022.
4. Schlegel, H. B.; Frisch, M. J. In Theoretical and Computational Models for Organic Chemistry; Formosinho, J. S.; Csizmadia, I. G.; Arnaut, L. G., Eds.; NATO-ASI Series C339; Kluwer Academic: The Netherlands, 1991, p. 5.
5. (a). Greengard, L.; Rokhlin, V. J Comput Phys 1987, 73, 325;
6. (b) Greengard, L. The Rapid Evaluation of Potential Fields in Particle Systems: MIT Press: Cambridge, 1988;
7. (c) Greengard, L. Science 1994, 265, 909;
8. (d) Burant, J. C.; Strain, M. C.; Scuseria, G. E.; Frisch, M. J. Chem Phys Lett. 1996, 258, 45;
9. (e) Burant, J. C.; Strain, M. C.; Scuseria, G. E.; Frisch, M. J. Chem Phys Lett 248, 43;
10. (f) Strain, M. C.; Scuseria, G. E.; Frisch, M. J. Science 1996, 271, 51.
11. van Alsenoy, C.; Yu, C.-H.; Peeters, A.; Martin, J. M. L.; Schäfer, L. J Phys Chem 1998, 102, 2245.
12. Moller, C.; Plesset, M. S. Phys Rev 1934, 46, 618.
13. Pople, J. A.; Krishman, R.; Schlegel, H. B.; Binkley, J. S. Int J Quantum Chem 1978, XIV, 545.
14. Pople, J. A.; Head-Gordon, M.; Raghavachari, K. J Chem Phys 1987, 84, 5968.
15. Jákli, I.; Perczel, A.; Parkas, Ö.; Csázár, A. G.; Sosa, C.; Csizmadia, I. G. J Comp Chem 2000, 21, 626.
16. (a) Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. J Mol Biol 1963, 7, 95;
17. (b) Ramachandran, G. N.; Sasisekharan, V. Adv Protein Chem 1968, 23, 283;
18. (c) Ramachandran, G. N.; Venkatachalam, C. M.; Krimm, S. Biophys J 1966, 6. 849.
19. Zimmerman, S. S.; Pottle, M. A.; Nemethy, G.; Scheraga, H. A. Macromolecules 1977, 10, 1.
20. (a) Leach, S. J.; Nemethy, G.; Scheraga, H. A. Biopol 1966, 4, 369;
21. (b) Howard, J. C.; Ali, A.; Scheraga, H. A.; Momany, F. A. Macromolecules 1975, 8, 607.
22. Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Brooks, C. L., III; Pople, J. A. Int J Quantum Chem Quantum Biol 1989, 16, 311.
23. Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Brooks, C. L., III; Pople, J. A. J Am Chem Soc 1991, 113, 5989.
24. Perczel, A.; Ángyán, J. G.; Kajtár, M.; Viviani, W.; Rivail, J.-L.; Marcoccia, J. F.; Csizmadia, I. G. J Am Chem 1991, 113, 6256.
25. Yu. C. H.; Norman, M. A.; Schäfer, L.; Ramek, M.; Peeters, A.; van Alsenoy, C. J Mol Struct 2001, 567, 361.
26. Vargas, R.; Garza, J.; Hay, B. P.; Dixon, D. A. J Phys Chem A 2002, 106, 3213.
27. McAllister, M. A.; Perczel, A.; Csázár, P.; Csizmadia, I. G. J Mol Struct (Thechem) 1993, 290, 181.
28. McAllister, M. A.; Perczel, A.; Csázár, P.; Viviani, W.; Rivail, J.-L.; Csizmadia, I. G. J Mol Struct (Theochem) 1993, 290, 161.
29. Perczel, A.; Farkas, Ö.; Csizmadia, I. G. J Am Chem Soc 1995, 117, 1653.
30. Perczel, A.; Csizmadia, I. G. Int Rev Phys Chem 1995 14, 127.
31. Perczel, A.; Farkas, Ö.; Csizmadia, I. G. J Comp Chem 1996,17, 821.
32. Perczel, A.; Farkas, Ö.; Csizmadia, I. G. J Am Chem Soc 1996, 188, 7809.
33. Rodriguez, A. M.; Baldoni, H. A.; Suvire, F.; Vázquez, F. N.; Zamabide, G.; Enriz, R. D.; Farkas, Ö.; Perczel, A.; McAllister, M. A.; Torday, L. L.; Papp, J. G.; Csizmadia, I. G. J Mol Struct (Thechem) 1998, 455, 275.
34. Endrédi, G.; Perczel, A.; Farkas, Ö.; McAllister, M. A.; Csonka, G. I.; Ladik, J.; Csizmadia, I. G. J Mol Struct (Theochem) 1997, 391, 15.
35. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E.; Durant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, Ö.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G.A.; Ayala, P.Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komáromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98 (Revision A.7); Gaussian. Inc.: Pittsburgh, PA, 1998.
36. Farkas, Ö.; Schlegel, H. B. J Chem Phys (to appear).
37. (a) Pulay, P. Chem Phys Lett 1980, 73, 393;
38. (b) Pulay, P. J Comp Chem 1982, 3, 556;
39. (c) Császár, P.; Pulay, P. J Mol Struct (Thechem) 1984, 114, 31.
40. Ramakrishman, C.; Ramachandran, G. N. Biophys J 1965, 5, 909.
41. IUPAC-IUB Commission on Biochemical Nomenclature. Biochemistry 1970, 9, 3471.
42. Perczel, A.; Hudáky, P.; Csizmadia, I. G. J Mol Struct (Theochem) 2000, 500
43. Julkamen, K. J.; Suhai, S. Chem Phys 1996, 208, 81.