Conformations of the glycine tripeptide analog Ac-Gly-Gly-NHMe: A computational study including aqueous solvation effects.

Journal of Physical Chemistry A

Volumn 116, Issue 5, 2012, Pages 1396-1408

  Atwood, Rex E ^a   Urban, Joseph J ^a  

^a UNITED STATES NAVAL ACADEMY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO MOLECULAR ORBITAL THEORY; AQUEOUS SOLVATION; COMPUTATIONAL STUDIES; CONFORMATIONAL PREFERENCES; CONTINUUM MODEL; EMPIRICAL FORCE; LOW ENERGIES; TRIPEPTIDE; TURN STRUCTURE; TYPE II;

AMINO ACIDS; CALCULATIONS; CONTINUUM MECHANICS; MOLECULAR ORBITALS; SOLVATION;

CONFORMATIONS;

GLYCINE; PEPTIDE; SOLVENT; WATER;

CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; GAS; QUANTUM THEORY; REVIEW;

COMPUTER SIMULATION; GASES; GLYCINE; MOLECULAR CONFORMATION; PEPTIDES; QUANTUM THEORY; SOLVENTS; WATER;

EID: 84856912813     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp206152d     Document Type: Review

References (62)

1. Jakli, I.; Perczel, A.; Farkas, O.; Hollosi, M.; Csizmadia, I. G. J. Mol. Struct. (THEOCHEM) 1998, 455, 303-314
2. Perczel, A.; Angyan, J. G.; Kajtar, M.; Viviani, W.; Rivail, J. L.; Marcoccia, J. F.; Csizmadia, I. G. J. Am. Chem. Soc. 1991, 113, 6256-6265
3. Perczel, A.; Farkas, O.; Jakli, I.; Csizmadia, I. G. J. Mol. Struct. (THEOCHEM) 1998, 455, 315-338
4. Pohl, G.; Perczel, A.; Vass, E.; Magyarfalvi, G.; Tarczay, G. Phys. Chem. Chem. Phys. 2007, 9, 4698-4708
5. Wang, Z. X.; Duan, Y. J. Comput. Chem. 2004, 25, 1699-1716
6. Kaminsky, J.; Jensen, F. J. Chem. Theory Comput. 2007, 3, 1774-1788
7. Echenique, P.; Calvo, I.; Alonso, J. L. J. Comput. Chem. 2006, 27, 1733-1747
8. Freedman, H.; Truong, T. N. J. Chem. Phys. 2004, 121, 12447-12456
9. Mehta, M. A.; Fry, E. A.; Eddy, M. T.; Dedeo, M. T.; Anagnost, A. E.; Long, J. R. J. Phys. Chem. B 2004, 108, 2777-2780
10. Mukhopadhyay, P.; Zuber, G.; Beratan, D. N. Biophys. J. 2008, 95, 5574-5586
11. Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Charles, L.; Brooks, I.; Pople, J. A. J. Am. Chem. Soc. 1991, 113, 5989-5997
12. Lee, H.-J.; Park, H.-M.; Lee, K.-B. J. Theor. Comput. Chem. 2009, 8, 799-811
13. Gorbunov, R. D.; Stock, G. Chem. Phys. Lett. 2007, 437, 272-276
14. Gutierrez, L. J.; Baldoni, H. A.; Enriz, R. D. J. Mol. Struct. 2009, 934, 103-111
15. Yu, C. H.; Schafer, L.; Ramek, M. J. Phys. Chem. A 1999, 103, 8337-8345
16. Rosso, L.; Abrams, J. B.; Tuckerman, M. E. J. Phys. Chem. B 2005, 109, 4162-4167
17. Jono, R.; Shimizu, K.; Terada, T. Chem. Phys. Lett. 2006, 432, 306-312
18. Zhang, Y.; Wang, C. S. J. Comput. Chem. 2009, 30, 1251-1260
19. McKinney, B. E.; Urban, J. J. J. Phys. Chem. A 2010, 114, 1123-1133
20. Urban, J. J.; Tillman, B. G.; Cronin, W. A. J. Phys. Chem. A 2006, 110, 11120-11129
21. Chin, W.; Dognon, J.-P.; Piuzzi, F.; Tardivel, B.; Dimicoli, I.; Mons, M. J. Am. Chem. Soc. 2005, 127, 707-712
22. Zimmerman, S. S.; Pottle, M. S.; Nemethy, G.; Scheraga, H. A. Macromolecules 1977, 10, 1-9
23. Karplus, P. A. Protein Sci. 1996, 5, 1406-1420
24. Spartan06, software for molecular modeling; version 1.1.2; Wavefunction, Inc: Irvine, CA, 2006.
25. Halgren, T. A. J. Comput. Chem. 1996, 17, 490-519
26. Halgren, T. A. J. Comput. Chem. 1996, 17, 520-552
27. Halgren, T. A. J. Comput. Chem. 1996, 17, 553-586
28. Halgren, T. A. J. Comput. Chem. 1996, 17, 615-641
29. Halgren, T. A.; Nachbar, R. J. Comput. Chem. 1996, 17, 587-615
30. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. Gaussian09, Revision A.1; Gaussian Inc.: Wallingford, CT, 2009.
31. Becke, A. D. Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100
32. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785-789
33. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618
34. Dunning, T. H., Jr. J. Chem. Phys. 1989, 90, 1007-1023
35. Cances, E.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 107, 3032-3041
36. Cossi, M.; Barone, V.; Mennucci, B.; Tomasi, J. Chem. Phys. Lett. 1998, 286, 253-260
37. Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 106, 5151-5158
38. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V. J. Chem. Phys. 2002, 117, 43-54
39. Richardson, J. S.; The Anatomy and Taxonomy of Protein Structure. In Advances in Protein Chemistry; Anfinsen, C. B.; Edsall, J. T.; Richards, F. M., Eds.; Academic Press: New York, 1981; Vol. 34, pp 167-339.
40. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
41. Grimme, S. J. Comput. Chem. 2006, 27, 1787-1799
42. Chai, J. D.; Head-Gordon, M. Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
43. ChemBio3D, software for molecular modeling, version 12.0; Cambridge Scientific Computing: Cambridge, MA. 2009.
44. PCModel, software for molecular modeling, version 9.3; Serena Sofware: Bloomington, IN. 2010.
45. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197
46. Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J. Am. Chem. Soc. 1992, 114, 10024-10035
47. Rappé, A. K.; William A. Goddard, I. J. Phys. Chem. 1991, 95, 3358-3363
48. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129
49. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 19824-19839
50. Wang, Z. X.; Wu, C.; Lei, H.; Duan, Y. J. Chem. Theory Comput. 2007, 3, 1527-1537
51. Gloaguen, E.; Pollet, R.; Piuzzi, F.; Tardivel, B.; Mons, M. Phys. Chem. Chem. Phys. 2009, 11, 11385-11388
52. Csaszar, A. G.; Perczel, A. Prog. Biophys. Mol. Biol. 1999, 71, 243-309
53. Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436
54. Li, Y.; Wang, C.-S. J. Comput. Chem. 2011, 32, 2765-2773
55. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157-167
56. Schwabe, T.; Grimme, S. Acc. Chem. Res. 2008, 41, 569-579
57. Wodrich, M. D.; Corminboeuf, C.; Schreiner, P. R.; Fokin, A. A.; Von Schleyer, P. Org. Lett. 2007, 9, 1851-1854
58. Toroz, D.; Van Mourik, T. Mol. Phys. 2006, 104, 559-570
59. van Mourik, T.; Karamertzanis, P. G.; Price, S. L. J. Phys. Chem. A 2006, 110, 8-12
60. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. J. Am. Chem. Soc. 1997, 119, 5908-5920
61. Biswal, H. S.; Loquais, Y.; Tardivel, B.; Gloaguen, E.; Mons, M. J. Am. Chem. Soc. 2011, 133, 3931-3942
62. Tomita, K.; Narumi, T.; Niida, A.; Oishi, S.; Ohno, H.; Fujii, N. Biopolymers 2007, 88, 630-630