The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods

Journal of Chemical Physics

Volumn 138, Issue 24, 2013, Pages

  Pohl, Gabor ^a   Plumley, Joshua A ^a,b   Dannenberg, J J ^a  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b QUANTUMBIO INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID FORMATION; DISPERSION EFFECT; FUNCTIONALS; GLOBAL MINIMA; LOCAL MINIMUMS; OPTIMIZED GEOMETRIES; SHEET-LIKE STRUCTURE; STACKING INTERACTION;

AMINO ACIDS; GLYCOPROTEINS; ORBITAL CALCULATIONS;

DENSITY FUNCTIONAL THEORY;

PEPTIDE; PHENYLALANINE;

ARTICLE; CHEMISTRY; HYDROGEN BOND; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY;

HYDROGEN BONDING; PEPTIDES; PHENYLALANINE; PROTEIN STRUCTURE, SECONDARY; QUANTUM THEORY;

EID: 84879978215     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4811712     Document Type: Article

References (38)

1. E. Gazit, FASEB J. 16, 77-83 (2002); 10.1096/fj.01-0442hyp
2. P. Tamamis, L. Adler-Abramovich, M. Reches, K. Marshall, P. Sikorski, L. Serpell, E. Gazit, and G. Archontis, Biophys. J. 96, 5020-5029 (2009); 10.1016/j.bpj.2009.03.026
3. A. Dutta, D. Chattopadhyay, and A. Pramanik, Supramol. Chem. 22 (2), 95 (2010); 10.1080/10610270903254142
4. S. Marsili, R. Chelli, V. Schettino, and P. Procacci, Phys. Chem. Chem. Phys. 10 (19), 2673 (2008); 10.1039/b718519g
5. A. Acharya, B. Ramanujam, A. Mitra, and C. P. Rao, ACS Nano 4 (7), 4061 (2010). 10.1021/nn1006286
6. S. K. Kundu, P. A. Mazumdar, A. K. Das, V. Bertolasi, and A. Pramanik, J. Chem. Soc., Perkin Trans. 2 2002 (9), 1602. 10.1039/b203164g
7. D. M. Chung, Y. Dou, P. Baldi, and J. S. Nowick, J. Am. Chem. Soc. 127 (28), 9998 (2005). 10.1021/ja052351p
8. M. Marianski, A. Asensio, and J. J. Dannenberg, J. Chem. Phys. 137 (4), 044109 (2012). 10.1063/1.4737517
9. M. O. Sinnokrot and C. D. Sherrill, J. Phys. Chem. A 108 (46), 10200 (2004). 10.1021/jp0469517
10. A. D. Becke, J. Chem. Phys. 98, 5648 (1993); 10.1063/1.464913
11. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988). 10.1103/PhysRevB.37.785
12. C. Adamo and V. Barone, J. Chem. Phys. 110 (13), 6158 (1999). 10.1063/1.478522
13. X. Xu and W. A. Goddard, Proc. Natl. Acad. Sci. U.S.A. 101 (9), 2673 (2004). 10.1073/pnas.0308730100
14. S. Grimme, J. Comput. Chem. 27 (15), 1787 (2006). 10.1002/jcc.20495
15. J.-D. Chai and M. Head-Gordon, Phys. Chem. Chem. Phys. 10 (44), 6615 (2008). 10.1039/b810189b
16. Y. Zhao and D. G. Truhlar, Acc. Chem. Res. 41, 157 (2008). 10.1021/ar700111a
17. S. Simon, M. Duran, and J. J. Dannenberg, J. Chem. Phys. 105 (24), 11024 (1996). 10.1063/1.472902
18. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 09, Revision A.2, Gaussian, Inc., Wallingford, CT, 2009.
19. G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B 102 (17), 3257 (1998). 10.1021/jp973306+
20. V. Barone and M. Cossi, J. Phys. Chem. A 102 (11), 1995 (1998); 10.1021/jp9716997
21. M. Cossi, N. Rega, G. Scalmani, and V. Barone, J. Comput. Chem. 24 (6), 669 (2003). 10.1002/jcc.10189
22. AMPAC (Semichem, Inc., Shawnee, KS, AMPAC 8.16).
23. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107 (13), 3902 (1985). 10.1021/ja00299a024
24. M. Marianski and J. J. Dannenberg, J. Phys. Chem. B 116 (4), 1437 (2012); 10.1021/jp209177u
25. M. I.-H. Tsai, Y. Xu, and J. J. Dannenberg, J. Phys. Chem. B 113 (1), 309 (2009). 10.1021/jp8063646
26. M. Marianski, A. Oliva, and J. J. Dannenberg, J. Phys. Chem. A 116 (30), 8100 (2012). 10.1021/jp3050274
27. E. G. Cox, Rev. Mod. Phys. 30 (1), 159 (1958). 10.1103/RevModPhys.30.159
28. D. Roy, M. Marianski, N. Maitra, and J. J. Dannenberg, J. Chem. Phys. 137, 134109 (2012). 10.1063/1.4755990
29. J. A. Plumley and J. J. Dannenberg, J. Comput. Chem. 32 (8), 1519 (2011). 10.1002/jcc.21729
30. D. Sharma, S. Sharma, S. Pasha, and S. K. Brahmachari, FEBS Lett. 456, 181 (1999); 10.1016/S0014-5793(99)00933-3
31. S. Sen, D. Dash, S. Pasha, and S. K. Brahmachari, Protein Sci. 12, 953 (2003). 10.1110/ps.0224403
32. Y. Nozaki and C. Tanford, J. Biol. Chem. 246, 2211 (1971).
33. N. Kobko, M. Marianski, A. Asensio, R. Wieczorek, and J. J. Dannenberg, Comput. Theor. Chem. 990, 214 (2012). 10.1016/j.comptc.2011.11.022
34. R. J. Ouellette and S. Williams, J. Am. Chem. Soc. 93 (2), 466 (1971). 10.1021/ja00731a027
35. L. Adler-Abramovich, L. Vaks, O. Carny, D. Trudler, A. Magno, A. Caflisch, D. Frenkel, and E. Gazit, Nat. Chem. Biol. 8 (8), 701 (2012). 10.1038/nchembio.1002
36. J. A. Plumley and J. J. Dannenberg, J. Phys. Chem. B 115, 10560 (2011); 10.1021/jp205388q
37. J. A. Plumley, M. I.-H. Tsai, and J. J. Dannenberg, J. Phys. Chem. B 115 (6), 1562 (2011). 10.1021/jp111501d
38. See supplementary material at http://dx.doi.org/10.1063/1.4811712 E-JCPSA6-138-033325 for complete Cartesian coordinates for all optimized structures.