Variety of the molecular conformation in peptide nanorings and nanotubes

Journal of the American Chemical Society

Volumn 125, Issue 9, 2003, Pages 2756-2769

  Okamoto, Hajime ^a   Nakanishi, Tsutomu ^a   Nagai, Yukiko ^a   Kasahara, Maki ^a   Takeda, Kyozaburo ^a  

^a WASEDA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MATHEMATICAL CONFORMATIONS;

AMINO ACIDS; CONFORMATIONS; ENERGY GAP; HYDROGEN BONDS; MOLECULAR DYNAMICS; SUBSTITUTION REACTIONS;

NANOTUBES;

NANOPARTICLE; PEPTIDE;

AB INITIO CALCULATION; AMINO ACID SUBSTITUTION; ARTICLE; ELECTRONICS; MATHEMATICAL ANALYSIS; PREDICTION; PROTEIN CONFORMATION; THEORY; TUBE;

HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; NANOTECHNOLOGY; PEPTIDES, CYCLIC; PROTEIN CONFORMATION;

EID: 0037420311     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0212720     Document Type: Article

References (38)

1. Ghadiri, M. R.; Granja, J. R.; Milligan, R. A.; McRee, D. E.; Khazanovich, N. Nature 1993, 366, 324.
2. Ghadiri, M. R.; Granja, J. R.; Buehler, L. K. Nature 1994, 369, 301.
3. Khazanovich, N.; Granja, J. R.; McRee, D. E.; Milligan, R. A.; Ghadiri, M. R. J. Am. Chem. Soc. 1994, 116, 6011.
4. Ghadiri, M. R. Adv. Matter. 1995, 7, 675.
5. Hartgerink, J. D.; Granja, J. R.; Milligan, R. A.; Ghadiri, M. R. J. Am. Chem. Soc. 1996, 118, 43.
6. Clark, T. D.; Buehler, L. K.; Ghadiri, M. R. J. Am. Chem. Soc. 1998, 120, 651.
7. Bong, D. T.; Clark, T. D.; Granja, J. R.; Ghadiri, M. R. Angew. Chem., Int. Ed. 2001, 40, 988.
8. Fernandez-Lopez, S.; Kim, Hui-Sun; Choi, E. C.; Delgado, M.; Granja, J. R.; Khasanov, A.; Krachenbuehl, K.; Long, G.; Weinberger, D. A.; Wilcoxen, K. M.; Ghadiri, M. R. Nature 2001, 412, 452.
9. Fukasaku, K.; Takeda, K.; Shiraishi, K. J. Phys. Soc. Jpn. 1997, 66, 3387; ibid. 1998, 67, 3751.
10. Fukasaku, K.; Takeda, K.; Shiraishi, K. J. Phys. Soc. Jpn. 1997, 66, 3387; ibid. 1998, 67, 3751.
11. Okamoto, H.; Takeda, K.; Shiraishi, K. Phys. Rev. B 2001, 64, 115 425.
12. Shimanouchi, T.; Mizushima, S. J. Chem. Phys. 1955, 23, 707.
13. Miyazawa, T. J. Polym. Sci. 1961, 55, 215.
14. De Santis, P.; Morosetti, S.; Rizzo, R. Macromolecules 1974, 7, 52.
15. n symmetry.
16. Nakanishi, T. Thesis of Waseda University 2000.
17. Tables in Chemistry (Kagaku Binran in Japanese), ed.; The Chemical Society of Japan: Maruzen, Tokyo, 1984.
18. In section III, we also use those values as the initial values for the geometry optimization.
19. Shimanouchi, T.; Mizushima, S. Kagaku 1947, 17, 24.
20. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; 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.; Komaromi, 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; Gaussian, Inc.: Pittsburgh, PA, 1998.
21. 10 Therefore, the total energy of the E-type MR slightly decreases with increasing n number.
22. For E-type PCRs, the equatorial substitution appears in the region of ψ > φ + π, and the axial substitution appears in the region of ψ < φ - π (Figure 3b). For B-type PCRs, on the other hand. the equatorial substitution appears in the region of φ - π < ψ < φ, and the axial substitution appears in the region of φ < ψ < φ + π.
23. 1 angles and rotamer type are also listed in Table 2. The PCRs might also have the other rotamer types for the local minimum forms. However, the other rotamer types are out of consideration in the present paper because of the large number of degrees of freedom in the calculations.
24. Only the horno-Pro PCR shows a considerably large energetic stability in the E-type conformation (by 20.6 kcal/mol per residue). This is because the peculiar atomic loop included in the Pro residue generates the large backbone distortion especially in the B-type conformation as shown in Table 2.
25. Homo-residue PCRs of Trp and His also show the large energetic stability in the E-type conformation, despite the fact that they include no HB between the side chains and the backbone.
26. Takeda, K.; Shiraishi, K. J. Phys. Soc. Jpn. 1996, 65, 421.
27. β atom. However, the individual levels still maintain the 6-fold degeneracy.
28. π* = α - 1.62β when the atomicity of the membered ring is changed to m = 5 as illustrated in Figure 15. Therefore, the π* levels are put into the conduction band, while the π levels are still within the energy gap.
29. j = α + 2β cos 2πjm, where j = 0, 1, 2, ..., m/2 if j is an even number, or j = 0, 1, 2, ..., (m - 1)/2 ifj is an odd number.
30. 30
31. Okamoto, H.; Nakanishi, T.; Nagai, Y.; Takeda, K.; Obataya, I.; Mihara, H.; Azehara, H.; Mizutani, W. Jpn. J. Appl. Phys. 2003, 42, 1.
32. The resulting energy difference between E-type and B-type parallel PNTs is as small as 0.14 kcal/mol per residue (Figure 18).
33. Saunders, V. R.; Dovesi, R.; Roetti, C.; Causà, M.; Harrison, N. M.; Orlando, R.; Zicovich-Wilson, C. M. CRYSTAL 98, University of Torino, 1998.
34. Lewis, J. P.; Pawley, N. H.; Sankey, O. F. J. Phys. Chem. B 1997, 101, 10 576.
35. Carloni, P.; Andreoni, W.; Parrinello, M. Phys. Rev. Lett. 1997, 79, 761.
36. Jishi, R. A.; Braier, N. C.; White, C. T.; Mintmire, J. W. Phys. Rev. B 1998, 58, R16 009.
37. Jishi, R. A.; Flores, R. M.; Valderrama, M.; Lou, L.; Bragin, J. J. Phys. Chem. A 1998, 102, 9858.
38. 10 This is because ab initio Hartree-Fock calculations overestimate the energy gap due to the neglect of the inter-electron correlation, whereas the first principles DFT calculations underestimate the corresponding value. Therefore, these values should be calibrated.