Electronic Structures of Polyglycine and Active Sites of Cytochrome c Oxidase

Journal of the Physical Society of Japan

Volumn 73, Issue 11, 2004, Pages 3198-3208

  Kamiya, Katsumasa ^a   Shiraishi, Kenji ^a   Oshiyama, Atsushi ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

cytochrome c oxidase; density functional theory; electronic structure; nearly free electron state; polyglycine

Indexed keywords

EID: 33645774468     PISSN: 00319015     EISSN: 13474073     Source Type: Journal    
DOI: 10.1143/JPSJ.73.3198     Document Type: Article

References (30)

1. See, for example, H. Lodish, A. Berk, S. L. Zipursky, P. Matsudaira, D. Baltimore and J. Darnell: Molecular Cell Biology (W. H. Freeman & Co., New York, 2001) 4th ed.
2. P. Hohenberg and W. Kohn: Phys. Rev. 136 (1964) B864.
3. W. Kohn and L. J. Sham: Phys. Rev. 140 (1965) A1133.
4. See, for example, R. G. Parr and W. Yang: Density Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
5. M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias and J. D. Joannopoulos: Rev. Mod. Phys. 64 (1992) 1045.
6. M. Boero, K. Terakura, T. Ikeshoji, C. C. Liew and M. Parrinello: Phys. Rev. Lett. 85 (2000) 3245.
7. M. Boero, K. Terakura, T. Ikeshoji, C. C. Liew and M. Parrinello: J. Chem. Phys. 115 (2001) 2219.
8. M. Boero, M. Parrinello, K. Terakura, T. Ikeshoji and C. C. Liew: Phys. Rev. Lett. 90 (2003) 226403.
9. K. Takeda and K. Shiraishi: J. Phys. Soc. Jpn. 65 (1996) 421.
10. M. Marchi, J. Hutter and M. Parrinello: J. Am. Chem. Soc. 118 (1996) 7847.
11. M. Boero, K. Terakura and M. Tateno: J. Am. Chem. Soc. 124 (2002) 8949.
12. F. Sato, T. Yoshihiro, M. Era and H. Kashiwagi: Chem. Phys. Lett. 341 (2001) 645.
13. S. Ferguson-Miller and G. T. Babcock: Chem. Rev. 96 (1996) 2889.
14. S. Yoshikawa, K. Shinzawa-Itoh, R. Nakashima, R. Yaono, E. Yamashita, N. Inoue, M. Yao, M. J. Fei, C. P. Libeu, T. Mizushima, H. Yamaguchi, T. Tomizaki and T. Tsukihara: Science 280 (1998) 1723.
15. S. Munoz-Guerra, J. Puiggali, A. Rodriguez and J. A. Subirana: J. Mol. Biol. 167 (1983) 223.
16. S. Saito and A. Oshiyama: Phys. Rev. Lett. 71 (1993) 121.
17. Y. Miyamoto, A. Rubio, X. Blase, M. L. Cohen and S. G. Louie: Phys. Rev. Lett. 74 (1995) 2993.
18. S. Okada, A. Oshiyama and S. Saito: Phys. Rev. B62 (2000) 7634.
19. Codes used in the present work are based on Tokyo Ab initio Program Package (TAPP) developed by us; J. Yamauchi, M. Tsukada, S. Watanabe and O. Sugino: Phys. Rev. B54 (1996) 5586
20. H. Kageshima and K. Shiraishi: Phys. Rev. B56 (1997) 14985
21. O. Sugino and A. Oshiyama: Phys. Rev. Lett. 68 (1992) 1858.
22. D. Vanderbilt: Phys. Rev. B41 (1990) 7892.
23. J. P. Perdew, K. Burke and M. Ernzerhof: Phys. Rev. Lett. 77 (1996) 3865.
24. J. Rossmeisl, B. Hinnemann, K. W. Jacobsen, J. K. Norskov, O. H. Olsen and J. T. Pedersen: J. Chem. Phys. 118 (2003) 9783.
25. S. Okada, Y. Enomoto, K. Shiraishi and A. Oshiyama: unpublished.
26. The importance of the cavity for NFE states has been reported by S. Okada, A. Oshiyama and S. Saito: Phys. Rev. B62 (2000) 7634 in the context of electronic structure of carbon nanotubes.
27. T. Tsukihara, H. Aoyama, E. Yamashita, T. Tomizaki, H. Yamaguchi, K. Shinzawa-Itoh, R. Nakashima, R. Yaono and S. Yoshikawa: Science 272 (1996) 1136.
28. S. Okada, M. Otani and A. Oshiyama: Phys. Rev. B67 (2003) 205411.
29. M. Otani, S. Okada and A. Oshiyama: Phys. Rev. B68 (2003) 125424.
30. M. K. F. Wikström: Nature 266 (1977) 271.