Transfer of noncovalent chiral information along an optically inactive helical peptide chain: Allosteric control of asymmetry of the C-terminal site by external molecule that binds to the N-terminal Site

Journal of Organic Chemistry

Volumn 74, Issue 4, 2009, Pages 1429-1439

  Ousaka, Naoki ^a,b   Inai, Yoshihito ^a  

^a NAGOYA INSTITUTE OF TECHNOLOGY   (Japan)

^b JST ERATO SORST Kuroda Chiromorphology Team   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERIC CONTROLS; ALLOSTERIC MODELS; AMINOISOBUTYRIC ACIDS; CD SIGNALS; CD SPECTRUM; CHIRAL INDUCTIONS; CHIRAL INFORMATIONS; CHIRAL MOLECULES; CIRCULAR DICHROISMS; HELICAL CONFORMATIONS; HELICAL PEPTIDES; HELICAL SENSE; HELICITY; HELICITY INDUCTIONS; L PROLINES; N TERMINALS; NONCOVALENT; PEPTIDE CHAINS; TERMINAL SITES;

AMINES; BINDING ENERGY; DATA STORAGE EQUIPMENT; DICHROISM; POLYPEPTIDES; STEREOCHEMISTRY;

BINDING SITES;

AMIDE; AMINO ACID; PEPTIDE; PROLINE;

ABSORPTION SPECTROSCOPY; ALLOSTERISM; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CHIRALITY; CIRCULAR DICHROISM; COMPUTER SIMULATION; CONFORMATION; DIPOLE; ENERGY; FOURIER TRANSFORMATION; INFRARED SPECTROSCOPY; MOLECULE; PEPTIDE ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE; SYNTHESIS; TEMPERATURE DEPENDENCE;

ABSORPTION; ALLOSTERIC REGULATION; BIOMIMETICS; CIRCULAR DICHROISM; COMPUTER SIMULATION; MODELS, MOLECULAR; OPTICAL PROCESSES; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTROPHOTOMETRY, ULTRAVIOLET; STEREOISOMERISM;

EID: 64349116529     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo801686m     Document Type: Article

References (181)

1. For elegant articles of helical polymers, see: (a) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. Rev. 2001, 101, 3893-4011.
2. (b) Green, M. M.; Park, J.-W.; Sato, T.; Teramoto, A.; Lifson, S.; Selinger, R. L. B.; Selinger, J. V. Ansew. Chem., Int. Ed. 1999, 38, 3138-3154.
3. (c) Nakano, T.; Okamoto, Y. Chem. Rev. 2001, 101, 4013-4038.
4. (d) Yashima, E.; Maeda, K.; Nishimura, T. Chem. Eur. J. 2004, 10, 42-51.
5. (e) Brunsveld, L.; Folmer, B. J. B.; Meijer, E. W.; Sijbesma, R. P. Chem. Rev. 2001, 101, 4071-4097.
6. (f) Cornelissen, J. J. L. M.; Rowan, A. E.; Nolte, R. J. M.; Sommerdijk, N. A. J. M. Chem. Rev. 2001, 101, 4039-4070.
7. (g) Dolain, C.; Léger, J.-M.; Delsuc, N.; Gornitzka, H.; Huc, I. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16146-16151.
8. (a) Aurora, R.; Srinivasan, R.; Rose, G. D. Science 1994, 264, 1126-1130.
9. (b) Schellman, C. In Protein Foldins; Jaenicke, R., Ed.; North-Holland Biomedical Press, Elsevier: Amsterdam, 1980; pp 53-61.
10. (c) Sagermann, M.; Mårtensson, L.-G.; Baase, W. A.; Matthews, B. W. Protein Sci. 2002, 11, 516-521.
11. (d) Jiménez, M. A.; Muñoz, V.; Rico, M.; Serrano, L. J. Mol. Biol. 1994, 242, 487-496.
12. (e) Harper, E. T.; Rose, G. D. Biochemistry 1993, 32, 7605-7609.
13. (f) Kim, P. S.; Baldwin, R. L. Nature 1984, 307, 329-334.
14. (g) Storrs, R. W.; Truckses, D.; Wemmer, D. E. Biopolymers 1992, 32, 1695-1702.
15. (h) Lawrence, J. R.; Johnson, W. C. Biophys. Chem. 2002, 101-102, 375-385.
16. (i) Monticelli, L.; Tieleman, D. P.; Colombo, G. J. Phys. Chem. B 2005, 109, 20064-20067. For C-terminal hydrogen-bonding patterns of helical model peptides, see also:
17. (j) Datta, S.; Uma, M. V.; Shamala, N.; Balaram, P. Biopolymers 1999, 50, 13-22.
18. (k) Benedetti, E.; Di Blasio, B.; Pavone, V.; Pedone, C.; Santini, A.; Bavoso, A.; Toniolo, C.; Crisma, M.; Sartore, L. J. Chem. Soc., Perkin Trans. 2 1990, 1829-1837.
19. For insightful simulation of heterochiral/homochiral helices, see: (a) Nanda, V.; DeGrado, W. F. J. Am. Chem. Soc. 2004, 126, 14459-14467.
20. (b) Nanda, V.; DeGrado, W. F. J. Am. Chem. Soc. 2006, 128, 809-816.
21. Kuroda, R. Enantiomer 2000, 5, 439-450.
22. For leading examples of covalent chiral effects on helix sense, see: (a) Green, M. M.; Reidy, M. P.; Johnson, R. D.; Darling, G.; O'Leary, D. J.; Willson, G. J. Am. Chem. Soc. 1989, 111, 6452-6454.
23. (b) Tian, G.; Lu, Y.; Novak, B. M. J. Am. Chem. Soc. 2004, 126, 4082-4083.
24. (c) Tang, H.-Z.; Lu, Y.; Tian, G.; Capracotta, M. D.; Novak, B. M. J. Am. Chem. Soc. 2004, 126, 3722-3723.
25. (d) Dolain, C.; Jiang, H.; Léger, J.-M.; Guionneau, P.; Huc, I. J. Am. Chem. Soc. 2005, 127, 12943-12951.
26. (e) Okamoto, Y.; Matsuda, M.; Nakano, T.; Yashima, E. Polym. J. 1993, 25, 391-396.
27. (f) Maeda, K.; Okamoto, Y. Polym. J. 1998, 30, 100-105.
28. (g) Nath, G. Y.; Samal, S.; Park, S.-Y.; Murthy, C. N.; Lee, J.-S. Macromolecules 2006, 39, 5965-5966.
29. (h) Tabei, J.; Shiotsuki, M.; Sato, T.; Sanda, F.; Masuda, T. Chem. Eur. J. 2005, 11, 3591-3598.
30. (i) Kamer, P. C. J.; Cleij, M. C.; Nolte, R. J. M.; Harada, T.; Hezemans, A. M. F.; Drenth, W. J. Am. Chem. Soc. 1988, 110, 1581-1587.
31. (a) Prince, R. B.; Barnes, S. A.; Moore, J. S. J. Am. Chem. Soc. 2000, 122, 2758-2762.
32. (b) Yashima, E.; Matsushima, T.; Okamoto, Y. J. Am. Chem. Soc. 1997, 119, 6345-6359.
33. (c) Yashima, E.; Maeda, K.; Okamoto, Y. Nature 1999, 399, 449-451.
34. (d) Maeda, K.; Ishikawa, M.; Yashima, E. J. Am. Chem. Soc. 2004, 126, 15161-15166.
35. (e) Schlitzer, D. S.; Novak, B. M. J. Am. Chem. Soc. 1998, 120, 2196-2197.
36. (f) Maurizot, V.; Dolain, C.; Huc, I. Eur. J. Ore. Chem. 2005, 2005, 1293-1301.
37. (g) Majidi, M. R.; Kane-Maguire, L. A. P.; Wallace, G. G. Polymer 1994, 35, 3113-3115.
38. (h) Green, M. M.; Khatri, C.; Peterson, N. C. J. Am. Chem. Soc. 1993, 115, 4941-4942.
39. (i) Nakashima, H.; Koe, J. R.; Torimitsu, K.; Fujiki, M. J. Am. Chem. Soc. 2001, 123, 4847-4848.
40. For transfer of chiral information in supramolecular assemblies, see: (a) Smulders, M. M. J.; Schenning, A. P. H. J.; Meijer, E. W. J. Am. Chem. Soc. 2008, 130, 606-611.
41. (b) van Gestel, J.; Palmans, A. R. A.; Titulaer, B.; Vekemans, J. A. J. M.; Meijer, E. W. J. Am. Chem. Soc. 2005, 127, 5490-5494.
42. (c) Lauceri, R.; Raudino, A.; Scolaro, L. M.; Micali, N.; Purrello, R. J. Am. Chem. Soc. 2002, 124, 894-895.
43. (d) Mammana, A.; D'Urso, A.; Lauceri, R.; Purrello, R. J. Am. Chem. Soc. 2007, 129, 8062-8063.
44. (e) Prins, L. J.; Timmerman, P.; Reinhoudt, D. N. J. Am. Chem. Soc. 2001, 123, 10153-10163.
45. For biorelated helical backbones, see: (a) Kozlov, I. A.; Orgel, L. E.; Nielsen, P. E. Ansew. Chem., Int. Ed. 2000, 39, 4292-4295.
46. (b) Mazaleyrat, J.-P.; Wright, K.; Gaucher, A.; Toulemonde, N.; Wakselman, M.; Oancea, S.; Peggion, C.; Formaggio, F.; Setnicka, V.; Keiderling, T. A.; Toniolo, C. J. Am. Chem. Soc. 2004, 126, 12874-12879.
47. (c) Benedetti, E.; Saviano, M.; Iacovino, R.; Pedone, C.; Santini, A.; Crisma, M.; Formaggio, F.; Toniolo, C.; Broxterman, Q. B.; Kamphuis, J. Biopolymers 1998, 46, 433-443.
48. (d) Benedetti, E.; Saviano, M.; Iacovino, R.; Crisma, M.; Formaggio, F.; Toniolo, C. Z. Kristalloer. 1999, 214, 160-166.
49. (e) Crisma, M.; Valle, G.; Formaggio, F.; Toniolo, C. Z Kristallogr. 1998, 213, 599-604.
50. (f) Pengo, B.; Formaggio, F.; Crisma, M.; Toniolo, C.; Bonora, G. M.; Broxterman, Q. B.; Kamphuis, J.; Saviano, M.; Iacovino, R.; Rossi, F.; Benedetti, E. J. Chem. Soc., Perkin Trans. 2 1998, 1651-1657.
51. (g) Pieroni, O.; Fissi, A.; Pratesi, C.; Temussi, P. A.; Ciardelli, F. J. Am. Chem. Soc. 1991, 113, 6338-6340.
52. (h) Tuzi, A.; Ciajolo, M. R.; Guarino, G.; Temussi, P. A.; Fissi, A.; Pieroni, O. Biopolymers 1993, 33, 1111-1121.
53. (i) Pieroni, O.; Fissi, A.; Pratesi, C.; Temussi, P. A.; Ciardelli, F. Biopolymers 1993, 33, 1-10.
54. (j) Ramagopal, U. A.; Ramakumar, S.; Joshi, R. M.; Chauhan, V. S. J. Pept. Res. 1998, 52, 208-215.
55. (a) Sone, E. D.; Zubarev, E. R.; Stupp, S. I. Aneew. Chem. Int. Ed. 2002, 41, 1705-1709.
56. (b) Sakurai, S.; Ohsawa, S.; Nagai, K.; Okoshi, K.; Kumaki, J.; Yashima, E. Aneew. Chem., Int. Ed. 2007, 46, 7605-7608.
57. (c) Sakurai, S.; Okoshi,K.; Kumaki, J.; Yashima, E. J. Am. Chem. Soc. 2006, 128, 5650-5651.
58. (d) Maeda, T.; Furusho, Y.; Sakurai, S.; Kumaki, J.; Okoshi, K.; Yashima, E. J. Am. Chem. Soc. 2008, 130, 7938-7945.
59. (e) Shinohara, K.; Yasuda, S.; Kato, G.; Fujita, M.; Shigekawa, H. J. Am. Chem. Soc. 2001, 123, 3619-3620.
60. (a) Inai, Y.; Tagawa, K.; Takasu, A.; Hirabayashi, T.; Oshikawa, T.; Yamashita, M. J. Am. Chem. Soc. 2000, 122, 11731-11732.
61. (b) Inai, Y.; Ousaka, N.; Okabe, T. J. Am. Chem. Soc. 2003, 125, 8151-8162.
62. (c) Ousaka, N.; Inai, Y.; Okabe, T. Biopolymers 2006, 83, 337-351.
63. (d) Inai, Y.; Hirano, T. ITE Lett. Batteries. New Technol. Med. 2003, 4, 485-488.
64. (e) Inai, Y.; Ousaka, N.; Ookouchi, Y. Biopolymers 2006, 82, 471-481.
65. For the control of helix sense of sequence containing chiral residue, see: (a) Inai, Y.; Ishida, Y.; Tagawa, K.; Takasu, A.; Hirabayashi, T. J. Am. Chem. Soc. 2002, 124, 2466-2473.
66. (b) Inai, Y.; Komori, H.; Takasu, A.; Hirabayashi, T. Biomacromolecules 2003, 4, 122-128.
67. (c) Inai, Y.; Komori, H. Biomacromolecules 2004, 5, 1231-1240.
68. (d) Komori, H.; Inai, Y. J. Ore. Chem. 2007, 72, 4012-4022.
69. Inai, Y.; Komori, H.; Ousaka, N. Chem. Rec. 2007, 7, 191-202.
70. (a) Ousaka, N.; Inai, Y. J. Am. Chem. Soc. 2006, 128, 14736-14737.
71. (b) Inai, Y.;Ashitaka, S.; Hirabayashi, T. Polym. J. 1999, 31, 246-253.
72. 10-/ α-helical propensity: (a) Karle, I. L.; Gopi, H. N.; Balaram, P. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13946-13951.
73. (b) Venkatraman, J.; Shankaramma, S. C.; Balaram, P. Chem. Rev. 2001, 101, 3131-3152.
74. (c) Karle, I. L.; Flippen-Anderson, J. L.; Uma, K.; Balaram, H.; Balaram, P. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 765-769.
75. (d) Benedetti, E.; Bavoso, A.; Di Blasio, B.; Pavone, V.; Pedone, C.; Crisma, M.; Bonora, G. M.; Toniolo, C. J. Am. Chem. Soc. 1982, 104, 2437-2444.
76. (e) Yanagisawa, K.; Morita, T.; Kimura, S. J. Am. Chem. Soc. 2004, 126, 12780-12781.
77. (f) Okuyama, K.; Saga, Y.; Nakayama, M.; Narita, M. Biopolymers 1991, 31, 975-985.
78. (g) Toniolo, C.; Benedetti, E. Trends Biochem. Sci. 1991, 16, 350-353.
79. (h) Toniolo, C.; Bonora, G. M.; Bavoso, A.; Benedetti, E.; Di Blasio, B.; Pavone, V.; Pedone, C. Biopolymers 1983, 22, 205-215.
80. (i) Rajashankar, K. R.; Ramakumar, S.; Chauhan, V. S. J. Am. Chem. Soc. 1992, 114, 9225-9226.
81. (j) Jain, R. M.; Rajashankar, K. R.; Ramakumar, S.; Chauhan, V. S. J. Am. Chem. Soc. 1997, 119, 3205-3211.
82. (k) Ramagopal, U. A.; Ramakumar, S.; Sahal, D.; Chauhan, V. S. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 870-874.
83. (l) Ciajolo, M. R.; Tuzi, A.; Pratesi, C. R.; Fissi, A.; Pieroni, O. Biopolymers 1990, 30, 911-920.
84. (m) Ciajolo, M. R.; Tuzi, A.; Pratesi, C. R.; Fissi, A.; Pieroni, O. Biopolymers 1992, 32, 717-724.
85. (n) Mitra, S. N.; Dey, S.; Karthikeyan, S.; Singh, T. P. Biopolymers 1997, 41, 97-105.
86. (o) Chauhan, V. S.; Uma, K.; Kaur, P.; Balaram, P. Biopolymers 1989, 28, 763-771.
87. (p) Gupta, A.; Bharadwaj, A.; Chauhan, V. S. J. Chem. Soc., Perkin Trans. 2 1990, 1911-1916.
88. (a) Inai, Y.; Oshikawa, T.; Yamashita, M.; Tagawa, K.; Hirabayashi, T. Biopolymers 2003, 70, 310-322.
89. (b) Inai, Y.; Oshikawa, T.; Yamashita, M.; Hirabayashi, T.; Ashitaka, S. J. Chem. Soc., Perkin. Trans. 2 2001, 892-897.
90. Nandel, F. S.; Khare, B. Biopolymers 2005, 77, 63-73.
91. zPhe-containing peptides, see: (a) Pieroni, O.; Fissi, A.; Jain, R. M.; Chauhan, V. S. Biopolymers 1996, 38, 97-108.
92. (b) Pieroni, O.; Montagnoli, G.; Fissi, A.; Merlino, S.; Ciardelli, F. J. Am. Chem. Soc. 1975, 97, 6820-6826.
93. ZPhe)n-, see:
94. (d) Komori, H.; Inai, Y. J. Phys. Chem. A 2006, 110, 9099-9107.
95. For the exciton chirality method, see: (a) Harada, N.; Chen, S. L.; Nakanishi, K. J. Am. Chem. Soc. 1975, 97, 5345-5352.
96. (b) Harada, N.; Nakanishi, K. Circular Dichroic Spectroscopy. Exciton Coupling in Organic Stereochemistry; University Science Books: Mill Valley, CA, 1983.
97. Elegant models have been proposed for the remote control of conformational information along a molecular frame: (a) Clayden, J.; Lund, A.; Vallverdu, L.; Helliwell, M. Nature 2004, 437, 966-971.
98. (b) Mizutani, T.; Sakai, N.; Yagi, S.; Takagishi, T.; Kitagawa, S.; Ogoshi, H. J. Am. Chem. Soc. 2000, 722, 748-749.
99. (a) Johnson, N. P.; Baase, W. A.; von Hippel, P. H. Proc. Natl. Acad. Sci.U.S.A. 2004,707,3426-3431.
100. (b)Johnson,N.P.;Baase,W.A.;vonHippel, P. H. Proc. Natl. Acad. Sci. U.S.A. 2005, 702, 7169-7173.
101. (c) Inai, Y.; Sisido, M.; Imanishi, Y. J. Phys. Chem. 1990, 94, 6237-6243.
102. (d) Inai, Y.; Sisido, M.; Imanishi, Y. J. Phys. Chem. 1990, 94, 8365-8370.
103. (21) For allosteric proteins, see: Monod, J.; Changeux, J. P.; Jacob, F. J.
104. Mol. Biol. 1963, 6, 306-329.
105. (a) Shinkai, S.; Ikeda, M.; Sugasaki, A.; Takeuchi, M. Acc. Chem. Res.
106. 2001, 34, 494-503. (b) Takeuchi, M.; Ikeda, M.; Sugasaki, A.; Shinkai, S. Acc. Chem. Res. 2001, 34, 865-873.
107. (c) Kovbasyuk, L.; Kramer, R. Chem. Rev. 2004, 704, 3161-3187.
108. 3-helix, see ref14g. See also: Barlow, D. J.; Thornton, J. M. J. Mol. Biol. 1988, 207, 601-619.
109. 10a-d Thus the choice of the N-terminal amino acid or Boc-amino acid is not an essential factor in the current theme.
110. (a) Inai, Y.; Oshikawa, T.; Yamashita, M.; Hirabayashi, T.; Hirako, T. Biopolymers 2001, 58, 9-19.
111. (b) Inai, Y.; Hirabayashi, T. Biopolymers 2001, 59, 356-369.
112. (c) Inai, Y.; Oshikawa, T.; Yamashita, M.; Hirabayashi, T.; Kurokawa, Y. Bull. Chem. Soc. Jpn. 2001, 74, 959-966.
113. (a) Kuragaki, M.; Sisido, M. J. Phys. Chem. 1996, 100, 16019-16025.
114. (b) Butterfield, S. M.; Patel, P. R.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9751-9755.
115. Although FT-IR absorption data of peptide 3 were reported in ref 10a, the data have been updated here. FT-IR absorption spectra of 2 and 3 are shown in Figure S1, Supporting Information.
116. (a) Inai, Y.; Sakakura, Y.; Hirabayashi, T. Polym. J. 1998, 30, 828-832.
117. zPhe residues, see:
118. (c) Gupta, A.; Mehrotra, R.; Tewari, J.; Jain, R. M.; Chauhan, V. S. Biopolymers 1999, 50, 595-601.
119. For example, see refs 10, 11, 13, 14o, 14p, and 15.
120. For intramolecular hydrogen-bonding NH and temperature coefficient, see: (a) Andersen, N. H.; Neidigh, J. W.; Harris, S. M.; Lee, G. M.; Liu, Z.; Tong, H. J. Am. Chem. Soc. 1997, 119, 8547-8561.
121. (b) Baxter, N. J.; Williamson, M. P. J. Biomol. NMR 1997, 9, 359-369.
122. (c) Stevens, E. S.; Sugawara, N.; Bonora, G. M.; Toniolo, C. J. Am. Chem. Soc. 1980, 102, 7048-7050.
123. 10b,c
124. Pitner, T. P.; Urry, D. W. J. Am. Chem. Soc. 1972, 94, 1399-1400.
125. (a) Gaussian 03, Revision C.02 Frisch, M. J. et al. Gaussian, Inc.: Wallingford CT, 2004. (b) For the manual and full references for Gaussian 03, see also: The Official Gaussian 03 Website (http://www.gaussian.com/).
126. For the AM1 method, see: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 707, 3902-3909.
127. For the B3LYP method, see: (a) Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
128. (b) Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627.
129. (c) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev.B. 1988, 37, 785-789.
130. Foresman, J. B.; Frisch, iE. Exploring Chemistry with Electronic Structure Methods, 2nd ed.; Gaussian, Inc.: Pittsburgh, PA, 1996; Chapters 6-7.
131. For molecular graphics in the present paper, see: Thompson, M. A. ArgusLab 4.0.7; Planaria Software LLC: Seattle, WA (http://www.arguslab. com).
132. (a) Pavone, V.; Benedetti, E.; Di Blasio, B.; Pedone, C.; Santini, A.; Bavoso, A.; Toniolo, C.; Crisma, M.; Sartore, L. J. Biomol. Struct. Dyn. 1990, 7, 1321-1331.
133. (b) Karle, I. L.; Flippen-Anderson, J. L.; Gurunath, R.; Balaram, P. Protein Sci. 1994, 3, 1547-1555.
134. (c) Fiori, W. R.; Miick, S. M.; Millhauser, G. L. Biochemistry 1993, 32, 11957-11962.
135. (d) Basu, G.; Kuki, A. Biopolymers 1992, 32, 61-71.
136. 10a the updated data were analyzed. The values ranging between 17 and 25 indicate similar interaction for the chiral induction.
137. For the nature of helix termini in proteins and peptides, see: (a) Aurora, R.; Rose, G. D. Protein Sci. 1998, 7, 21-38.
138. (b) Baldwin, R. L.; Rose, G. D. Trends Biochem. Sci. 1999, 24, 26-33.
139. (c) Harper, E. T.; Rose, G. D. Biochemistry 1993, 32, 7605-7609.
140. (d) Seale, J. W.; Srinivasan, R.; Rose, G. D. Protein Sci. 1994, 3, 1741-1745.
141. (e) Karpen, M. E.; DeHaseth, P. L.; Neet, K. E. Protein Sci. 1992, 7, 1333-1342.
142. For the ZINDO/S method, see: (a) Ridley, J. E.; Zerner, M. C. Theor. Chim. Acta 1973, 32, 111-134.
143. (b) Ridley, J. E.; Zerner, M. C. Theor. Chim. Acta 1976, 42, 223-236.
144. (c) Zerner, M. C.; Loew, G. H.; Kirchner, R. F.; Mueller-Westerhoff, U. T. J. Am. Chem. Soc. 1980, 702, 589-599.
145. (d) Thompson, M. A.; Zerner, M. C. J. Am. Chem. Soc. 1991, 773, 8210-8215.
146. A similar helical arrangement of each TDM in the length form was obtained; see Figure S12, Supporting Information.
147. For the ZINDO-based CD simulation, see: (a) Telfer, S. G.; Tajima, N.; Kuroda, R. J. Am. Chem. Soc. 2004, 726, 1408-1418.
148. (b) Ankai, E.; Sakakibara, K.; Uchida, S.; Uchida, Y.; Yokoyama, Y.; Yokoyama, Y. Bull. Chem. Soc. Jpn. 2001, 75, 1101-1108.
149. (c) Kawai, M.; Nagai, U.; Inai, Y.; Yamamura, H.; Akasaka, R.; Takagi, S.; Miwa, Y.; Taga, T. Biopolymers 2005, 80, 186-198.
150. (d) Fujii, T.; Shiotsuki, M.; Inai, Y.; Sanda, F.; Masuda, T. Macromolecules 2007, 40, 7079-7088.
151. The TD SCF MO method for simulation of CD spectra has been recently advanced: (a) Stephens, P. J.; McCann, D. M.; Devlin, F. J.; Cheeseman, J. R.; Frisch, M. J. J. Am. Chem. Soc. 2004, 126, 7514-7521.
152. (b) Furche, F.; Ahlrichs, R.; Wachsmann, C.; Weber, E.; Sobanski, A.; Vogtle, F.; Grimme, S. J. Am. Chem. Soc. 2000, 122, 1717-1724.
153. (c) Autschbach, J.; Ziegler, T.; Gisbergen, S. J. A.; Baerends, E. J. J. Chem. Phys. 2002, 116, 6930-6940.
154. (d) Diedrich, C.; Grimme, S. J. Phys. Chem. A 2003, 107, 2524-2539.
155. (e) Brown, A.; Kemp, C. M.; Mason, S. F. J. Chem. Soc. 1971, 751-755.
156. zBip-NMA (Ac = acetyl; NMA = N-methylamide) were produced by using the atomic coordinates extracted from the 310-helical structures of1-2 (Figure S13, Supporting Information). CD spectra of these short helical fragments, obtained from both the DFT and ZINDO/S methods, yielded split-type CD patterns essentially (Figure S13, Supporting Information). Split CD patterns were shifted to a longer wavelength with increasing the aromatic size of ΔAA residue. At the DFT method, there is no essential difference between the velocity- and length-based CD spectra of which all are identified as split-type patterns. Meanwhile, at the ZINDO/S method, the velocity-based CD spectra are regarded as split types, but such split patterns are distorted in the length-based spectra of 1-4 and 1-2. As a result, CD profiles at the DFT level were essentially obtained by using velocity-based parameters at the ZINDO/S level. This supports the validity of the current CD simulation of 1-m.
157. Forinstance, see: (a) Toniolo, C.; Crisma, M.; Bonora, G. M.; Benedetti, E.; Di Blasio, B.; Pavone, V.; Pedone, C.; Santini, A. Biopolymers 1991, 37, 129-138.
158. (b) Gessmann, R.; Bruckner, H.; Petratos, K. J. Pept. Sci. 2003, 9, 753-762.
159. (c) Rudresh; Gupta, M.; Ramakumar, S.; Chauhan, V. S. Biopolymers 2005, 80, 617-627.
160. (d) Ramagopal, U. A.; Ramakumar, S.; Mathur, P.; Joshi, R.; Chauhan, V. S. Protein Eng. 2002, 75, 331-335.
161. (e) Pavone, V.; Di Blasio, B.; Santini, A.; Benedetti, E.; Pedone, C.; Toniolo, C.; Crisma, M. J. Mol. Biol. 1990, 274, 633-635.
162. For instance, see: Malcolm, B. R.; Walkinshaw, M. D. Biopolymers 1986, 25, 607-625.
163. (a) Kottas, G. S.; Clarke, L. I.; Horinek, D.; Michl, J. Chem. Rev. 2005, 105, 1281-1376.
164. (b) Feringa, B. L. Acc. Chem. Res. 2001, 34, 504-513.
165. (c) Kinbara, K.; Aida, T. Chem. Rev. 2005, 105, 1377-1400.
166. (d) Kelly, T. R. Acc. Chem. Res. 2001, 34, 514-522.
167. Absolute CD values of (1S)- and (1R)-CSAAS were assumed to be the same. For the calibration with (1 S)-CSAAS, see the spectroscopic manual of JASCO J-820.
168. See also: Takakuwa, T.; Konno, T.; Meguro, H. Anal. Sci. 1985, 1, 215-218.
169. Bodenhausen, G.; Kogler, H.; Ernst, R. R. J. Maen. Reson. 1984, 58, 370-388.
170. Wuthrich, K. NMR of Proteins and Nucleic Acids; John Wiley and Sons: New York, 1986.
171. Marat, K. SpinWorks; University of Manitoba: Canada, 1999-2006 (http://www.umanitoba.ca/chemistry/nmr/spinworks/index.html).
172. (a) Paterson, Y.; Rumsey, S. M.; Benedetti, E.; Nemethy, G.; Scheraga, H. A. J. Am. Chem. Soc. 1981, 703, 2947-2955.
173. (b) Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436.
174. (a) Arnott, S.; Dover, S. D. J. Mol. Biol. 1967, 30, 209-212.
175. (b) Arnott, S.; Wonacott, A. J. J. Mol. Biol. 1966, 27, 371-383.
176. (c) IUPAC-IUB Commission on Biochemical Nomenclature. Biochemistry 1970, 9, 3471-3479. For the definition of torsion angles for peptide conformation, see ref 54c.
177. (a) Ajo, D.; Casarin, M.; Granozzi, G. J. Mol. Struct. (THEOCHEM)1982, 86, 297-300.
178. (b) For the side chain conformation (%2)of AAA residues, see also ref 25c.
179. (a) Hafelinger, G.; Regelmann, C. J. Comput. Chem. 1987, 8, 1057-1065.
180. (b) Tsuzuki, S.; Tanabe, K. J. Phys. Chem. 1991, 95, 139-144.
181. zPhe-phenyl group by the biphenyl group, see: GaussView 3.09, Dennington, R., III.; Keith, T.; Millam, J.; Eppinnett, K.; Hovell, W. L.; Gilliland, R. Semichem, Inc.: Shawnee Mission, KS, 2003.