Water-Mediated Association Provides an Ion Pair Receptor

Journal of the American Chemical Society

Volumn 125, Issue 49, 2003, Pages 15140-15150

  Kotch, Frank W ^a   Sidorov, Vladimir ^a   Lam, Yiu Fai ^a   Kayser, Katherine J ^a   Li, Hojun ^a   Kaucher, Mark S ^a   Davis, Jeffery T ^a  

^a University of Maryland   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ION PAIR RECEPTOR;

CHROMATOGRAPHIC ANALYSIS; DIFFUSION; DIMERIZATION; DIMERS; NUCLEAR MAGNETIC RESONANCE; POSITIVE IONS; SALTS; STOICHIOMETRY;

WATER;

CALIX[4]ARENE; CALIXARENE; DIMER; GUANOSINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; DIFFUSION COEFFICIENT; EXTRACTION; ION PAIR CHROMATOGRAPHY; MOLECULAR MECHANICS; PRECIPITATION; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; SOLUBILITY; STOICHIOMETRY; THERMOSTABILITY;

CALIXARENES; CIRCULAR DICHROISM; DIMERIZATION; GUANOSINE; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR CONFORMATION; PHENOLS; WATER;

EID: 0344667432     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0364165     Document Type: Article

References (109)

1. Westhof, E., Ed.; Water and Biological Macromolecules: CRC Press: Boca Raton, FL, 1993.
2. Dunitz, J. D. Science 1994, 264, 670.
3. (a) Ladbury, J. E. Chem. Biol. 1996, 3, 973-980.
4. (b) Janin, J. Struct. Fold. Des. 1999, 7, R277-R279.
5. Bhat, T. N.; Bentley, G. A.; Boulot, G.; Greene, M. I.; Tello, D.; Dallacqua, W.; Souchon, H.; Schwarz, F. P.; Mariuzza, R. A.; Poljak, R. J. Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 1089-1093.
6. For references on structure: (a) Drew, H. R.; Dickerson, R. E. J. Mol. Biol. 1981, 151, 535-556.
7. (b) Shui, X. Q.; McFail-Isom, L.; Hu, G. G.; Williams, L. D. Biochemistry 1998, 37, 8341-8355.
8. This hydration spine is critical for the thermodynamic stability of duplex DNA: Lan, T.; McLaughlin, L. W. J. Am. Chem. Soc. 2000, 122, 6512-6513.
9. Schirmer, T.; Evans, P. R. Nature 1990, 343, 140-145.
10. Adrian, J. C.; Wilcox, C. S. J. Am. Chem. Soc. 1992, 114, 1398-1403.
11. Bonar-Law, R. P.; Sanders, J. K. M. J. Am. Chem. Soc. 1995. 117, 259-271.
12. Arena, G.; Casnati, A.; Mirone, L.; Sciotto, D.; Ungaro, R. Tetrahedron Lett. 1997, 38, 1999-2002.
13. Far, A. R.; Shivanyuk, A.; Rebek, J., Jr. J. Am. Chem. Soc. 2002, 124, 2854-2855.
14. (a) Murayama, K.; Aoki, K. Chem. Commun. 1998, 607-608.
15. (b) Shivanyuk, A.; Rissanen, K.; Kolehmainen, E. Chem. Commun. 2000, 1107-1108.
16. (c) Mansikkamaki, H.; Nissinen, M.; Rissanen, K. Chem. Commun. 2002, 1902-1903.
17. (a) Shivanyuk, A.; Rebek, J., Jr. Chem. Commun. 2001, 2374-2375.
18. (b) Shivanyuk, A.; Friese, J. C.; Doring, S.; Rebek, J., Jr. J. Org. Chem. 2003, 68, 6489-6496.
19. MacGillivray, L. R.; Atwood, J. L. Nature 1997, 389, 469-472.
20. (a) Shivanyuk, A.; Rebek, J., Jr. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 7662-7665.
21. (b) Shivanyuk, A.; Rebek, J., Jr. Chem. Commun. 2001, 2424-2425.
22. (a) Avram, L.; Cohen, Y. J. Am. Chem. Soc. 2002, 124, 15 148-15 149.
23. (b) Avram, L.; Cohen, Y. Org. Lett. 2002, 4, 4365-4368.
24. (c) Avram, L.; Cohen, Y. Org. Lett. 2003, 5, 1099-1102.
25. Shivanyuk, A.; Rebek, J., Jr. J. Am. Chem. Soc. 2003, 125, 3432-3233.
26. (a) Perez, C.; Espinola, G.; Foces-Foces, C.; Nunez-Coello, P.; Carrasco, H.; Martin, J. D. Org. Lett. 2000, 2, 1185-1188.
27. (b) Carrasco, H.; Foces-Foces, C.; Perez, C.; Rodriguez, M. L.; Martin, J. D. J. Am. Chem. Soc. 2001, 123, 11 970-11 981.
28. Hong, B. H.; Lee, J. Y.; Lee, C. W.; Kim, J. C.; Bae, S. C.; Kim, K. S. J. Am. Chem. Soc. 2001, 123, 10 748-10 749.
29. Sidorov, V.; Kotch, F. W.; Abdrakhmanova, G.; Mizani, R.; Fettinger, J. C.; Davis, J. T. J. Am. Chem. Soc. 2002, 124, 2267-2278.
30. For a recent review, see: Kirkovits, G. J.; Shriver, J. A.; Gale, P. A.; Sessler, J. L. J. Incl. Phenom. Macrocycl. Chem. 2001, 41, 69-75.
31. Selected examples: (a) Reetz, M. T.; Niemeyer, C. M.; Harms, K. Angew. Chem., Int. Ed. Engl. 1991, 30, 1472-1474.
32. (b) Scheerder, J.; van Duynhoven, J. P. M.; Engbersen, J. F. J.; Reinhoudt, D. N. Angew. Chem., Int. Ed. Engl. 1996, 35, 1090-1093.
33. (c) Mahoney, J. M.; Beatty, A. M.; Smith, B. D. J. Am. Chem. Soc. 2001, 123, 5847-5848.
34. (d) Deetz, M. J.; Shang, M.; Smith, B. D. J. Am. Chem. Soc. 2000, 122, 6201-6207.
35. (e) Koulov, A. V.; Mahoney, J. M.; Smith, B. D. Org. Biomol. Chem. 2003, 1, 27-29.
36. (f) Webber, P. R. A.; Beer. P. D. J. Chem. Soc., Dalton Trans. 2003, 2249-2252.
37. For a hydrogen bond based assembly that binds cations and organic anions: (a) Shi, X.; Fettinger, J. C.; Davis, J. T. Angew. Chem., Int. Ed. 2001, 40, 2827-2831.
38. (b) Shi, X.; Mullaugh, K. M.; Fettinger, J. C.; Jiang, Y.; Hofstadler, S. A.; Davis, J. T. J. Am. Chem. Soc. 2003, 125, 10830-10841.
39. For an approach that uses coordination chemistry to build a LiCl receptor: Piotrowski, H.; Severin, K. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 4997-5000.
40. Other ion pair receptors that are formed by noncovalent self-assembly: (a) Casnati, A.; Massera, C.; Pelizzi, N.; Stibor, I.; Pinkassik, E.; Ugozzoli, F.; Ungaro, R. Tetrahedron Lett. 2002, 43, 7311-7314.
41. (b) Barboiu, M.; Vaughan, G.; van der Lee, A. Organic Lett. 2003, 5, 3073-3076.
42. There are many dimeric calixarenes. For a review, see: (a) Hof, F.; Craig, S. L.; Nuckolls, C.; Rebek, J., Jr. Agew. Chem., Int. Ed. 2002, 41, 1488-1508.
43. For recent examples of calix[4]arene dimers, see: (b) Vysotsky, M. O.; Thondorf, I.; Böhmer, V. Angew. Chem., Int. Ed. 2000, 39, 1264-1267.
44. (c) Castellano, R. K.; Craig, S. L.; Nuckolls, C.; Rebek, J., Jr. J. Am. Chem. Soc. 2000, 122, 7876-7882.
45. (d) Rincon, A. M.; Prados, P.; de Mendoza, J. J. Am. Chem. Soc. 2001, 123, 3493-3498.
46. (e) Corbellini, F.; Fiammengo, R.; Timmerman, P.; Crego-Calama, M.; Versluis, K.; Heck, A. J. R.; Luyten, I.; Reinhoudt, D. N. J. Am. Chem. Soc. 2002, 124, 6569-6575.
47. (f) Brewster, R. E.; Shuker, S. B. J. Am. Chem. Soc. 2002, 124, 7902-7903.
48. (h) Corbellini, F.; Di Costanzo, L.; Crego-Calama, M.; Geremia, S.; Reinhoudt, D. N. J. Am. Chem. Soc. 2003, 125, 9946-9947.
49. G-quartet review: Guschlbauer, W.; Chantot, J. F.; Thiele, D. J. Biomol. Struct. Dyn. 1990, 8, 491-511.
50. Gottarelli, G.; Masiero, S.; Spada, G. P. Chem. Commun. 1995, 2555-2557.
51. Forman, S. L.; Fettinger, J. C.; Pieraccini, S.; Gottarelli, G.; Davis, J. T. J. Am. Chem. Soc. 2000, 122, 4060-4067.
52. For other calix[4]arene-nucleosides, see: (a) Vreekamp, R. H.; Verboom, W.; Reinhoudt, D. N. Rec. Trav. Chim. Pays-Bas 1996, 115, 363-370.
53. (b) Zeng, C.-C.; Tang, Y.-L.; Zheng, Q.-Y.; Huang, L.; Xin, B.; Huang, Z.-T. Tetrahedron Lett. 2001, 42, 6179-6181.
54. (c) Zeng, C.-C.; Zheng, Q.-Y.; Tang, Y.-L.; Huang, Z.-T. Tetrahedron 2003, 59, 2539-2548.
55. (d) Kim, S. J.; Kim, B. H. Nucleic Acids Res. 2003, 31, 2725-2734.
56. (a) Ikeda, A.; Shinkai, S. Chem. Commun. 1994, 2375-2376.
57. (b) Mislin, G.; Graf, E.; Hosseini, M. W.; De Cian, A.; Kyntsakas, N.; Fischer, J. Chem. Commun. 1998, 2545-2546.
58. (c) Jaunky, W.; Hosseini, M. W.; Planeix, J. M.; De Cian, A.; Kyritsakas, N.; Fischer. J. Chem. Commun. 1999, 2313-2314.
59. (d) Kleina, C.; Graf, E.; Hosseini, M. W.; De Cian, A.; Fischer, J. Chem. Commun. 2000, 239-240.
60. (e) Budka, J.; Lhotak, P.; Stibor, I.; Sykora, J.; Cisarova, I. Supramol. Chem. 2003, 15, 353-357.
61. de Mendoza, J.; Cuevas, F.; Prados, P.; Meadows, E. S.; Gokel, G. W. Angew. Chem., Int. Ed. 1998. 37, 1534-1537.
62. Sidorov, V.; Kotch, F. W.; El-Khouedi, M.; Davis, J. T. Chem. Commun. 2000, 2369-2370.
63. An adenosine tetrad in a DNA oligonucleotide occurs only when stacked above a G-quadruplex: Patel, P. K.; Koti, A. S. R.; Hosur, R. V. Nucleic Acids Res. 1999, 27, 3836-3843.
64. Huang, Z. T.; Wang, G. Q.; Yang, L. M.; Lou, Y. X. Synth. Commun. 1995, 25, 1109-1118.
65. (a) Verboom. W.; Datta, S.; Asfari, Z.; Harkema, S.; Reinhoudt, D. N. J. Org. Chem. 1992, 57, 5394-5398.
66. (b) Iwamoto, K.; Shinkai, S. J. Org. Chem. 1992, 57, 7066-7073.
67. Li, H.; Miller, M. J. J. Org. Chem. 1999, 64, 9289-9293.
68. Seela, F.; Ott, J.; Potter, B. V. L. J. Am. Chem. Soc. 1983, 105, 5879-5886.
69. Attempts to convert 11 directly to 14 under Mitsunobu conditions failed due to N2 iminophosphorane formation, thus necessitating use of the protecting group.
70. Iminophosphorane formation under Mitsunobu conditions at guanine N2 has been previously described: Chien, T. C.; Chen, C. S.; Yeh, J. Y.; Wang, K. C.; Chern, J. W. Tetrahedron Lett. 1995, 36, 7881-7884.
71. Parzuchowski, P.; Böhmer, V.; Biali, S. E.; Thondorf, I. Tetrahedron: Asymmetry 2000, 11 2393-2402.
72. 3, see refs 12b and 13.
73. 6 concentration due to denaturation of the hydrogen-bonded dimer.
74. - binding.
75. Marcus, Y. J. Chem. Soc., Faraday Trans. 1991, 87, 2995-2999.
76. +." Hud, N. V.; Smith, F. W.; Anet. F. A. L.; Feigon, J. Biochemistry 1996, 35, 15 383-15 390.
77. (a) Stejskal, E. O.; Tanner, J. E. J. Chem. Phys. 1965, 42, 288-292.
78. (b) Tanner, J. E. J. Chem. Phys. 1970, 52, 2523-2526.
79. n had a large unit cell (a = 26 Å, b = 30.6 Å, c = 30.8 Å) but they did not diffract strongly enough to obtain a structure.
80. (a) Altieri, A. S.; Hinton, D. P.; Byrd, R. A. J. Am. Chem. Soc. 1995. 117, 7566-7567.
81. (b) Krishnan, V. V. J. Magn. Reson. 1997, 124, 468-473.
82. (a) Gafni, A.; Cohen, Y. J. Org. Chem. 1997, 62, 120-125.
83. (b) Frish, L.; Matthews, S. E.; Böhmer, V.; Cohen, Y. Perkin Trans. 2 1999, 669-671.
84. (c) Timmerman, P.; Weidmann, J. L.; Jolliffe, K. A.; Prins, L. J.; Reinhoudt, D. N.; Shinkai, S.; Frish, L.; Cohen, Y. Perkin Trans. 2 2000, 2077-2089.
85. (d) Frish, L.; Sansone, F.; Casnati, A.; Ungaro, R.; Cohen, Y. J. Org. Chem. 2000, 65, 5026-5030.
86. (e) Cameron, K. S.; Fielding, L. J. Org. Chem. 2001, 66, 6891-6895.
87. Lo, M. C.; Helm, J. S.; Sarngadharan, G.; Pelczer, I.; Walker, S. J. Am. Chem. Soc. 2001, 123, 8640-8641.
88. ten Cate, A. T.; Dankers, P. Y. W.; Kooijman, H.; Speck, A. L.; Sijbesma, R. P.; Meijer, E. W. J. Am. Chem. Soc. 2003, 125, 6860-6861.
89. Wills, P. R.; Georgalis, Y. J. Phys. Chem. 1981, 85, 3978-3984.
90. de la Torre, J. G.; Bloomfield, V. A. Q. Rev. Biophys. 1981, 14, 81-139.
91. Otto, W. H.; Keefe, M. H.; Splan, K. E.; Hupp, J. T.; Larive, C. K. Inorg. Chem. 2002, 41, 6172-6174.
92. Marlow, A. L.; Mezzina, E.; Spada, G. P.; Masiero, S.; Davis, J. T.; Gottarelli, G. J. Org. Chem. 1999, 64, 5116-5123.
93. Otting, G. Prog. Nucl. Magn. Reson. Spectrosc. 1997, 31, 259-285.
94. (a) Newby, M. I.; Greenbaum, N. L. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12 697-12 702.
95. (b) Bagno, A.; Campulla, M.; Pirana, M.; Scorrano, G.; Stiz, S. Chem.-Eur. J. 1999, 5, 1291-1300.
96. (c) Angulo, M.; Hawat, C.; Hofmann, H. J.; Berger, S. Org. Biomol. Chem. 2003, 1, 1049-1052.
97. (d) Pinkhassik, E.; Sidorov, V.; Stibor, I. J. Org. Chem. 1998, 63, 9644-9651.
98. (a) Arimura, T.; Kawabata, H.; Matsuda, T.; Muramatsu, T.; Satoh, H.; Fujio, K.; Manabe, O.; Shinkai, S. J. Org. Chem. 1991, 56, 301-306.
99. (b) Ikeda, A.; Nagasaki, T.; Shinkai, S. J. Phys. Org. Chem. 1992, 5, 699-710.
100. Castellano, R. K.; Nuckolls, C.; Rebek, J., Jr. J. Am. Chem. Soc. 1999, 121, 11 156-11 163.
101. Gottarelli, G.; Masiero, S.; Spada, G. P. Enantiomer 1998, 3, 429-436.
102. For a review on noncovalent polymers, see: Brunsveld, L.; Folmer, B. J. B.; Meijer, E. W.; Sijbesma, R. P. Chem. Rev. 2001, 101, 4071-4097.
103. 1,3-alternate calixarenes can exhibit allosteric effects induced by conformational change. (a) For a negative allosteric effect, see: Budka, J.; Lhotak, P.; Michlova, V.; Stibor, I. Tetrahedron Lett. 2001, 42, 1583-1586.
104. (b) For a positive allosteric effect, see ref 22b.
105. A templating cation is not always required for G-quartet formation; see: Sessler, J. L.; Sathiosatham, M.; Doerr, K.; Lynch, V.; Abboud, K. A. Angew. Chem., Int. Ed. 2000, 39, 1300-1303.
106. Gellert, M.; Lipsett, M. N.; Davies, D. R. Proc. Natl. Acad. Sci. U. S. A. 1962, 48, 2013-2018.
107. X-ray structures of DNA G-quadruplexes show that the coordination spheres of terminal cations are completed by water: (a) Phillips, K.; Dauter, Z.; Murchie, A. I. H.; Lilley, D. M. J.; Luisi, B. J. Mol. Biol. 1997, 273, 171-182.
108. (b) Horvath, M. P.; Schultz, S. C. J. Mol. Biol. 2001, 310, 367-377.
109. (c) Haider, S.; Parkinson, G. N.; Neidle, S. J. Mol. Biol. 2002, 320, 189-200.