Helical Aromatic Oligoamides
A R T I C L E S
fied backbone forces an oligomer of a sufficient length to adopt
a helical conformation containing a large, hydrophilic interior
cavity. Our previous results revealed that the helical conforma-
tion was present both in solution and in solid state. The folded
structures were independent of the nature of the side chains
carried by the corresponding oligomers. Despite their rigidity,
the folded conformations of these oligoamides are effected by
reversible intramolecular H-bonding interactions. These oligo-
mers are therefore true foldamers that should undergo dynamic
exchange between folded and partially folded (or even unfolded)
states as environmental factors such as temperature and solvent
change. To use these backbone-rigidified folding oligomers as
reliable, shape-persistent molecular building blocks for con-
structing large nanostructures, it is necessary to understand the
stability of their folded conformations. For example, although
we previously found that the three-center H-bonds were
stabilized by positive cooperativity, it is still not clear how these
three-center H-bonds, which play the critical role of defining
the local conformational preference, would differ in their
stabilities when placed in different locations along the backbone
of a folded oligomer. What is the effect of temperature change
on the overall folded conformation of an oligomer? Another
concern about these oligomers is related to their H-bond-
rigidified backbones. Is it possible that in long oligomers, the
steric hindrance becomes so severe that some of the backbone-
rigidifying intramolecular H-bonded rings will be broken,
leading to interruption of the H-bonded crescent and helical
conformations? Finally, since long oligomers are constructed
by simple repetition of the same structural motif and local
conformational preference, is it possible to accurately predict
the folded conformations of long oligomers based on structural
data from their shorter homologues?
In this paper, we first describe a method for quantifying the
stability of the local three-center H-bonds based on the deter-
mination of the half-lives of amide proton-deuterium exchange.
We then investigate the effect of temperature changes on the
folded helical conformation of nonamer (9-mer) 1. To probe
the effect of chain length on folded conformations, we synthe-
sized and characterized undecamer (11-mer) 2. Results from
extensive NMR studies suggest that this longer oligomer still
adopts H-bond enforced, helical conformations. Finally, we have
developed a modeling method for predicting the folded struc-
tures of oligomers 1b and 2b based on data from the crystal
structures of short oligoamides. The reliability of the modeled
structures was shown by their excellent agreement with results
from two-dimensional (2D) nuclear Overhauser enhancement
spectroscopy (NOESY) studies.
(18) (a) Goto, H.; Heemstra, J. M.; Hill, D. J.; Moore, J. S. Org. Lett. 2004, 6,
889. (b) Heemstra, J. M.; Moore, J. S. Org. Lett. 2004, 6, 659. (c) Heemstra,
J. M.; Moore, J. S. J. Am. Chem. Soc. 2004, 126, 1648. (d) Stone, M. T.;
Moore, J. S. Org. Lett. 2004, 6, 469. (e) Oh, K.; Jeong, K. S.; Moore, J. S.
J. Org. Chem. 2003, 68, 8397. (f) Cary, J. M.; Moore, J. S. Org. Lett.
2002, 4, 4663. (g) Matsuda, K.; Stone, M. T.; Moore, J. S. J. Am. Chem.
Soc. 2002, 124, 11836. (h) Zhao, D. H.; Moore, J. S. J. Am. Chem. Soc.
2002, 124, 9996. (i) Hill, D. J.; Moore, J. S. Proc. Natl. Acad. Sci. U.S.A.
2002, 99, 5053. (j) Tanatani, A.; Hughes, T. S.; Moore, J. S. Angew. Chem.,
Int. Ed. 2001, 41, 325. (k) Oh, K.; Jeong, K. S.; Moore, J. S. Nature 2001,
414, 889. (l) Prince, R. B.; Moore, J. S.; Brunsveld, L.; Meijer, E. W.
Chem.-Eur. J. 2001, 7, 4150. (m) Brunsveld, L.; Meijer, E. W.; Prince, R.
B.; Moore, J. S. J. Am. Chem. Soc. 2001, 123, 7978. (n) Tanatani, A.;
Mio, M. J.; Moore, J. S. J. Am. Chem. Soc. 2001, 123, 1792. (o) Lahiri, S.;
Thompson, J. L.; Moore, J. S. J. Am. Chem. Soc. 2000, 122, 11315. (p)
Mio, M. J.; Prince, R. B.; Moore, J. S.; Kuebel, C.; Martin, D. C. J. Am.
Chem. Soc. 2000, 122, 6134. (q) Yang, W. Y.; Prince, R. B.; Sabelko, J.;
Moore, J. S.; Gruebele, M. J. Am. Chem. Soc. 2000, 122, 3248. (r) Prince,
R. B.; Barnes, S. A.; Moore, J. S. J. Am. Chem. Soc. 2000, 122, 2758. (s)
Prest, P. J.; Prince, R. B.; Moore, J. S. J. Am. Chem. Soc. 1999, 121, 5933.
(t) Prince, R. B.; Saven, J. G.; Wolynes, P. G.; Moore, J. S. J. Am. Chem.
Soc. 1999, 121, 3114. (u) Gin, M. S.; Yokozawa, T.; Prince, R. B.; Moore,
J. S. J. Am. Chem. Soc. 1999, 121, 2643. (v) Prince, R. B.; Okada, T.;
Moore, J. S. Angew. Chem., Int. Ed. 1999, 38, 233. (w) Nelson, J. C.;
Saven, J. G.; Moore, J. S.; Wolynes, P. G. Science 1997, 277, 1793.
(19) (a) Gabriel. G. J.; Iverson, B. L. J. Am. Chem. Soc. 2002, 124, 15174. (b)
Zych, A. J.; Iverson, B. L. J. Am. Chem. Soc. 2000, 122, 8898. (c) Nguyen,
J. Q.; Iverson, B. L. J. Am. Chem. Soc. 1999, 121, 2639. (d) Lokey, R. S.;
Iverson, B. L. Nature 1995, 375, 303. (e) Nowick, J. S.; Cary, J, M.; Tsai,
J. H. J. Am. Chem. Soc. 2001, 123, 5176. (f) Nowick, J. S.; Mahrus, S.;
Smith, E. M.; Ziller, J. W. J. Am. Chem. Soc. 1996, 118, 1066. (g) Hagihara,
M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber, S. L. J. Am. Chem.
Soc. 1992, 114, 6568. (h) Gennari, C.; Salom, B.; Potenza, D.; Williams,
A. Angew. Chem., Int. Ed. Engl. 1994, 33, 2067. (i) Cho, C. Y.; Moran, E.
J.; Cherry, S. R.; Stephans, J. C.; Fodor, S. P.; Adams, C. L.; Sundaram,
A.; Jacobs, J. W.; Schultz, P. G. Science 1993, 261, 1303. (j) Smith, A. B.,
III; Keenan, T. P.; Holcomb, R. C.; Sprengeler, P. A.; Guzman, M. C.;
Wood, J. L.; Carroll, P. J.; Hirschmann, R. J. Am. Chem. Soc. 1992, 114,
10672. (k) Winkler, J. D.; Piatnitski, E. L.; Mehlmann, J.; Kasparec, J.;
Axelsen, P. H. Angew. Chem., Int. Ed. 2001, 40, 743. (l) Jones, T. V.;
Blatchly, R. A.; Tew, G. N. Org. Lett. 2003, 5, 3297.
(20) (a) Zeng, H. Q.; Yang, X. W.; Brown, A. L.; Martinovic, S.; Smith, R. D.;
Gong, B. Chem. Commun. 2003, 1556. (b) Zeng, H. Q.; Ickes, H.; Flowers,
R. A.; Gong, B. J. Org. Chem. 2001, 66, 3574. (c) Zeng, H. Q.; Yang, X.
W.; Flowers, R. A.; Gong, B. J. Am. Chem. Soc. 2002, 124, 2903. (d)
Hirschberg, J. H. K. K.; Brunsveld, L.; Ramzi, A.; Vekemans, J. A. J. M.;
Sijbesma, R. P.; Meijer, E. W. Nature 2000, 407, 167. (e) Prins, L. J.; De
Jong, F.; Timmerman, P.; Reinhoudt, D. N. Nature 2000, 408, 181.
(21) (a) Yang, X. W.; Yuan, L. H.; Yamato, K.; Brown, A. L.; Feng, W.;
Furukawa, M.; Zeng, X. C.; Gong, B. J. Am. Chem. Soc. 2004, 126, 3148.
(b) Yang, X. W.; Martinovic, S.; Smith, R. D.; Gong, B. J. Am. Chem.
Soc. 2003, 125, 9932. (c) Yang, X. W.; Brown, A. L.; Furukawa, M.; Li,
S.; Gardinier, W. E.; Bukowski, E. J.; Bright, F. V.; Zheng, C.; Zeng, X.
C.; Gong. B. Chem. Commun. 2003, 56. (d) Gong, B.; Zeng, H. Q.; Zhu,
J. Yuan L. H.; Han, Y. H.; Cheng, S. Z.; Furukawa, M.; Parra, R. D.;
Kovalevsky, A. Y.; Mills, J. L.; Skrzypczak-Jankun, E.; Martinovic, S.;
Smith, R. D.; Zheng, C.; Szyperski, T.; Zeng, X. C. Proc. Natl. Acad. Sci.
U.S.A. 2002, 99, 11583. (e) Parra, R. D.; Zeng, H. Q.; Zhu, J.; Zheng, C.;
Zeng, X. C.; Gong, B. Chem.-Eur. J. 2001, 7, 4352. (f) Parra, R. D.;
Furukawa, M.; Gong, B.; Zeng. X. C. J. Chem. Phys. 2001, 115, 6030. (g)
Parra, R. D.; Gong, B.; Zeng. X. C. J. Chem. Phys. 2001, 115, 6036. (h)
Zhu, J.; Parra, R. D.; Zeng, H.; Skrzypczak-Jankun, E.; Zeng, X. C.; Gong,
B. J. Am. Chem. Soc. 2000, 122, 4219.
(22) (a) Hamuro, Y.; Geib, S. J.; Hamilton, A. D. J. Am. Chem. Soc. 1997, 119,
10587. (b) Berl, V.; Khoury, R. G.; Huc, I.; Krische, M. J.; Lehn, J.-M.
Nature 2000, 407, 720. (c) Huc, I.; Maurizot, V.; Gornitzka, H.; Leger, J.
M. Chem. Commun. 2002, 578. (d) Jiang, H.; Leger, J. M.; Huc, I. J. Am.
Chem. Soc. 2003, 125, 3448. (e) Jiang, H.; Le´ger, J.-M.; Dolain, C.;
Guionneau, P.; Huc, I. Tetrahedron 2003, 59, 8365. (f) Jiang, H.; Dolain,
C.; Leger, J. M.; Gornitzka, H.; Huc, I. J. Am. Chem. Soc. 2004, 126, 1034.
(23) Berstein, J.; Davis, R. E.; Shimoni, L.; Chang, N.-L. Angew. Chem., Int.
Ed. Engl. 1995, 34, 1555.
Results and Discussion
Synthesis. The synthesis of nonamer 1a was reported by us
before.21d Nonamer 1 was synthesized on the basis of the same
procedures for synthesizing 1a and other similar 9-mers. The
symmetrical 11-mer 2, consisting of a central isophthalic acid
residue and two identical oligoamide “arms”, was synthesized
on the basis of a convergent route by coupling the corresponding
4,6-disubstituted isophthaloyl chlorides with the amino-
terminated pentamer (Scheme 1a). Hexamer 2a was similarly
prepared by acylating the amino-terminated pentamer with
9
J. AM. CHEM. SOC. VOL. 126, NO. 50, 2004 16529