Hydrogen Bond-Stabilized Helix Formation of a m-Phenylene Ethynylene Oligomer

Article abstract of DOI:10.1021/ol0270982

(Matrix Presented) Incorporation of a single hydrogen bonded β-turn mimic in the backbone of a m-phenylene ethynylene oligomer is shown to affect the thermodynamic properties of the folding reaction. Oligomers 1 and 2 both undergo solvophobic helix formation, but hydrogen bonded oligomer 1 was found to form a more stable helix with a higher tolerance to solvent denaturation than isomeric, non-hydrogen bonded oligomer 2.

Full text of DOI:10.1021/ol0270982

ORGANIC
LETTERS
2002
Vol. 4, No. 26
4663-4666
Hydrogen Bond-Stabilized Helix
Formation of a m-Phenylene Ethynylene
Oligomer
Jennifer M. Cary and Jeffrey S. Moore*
Departments of Chemistry and Materials Science & Engineering,
600 South Mathews AVenue, The UniVersity of Illinois at Urbana-Champaign,
Urbana, Illinois 61801
moore@scs.uiuc.edu
Received October 14, 2002
ABSTRACT
Incorporation of a single hydrogen bonded â-turn mimic in the backbone of a m-phenylene ethynylene oligomer is shown to affect the
thermodynamic properties of the folding reaction. Oligomers 1 and 2 both undergo solvophobic helix formation, but hydrogen bonded oligomer
1 was found to form a more stable helix with a higher tolerance to solvent denaturation than isomeric, non-hydrogen bonded oligomer 2.
Biomolecules rely on precise combinations of noncovalent
interactions to interconvert between various folded and
unfolded states in response to ligand binding or changes in
their environment.1 Foldamer research focuses on designing
synthetic macromolecules that replicate characteristics of
their natural counterparts.2 These synthetic molecules use
noncovalent interactions to drive the folding reaction, so they
are able to reversibly change conformation in response to
environmental stimuli. In supramolecular systems, the use
of combinations of noncovalent interactions presents many
challenges3 but offers the potential for increased control. Here
we show how the combination of hydrogen bonding and
π-stacking interactions can be used to shift the conforma-
tional transition of a m-phenylene ethynylene foldamer.
One class of foldamers that has attracted recent interest is
single-stranded oligomers that mimic proteins in their ability
to undergo cooperative transitions between random and
helical conformations.4-6 Phenylene ethynylene (PE) oligo-
mers 3 previously studied by our group have been found to
exhibit a reversible transition from random to helical
conformations in response to changes in solvent quality.7,8
The equilibrium constant for this folding reaction (eq 1)
Keq
random conformation y z helix
(1)
(1) Anfinsen, C. B. Science 1973, 181, 223-230.
(2) (a) Hill, D. J. Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S.
Chem. ReV. 2001, 101, 3893-4011. (b) Gellman, S. H. Acc. Chem. Res.
1998, 31, 173-180. (c) Stigers, K. D.; Soth, M. J.; Nowick, J. S. Curr.
Opin. Chem. Biol. 1999, 3, 714-723. (d) Archer, E. A.; Gong, H.; Krische,
M. J. Tetrahedron 2001, 57, 1139-1159.
represents the ratio between folded and unfolded oligomers
(3) Hirschberg, J. H. K. K.; Brunsveld, L.; Ramzi, A.; Vekemans, J. A.
J. M.; Sijbesma, R. P.; Meijer, E. W. Nature 2000, 407, 167-170.
10.1021/ol0270982 CCC: $22.00 © 2002 American Chemical Society
Published on Web 12/07/2002

and is related to the thermodynamic parameters s and σ from
the helix coil model9 as shown in eq 2.
Keq ) σsn - n
(2)
o
In this equation, s accounts for the enthalpic gain from
monomer-monomer interactions; no is equal to the number
of monomers required to form one turn of the helix, and σ
accounts for the entropic cost of sacrificing free rotation
between monomers to form the first turn of the helix. The
We concluded that 5 was a suitable â-turn mimic for use
in PE oligomers, while isomer 6 served as a control having
similar ring electronics but a disengaged hydrogen bond.
Next, we synthesized oligomers incorporating either the
â-turn mimic or the control unit (Scheme 1). Synthesis of
the oligomers began with acylation of 2-bromo-4-nitro-
aniline13 by acetic anhydride in the presence of catalytic
copper(II) trifluoromethanesulfonate.14 Reduction of the
nitroarene, followed by protection of the resulting aniline
as a bis-diethyltriazine and subsequent Pd-catalyzed cross-
coupling with trimethylsilylacetylene, gave amide monomer
7. Esterification of 2-iodo-4-nitrobenzoic acid15 gave the
methyl ester. Reduction of this second nitroarene, followed
by protection of the resulting aniline as a bis-diethyltriazine,
yielded methyl ester monomer 8. Coupling of monomer 7
with either 8 or 95 followed by deprotection of the bis-
diethyltriazine groups gave the corresponding iodides. Fi-
nally, Pd-catalyzed cross-coupling with trimethylsilyl-
acetylene yielded â-turn monomers 10 and 11. Coupling of
either monomer 10 or 11 with 2 equiv of chiral octamer
iodide 12 gave the desired octadecamers 1 and 2.
free energy change for the helix nucleation process (∆Gnuc
)
is given by -RTln(σ), while the free energy change for helix
propagation (∆Gprop) is given by -RT(n - no)ln(s).
Previous work in our group has demonstrated that the
thermodynamics of the folding reaction for oligomer 3 can
be altered through variations in chain length (n),5 side chain
polarity,4g and hydrophobic packing of the helical cavity.10
However, because only aromatic stacking interactions are
utilized for stabilizing the helical conformation, control over
the folding properties of oligomers having a homogeneous
backbone is limited. By using a combination of noncovalent
interactions, we demonstrate here an increased ability to
manipulate the equilibrium constant of the folding reaction.
On the basis of the value of ∆Gnuc for oligomers 3, we
calculate the free energy change associated with locking each
acetylene bond in the folded conformation to be ap-
proximately 0.9 kcal/mol.11 From this we predict that the
incorporation of a â-turn mimic having a hydrogen bond
bridging adjacent phenyl units would restrict rotation about
one acetylene bond. This would lower the value of ∆Gnuc
and increase the equilibrium constant for the folding reaction.
Diphenylacetylene is known to function as a â-turn unit
in artificial â-sheet 4,12 so we adapted the structure to give
5 as our model of a hydrogen bonded PE monomer. We were
able to obtain crystals of 5, and the X-ray structure revealed
that the molecule adopts the desired â-turn conformation with
an Ndonor-Oacceptor hydrogen bond length of 3.10 Å (Figure
1). NMR spectroscopy showed that the â-turn conformation
To compare the folding properties of octadecamers 1 and
2, UV absorption spectra of the two isomers were obtained
in a series of solvent mixtures ranging from pure acetonitrile
to pure chloroform. In acetonitrile, the PE backbone is poorly
(4) Examples of single-stranded oligomers that undergo cooperative
conformational transitions include: (a) Kirshenbaum, K.; Barron, A. E.;
Goldsmith, R. A.; Armand, P.; Bradley, E. K.; Truong, K. T. V.; Dill, K.
A.; Cohen, F. E.; Zuckermann, R. N. Proc. Natl. Acad. Sci. U.S.A. 1998,
95, 4303-4308. (b) Martinez de Ilarduya, A.; Alema´n, C.; Garc´ıa-Alvarez,
M.; Lo´pez-Carrasquero, F.; Mun˜oz-Guerra, S. Macromolecules 1999, 32,
3257-3263. (c) Cheng, J.; Deming, T. J. Macromolecules 2001, 34, 5169-
5174. (d) Wu, C. W.; Sanborn, T. J.; Huang, K.; Zuckermann, R. N.; Barron,
A. E. J. Am. Chem. Soc. 2001, 123, 6778-6784. (e) Ferna´ndez-Sant´ın, J.
M.; Mun˜oz-Guerra, S.; Rodr´ıguez-Gala´n, A.; Aymam´ı, J.; Lloveras, J.;
Subirana, J. A. Macromolecules 1987, 20, 62-68. (f) Prince, R. B.; Moore,
J. S.; Brunsveld, L.; Meijer, E. W. Chem. Eur. J. 2001, 7, 4150-4154. (g)
Brunsveld, L.; Prince, R. B.; Meijer, E. W.; Moore, J. S. Org. Lett. 2000,
2, 1525-1528. (h) Gin, M. S.; Moore, J. S. Org. Lett. 2000, 2, 135-138.
(i) Petitjean, A.; Cuccia, L. A.; Lehn, J.-M.; Nierengarten, H.; Schmutz,
M. Angew. Chem., Int. Ed. 2002, 41, 1195-1198.
(5) Prince, R. B.; Saven, J. G.; Wolynes, P. G.; Moore, J. S. J. Am.
Chem. Soc. 1999, 121, 3114-3121.
(6) Nelson, J. C.; Saven, J. G.; Moore, J. S.; Wolynes, P. G. Science
1997, 277, 1793-1796.
(7) Hill, D. J., Moore, J. S. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5053-
5057.
(8) Defined according to classic polymer chemistry: Flory, P. J.
Principles of Polymer Chemistry; Cornell University Press: Ithaca, NY,
1953.
(9) Zimm, B. H.; Bragg, J. K. J. Chem. Phys. 1959, 31, 526-535.
(10) Prince, R. B. Ph.D. Thesis, University of Illinois at Urbana-
Champaign, Urbana, 2000.
Figure 1. Model compound 5 and control isomer 6. X-ray structure
of 5 shows the hydrogen bonding interaction between adjacent units.
(11) See supplemental information
(12) Kemp, D. S.; Li, Z. Q. Tetrahedron Lett. 1995, 36, 4179-4180.
(13) Roche, D.; Prasad, K.; Repic, O.; Blacklock, T. J. Tetrahedron Lett.
2000, 41, 2083-2085.
(14) Saravanan, P.; Singh, V. K. Tetrahedron Lett. 1999, 40, 2611-
was retained in solution, as the amide N-H proton of 5 was
shifted 1.42 ppm in chloroform and 0.97 ppm in acetonitrile
relative to the amide N-H proton of control compound 6.
2614.
(15) Katritzky, A. R.; Savage, G. P.; Gallos, J. K.; Durst, H. D. Org.
Prep. Proced. Int. 1989, 21, 157-162.
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Org. Lett., Vol. 4, No. 26, 2002

Scheme 1a
a Reagents and conditions: (a) Ac2O, Cu(OTf)2, CH2Cl2. (b) Pt/C, HCO2H, Et3N. (c) (i) NaNO2, HCl, H2O, CH3CN, 5 °C; (ii) Et2NH,
K2CO3, H2O. (d) TMS acetylene, Pd2(dba)3, CuI, PPh3, Et3N, 70 °C. (e) MeOH, H2SO4, ∆. (f) Na2S2O4, MeOH, THF, H2O. (g) (i) TBAF,
THF; (ii) 8, Pd2(dba)3, CuI, PPh3, Et3N, 50 °C. (h) CH3I, 110 °C. (i) TMS acetylene, Pd2(dba)3, CuI, PPh3, Et3N, 50 °C. (j) (i) TBAF, THF;
(ii) 9, Pd2(dba)3, CuI, PPh3, Et3N, 70 °C. (k) (i) TBAF, THF; (ii) 12, Pd2(dba)3, CuI, PPh3, Et3N, 50 °C.
solvated causing the oligomer to collapse into a helical
conformation, whereas in chloroform, the PE backbone is
better solvated and the oligomer unfolds into a random
conformation. This transition from the helix to a random
conformational state was monitored by the ratio of the
oligomer absorbance bands at 303 and 289 nm, with low
values of A303/289 indicating a high degree of folding.5,6
Assuming that both 1 and 2 undergo a complete transition
between their folded and unfolded states over the observed
range of solvent mixtures, the UV absorbance data can be
fitted to give the fraction of oligomer in the unfolded state
for each solvent mixture.
midpoint of denaturation for 1 and 2 is presented in Table
1. These data reveal that the hydrogen bonded â-turn mimic
Table 1. Comparison of the Free Energy of Folding and
Midpoint of Denaturation for Octadecamers 1 and 2
∆G(CH3CN)
(kcal/mol)
m
[CHCl3]1/2
(vol %)
oligomer
(cal/mol)
1
2
-7.0 ( 0.7
-5.8 ( 0.6
90 ( 8
80 ( 8
78.0 ( 0.8
72.7 ( 0.8
Figure 2 displays the absorption data obtained for 1 and 2
as a function of solvent composition. Assuming that the free
energy difference between the folded and unfolded states
depends linearly on solvent composition,16 the free energy
of folding in pure acetonitrile, ∆G(CH3CN), can be deter-
mined from eq 3 where [CHCl3] represents the chloroform
composition expressed as vol % and m indicates how rapidly
the stabilization energy of the helix (∆G) changes in response
to changes in solvent composition.5
of oligomer 1 lowers the energy of the helical conformation
by ca. 1.2 kcal/mol. This stabilization results in a higher
tolerance to denaturation, as the percentage of chloroform
required to reach the midpoint of denaturation increases by
5.3 vol % for the hydrogen bonded oligomer.17
The experimentally observed stabilization of 1.2 kcal/mol
provided by the hydrogen bonded â-turn mimic is on the
(16) (a) Jasanoff, A.; Fersht, A. R. Biochemistry 1994, 33, 2129-2135.
(b) Pace, C. N. Methods in Enzymology; Hirs, C. H. W., Timasheff, S. N.,
Eds.; Academic Press: New York, 1986; Vol. 131, pp 266-280. (c) Pace,
C. N.; Shirley, B. A.; Thomson J. A. In Protein Structure: A Practical
Approach; Creighton, T. E., Ed.; IRL Press: New York, 1989; pp 311-
330.
∆G ) ∆G(CH3CN) - m[CHCl3]
(3)
(17) The predicted decrease in free energy of folding corresponding to
the observed shift in denaturation midpoint is approximately 1 kcal/mol.
While the calculated change in ∆G(CH3CN) is on the edge of statistical
significance, the shift in [CHCl3]1/2 is well beyond the error limits.
The composition of chloroform required to reach the mid-
point of denaturation ([CHCl3]1/2) is given by ∆G(CH3CN)/
m. A comparison of the free energy of folding and the
Org. Lett., Vol. 4, No. 26, 2002
4665

yet know if the placement of the hydrogen bond in the middle
of the helix rather than at the terminus leads to a more
pronounced effect on the thermodynamics of helix nucle-
ation. We are also unable to comment on the role of the
slight electronic differences between the â-turn mimic and
the control unit with regards to imparting greater stabilization
to the helical conformation of the hydrogen bonded oligomer.
Nonetheless, we believe that the results are in good agree-
ment with the predicted behavior, and we feel that this â-turn
mimic provides added versatility to our PE monomer pool.
In conclusion, the incorporation of a single hydrogen
bonded â-turn mimic into a m-phenylene ethynylene oligo-
mer provides an additional noncovalent interaction that can
be used to control the folding properties of the oligomer.
The effect on the thermodynamics of the folding reaction is
apparent from a comparison of the free energy of folding
and the midpoint of solvent denaturation for hydrogen
bonded oligomer 1 and isomeric, non-hydrogen bonded
oligomer 2. The hydrogen bond was found to stabilize the
folded conformation of the oligomer, making it more tolerant
to denaturation by chloroform. As more types of noncovalent
interactions are adapted for use in oligomers, these systems
will better mimic proteins in their ability to use a monomer
sequence to specify precise folding properties. Future studies
may include use of the PE backbone as a scaffold for
incorporation of multiple-peptide â-sheets to create a â-sand-
wich structure.
Acknowledgment. This research was funded by the
National Science Foundation (CHE 00-91931). J.M.C. thanks
Abbott Laboratories for a doctoral fellowship.
Figure 2. (a) UV spectra of 1 (red) and 2 (blue) in chloroform
and acetonitrile. (b) UV titration curve of 1 (red diamonds) and 2
(blue squares).
Supporting Information Available: Detailed descrip-
tions of all experimental procedures and accompanying
analytical data. This material is available free of charge via
the Internet at http://pubs.acs.org.
order of the predicted value of 0.9 kcal/mol for locking the
rotation about one acetylene bond in the PE backbone. In
other words, the hydrogen bond of the â-turn mimic provides
enough energy to lock one diphenylacetylene unit in the
cisoid conformation required for helix formation. We do not
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Org. Lett., Vol. 4, No. 26, 2002