Efficient macrocyclization of preorganized palindromic oligosquaramides

Article abstract of DOI:10.1002/anie.200602790

(Figure Presented) Hydrogen-bonding interactions drive oligosquaramides of different lengths to fold into hairpin-like structures both in nonprotic and protic solvents. These compounds are useful preorganized precursors in macrocyclization reactions.

Full text of DOI:10.1002/anie.200602790

Communications
Macrocycles
DOI: 10.1002/anie.200602790
Efficient Macrocyclization of Preorganized
Palindromic Oligosquaramides**
Carmen Rotger,* M. Neus Piæa, Manuel Vega,
Pablo Ballester, Pere M. Deyà, and Antoni Costa*
Nature has evolved polymers with highly specific functions. In
the last decade, a new generation of natural circular proteins
has been found in bacteria, plants, and mammals.[1] These
large cycles show exceptional stability and a wide range of
[*] Dr. C. Rotger, Dr. M. N. Piæa, M. Vega, Prof. P. M. Deyà, Prof. A. Costa
Departament de Química
Universitat de les Illes Balears
Ctra. Valldemossa km 7.5
07122 Palma de Mallorca (Spain)
Fax: (+34)971-173-426
E-mail: carmen.rotger@uib.es
antoni.costa@uib.es
Dr. P. Ballester
ICREA and Institute ofChemical Research ofCatalonia (ICIQ)
Avgda. Països Catalans
s/n, 43007, Tarragona (Spain)
[**] We thank the DGI ofSpain of r support ofthis study (CTQ2005-
08989) and Dr. Gabriel Martorell (SCT) for technical assistance. C.R.
thanks the MEC and the DGR+D+I (Govern Balear) for cofunding
within the Ramón y Cajal program, and M.N.P. thanks the
DGR+D+I (Govern Balear) for a predoctoral fellowship.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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biomedical activities, from insecticidal and antimicrobial to
anti-HIV properties. Furthermore, they are ideal templates
for engineering similar macromolecules of non-natural
oligomers for potential biomedical applications.[2]
The incorporation of turn segments in the linear precursor
is frequently the strategy of choice for cyclization reactions.[3]
However, to our knowledge, examples of successful macro-
cyclization that occur with non-natural hydrogen-bonded self-
templated precursors in polar solvents are rare.[4] Herein, we
report on the application of preorganized oligosquaramides
of different sizes, for the synthesis of tailor-made macrocycles
in methanol.
The most studied families of non-natural oligomers with
well-defined conformations in solution are aliphatic,[5] but
several aromatic oligomers based on amide,[6] urea,[7] and
hydrazide[8] linkages have also been shown to adopt stable
conformations in solution. Such molecules, termed folda-
mers,[9,5b] represent a significant step forward to achieving
fully synthetic protein analogues. Among those, squaramides,
which can be considered as vinylogous amides, are versatile
molecules with considerable hydrogen-bonding capabilities
and favorable dynamic properties that allow them to adopt
secondary structures. Previously, we have shown the ability of
some secondary disquaramides, stabilized by an intramolec-
ular hydrogen bond, to fold into a U-turn module in polar and
nonpolar solvents.[10]
independent (0.5–20 mm) and shifted downfield relative to
the corresponding chemical shift found for squaramide
hydrogen atoms (d = 6.2–5.4 ppm), which lack hydrogen-
bonding potential.[10] Compounds 2–5 show two different
peaks assignable to the squaramide hydrogen atoms at d = 7.5
and 8.2 ppm, respectively, thus suggesting that they reside in
different chemical environments. The downfield area of the
squaramide hydrogen peaks varies depending on the number
of squaramide modules in the oligomer skeleton, and the
integrated area of the upfield peak remains equal to two in all
the oligomers.
Stabilization of a well-defined and stable folded confor-
mation with common structural features to all the oligomers
was studied by 1HNMR and UV/Vis spectroscopy. A
diffusion NMR experiment (DOSY) of 1–5 in CDCl3
completely discards any aggregation at the oligomer level,
and a good correlation was found for the logarithms of
molecular weight and the diffusion coefficients (Figure 2).
The new family of oligomer reported herein is based on
squaramide modules and aliphatic linkages, as represented by
the general structure shown in Figure 1. These oligomers are
palindromically constituted with a flexible backbone and
have a related structure to the foldable module.
The modular synthesis of the novel oligosquaramides 1–5
was achieved through standard condensation reactions of the
squaramide building blocks in good-to-moderate yields (55–
95%).[11]
The resulting structural symmetry of 1–5 is readily
apparent in the 1D 1HNMR spectra recorded in CDCl 3
(Figure 1). The peaks are relatively sharp, and the resonance
for the squaramide hydrogen atoms are concentration-
Figure 2. A) The molar extinction coefficients (e at 292 nm) in CHCl3 versus
oligomer length (n). B) Logarithmic plot of the diffusion coefficient (D)
versus the molecular weight (Mw) ofthe oligomer.
Furthermore, variable-temperature (VT) 1HNMR experi-
ments from 243 to 298 K performed in CDCl3 of samples of 1–
5 (2 mm) revealed a small upfield shift for all the squaramide
protons signals. The observed coefficients for the rate of
change of the NHsquaramide protons with temperature are
less than or equal to À6.56 ppbKÀ1, as expected for intra-
molecularly hydrogen-bonded protons.[12] It is also observed
that the values of these coefficients decrease when the
number of squaramide units in the oligomer skeleton
increase. The NHsquaramide peak at d = 8.2 ppm in 3–5
splits at 283 K, thus suggesting the existence of a dynamic
process involving the hydrogen-bonded protons.
The UV/Vis spectra of 1–5 were also recorded in CDCl3.
The molar extinction coefficient (e) was determined for each
oligomer over the range of concentrations 10À4–10À5 m. The
Lambert–Beer law was observed for each compound, as
expected for monomeric systems. The calculated e values at
292 nm (e = 23088, 41585, 64921, 79544, and 100559mÀ1 cmÀ1
for 1–5, respectively) exhibit linear relationships with the
number of squaramide residues in the strand, thus implying an
absence of stacking for the squaramide chromophore as a
result of the secondary structure (Figure 2).
From these data, we obtained preliminary results that
support the hypothesis that the oligosquaramides prefer a
folded structure in solution, driven by intramolecular hydro-
gen-bonding interactions that increase with oligomer length.
Figure 1. Top: General structure ofthe oligosquaramides ( n=1–5 for
1–5, respectively; Boc=tert-butyloxycarbonyl). Bottom: Partial 1H NMR
(300 MHz) spectra of 1–5 in CDCl3.
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To further characterize the U-turn module for the folded
NOE correlations were more difficult to identify for
longer oligomers because of the C2 symmetry of the strand.
Under the assumption that all the oligomers have the
characterized U-turn in common and all the NHprotons
are intramolecularly hydrogen-bonded and distributed in two
different chemical environments, related folded structures
can be anticipated to occur in longer oligosquaramide
skeletons in a hairpin-like structure. In these cases, more
interactions between the two strands occur and contribute to
the stabilization of the folded conformation (Figure 4). As a
result of the palindromic nature of these molecules, a dynamic
process will occur in which the hydrogen-bonding pattern
slips from one end to other, thus yielding conformational and
energetically equivalent structures in solution.
oligosquaramides, 6 was synthesized and an NMR ROESY
spectroscopic experiment was conducted in CDCl3 (Figure 3).
Cross-peaks were observed between the tert-butyl protons (f)
and the NH(a) and a-methylene (c) protons of the n-butyl
side chain. The a’-methylene protons (d) give also a cross-
peak with the methylene protons (e) of the Boc-protected
alkylamino chain. From this data, we propose a folded
structure for 6 in which the squaramide proton (b) is
hydrogen-bonded to the N-methyl donor atom, thus forming
a six-membered ring as observed in related systems.[10]
Moreover, an additional hydrogen-bond interaction occurs
between the carbamate carbonyl group and the squaramide
proton (a), which stabilizes the folded structure.
Figure 4. Proposed folded structure for 2 and the slipping equilibrium
end-to-end ofthe hydrogen-bonding pattern.
Typically, the folded structures driven essentially by
hydrogen-bonding interactions have been detected in non-
protic solvents.[5] The proposed folded state for the oligos-
quaramides resists competition from externally added protic
solvents, such as MeOH.[13] The 1HNMR spectra of 2 and 4 at
285 K (3mm) in CDCl3/MeOHmixtures containing up to
40% MeOHdisplay little perturbation and persistent
deshielded squaramide NHsignals, as expected for intra-
molecular hydrogen bonds; however, the NHcarbamate
signals move upfield, thus showing solvent exposure.
Differential scanning calorimetry (DSC) experiments
were run on the oligosquaramides 2–5 to fully characterize
the folded structures in protic solvents, (EtOH/CHCl3 (95:5,
v/v)) by increasing the temperature from 10 to 808C at a rate
of 108ChÀ1 (Figure 5). All the tested oligomers undergo a
sharp and reversible structural transition as a function of
temperature, thus indicating the existence of a well-defined
secondary structure. The excess heat capacity peak is
complete within a 15–208C range, evident of a cooperative
nature of the oligomer unfolding.[14] The DH values obtained
for the unfolding processes (0.16, 0.32, 0.48, and 0.61 kcal
molÀ1 for 2–5, respectively) show a clear dependence on the
chain length of the oligomers, which is consistent with other
observed data.
Figure 3. Top: Folded conformation of 6 showing H atom labels and
the corresponding NOE interactions. Bottom: NOE interactions as
revealed by the NOESY spectrum of 6 in CDCl3.
The melting temperature (Tm = 63 Æ 28C) was found to be
similar for all the tested oligomers and comparable to those
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As we have shown, the proposed folded structures for the
oligosquaramides constitute a series of self-organized pre-
cursors applicable to one-step macrocyclization reactions in
protic solvents without standard high-dilution conditions.
Squaramides are particularly well suited to take advantage of
the template effect in alcoholic solvents, given that the
condensation of amines with squaramide esters is routinely
carried out in ethanol or methanol. Cleavage of the Boc
groups leaves two reactive amino groups in each oligomer
that are close enough to react with a molecule of diethyl-
squarate in a one-step cyclization reaction to obtain the
corresponding macrocycles. Therefore, the corresponding
diamines of oligosquaramides 2–5 were condensed in meth-
anol at millimolar concentrations with one equivalent of
diethylsquarate. In all the cases, the macrocyclization of the
oligosquaramides gave very high and comparable yields
(80%) of the corresponding macrocycles 7–10 (Figure 6).[11]
Further oligomerization was not detected by ESI MS studies
of the crude product. These results support the dominance of
the folded structure for the oligosquaramides under the
macrocyclization reaction conditions. The generality of the
oligosquaramides macrocyclization is also manifest. In some
examples of highly efficient one-step macrocyclizations
Figure 5. DSC melting curves of 2 (blue), 3 (green), 4 (red), and 5
(purple).
determined for unfolding of the hairpin peptide structure in
water.[15] The DH value per residue ( ꢀ 0.1 kcalmolÀ1) reflects,
mainly, the hydrogen-bond component because the solvo-
phobic effect, as a result of the alkyl chains of the oligoamide
skeleton, is assumed to have a minimum contribution on the
overall folding–unfolding process.
Figure 6. A) Synthesis ofmacrocycle 7: a) HCl, 508C, 3 h; b) diethyl squarate, MeOH, room temperature, 12 h. B) Structures ofmacrocycles 8–10.
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[15] R. M. Fesinmeyer, F. M. Hudson, N. H. Andersen, J. Am. Chem.
Soc. 2004, 126, 7238 – 7243.
assisted by folding of precursor oligomers, the macrocycle
sizes are limited to a determined length because of the rigidity
of their backbones.[16] The nature of the folded structure
adopted by the squaramides permits no size restrictions on
the macrocycle synthesis. Therefore, a versatile synthetic
strategy to obtain tailor-made macrocycle cavities with
squaramide groups, which maintain their considerable hydro-
gen-bonding capability, has been demonstrated.
[16] L. Yuan, W. Feng, K. Yamato, A. R. Sanford, D. Xu, H. Guo, B.
Gong, J. Am. Chem. Soc. 2004, 126, 11120 – 11121.
[17] The macrocyclation reaction fails when the donor atom in the
d position on the alkyl chain is absent;[10] moreover, unpublished
results show that a different atom sequence in the linker chain
gives insoluble squaramide compounds in CHCl3 and protic
solvents.
In summary, we have demonstrated that oligosquaramides
of different length that contain a donor atom (N) in the
d position of the alkyl linker chains, fold to form stable
monomeric structures that possess a hairpin-like pattern driven
by intramolecular hydrogen-bonding interactions.[17] The sta-
bility of the folded structure increases with oligomer length,
but the shortest oligomers also display a well-defined and
stable conformation. The characterized folded structures are
stable in polar solvents, as indicated by denaturation studies
and DSC experiments. Thus, the preorganization shown by the
oligosquaramide skeleton make them useful precursors in
macrocyclization reactions. The study presented herein is the
first example of how unnatural oligomers with designed folded
structures driven by hydrogen-bonding interactions can be
used to efficiently yield large macrocyclic structures.
Received: July 13, 2006
Published online: September 26, 2006
Keywords: foldamers · hydrogen bonds · macrocyclization ·
.
squaramides
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