Quadruple and double helices of 8-fluoroquinoline oligoamides

Article abstract of DOI:10.1002/anie.200704938

(Figure Presented) Winding and rewinding: How many times can helical aromatic oligomers wind around one another? At least four, as judged by the aggregation behavior of oligoamides based on 8-fluoroquinoline (see scheme depicting the formation of a quadruple helix; red spheres: sites in the hollow space partially occupied by water molecules).

Full text of DOI:10.1002/anie.200704938

Angewandte
Chemie
DOI: 10.1002/anie.200704938
Helical Structures
Quadruple and Double Helices of 8-Fluoroquinoline Oligoamides**
Quan Gan, Chunyan Bao, Brice Kauffmann, Axelle GrØlard, Junfeng Xiang, Shenghua Liu,
Ivan Huc,*and Hua Jiang*
Dedicated to Professor Huijun Xu
The assembly of molecular strands into multiple helical
hybrids represents a major strategy that nature uses to control
elongated supramolecular architectures such as nucleic acids,
collagen, or other coiled strands. Multiple-helix formation
from non-natural oligomers has thus emerged as an important
subject.[1] Nucleic acids[2] and some artificial oligomers[3]
adopt a single-stranded helical conformation in the mono-
meric state and can wind around one another without
significantly changing their helical pitch. In other hybrids,
for example, pyridine carboxamide oligomers[4,5] and grami-
cidin D,[6] compact single-helical conformers must increase
their helical pitch and undergo a springlike extension to
accommodate a complementary strand and wind into a
double helix (Scheme 1, top). For those latter hybrids,
double-helix formation thus critically depends on the ease
of increasing the helical pitch.
Scheme 1. Schematic representation of the hybridization of a single
helix to a double helix (top), and of a double helix to a quadruple helix
(bottom), both through springlike extension.
We recently found that the hybridization of pyridine
carboxamide oligomers is dramatically enhanced when one
unit that is designed to enlarge the helix diameter—that is,
consisting of three fused aromatic rings—is introduced in the
sequence, precisely because this unit lowers the enthalpic cost
ization are also promoted in helical pyridine–pyridazine
oligomers because of their large diameter.[7] Intrigued by
the possible outcomes of using exclusively units that give rise
to a large helix diameter, we designed tetrameric and
octameric amides of 7-amino-8-fluoro-2-quinolinecarboxylic
acid, compounds 1 and 2. Herein, we present their remarkable
of springlike extension.[5] Aggregation and, possibly, hybrid-
[*] Q. Gan, Dr. J. Xiang, Prof. H. Jiang
Beijing National Laboratory for Molecular Sciences
CAS Key Laboratory of Photochemistry
Institute of Chemistry, Chinese Academy of Sciences
Beijing 100080 (China)
Fax: (+86)10-8261-7315
E-mail: hjiang@iccas.ac.cn
Dr. C. Bao, A. GrØlard, Dr. I. Huc
UniversitØ Bordeaux 1—CNRS UMR5248
Institut EuropØen de Chimie et Biologie
2 rue Robert Escarpit, 33607 Pessac (France)
Fax: (+33)5-4000-2215
aggregation behavior; we notably show that 1 is able to adopt
a helical conformation with a large pitch, which allows the
formation of an unprecedented quadruple helix and that 2
dimerizes as an antiparallel double helix.
E-mail: i.huc@iecb.u-bordeaux.fr
Dr. B. Kauffmann
UniversitØ Bordeaux 1
UniversitØ Victor Segalen Bordeaux 2
CNRS UMS3033
Institut EuropØen de Chimie et Biologie
2 rue Robert Escarpit, 33607 Pessac (France)
Several families of aromatic oligoamides have been shown
to adopt helical conformations when an aromatic endocyclic
nitrogen atom[4,5,8] or exocyclic fluorine atom[9] is placed
adjacent to each amide group.[10] In aromatic oligomers, the
helix diameter can be tuned upon incorporating larger
aromatic subunits with multiple fused rings[5,10,11] and upon
manipulating the orientations of the linkages on the aromatic
rings.[7,10,12] The motivation to develop helices with a large
diameter is generally the potential use of their hollow spaces
in molecular recognition.[13,14] Nevertheless, large diameters
Q. Gan, Prof. S. Liu
College of Chemistry, Central China Normal University
Wuhan, Hubei, 430079 (China)
[**] This work was supported by a French ANR grant (project no. NT05-
3_44880) and the Chinese Academy of Sciences “Hundred Talents
Program”. We thank J. Lefeuvre for the preparation of Scheme 1.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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may be associated with characteristic aggregation behaviors,
approximately 3.5 Š. Consistent with the spectral features of
other helical aromatic oligoamides,[12,16] the low-concentra-
tion H NMR spectrum of 1 is sharp and shows three amide
signals at low field (d > 11 ppm), which is in agreement with
the involvement of these protons in intramolecular hydrogen
bonds.
including, as shown below, the formation of a quadruple helix.
Monomer design, monomer preparation, and oligomer
assembly for the synthesis of 1 and 2 were inspired from the
design and synthesis of oligomers of 8-amino-2-quinolinecar-
boxylic acid[8] and are described in the Supporting
Information. To ensure the preference for helical conforma-
tions, an exocyclic fluorine atom (a hydrogen-bonding
acceptor)[9] was introduced in the 8-position of each quinoline
ring (Scheme S1 in the Supporting Information). Fluorine was
preferred to an endocyclic nitrogen atom because of the
synthetic hurdles, low solubility, and poor amide stability of
1,8-naphthyridine derivatives.[15] The orientation of the amine
and acid functions in 1 and 2 are similar to those in 2,6-
disubstituted pyridine oligomers.[4,5] The two families of
helices are thus expected to possess the same numbers of
units per turn (about four), the quinoline helices being wider
owing to the larger size of the monomers. These predictions
were verified in the structure of the single-helical conformer
of 1 observed in crystals grown from chlorobenzene/hexane
(Figure 1a). In the solid state, this tetramer spans just about
one turn and, because of steric hindrance, its two ends deviate
from planarity and overlap into a single helix with a pitch of
1
Crystals of 1 obtained from a different solvent mixture
(toluene/dichloroethane/hexane) were also analyzed by X-ray
diffraction and revealed an unprecedented quadruple helix
(Figure 1c) in which two molecules of 1 stack in a head-to-tail
dimer, and two such dimers are further entwined with offset
helical axes so that the four bulky tert-butoxycarbonyl (Boc)
groups stick out of the quaduplex while the methyl ester
groups remain buried in the helix. The structure thus shows
two pairs of grooves within and between the head-to-tail
dimers, respectively (Scheme 1). Owing to the large diameter
of the helix, the vertical rise per turn is accommodated with a
tilt angle of the strands with respect to the helix axis
comparable to that seen in double helices of pyridine
carboxamide oligomers (Figure 1b) and does not require
large twist angles at the aryl–amide linkages. In fact, the
vertical rise originates from a single twist between the two
central quinoline units (318), while the terminal quinoline
rings are essentially coplanar. This partic-
ular quadruplex structure arises from two
duplexes clipped into one another. It
appears to be made possible by the fact
that tetramer 1 spans only one helix turn.
We studied the aggregation of 1 in
CDCl3 solutions by 1H and 19F NMR.
Upon increasing the concentration (0.5–
40 mm), the BocNH, ester CH3, and aro-
matic signals are shifted upfield (Dd up to
À0.39, À0.41, and À0.31 ppm, respec-
tively). Similar shifts of even larger ampli-
tudes and broadening were observed upon
cooling the samples at various concentra-
tions (2–40 mm) from 298 to 223K (at
2 mm, Dd up to À1.07, À1.09, and
À0.60 ppm, respectively; Table S1 in the
Supporting Information). The 19F NMR
signals are shifted as well upon cooling
(Dd > 1 ppm; Figure S5 in the Supporting
Information). Such chemical-shift varia-
tions are a typical signature of ring-current
effects arising from intermolecular p–p
stacking within aggregates of 1 that are in
fast exchange with monomeric species on
the NMR timescale. Diffusion coefficients
1
were calculated from H DOSY measure-
ments recorded at 296 K using 2 mm and
40 mm samples (Figure S6 in the
Figure 1. Side views and top views of the crystal structures at the same scale of:
a) compound 1 as a single helix; the fluorine atoms converging towards the helix hollow
space are shown as spheres; b) a narrow double helix composed of pyridine rings only
(shown for comparison);[4a] c) compound 1 as a quadruple helix; a string of sites partially
occupied by water molecules is shown as spheres; d) compound 2 as a double helix; alkoxy
residues and solvent molecules are omitted for clarity. The similarity between the head-to-tail
duplex of 2 and the head-to-tail duplexes that constitute the quadruplex of 1 appears clearly
when focusing on the orange and dark blue strands in (c) and (d).
Supporting Information), a concentration
range that spans most of the variation in
chemical shift. The diffusion coefficients
are 5.6 ” 10À10 and 3.8 ” 10À10 m2 sÀ1 at 2 and
40 mm, respectively. According to the
Stokes–Einstein equation, the ratio
between these values is consistent with a
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volume ratio of 3in the approximation that the average
entities at 2 and 40 mm are assimilated into spheres. Though
the approximation of molecular shape to spheres prevents a
refined analysis of such data, this ratio is within the range
expected for single helix–duplex and duplex–quadruplex
equilibria (Scheme 1). The concentration-dependant chem-
ical-shift values at 298 K are well fitted by a simple
dimerization isotherm yielding Kdim = 66 LmolÀ1.[17] Addi-
tionally, NOESYexperiments reveal correlations between the
quinoline protons at C3(the only aromatic singlets) and the
quinoline protons at C5 and C6 (the aromatic multiplets).
Given the distance between these protons on the same
quinoline ring, these correlations are unlikely to be intra-
molecular and are not observed in the NOESY spectra of a
precursor of 1 consisting of only two quinoline rings
(Figure S7 in the Supporting Information). They may
emerge from a stacked head-to-tail dimeric arrangement, as
seen in each of the duplexes that constitute the quadruplex
crystal structure. Altogether, these data suggest that aggre-
gation does occur in solution in a way that is consistent with
the structure observed in the solid state. These aggregates,
possibly duplexes or quadruplexes, are labile and remain in
fast exchange with monomeric helical species at room
temperature.
temperatures (243K), and at even higher temperatures
(273K) the signals of the aggregate were not intense
enough. However, the slow exchange and the sharp NMR
lines point to a well-defined species. Since the solid-state
quadruplex structure consists of two head-to-tail duplexes
and given the size estimate of the aggregates observed at
room temperature, the new species observed at low temper-
ature by NMR could well be the quadruplex itself. Yet other
aggregation modes cannot be ruled out.
The structure and aggregation behavior of octamer 2 was
investigated as well. In the solid state, it forms an antiparallel
double helix (Figure 1d) wherein the relative arrangement of
the two strands is very similar to the head-to-tail stacks of two
molecules of 1 found in the quadruplex. The first quinoline
ring of each strand largely overlaps—with a small offset—
with the last quinoline ring of the other strand, thus bringing
the terminal ester and tert-butyl groups of opposite strands in
close proximity. Within each strand, the position and ori-
entation of the fluoroquinoline and amide units are consistent
with the initial design and with the two structures of the
tetramer. In particular, all fluorine atoms are found within the
hollow space of the helix. The strands of (2)2 span about two
helical turns.
1
The H NMR spectra of 2 in solution (CDCl3) show a
At low temperature, the spectra of a concentrated sample
of 1 (40 mm) reveal the emergence of a second set of signals
(Figure 2). The proportion of these signals increases upon
decreasing the temperature (up to 35% at 233 K), thus
showing that a higher aggregate exists that is in slow exchange
on the NMR timescale with the monomeric and aggregated
species observed at room temperature. The signals of this
aggregate are found at even higher field, suggesting that it
involves additional intermolecular p–p stacking. Attempts to
assess the size of this aggregate through DOSY experiments
were hampered by its precipitation at 233 K over long
acquisition times. This problem persisted at slightly higher
single set of slightly broad signals, which are all found
considerably upfield from the corresponding signals of
tetramer 1. Upon increasing the concentration (from 1 to
20 mm) or upon cooling (from 298 K to 223K), only minor
variations in chemical shift are observed, the largest varia-
tions being for the signals of the BocNH and ester CH3 groups
(Dd < 0.22 ppm). In contrast to the corresponding shifts
observed for tetramer 1, these are downfield and not upfield
shifts. In pyridine, a solvent in which double helices of
aromatic oligoamides tend to dissociate,[5] no significant
change occurs. However, whether in chloroform or pyridine,
heating or high dilution results in the onset of a second set of
Figure 2. Excerpts of the 1H NMR spectra of 1 in CDCl3. a) 2 mm at
298 K; b) 40 mm at 298 K; c) 40 mm at 243 K. Increasing the concen-
tration at room temperature causes chemical-shift variations indicative
of aggregate formation. Cooling at high concentration leads to the
onset of a second species (black circles) corresponding to a higher
aggregate. This species is not observed upon cooling a 2 mm solution
(spectrum not shown).
Figure 3. Excerpts of the 1H NMR spectra of 2 in [D5]pyridine. a) 6 mm
at 298 K; b) 6 mm at 360 K; c) 1 mm at 298 K; d) 1 mm at 360 K. Both
decreasing the concentration and increasing the temperature lead to
the onset of a new species in slow exchange on the NMR timescale
(black circles).
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pyridine-based oligomers[4,5] and in view of the solid-state
structure of 2, this behavior suggests that 2 forms a very stable
double helix in solution that prevails even at low concen-
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8.5 ” 105 LmolÀ1 in CDCl3. The enthalpy and entropy of
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In conclusion, we have found that the ability of helical
aromatic amides to hybridize into double helices is not
restricted to the pyridine-based oligomers studied previously
but also applies to fluoroquinoline carboxamide oligomers,
the structures of which are quite remote from the former. One
may speculate that this behavior bears some generality,
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Received: October 24, 2007
Published online: January 23, 2008
Keywords: chirality · helical structures · structure elucidation ·
.
supramolecular chemistry · X-ray diffraction
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