Converting sequences of aromatic amino acid monomers into functional three-dimensional structures: Second-generation helical capsules

Article abstract of DOI:10.1002/anie.200800625

New codes for sequence-structure-function relationships can be elaborated in aromatic oligoamide foldamers upon varying main-chain components. Each monomer carries its own structural and functional features and enables oligomeric sequences to be designed

Full text of DOI:10.1002/anie.200800625

Angewandte
Chemie
DOI: 10.1002/anie.200800625
Oligoamide Foldamers
Converting Sequences of Aromatic Amino Acid Monomers into
Functional Three-Dimensional Structures: Second-Generation Helical
Capsules**
Chunyan Bao, Brice Kauffmann, Quan Gan, Kolupula Srinivas, Hua Jiang, and Ivan Huc*
The relationships between primary sequence, folded struc-
ture, and function are the basic tenets of nucleic acids and
protein machineries. Both comprise a main chain that consists
of a constant repeat unit—the sugar–phosphate backbone and
the a-peptidic backbone—and variable sequences of side
chains—nucleobases
and by intramolecular aryl–aryl interactions. It is composed of
five different units that have all been characterized inde-
pendently in the context of simpler sequences consisting of
only one or two types of units: 8-amino-2-quinolinecarboxylic
acid (Q),[5] 2,6-diaminopyridine and 2,6-pyridinedicarboxylic
and amino acid resi-
dues—that determine
their structure and,
ultimately, their func-
tion. Foldamers are
synthetic oligomers
that adopt stable
folded conformations.[1] As biopolymers, many foldamers
are based on a constant main chain and variable side chains.
However, increasing attention is being paid to sequences in
which the main chain also features variable components.
Some prime examples include hybrid sequences of a and b
peptides[2] and hybrid sequences of aliphatic and aromatic
units.[3] Here we present our investigation of an oligoamide
foldamer sequence containing five different aromatic units.
Its folded structure and its function, namely, specific molec-
ular recognition of alkane diols and alkane diamines, are
essentially defined by main-chain sequence variations, and
the role of side chains is limited to determining solubility.
These results represent significant steps towards the elabo-
ration of new, nonnatural codes for sequence–structure–
function relationships.
acid (P),[6] 7-amino-8-fluoro-2-quinolinecarboxylic acid
(QF),[7] and 1,8-diaza-9-fluoro-2,7-anthracenedicarboxylic
acid (AF).[8] The sequence of 1 was designed according to
two criteria. Firstly, each monomer type should code for an
increasing helix diameter from the sequence termini to its
center, thus defining a sizeable hollow space inside the helix
in which guest molecules can potentially reside. This is
ensured by the fact that P, QF, and AF monomers have one,
two, and three fused rings, respectively, while all present their
amino and/or carboxylic acid functions at a 1208 angle.
Second, the monomers should display suitable recognition
functions towards the hollow so as to establish specific
interactions with the guest. In the case of 1, amide protons,
pyridine and quinoline endocyclic nitrogen atoms, and
fluorine atoms are expected to converge towards the helix
hollow. The quinoline trimers (Q3) at each end of the
sequence are known to form a helix too narrow to accom-
modate any guest[9] and should thus cap the cavity of 1. Three
quinoline units were used so as to prevent the hybridization of
1 into double helices, as was observed with a Q2P3AP3Q2
sequence.[8c]
Like other aromatic oligoamide foldamers,[4] compound 1
was designed to fold into a robust helical structure stabilized
by local conformational preferences at each rotatable bond
[*] Dr. C. Bao, Dr. B. Kauffmann, Dr. K. Srinivas, Dr. I. Huc
UniversitØ Bordeaux 1, CNRS UMR5248 and UMS3033
Institut EuropØen de Chimie et Biologie
2 rue Robert Escarpit, 33607 Pessac (France)
Fax: (+33)5-4000-2215
Compound 1 represents an extension of prototypical
sequences Q2PnQ2 that were shown to host one water
molecule (n = 3 or 5) or small polar guests such as formic
acid and methanol (n = 7).[9] It is related both to receptors
based on helically folded oligomers with open hollows[10] and
to macropolyclic containers and self-assembled capsules that
completely seclude their guests and isolate them from the
surrounding medium.[11] As reported in detail in the Support-
ing Information, 1 was synthesized following a convergent
approach. A Q3 acid chloride module and a monoprotected P3
E-mail: i.huc@iecb.u-bordeaux.fr
Q. Gan, Prof. H. Jiang
Beijing National Laboratory for Molecular Sciences
CAS Key Laboratory of Photochemistry
Institute of Chemistry, Chinese Academy of Sciences
Beijing 100080 (China)
[**] This work was supported by a French ANR grant (project no.
NT05-3_44880) and the Chinese Academy of Sciences “Hundred
Talents Program”. For the first generation of helical capsules, see
reference [9].
module were first assembled then coupled to a dimer QF . In a
2
final step, a Q3P3QF2 amine was reacted with 0.5 equiv of the
diacid chloride of AF to yield 1. Speculations as to which
guests would be suitable for 1 were made at the time of its
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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design so as to define its sequence. Pyridine monomers have
glycol and 1,4-butanediol results in a moderate discrimination
by the host: a factor of five in favor of the latter. However,
complete selectivity was observed against guests that are
presumably too large to be accommodated in the capsule: no
binding was detected with 1,3-butanediol, a branched isomer
of 1,4-butanediol, and with 1,5-pentanediol, which is only one
CH2 unit longer than 1,4-butanediol (entries 4 and 6, Table 1).
No binding is also observed when terminal hydroxy groups
are replaced by either methyl groups or thiols. For instance,
n-butanol, an isostere of 1,3-propanediol, and n-hexane and
1,4-butanedithiol, two isosteres of 1,4-butanediol, do not bind
to 1 (entries 4 and 6, Table 1). On the other hand, amine
functions appear to show affinity for 1 comparable—within
experimental error—to that of hydroxy functions (entries 10–
11, Table 1). Another two guests, 2-butyne-1,4-diol and
2,2,3,3-tetrafluoro-1,4-butanediol, were tested inconclusively
because they are insoluble in chloroform: cooling a hot
solution resulted in precipitation of the guest with no
observable binding.
been shown to bind to hydroxy functions.[6,9] Molecular
modeling shows that the QF AFQF central module should
2
2
span over one helical turn and define a hollow large enough to
accommodate an alkyl chain. Alkanediols thus appeared to be
suitable guests for 1.
The ability of 1 to bind various guests was assessed by
1
titrations in anhydrous CDCl3 monitored by H NMR spec-
troscopy. For all guests except water, guest binding and
release was found to be slow on the NMR timescale at 298 K;
the full and empty hosts give rise to distinct and well-resolved
NMR signals. Spectra from a typical titration experiment are
shown in Figure 1. Binding constants, within the 500–
5000 LmolÀ1 range, were calculated for a series of guests by
integrating NMR spectra (Table 1). All titrations were
performed twice and the standard deviation was estimated
to be less than 20%. As expected, several linear alkanediols
(entries 1–3, Table 1) as well as an unsaturated diol (entry 5,
Table 1) bind to 1. The size difference between ethylene
The binding into the capsule hollow does not lead to
considerable variations in the CH2 NMR signals of the guest
(Dd < 0.25 ppm). This contrasts with numerous binding
studies within macrocyclic or self-assembled containers
whose walls also consist of aromatic units.[11] Unlike in most
of these hosts, the aryl groups of 1 are expected to expose
their edges and not their faces to the guest; thus, ring current
effects do not come into play. Nevertheless, the chiral
environment of 1 leads to diasterotopic patterns in the guest
signals (Dd up to 0.4 ppm, see the Supporting Information).
The multiplicity of the NMR signals of the capsule indicates
that, for all symmetrical guests, the complex also is sym-
metrical on average. Even though smaller guests such as
ethylene glycol may find several suitable positions within the
capsule hollow, these structures rapidly equilibrate. On the
other hand, 4-amino-1-butanol, a dissymmetrical guest,
breaks the symmetry of the helix whose signals split into
two when the complex forms (see the Supporting Informa-
tion). This indicates that the amine and hydroxy functions
create different environments in the host cavity and that any
flip-flop motion of the guest is slow, if at all possible.
In the absence of any specific guest, some amide
resonance chemical shift values were shown to increase with
the water content of the sample. As was previously charac-
terized with Q2PnQ2 sequences (n = 3, 5, 7), this finding
indicates that water is also bound in the capsule but that its
binding and release is fast on the NMR timescale, as could be
expected for a smaller guest.[9] The binding constant of water
could not be accurately measured because it is difficult to
assess the amount of guest in the sample. An estimate based
on previous studies of smaller helical capsules gives a binding
constant of the order of 100 LmolÀ1 in CDCl3.[9] When the
titrations of Table 1 are performed in chloroform “from the
bottle”, that is, containing residual water, apparent binding
drops by about 50% because water competes with the guest.
Although accurate binding constants cannot be calculated in
this case, competition experiments clearly show that the
overall trend in guest preferences is unchanged.
Figure 1. Representative 300 MHz NMR spectra of 1 in CDCl3 (2 mm)
at 258C titrated with 1,4-butanediol: a) 0 equiv, b) 0.5 equiv, c) 1 equiv,
d) 2 equiv, and e) 4.5 equiv. The selected window mostly shows amide
resonances. A few aromatic resonances are marked with stars. Some
signals of the empty host and of the host–guest complex are marked
with white and black circles, respectively.
Table 1: Binding constants between 1 and various guests in CDCl3 at
258C.
Entry
Guest
K [LmolÀ1
]
1
2
3
4
5
6
7
8
ethylene glycol
1,3-propanediol
1,4-butanediol
1,3-butanediol
cis-2-butene-1,4-diol
1,5-pentanediol
n-butanol
0.64”103
2.5”103
3.3”103
[a]
–
5.2”103
[a]
–
[a]
–
[a]
n-hexane
–
[a]
9
10
11
1,4-butanedithiol
4-amino-1-butanol
1,4-butanediamine
–
3.0”103
4.2”103
Detailed information about host–guest interactions were
obtained through crystallographic studies. Single crystals of 1
[a] No binding was detected by NMR spectroscopy in the presence of
over 20 equiv of guest.
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containing 1,3-propanediol, 1,4-butanediol, and 1-amino-4-
butanol suitable for X-ray analysis were all obtained by
diffusion of hexane into chloroform solutions (see the
Supporting Information). The three structures possess
almost identical unit cells and are essentially superimposable
(Figure 2). The polar hydroxy or amine groups of the guests
are hydrogen bonded to the NH functions of a 2,6-pyridine-
dicarboxamide (dN-O/N: 2.91–3.11 Š, N-H-O/N: 143–1608).
molecules, two of which are also bound to the 2,6-pyridine-
dicarboxamide units. The central part of the capsule contains
one water molecule. One of the two peripheral water
molecules is found at the same position as the hydroxy
groups of the other guests. However, the other water
molecule is found at a position offset by over 1.5 Š from
the position occupied by hydroxy and amine functions in the
other complexes (Figure 2b). A closer look at the structure
reveals that this peculiar position in fact results from a
significant conformation change in the aryl–amide backbone
that in all cases adjust the position of 2,6-pyridinedicarbox-
amide units within hydrogen-bonding distance of the guest
(Figure 2b). This ability of the helical capsule to adjust
bending angles at the aryl–amide linkage and adapt its
conformation to the presence of one or another guest is a new
element in the field of aromatic amide foldamers, which are
generally depicted as rather rigid structures. It also represents
a new type of induced fit that could be compared to that of a
snake around its prey.
The crystal structures of 1 shed light on a number of NMR
results including the diastereotopic motifs in the guestsꢀ
signals, the slow guest binding and release which require
considerable conformational changes of the capsule, and the
probably impossible flip-flop motion of the guests within the
helix cavity. The structures also fully validate the initial
design. They show that 1 completely surrounds its guests and
confirm the respective role of each aromatic monomer in the
sequence. Terminal Q units cap the helix hollow and prevent
hybridization of the helix into a duplex.[6,8c] Pyridine units
define a binding site for polar hydroxy or amine moieties, and
QF and AF units provide a nonpolar environment in the center
of the sequence. On this basis, capsules with a high affinity for
1,5-pentanediol or 1,6-hexanediol might be designed through
the incorporation of additional QF units.
In conclusion, this study illustrates how sequence–struc-
ture–function relationships can be rationally established using
codes that are different from those nature uses. In addition to
the remarkable binding properties of 1, it clearly appears that
sequences slightly longer than 1 will accommodate more
challenging guests and possibly help mediate some chemical
transformations. Ultimately, the ability to tune the groups that
converge towards the cavity of molecular capsules, as made
possible by our design, may become a critical advantage to
implement function. Our current efforts concentrate on
developing strategies towards the synthesis of even larger
helical capsules and at unraveling the recognition modes
between the capsule inner wall and guest molecules.
Figure 2. Solid-state structures of host–guest complexes of 1. a) Side
views of CPK and stick representations of 1 containing 4-amino-1-
butanol. Q and P monomers are shown in blue and red, respectively.
QF and AF monomers are shown in gray. Isobutyl side chains and
included solvent molecules have been removed for clarity. b) Overlay
of the solid-state structures of 1 containing 4-amino-1-butanol, 1,4-
butanediol, 1,3-propanediol, and three water molecules. The latter
complex is shown in orange while the three former complexes are
depicted using dark and light blue. The blue helix backbone represents
the backbones of the three former complexes which are essentially
superimposable. All six terminal Q units, isobutyl side chains, hydro-
gen atoms, and included solvent molecules have been removed for
clarity. The structure on the right depicts a top view of the upper three
P units and the nearby guest heteroatoms (N or O) using the same
color code. This structure clearly shows that one water molecule
(orange sphere) occupies an offset position with respect to hydroxy
and amine functions in other complexes.
The methylene units are surrounded by a ring of fluorine
atoms of the host. The guestsꢀ butyl chains are slightly bent in
close to an eclipsed conformation (C-C-C-C torsion: 1448 and
1158 for 1,4-butanediol and 4-amino-1-butanol, respectively).
This conformation may explain the high affinity of 1 for cis-2-
butene-1,4-diol, which already has a similar shape. In contrast,
the propyl chain of 1,3-propanediol adopts an extended, all-
anti conformation. As a result, although it has one less CH2
unit, 1,3-propanediol is located in the center of the capsule. It
does not shift towards one end and its terminal oxygen atoms
occupy positions very near those of the two longer guests.
The structure of a crystal of 1 grown in the absence of any
specific guest but in the presence of a large excess of water
could also be resolved. The unit cell parameters are slightly
but reproducibly different from those of the first three
structures. This latter capsule contains exactly three water
Received: February 7, 2008
Published online: April 28, 2008
Keywords: helical structures · molecular recognition ·
.
structure elucidation · supramolecular chemistry
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