On-Demand Cyclophanes: Substituent-Directed Self-Assembling, Folding, and Binding

Article abstract of DOI:10.1021/acs.joc.5b02605

A family of p-cyclophanes based on bis- or tetrafunctionalized 1,4-bisthiophenol units linked by disulfide bridges was obtained by self-assembly on a gram scale and without any chromatographic purification. The nature of the functionalities borne by these so-called dyn[4]arenes plays a crucial role on their structural features as well as their molecular recognition abilities. Tuning these functions on demand yields tailored receptors for cations, anions, or zwitterions in organic or aqueous media.

Full text of DOI:10.1021/acs.joc.5b02605

Article
pubs.acs.org/joc
On-Demand Cyclophanes: Substituent-Directed Self-Assembling,
Folding, and Binding
Pierre-Thomas Skowron,† Melissa Dumartin,‡ Emeric Jeamet,‡ Florent Perret,‡ Christophe Gourlaouen,§
Anne Baudouin,‡ Bernard Fenet,‡ Jean-Valere Naubron,† Frederic Fotiadu,† Laurent Vial,∥
̀
́
́
and Julien Leclaire*,‡
†Institut des Sciences Molec
Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France
‡Institut de Chimie et Biochimie Molec
́
ulaires et Supramoleculaires, UMR 5246 CNRS − Universite Claude Bernard Lyon 1 − CPE
́
́
́
ulaires de Marseille, UMR 7313 CNRS − Universite d’Aix-Marseille − Ecole Centrale Marseille, Avenue
́
́
Lyon, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
§Institut de Chimie de Strasbourg, UMR 7177 CNRS − Universite
́
de Strasbourg, 1 rue Blaise Pascal, 67008 Strasbourg Cedex,
de Montpellier, Place Eugene Bataillon, 34296
France
∥Institut des Biomolec
́
ules Max Mousseron, UMR 5247 CNRS − Universite
́
̀
Montpellier Cedex 5, France
S
* Supporting Information
ABSTRACT: A family of p-cyclophanes based on bis- or
tetrafunctionalized 1,4-bisthiophenol units linked by disulfide bridges
was obtained by self-assembly on a gram scale and without any
chromatographic purification. The nature of the functionalities borne
by these so-called dyn[4]arenes plays a crucial role on their structural
features as well as their molecular recognition abilities. Tuning these
functions on demand yields tailored receptors for cations, anions, or
zwitterions in organic or aqueous media.
partner toward discrete molecular objects in solution or within
a condensed phase. Among the available reversible reactions,
the disulfide bond exchange, used by Nature to select the
optimal structures of proteins for a biological function, is
probably one of the most popular given its wide functional
group tolerance.7,8 The disulfide bond exchange reaction occurs
spontaneously in aqueous solution at pH values between 7 and
9 and may be quenched by simply lowering the pH. Sanders
and colleagues pioneered its use in DCC to produce in aqueous
media topologically complex architectures, receptors, and
catalysts.9−11 Yet, such an approach comes with two major
drawbacks. First, while expanding the constitutional diversity of
the system increases the probability of identification of a hit, it
simultaneously hampers the isolation and purification pro-
cesses. Even from biased libraries, high performance chromato-
graphic tools are required and only modest quantities of the hit
can be accessed. The second drawback is inherent to the
equilibrium displacement concept: library members of high
intrinsic stability combining strong affinity for the target will
INTRODUCTION
■
Pedersen’s seminal discovery of crown ethers simultaneously
brought two cornerstones to the emerging edifice of supra-
molecular chemistry.1 These macrocyclic entities were the first
nanocontainers with well-defined cavities dedicated to molec-
ular recognition. It also revealed how noncovalent interactions
can act as powerful driving forces during covalent self-assembly
processes. Since then, supramolecular chemists have learned to
produce various cavitands such as calixarenes,2 pillarenes,3
cyclodextrins,4 or cucurbiturils.5 While these architectures can
be obtained at relatively large scale from accessible starting
material, a few numbers of templates and functional groups are
unfortunately compatible with the generally harsh oligomeriza-
tion conditions, yielding mixtures that often require tedious
chromatographic purifications and postsynthetic functionaliza-
tion steps, respectively.
During the past 20 years, dynamic combinatorial chemistry
(DCC) has emerged as an interesting alternative to produce
robust covalent macrocyclic architectures in mild conditions.6
By operating under thermodynamic control, DCC relies on
noncovalent interactions as tunable driving forces to displace
equilibrium mixtures in the absence or presence of a molecular
Received: November 12, 2015
© XXXX American Chemical Society
A
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Figure 1. Dynamic combinatorial libraries from bisthiophenols 1−3 and templates 4−13, and subsequent isolation of dyn[4]arenes 14−34.
Electronic features: red = electron-rich, blue = electron-poor. See Supporting Information for full details.
behave as “false negative” during the dynamic screening
process.12
(8−10), and cationic (11−13) guests could potentially amplify
their optimal receptor, respectively.13
Libraries generated from 1 in chloroform invariably and
quantitatively yielded a single oligomeric product, which was
identical to the adduct obtained by Raasch who hypothesized a
cyclic tetrameric structure 14 from mass spectrometry data
(Figure 1).14 Interestingly, 14 could also be isolated from a
neutral aqueous medium (200 mM Tris buffer, pH 7.4) by
simultaneous self-assembly and precipitation (71% yield). A
crystal structure was obtained for the first time for this
compound, confirming its identity and conformation in the
solid state (see Supporting Information for details).
Libraries generated from 2 in the presence or absence of
template in Tris buffer (200 mM, pH 7.4) delivered an
alternative example of convergence, yielding quantitatively 24 as
a single insoluble species (Figure 1). The identity and purity of
the macrocycle was confirmed by HPLC coupled to mass
spectrometry, NMR, and elemental analysis.
Libraries generated from 3 surprisingly revealed that
fragment polyamines 12 and 13 have almost the same
templating effect as the parent spermine 11 previously reported
for its quantitative amplification of 34 (Figure 1).15 This
qualitative deconvolution suggested that the shorter 1,4-
diammonium motif already displays all the necessary
recognition features that are required to efficiently bind 34
(vide infra). Unlike the previous macrocycles, 34 remained
soluble in a neutral aqueous medium (200 mM Tris buffer, pH
7.4). Its isolation was simply achieved by precipitation upon
By exploring the DCC of 1,4-bisthiophenols, we report
herein the easy preparation of a family of p-cyclophanes that
incorporate dynamic disulfide linkages and various functional
groups through quantitative self-assembly. These so-called
dyn[4]arenes could be obtained in a gram scale by a
straightforward procedure that takes profit of intra- or
intermolecular noncovalent driving forces. These forces
dramatically depend on the chemical functions borne by the
monomers and further determine the structural and binding
features of the resulting macrocycles.
RESULTS AND DISCUSSION
■
Syntheses. A conventional dynamic combinatorial ap-
proach was first followed to screen for the best receptors for
ionic templates of different polarities from libraries of cyclic
homo-oligomers. We investigated the disulfide-based self-
assembly of three distinct bis- or tetrafunctionalized 1,4-
bisthiophenols 1−3 in the absence and in the presence of
potential ionic partners 4−13 (Figure 1). Substituents were
chosen to provide electronically contrasted donor/acceptor
sites on monomers 1, 2, and 3 to generate dynamic libraries of
oligomers that display π-acidic, π-basic combined with H-bond
donating/accepting, and π-basic combined with H-bond
accepting properties, from which anionic (4−7), zwitterionic
B
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Figure 2. Dyn[4]arene virtual conformational landscape from the rotation of phenyl units (A), and the inversion of the dihedral angle of disulfide
bonds (B).
neutralization of its anionic charges with trifluoroacetic acid
(66% yield). The identity and purity of the oligomer was again
confirmed by HPLC coupled to mass spectrometry and
elemental analysis.
Whereas high performance chromatography has been
systematically conducted so far for hit isolation from
disulfide-based libraries, highly dominant species can clearly
be accessed by simpler and more straightforward procedures.
Dyn[4]arenes 14, 24, and 34 can be prepared in a gram scale
with good yields (66−96%) and excellent purities and without
any chromatographic step. We therefore decided to explore the
structural features of these macrocycles to elucidate the driving
forces underpinning the remarkably efficient self-assembly
processes.
Conformational Analyses in Solution. Due to their
reduced synthetic accessibility16,17 and/or low solubility,18,19
Figure 3. Conformer structure and distribution in solution for
dyn[4]arene 14 from 19F NMR studies in CDCl3 and from DFT
disulfide-based cyclophanes have barely been characterized in
solution from a structural point of view. Attention has been
calculations. See Supporting Information for full details.
drawn to their binding properties, while often considering these
objects as members of a structurally and conformationally
homogeneous population. Yet, the synthesis of homologous
pillar[n]arenes is known to yield stereoisomers because the
NMR. DFT calculations in solution at the Møller−Plesset
second-order perturbation theory level (MP2) are in fair
agreement with the experimental data, allowing us to assign
these three species to the folded meso MPMP, meso MMPP,
rotation of each of the [n] phenyl units along the 1−4 axis leads
to structures displaying [n] planes of chirality with two opposite
and homochiral PPPP/MMM conformers, respectively.
pR/pS configurations (Figure 2A).20 For dyn[n]arenes, a
Although the flattened shape of 14 could be intuitively
second level of structural diversity arises from the chirality of
attributed to C−F/pi interactions, calculations also revealed
that it mostly originates from dispersive forces (see section
S4.1).
each of the [n] disulfide linkages, which can individually adopt
two stabilized enantiomeric P/M conformations (Figure 2B).
We decided to explore the conformational landscape of
dyn[4]arenes 14−34 in solution by NMR spectroscopy and
DFT calculations.
While the octamethoxydyn[4]arene was described to adopt
in the solid state a homochiral PPPP/MMMM conformation
with phenyl groups perpendicular to the average plane of the
polydisulfide ring,20 its perfluoro analogue 14 crystallizes in a
much more flattened conformation. Interestingly, this structural
feature survives the dissolution in an organic medium, which
indicates that it originates from intramolecular interactions.
Indeed, three tetrameric species could be identified on the 19F
NMR time scale (Figure 3 and section S3.1).
24, which is amplified by self-aggregation, also exemplifies the
dramatic impact of the functional groups borne by the
monomeric units on the conformational features of the
resulting dyn[4]arene. Three types of aromatic protons (Figure
4, Ha, Hb, and Hc) were observed in 1H NMR and appeared to
belong to a unique species (see section S3.1.2 for the full
multidimensional NMR analysis). Conformational analysis in
solution by DFT calculations (at the wB97XD/6-31G(d,p)
level, see section S4.2) exclusively yielded species involving an
internal N···H−N hydrogen bond between two nonadjacent
aromatic units. This internal interaction has two major
structural consequences: (i) the monomeric units engaged in
this bond are bent into the cavity with amino groups facing
each other, and (ii) the homochiral pRpRpSpR/MMMM and
pSpSpRpS/PPPP enantiomeric dynarenes are the only stable
conformers. This internal bond is extremely robust, and
coalescence could not be observed upon heating (up to 100
The two most abundant (87% and 11%) conformers each
displayed two sets of signals corresponding to internal
(shielded) and external (deshielded) fluorine nuclei in relatively
slow mutual exchange (60 kJ mol−1). The exchange is faster for
the third minor species (2%), resulting in a single signal in 19F
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respectively, have left a significant conformational imprint on
the resulting architectures. These contrasted conformational
features, which are dictated by the nature of substituents on the
monomeric units, should also substantially affect the binding
properties of dynarenes.
Binding Properties in Solution. As initially intended
during the preliminary dynamic combinatorial screening, the
homo-oligomers combining a π-acidic cavity surrounded by
hydrogen accepting sites (14), a π-basic cavity surrounded by
neutral hydrogen bond donating/accepting sites (24), and π-
basic cavities surrounded by anionic hydrogen bond accepting
sites (34) were respectively probed as receptors for anions,
zwitterions, and cations. In good agreement with DOSY
experiments, molecular modeling revealed that the three
dyn[4]arenes have similar diameters and hosting capacities
with a maximal cavity diameter of 5.3−6.0 Å (Figure 5), which
is comparable to pillar[5]arene, while being much less floppy
than their static homologues in terms of phenylene rotation
(see Supporting Information section S4.4 and references herein
for details). Still, their respective folding states, hence the
morphology and accessibility of their potential binding sites, are
radically different within the series. Binding properties of
dyn[4]arenes in solution were investigated by UV−vis titration
in organic media for 14 and 24 and by ITC in neutral aqueous
media for 34.
Figure 4. Conformer structure and distribution in solution for
dyn[4]arene 24 from H NMR studies in DMSO-d6 and from DFT
calculations. See Supporting Information for full details.
1
°C). In addition, the two sharp signals Hb and Hc tend to fuse
while Ha undergoes severe line broadening upon concentration,
suggesting a self-association event in solution. DOSY experi-
ments indeed revealed that two populations of monomeric 24
and dimeric 24·24, displaying hydrodynamic radii of 8.2 and
15.6 Å, respectively, coexist in solution with concentration-
dependent proportions (see section S3.3.3 for details).
Tetramer 34, which bears anionic monomeric units, was
1
characterized by a single sharp peak in H NMR (see section
According to its cavity size and π-acidic character, 14
displayed millimolar affinity for iodide, yielding a 1:1 complex
in chloroform accompanied by charge-transfer features (see
section S6.2.1). No binding could be detected with the smaller
bromide, chloride, and fluoride ions (Figure 5). No
modification of the 19F NMR spectrum of 14 was observed
upon iodide addition, which is in agreement with previous
reports on anion−pi interactions21−24 and suggests that the
conformational landscape of the host remains unchanged upon
guest binding (absence of induced fit). Despite the modest π-
acidic character of 1, a macrocyclic effect,25 partly relying on the
preorganization of 14, is suggested to explain the selective and
efficient binding of iodine in the halogen series through anion−
pi interactions.
S3.1.3). Our previous modeling study suggested that it
corresponds to the cylindrical-shaped homochiral (pS)4/(pR)4
species, which minimizes the repulsive Coulombic interactions
between nearest carboxylate neighbors. This homochiral
configuration of the dicarboxyphenyl units in turns directs the
disulfide bridges into a homochiral conformation. This analysis
agrees with the experimental detection of a unique C−H signal
(the kinetic barrier for the inversions of the disulfide bridge’s
dihedral angle was estimated to be around 75 kJ mol−1, a value
that should lead to signal splitting at the NMR time scale if
several conformers coexist).
Interestingly, the supramolecular forces that dictate the self-
assembly of tetramers 14, 24, and 34, intramolecular
stabilization, intermolecular self-stabilization, and templating,
Figure 5. Structure−binding relationships for dyn[4]arenes 14−34: hydrodynamic radii from DOSY experiments in CDCl3 (a) and DMSO-d6 (b);
cavity diameters, external diameter, and electrostatic potential surfaces from DFT calculations, and thermodynamic parameters for the binding events
with 4−13 from UV and ITC titrations in CHCl3 (c), 95% DMSO/5% aq AcONH4 (d), and 40 mM Tris buffer pH 7.4. See Supporting Information
for full details.
D
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While 14 adopts upon self-assembly a tetrahedral shape that
leads to a binding site for spherical anions, the cavity of 24 is
entirely occupied by bent hydrogen-bonded monomeric units.
As a consequence, the dyn[4]arene displays an electron-poor
cleft and an electron-rich area, both sites lying 6 Å away from
each other (Figure 5). UV-titrations with substituted α,ω-
amino acids in a DMSO/aqueous ammonium acetate mixture
revealed that glycine (8) is too short to bridge this gap through
noncovalent interactions, while both β-alanine (9) and γ-
aminobutyric acid (GABA, 10) form 1:1 complexes with
submillimolar affinities. No binding was observed with
monoanions such as carboxylates or primary ammoniums of
various chain lengths in the same conditions. The absence of
significant alteration in both the host and guest NMR spectrum
upon binding confirms that (i) this binding event follows a
lock-and-key scenario, without any induced-fit phenomenon,
and (ii) the methylene spacers of the guest remain exposed to
the outer solution in the complexes. Because the unfolding of
24 represents a prohibitive energetic cost, it narrows the
spectrum of potential guests to zwitterions that display an
appropriate distance between their end groups.
binding sites are desolvated upon binding hence involved in
complex formation. The evolution in enthalpy reveals that the
accompanying desolvation penalty overcomes the benefits of
supplementary binding site(s) but that a chelate effect can
indeed be observed when comparing spermidine to spermine.
1
Analysis of the H NMR spectrum of the complexes (see
section S5.2 for details) indicate that enantiotopic methylene
protons of the butanediamine thread become clearly diaster-
eotopic upon complexation, confirming the homochiral (pS)4/
(pR)4 configuration of the host 34.14 Yet, fast exchange between
two diastereoisomeric complexes occurs in the case of
spermidine (Figure 6b), which result in an average spectrum
displaying broad signals for the butanediamine moiety. The
loose nature of this complex agrees reasonably well with its
increased entropy and reduced enthalpy of formation with
respect to parent guests 11 and 13.
CONCLUSION
■
The functional group-directed self-assembly of 1,4-bisthiophe-
nol building blocks has led to the gram scale and
chromatography-free preparation of a family of p-cyclophanes
named dynarenes. Beyond the exciting perspectives offered by
this new class of highly accessible objects, this preliminary
report illustrates the power of the molecular programs
contained in simple building blocks. Indeed, the nature of the
functionalities borne by the precursors determines the selection
event (folding-, aggregation-, or guest-directed) that is
responsible for self-assembly. While the conformational land-
scape of this family is potentially vast, well-structured
architectures in solution (tetrahedral, flattened, or cylindrical)
result from these function-dependent driving forces. Finally,
these structural imprints also dramatically govern the guest
binding abilities of dyn[4]arenes by preferentially orienting the
association events toward a lock-and-key mode, hence tuning
the spectrum of selectivities toward electronically and
structurally complementary guests. In the present case,
receptors with milli- to submicromolar affinities and selectivities
for anions, zwitterions, and cations were obtained. We are
currently working toward the expansion of this new family of
macrocycles in terms of ring sizes and functionalities for future
exciting applications.
The new synthetic procedure described herein, which
provides a straightforward access to substantial amounts of
34, opens the ways to comprehensive analyses of the
complexing features of this type of architecture in aqueous
solution for various cationic guests. Butanediamine 13,
spermidine 12, and spermidine 11 were chosen as models to
provide a preliminary insight into the issues that can be
1
addressed through ITC titration and H NMR analyses. This
modest series formally consists of the successive mutation of
one binding N−H proton into an aminopropyl secondary
binding group on one or both nitrogens of the butanediamine
core. This core remains the main binding site on which the
pseudorotaxane structure of the complex is centered as
indicated by the almost identical and systematic strong
1
shielding of the corresponding C−H protons in H NMR.
Whereas substitution on the butanediamine ends only slightly
decreases the electrostatic potential of each of these main
binding sites (by less than 5% each, data not shown) it could be
expected to reinforce the association by providing additional
intramolecular cationic binding sites from which some chelate
effect may arise. Yet, if the binding is indeed reinforced by 1
order of magnitude, ITC reveals that this increase is
entropically driven (Figure 6). This phenomenon can only be
imputed to desolvation and confirms that the supplementary
EXPERIMENTAL SECTION
■
Synthesis of the Building Blocks. Building block 1 tetrafluor-
obenzene-1,4-dithiol):14 Tetrafluorohydroquinone (4.3 g, 23.63
mmol) was dissolved in 45 mL of anhydrous DMF under argon. At
0 °C, 4 equiv of DABCO (10.62 g, 94.51 mmol) was added, and after
5 min, 4 equiv of dimethylthiocarbamoyl chloride (11.70 g, 94.51
mmol) was added portionwise to the reaction mixture. The suspension
was allowed to warm to room temperature and stirred for 1 day. The
reaction mixture was poured on ice and filtered, and the residue was
washed extensively with water dried under vacuum to give O,O′-
(perfluoro-1,4-phenylene) bis(dimethylcarbamothioate) as a white
solid, which was crystallized in acetone to give 8.22 g (yield = 98%) of
a white powder. 1H NMR (300 MHz, CDCl3): δ = 3.46 (s, 6H), 3.38
(s, 6H); 13C NMR (75 MHz, CDCl3): δ = 184.8, 140.1, 140.0, 139.8,
44.2, 39.2; 19F NMR (282 MHz, CDCl3): δ = −153.79; HRMS (ESI
+): m/z: calcd for C12H12N2O2S2F4Ag+: 462.9322 [M + Ag]+; found:
462.9323; mp: 194 °C.
O,O′-(Perfluoro-1,4-phenylene) bis(dimethylcarbamothioate) (900
mg, 2.53 mmol) was suspended in 3 mL of diphenyl ether under argon
atmosphere and heated on a sand bath to 200−210 °C for 1 h 30 min.
The reaction mixture was allowed to slowly cool to room temperature.
The reaction mixture was poured on 200 mL of petroleum ether under
strong stirring. The resulting precipitate was then filtered, extensively
Figure 6. Binding models between 34 and guest 11−13 and associated
enthalpy and entropy. ΔH° and ΔS° are expressed in kcal·mol−1 and
cal·mol−1·K−1, respectively. See Supporting Information for full details.
E
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washed with large amount of petroleum ether, and then dried under
vacuum to give 850 mg (yield = 94%) of S,S′-(perfluoro-1,4-
phenylene) bis(dimethylcarbamothioate). 1H NMR (300 MHz,
CDCl3): δ = 3.15 (s, 6H), 3.03 (s, 6H); 13C NMR (75 MHz,
CDCl3): δ = 161.9, 145.8, 145.7, 145. 6, 37.4; 19F NMR (282 MHz,
Library Preparation and Analyses. Preliminary dynamic
combinatorial screening was conducted as follows: 10 mM stock
solution of building block (1, 2·2HCl, or 3) were prepared by
dissolution in 200 mM Tris buffer pH = 7.4 in Milli-Q water. In a 2
mL HPLC vial equipped with a stir bar, 400 μL of each of these
solutions was mixed with either 400 μL of a 10 mM template solution
in the same buffer and 200 μL of buffer solution or 600 μL of buffer
solution. Precipitation occurs for libraries involving building block 2
after several hours and 1 after 48 h. After filtration and washing with
water and methanol, libraries [1] and [2] are redissolved in CDCl3 and
DMSO-d6 respectively. Both libraries are analyzed by HPLC-MS and
NMR. Templated and untemplated libraries prepared from 1 and 2
lead to HPLC chromatograms and NMR spectra corresponding to
pure 14 and 24 in each case. For building block 1, additional libraries
were set in CDCl3 (4 mM, 0.2 mM Et3N) in the absence and presence
of 0.25 equiv of template and lead to identical 19F spectra
corresponding to pure tetramer 14. Additional libraries made from
building block 2·HCl in DMSO (4 mM, 4.2 mM Et3N) led to side
products involving overoxidized sulfur atoms. Libraries [3] were
analyzed by HPLC-MS.
Oligomer Identification/Quantification. Identification and
quantification of the oligomers and potential side products were
conducted by HPLC with a heated column compartment (35 °C), and
a triple quadrupole mass spectrometer. Mass spectra (ESI−/ESI+)
were acquired in ultrascan mode by using a drying temperature of 400
°C, a drying gas flow of 11 L/min, and a capillary voltage of 3000 V
(ESI+) or 2000 V (ESI−). Elution was conducted at 1.2 mL/min on a
C8 column, 4.6 × 150 mm, 3 μm column (T = 35 °C).
CDCl3):
δ = −131.10; HRMS (ESI+): m/z: calcd for
C12H13N2O2S2F4 : 357.0349 [M + H]+; found: 357.0350; mp: 237 °C.
S,S′-(Perfluoro-1,4-phenylene) bis(dimethylcarbamothioate) was
suspended under argon in 3 mL of a 4.2 M degassed solution of
KOH in MeOH/H2O (5/1). The mixture was then refluxed for 1 h 30
min. The reaction mixture was allowed to cool to room temperature,
and degassed water (13 mL) was added to the solution followed by
HCl (10%, 5 mL) to afford a white precipitate. The precipitate was
filtered, washed with degassed water, and dried under vacuum to give
tetrafluorobenzene-1,4-dithiol as a white solid (233 mg, 71% yield). 1H
NMR (500 MHz, CDCl3): δ = 3.66 (s, 2H); 13C NMR (126 MHz,
CDCl3): δ = 143.65, 143.61, 108.43, 108.41; 19F NMR (471 MHz,
CDCl3): δ = −136.95; mp: 65−67 °C.
+
Building block
2 (2,5-diaminobenzene-1,4-dithiol di-
(hydrotrifluoroacetate)):26 Potassium hydroxide (14.87 g; 265.07
mmol) was dissolved in water (18 mL) and degassed under inert
atmosphere and cooled to 0 °C with an ice bath. Then 2·2HCl (5g;
20.39 mmol) was added by portions to the previous solution. The ice
bath can be removed, and the reaction mixture was stirred 2 h at room
temperature. The precipitated product was collected by filtration,
affording a highly air sensitive white solid which was immediately
transfer to the next step. To a round-bottom flask was poured water
(100 mL) followed by trifluoroacetic acid (23.25g, 203.9 mmol, 15.6
mL), and the solution was cooled at 0 °C. Then the dibasic potassium
salt of 2 was dissolved in degassed water (15 mL) and added carefully
to the previous solution. The reaction mixture was stirred at room
temperature for 2 h. And the water was removed by evaporation. Then
the air-sensitive crude solid was dispersed in degassed methanol and
rapidly filtered and dried under vacuum to afford compound 2·2TFA.
(7.8 g; yield = 96%)
Synthesis of the Macrocycles. Dyn[4]arene 14. A 932 mg
amount of 1 was dissolved into 900 mL in 200 mM Tris buffer pH =
7.4. The reaction mixture was stirred for 72 h. The resulting precipitate
was then filtered, washed with degassed methanol, and dried under
vacuum to give a pale yellow solid (656 mg, 71% yield). Crystal
suitable for X-ray analyses were obtained upon recrystallization in
chloroform−methanol. 19F NMR (471 MHz, CDCl3): δ = 128.1 (s,
MPMP), −129.1 (s, MMPP), −129.3 (s, MMMM + PPPP), −132.2
(MPMP), −133.0 (s, MMPP); 13C NMR (126 MHz, CDCl3): 119.0,
147; HRMS (ESI−): m/z: calcd for C24F16S8 = 882.7204 [M + Cl]−,
found = 882.7238; mp: 248−251 °C (decomp); IR (ATR, cm−1) =
538 (S−S) ; 1250 (C−F) 1464 (CC), 1618 (CC).
Building block 3 (2,5-dimercaptoterephthalic acid):15 To a solution
of 2,5-dihydroxyterephthalic acid diethyl ester (10 g, 39 mmol) in 150
mL of DMF was added 4 equiv of neat DABCO (17.6 g, 156 mmol),
and after a few minutes 4 equiv of dimethylthiocarbamoyl chloride
(19.4 g, 156 mmol) was added. The suspension was allowed to warm
to room temperature and was stirred for 24 h. The reaction mixture
was poured on a large amount of water, and the resulting 2,5-
bis(dimethylthiocarbamoyloxy)terephthalic acid diethyl ester was
filtered off and then dried under vacuum to give 16.0 g (yield =
Dyn[4]arene 24. A 980 mg (3.84 mmol) amount of 2·2HCl was
dissolved into 1 L of a 200 mM Tris buffer solution adjusted to pH =
8. The reaction mixture stirred for 72 h. The resulting solid was filtered
off and then dried under vacuum. A Soxhlet extractor was used
overnight to wash the solid with warm methanol. The solid was then
dried under vacuum to give 630 mg (yield = 96%) of a dark red
powder. The same result was obtained from the bis-
(hydrotrifluoroacetate) salt 2·2TFA, confirming that the anion is not
1
97%) of a white powder. H NMR (300 MHz, CDCl3): δ = 7.72 (s,
2H), 4.30 (q, J = 7.1 Hz, 4H), 3.45 (s, 6H), 3.39 (s, 6H), 1.33 (t, J =
7.1 Hz, 6H); 13C NMR (75 MHz, CDCl3): δ = 187.1, 163.1, 150.6,
128.6, 127.8, 61.7, 43.4, 39.1, 14.2; Mp: 211 °C.
1
involved in the self-assembling process. H NMR (400 MHz, DMSO-
d6): δ = 6.73 (sl, 4H, Ha), 6.83 (s, 2H, Hb), 6.84 (s, 2H, Hc); 13C
NMR (126 MHz, DMSO-d6): δ = 119.3, 121.7, 140.1; HRMS
The 2,5-bis(dimethylthiocarbamoyloxy)terephthalic acid diethyl
ester (1g, 2.35 mmol) was heated under nitrogen at 230 °C for 1 h.
The mixture was then cooled to room temperature, and the product
was recrystallized in absolute EtOH to form pale brown crystals. The
crystals were filtered off, yielding 2,5-bis(dimethylthiocarbamoyl-
sulfanyl)terephthalic acid diethyl ester (900 mg, 90%). 1H NMR
(300 MHz, CDCl3): δ = 8.09 (s, 2H), 4.33 (q, J = 7.1 Hz, 4H), 3.14 (s,
6H), 3.04 (s, 6H), 1.35 (t, J = 7.1 Hz, 6H); 13C NMR (75 MHz,
CDCl3): δ = 165.4, 165.3, 138.8, 137.3, 131.0, 61.7, 37.1, 14.2; mp:
140 °C
+
(MALDI): m/z: calcd for C24H24N8S8 = 679.9884 [M+•], found =
679.9896; Elemental analysis: calcd for C24H24N8S8,H2O = C: 41.23,
H: 3.75, N: 16.03, S: 37.70; found = C: 41.02, H: 3.42, N: 15.61, S:
37.22; mp: ≈ 200 °C (decomp); IR (ATR, cm−1): 3373 (NH), 1587
(CC), 1217 (C−N), 875 (CH).
Dyn[4]arene 34. A 920 mg (4 mmol) amount of monomer 3 was
dissolved into 400 mL of a 200 mM Tris buffer pH = 7.4 in the
presence of spermine (910 mg, 4 mmol). The reaction mixture was
stirred open to the air. After 48 h, a few milliliters of TFA was added
and a fine yellow precipitate appeared. The resulting solid was filtered
off and taken up in a pH = 9 borate buffer, and then TFA was added.
The precipitate was collected by centrifugation, suspended in Milli-Q
water, collected by centrifugation again, and then dried under vacuum
To 20 mL of a 1.3 M solution of KOH in H2O/EtOH (1/1)
degassed solution was added the 2,5-bis(dimethylthiocarbamoyl-
sulfanyl)terephthalic acid diethyl ester (650 mg, 1.51 mmol). The
mixture was purged with argon for 15 min and then heated to reflux
overnight. The reaction mixture was allowed to cool to room
temperature, and concentrated HCl was added to afford a yellow
precipitate. The precipitate was filtered, washed with degassed water,
and dried under vacuum to give the pure 2,5-dimercaptoterephthalic
1
overnight to give 600 mg (0.66 mmol; 66%) of a yellow powder. H
NMR (500 MHz, DMSO): δ = 8.29 (s, 1H); 13C NMR (126 MHz,
DMSO): δ = 166.95, 137.18, 132.41, 128.93; HRMS (ESI−): m/z:
1
−
calcd for C32H15O16S8 = 910.8131 [M − H]−, found = 910.8166;
acid 3 as a yellow solid (310 mg, 88% yield). H NMR (300 MHz,
DMSO-d6): δ = 8.06 (s, 2H); 13C NMR (75 MHz, DMSO-d6): δ =
166.7, 133.2, 130.0; mp: degradation over 387 °C.
Elemental analysis: calcd for C32H15O16S8·5H2O = C: 38.3 H: 2.61 O:
33.5; S: 25.6; found = C: 36.8; H: 2.67; O: 34.8; S: 25.8; mp: 350 °C
F
DOI: 10.1021/acs.joc.5b02605
J. Org. Chem. XXXX, XXX, XXX−XXX

The Journal of Organic Chemistry
Article
(decomp); IR (ATR, cm−1) = 2887 (OH), 1678 (CO), 1583 (C
discarded from each data set to remove the effect of guest diffusion
across the syringe tip during the equilibration process.
C), 1213 (C−O), 779 (CH).
NMR Studies. Liquid-state NMR spectra were recorded in CDCl3,
DMSO-d6, methanol-d4, and heavy water buffered with CD3CO2ND4
or KD2PO4−NaOD on spectrometers operating at 300, 400, and 500
MHz. Solvent residual signals were used as internal standard (when
necessary, water suppression by presaturation was used). The
temperature was set to 22° C unless otherwise specified. A 2s
relaxation time allowed proton full relaxation. 13C spectra were
recorded using a 30° tilt angle and 2s relaxation time. ROESY
experiments were run using the 2D off-resonance version, with
adiabatic trapezoidal 200 ms shape pulse, at 10 kHz field strength. A
total of 256 increments of 8 scans were collected giving 1 h 30 min
experiment time. Solid-state NMR spectra were recorded on a 9.4 T
spectrometer.
Computational Details. Geometry optimizations were conducted
at the MP2 level of theory with the DEF2-SVP basis set. Solvent
corrections (dichloromethane) were included through the COSMO
model. Weak interactions in the system were investigated by means of
Non Covalent Interactions (NCI) analysis on the basis of the
theoretically optimized geometry.
UV/vis titration experiments were performed at 298 K. All
measurements have been run at least in triplicate. All spectra were
carried out in quartz UV cuvettes (l = 1 cm). Spectroscopic grade
solvents (chloroform, DMSO, Milli-Q water) and analytical grade salts
(AcONH4, nBu4NPF6). AcONH4 was used to buffer the aqueous
DMSO solution and ensure a constant ionic strength protonation state
of the amino acid guests used. Similarly, anion−pi interactions
between 14 and anionic guests were probed both in the presence and
absence of nBu4NPF6 to rule out any solvatochromic effect.
ASSOCIATED CONTENT
* Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.joc.5b02605.
■
S
Material and methods, HPLC chromatograms, NMR
spectra, and MS spectra (PDF)
X-ray crystallographic data (CIF)
Dyn[4]arene 14. The structures of the four conformers of 14
(namely PPPP, PPPM, MMPP, and MPMP) were optimized with
solvent corrections. The most stable structure was found to
correspond to the MPMP conformer. The MMPP and PPPP structures
are slightly less stable, with energies higher by 1.0 and 1.8 kcal·mol−1,
respectively. The less stable conformer is the PPPM structure, whose
energy is 4.6 kcal·mol−1 higher than for the MPMP. This scheme is
consistent with the abundance found by NMR analysis, with one major
compound (around 85%) and two minor species (15% total). The
compact structure observed in the crystalline state was retrieved from
the calculation in solution. NCI analysis was performed to understand
the origin of such folded structure on the four conformers (Figure
S46). A network of interaction favoring the compact structures can be
clearly observed. They are of two main types. Fluorine atoms of
different phenyl moieties clearly interact with each other through weak
dispersive forces. An electrostatic interaction can be observed between
one fluorine atom and the carbon of the opposite phenyl ring: one C−
F fragment can thereby interact with another F−C of the opposite
monomer. This interaction accounts for the lower stability of the
PPPM structure, as this network is partially broken in such a
conformation, as it can be seen in Figure S46.
Dyn[4]arene 24. The conformational study of 24 was performed
using a stochastic exploration of the potential energy surface (PES)
using simulated annealing with AM1 semiempirical level. A set of 100
geometries of conformations were generated using four simulated
annealings, each performed with a different geometry or parametrized
with a different initial temperature. All annealings were performed with
a geometry optimized with WB97XD/6-31G(d,p) as the starting
structure. Only the dihedral angles of the initial structure were allowed
to relax during the annealing; the bonds lengths and the valences
angles were kept constant. Then the conformations with energy down
to 2.5 kcal mol−1, compared to the lower energy conformation, were
kept and fully optimized. The geometry optimizations, vibrational
frequencies, and IR absorption intensities were calculated with Density
Functional Theory (DFT) using WB97XD functional combined with
6-31G(d,p) basis set.
AUTHOR INFORMATION
Corresponding Author
*E-mail: julien.leclaire@univ-lyon1.fr.
Author Contributions
J.L., L.V., F.P., and F.F. conceived the experiments. P.-T.S,
M.D., E.J., F.P., and J.L. performed the experiments. E.J., C.G.,
and J.-V.N. performed the theoretical analyses. A.B. and B.F.
designed and performed the NMR analyses. J.L., F.P., and L.V.
analyzed the experimental data and cowrote the paper.
■
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
This work was supported by the LABEX iMUST (ANR-10-
■
LABX-0064) of Universite
́
de Lyon, within the program
“Investissements d′Avenir” (ANR-11-IDEX-0007) operated by
the French National Research Agency (ANR) (fellowship for
E.J. and starting grant for J.L.). We are grateful to the CNRS
and ANRT for funding (fellowship for M.D. and P.-T.S.
respectively)
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