Pyridine-incorporated cyclo[6]aramide for recognition of urea and its derivatives with two different binding modes

Article abstract of DOI:10.1080/10610278.2017.1282614

A novel pyridine-incorporated cyclo[6]aramide is designed and synthesised for recognition of urea and its derivatives. Analysis of its single crystal structure reveals the presence of introverted amide NH protons and amide carbonyl groups that are supposed to contribute to the subsequent accommodation of neutral urea-related guest molecules via multiple hydrogen bonding interactions. Thiourea is found to be superior to urea in binding to the receptor. Particularly interesting is the observation of two binding modes in complexing urea/thiourea (contact mode) and ethylurea/diethylurea (threading mode) as supported by both NMR experiments and computational simulations. The finding of the threading mode may open up new opportunities for the development of pesudorotaxanes and related mechanically interlocked structures.

Full text of DOI:10.1080/10610278.2017.1282614

Supramolecular Chemistry
ISSN: 1061-0278 (Print) 1029-0478 (Online) Journal homepage: http://www.tandfonline.com/loi/gsch20
Pyridine-incorporated cyclo[6]aramide for
recognition of urea and its derivatives with two
different binding modes
Kang Kang, Wei Huang, Yonghong Fu, Lixi Chen, Jinchuan Hu, Yi Ren, Wen
Feng & Lihua Yuan
To cite this article: Kang Kang, Wei Huang, Yonghong Fu, Lixi Chen, Jinchuan Hu, Yi Ren,
Wen Feng & Lihua Yuan (2017): Pyridine-incorporated cyclo[6]aramide for recognition of
urea and its derivatives with two different binding modes, Supramolecular Chemistry, DOI:
10.1080/10610278.2017.1282614
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Date: 06 February 2017, At: 15:00

Supramolecular chemiStry, 2017
http://dx.doi.org/10.1080/10610278.2017.1282614
Pyridine-incorporated cyclo[6]aramide for recognition of urea and its derivatives
with two different binding modes
Kang Kang, Wei Huang, Yonghong Fu, Lixi Chen, Jinchuan Hu, Yi Ren, Wen Feng and Lihua Yuan
Key laboratory for radiation physics and technology of ministry of education, institute of Nuclear Science and technology, college of chemistry,
Sichuan university, chengdu, china
ABSTRACT
ARTICLE HISTORY
received 17 october 2016
accepted 7 January 2017
A novel pyridine-incorporated cyclo[6]aramide is designed and synthesised for recognition of
urea and its derivatives. Analysis of its single crystal structure reveals the presence of introverted
amide NH protons and amide carbonyl groups that are supposed to contribute to the subsequent
accommodation of neutral urea-related guest molecules via multiple hydrogen bonding
interactions. Thiourea is found to be superior to urea in binding to the receptor. Particularly
interesting is the observation of two binding modes in complexing urea/thiourea (contact
mode) and ethylurea/diethylurea (threading mode) as supported by both NMR experiments and
computational simulations. The finding of the threading mode may open up new opportunities for
the development of pesudorotaxanes and related mechanically interlocked structures.
KEYWORDS
cyclo[6]aramide; urea;
host–guest complexation;
hydrogen bonding
1. Introduction
popular macrocyclic compounds such as crown ethers
(5), calixarenes (6), cyclodextrins (7), cucurbiturils (8), pil-
lararenes (9) and other artificial cycles (10). Simultaneous
with the shape-persistency of their molecular backbones
is the preorganisation of functionalities or amide car-
bonyl groups that allow follow-up implementation of
host–guest (H–G) interactions. These H-bonded macr-
ocycles have found a variety of applications in catalysis
(11), sensors (12), separation technology (13), molecular
recognition (14) and transmembrane channels (15), etc.
One-pot H-bonding-directed macrocyclisation (1) boasts
high production of cyclic compounds and synthetic sim-
plicity and atom economy. Particularly appealing is its
utility in generating various classes of aromatic amide
macrocycles that result from such macrocyclisation (2).
The resultant macrocycles, termed H-bonded aromatic
amide macrocycles (3), have demonstrated a unique struc-
tural feature of two-dimensional shape-persistency (non-
collapsiblility) (4) that differentiates them from nowadays
CONTACT lihua yuan
lhyuan@scu.edu.cn
Supplemental data for this article can be accessed http://dx.doi.org/10.1080/10610278.2017.1282614.
© 2017 informa uK limited, trading as taylor & Francis Group

2
K. KANG ET AL.
R1
O
R1
O
O
S
m
n
o
1
H
N
O
N
H
N
O
N
G1
G2
G3
G4
H2N
NH2
NH2
q
O
N
O
p
O
O
O
2
O
O
H2N
H
O
r
R2
H
O
s
R2
v
H
H
O
t
N
3
u
N
H2N
N
O
H
4
w
x
O
1a
N
H
N
H
5
R2
R1
Figure 1. chemical structures of pyridine-incorporated cyclo[6]aramide 1a and guest G1,G2,G3 and G4.
Among them, H-bonded aromatic amide macrocycles
bearing introverted carbonyl oxygens in their interiors
(16) dubbed cycloaramides, and their derivatives, are
especially intriguing due to their rich H–G chemistry (17).
Our recent work has revealed the strong ability of cyclo[6]
aramides, the smallest member of this class of H-bonded
aromatic amide macrocycles to bind organic cations (18)
such as dialkylammonium ions and diquat, and even to
recognise amino acids (19). Cyclo[6]aramide with a larger
cavity could accommodate a depsipeptide antibiotic val-
inomycin or its potassium complex on a highly oriented
pyrolytic graphite surface (20). Interestingly, these macro-
cycles are able to serve as a class of macrocyclic mesogens
that cover a wide spectrum of phases as liquid crystalline
materials, whose inter-phase transition is tunable via H–G
interactions (21). However, the presence of all six carbonyl
groups preorganised inside the cavity prevents these cyclic
compounds from being used in binding ion-pair or neutral
guest species.
Recently, we have developed a strategy by depleting
partial internal H-bonds to construct convergent heterodi-
topic cyclo[6]aramides as ion-pair receptor (22). The design
exploits the synergistic action by both anion- and cati-
on-binding groups, and therefore significantly enhances
the binding affinity (>105 M−1 in CDCl3) towards binding
dibutylammonium chloride, leading to an increase in asso-
ciation constant (Ka) in chloroform by two orders of magni-
tude. Analysis of the single crystal structure of the receptor
shows that one of the two carbonyl groups from the phe-
nyl ring absent of intramolecular hydrogen bonds orients
outwards and the other carbonyl group points inwards.
This prompted us to consider an alternative design by
incorporating a pyridine unit rather than a phenyl ring to
give receptor 1a (Figure 1). In this molecule, two amide
groups are predisposed on the same side due to the pres-
ence of intramolecular three-centre H-bonds formed by
the nitrogen atom and two NH protons, partially hinder-
ing its rotation around two rotatable amide bonds. With
this conformation, we envisioned that 1a would be able
to easily accommodate a neutral guest, urea or thiourea.
More importantly, the installation of an electro-deficient
pyridyl ring relative to a phenyl ring should increase the
acidity of NH protons, and thus may likely improve the
binding ability of the receptor for the guest.
Urea represents a typical guest molecule in host–guest
chemistry that has arrested considerable attention dur-
ing the past years. This is largely due to the importance
of urea as a metabolism product (23) for detecting pur-
poses (24) and protein denaturant (25), and its use as a
thread component (26) in constructing mechanically
interlocked molecules (27). Numerous receptors on rec-
ognising urea and its derivatives have been reported since
1971 (28), among which most of their structures are based
on pyridine- or its analogue-based aromatic oligoamides
(29), but few are associated with macrocyclic hosts (30).
Crown ethers and their derivatives are one of the very
few examples that have demonstrated the complexation
of urea though their host–guest interactions are pretty
weak in water (31). Therefore, there is still need to search
for artificial macrocycles that would recognise urea or its
derivatives. H-bonded aromatic amide macrocycles with
removal of partial H-bonds are likely to be the right can-
didates because their interior cavities are decorated with
amide functionalities available for the formation of multi-
ple hydrogen bonds. Despite the progress made in recent
years in utilising cyclo[6]aramides for binding various

SUPRAMOLECULAR CHEMISTRY
3
guests, the complexation of a neutral guest like urea is still
lacking. Herein, we report the recognition of urea and its
derivatives (thiourea, ethylurea and diethylurea) G1–G4 by
a pyridine-incorporated cyclo[6]aramide 1a. The presence
of the intramolecular H-bonding for restricting rotation
of amide bonds is corroborated by X-ray crystallography.
Two different binding modes are proposed according to
the data collected from NMR techniques.
macrocycle 1b adopts a chair-like conformation seen from
side view (Figure 3(b)), which considerably deviates from
the shallow bowl conformation of its analogue (22) or the
almost flat conformation of classical cyclo[6]aramide 2
with the fully H-bonded backbone (21). Detailed inspec-
tion of the crystal structure reveals a pyridyl ring-localised
conformation where two intramolecular hydrogen bonds,
N2C–H2C⋯N4C (105.931˚, 2.3267 Å) and N1C–H1C⋯N4C
(106.653°, 2.3807 Å), each comprising one five-membered
ring, predispose two amide NH hydrogens orienting inside
(Figure 3(a)). The observed orientation of amide hydrogens
as H-bond donor is crucial to the subsequent formation of
hydrogen bonds with H-bond acceptor (guest). This local
conformation constitutes the ‘chair’ back of the defined
chair conformation, while the four phenyl rings (phenyls
2, 3 and 5, 6, see Figure S23) adjacent to the pyridyl ring
construct the ‘seat’ flanked by two side chains as ‘chair’
feet. The dihedral angle between the chair back and the
chair seat is 151.8°. We attribute this to diminished strains
caused by depletion of two intramolecular three-centre
H-bonds in 2 that leads to considerable conformational
distortion in 1a. Interestingly, the plane (phenyl 3 and 5,
see Figure S23) along with its side chains is twisted away
from the ‘seat’, actually constituting two front feet of the
chair conformation. This suggests that even locally rigidi-
fied backbone enforced by the presence of intramolecular
three-centre H-bonds (32) may still be subject to the fluctu-
ation of regional conformation change, which is supposed
to be otherwise impossible with fully H-bonded cyclo[6]
aramide (21). The diameter of cavity in 1a measures 6.82 Å,
which is large enough to engulf a guest molecule like urea
with a size of only 3.82 Å (33). Selected bond lengths and
angles for 1b from X-ray diffraction experiment are given
in Table 1.
2. Results and discussion
2.1. Synthesis and solid state structure
Receptor 1a was synthesised according to the synthesis
route as shown in Figure 2. Hydrogenation of pentamer
5a in the presence of 20% Pd/C in CHCl3/CH3OH led to
its reduced form 5b, which was used for the immediate
coupling reaction with acid chloride 6a′ prepared from
pyridine dicarboxylate 6a. Purification by chromatography
on silica gel (CH2Cl2/MeOH = 30:1) provided the pyridine-
incorporated cyclo[6]aramide 1a as a white solid in a yield
of 44.2%. To grow single crystals, compound 1b, which
shares the same backbone but bears shorter side chains,
was synthesised according to the same procedure above
in 30% yield. Syntheis of pentamer 5a and 5b and control
compound 2 was accomplished following the previously
describeded method (22). All the target molecules and
intermediates were characterised by 1H NMR, 13C NMR and
high resolution mass spectroscopy (HRMS) techniques.
Crystals suitable for the X-ray analysis were obtained
by slow evaporation of a solution of 1b in a mixed solvent
of dichloromethane and methanol (20:1). A summary of
the crystallographic data and structure refinement of 1b is
listed in Table S1 and detailed labelling of major atoms are
shown in supporting information (Figure S23). The crys-
tal belongs to the space group P2(1)/c (Table S1), and the
unit cell contains four macrocyclic molecules. Surprisingly,
analysis of the single crystal structure clearly shows that
In the packing diagram, the pyridyl ring in one macrocy-
clic molecule of 1b interacts with a phenyl ring in another
molecule via π–π stacking interactions (right side, Figure
Figure 2. Synthesis of pyridine-incorporated cyclo[6]aramide 1a.

4
K. KANG ET AL.
3(c)). The interplanar distance between the two adjacent
macrocycles is 3.583 Å with the dihedral angle of 7.68°
between the phenyl ring and the pyridyl ring. At the same
time, two phenyl rings, each of which comes from a macro-
cyclic constituent of two different macrocycles, stack upon
each other with a π–π stacking distance of 3.680 Å (left
side, Figure 3(c)). Noticeably, these two phenyl rings orient
in the same direction with the dihedral angle of 6.73°. The
observation that a phenyl ring (phenyl 4) protrudes out of
a regional plane comprising two phenyl rings (phenyl 3,
5) is quite unusual because it is less likely for a rigidified
backbone enforced by two three-centre H-bonds to twist
to such an extent (23). The concurrent formation of two
very close dihedral angles (7.68° and 6.73°) as a result of
intermolecular π–π stacking interactions explains why one
of the five phenyl rings and the pyridyl ring in a single
macrocyclic molecule are oriented in the same orientation,
leading to the observed stacking mode and subsequent
linear arrangement of macrocycles (Figure 3(c)). Therefore,
the stacking interaction is considered here as a major
non-covalent linking bridge to another macrocycle in the
molecular packing.
finally the downfield shifting of signals of amide protons
Hv by 0.88 ppm. Contrary to the downfield shifting, Protons
H1 on urea experienced an upfield shift by 0.17 ppm. This
indicates that G1 interacts with the macrocycle possibly
as a result of the formation of hydrogen bonds via both
amide protons and urea protons. It should be noted that
the sample used was sonicated for ca. 1 h followed by filtra-
tion to remove excess solid urea before NMR experiments.
In the presence of thiourea (Figure 5), receptor 1a expe-
rienced significant downfield shifts for both two intro-
verted amide protons Hv and interior aromatic protons Hp,
Hn and Hs, (0.32, 0.32 and 0.71 ppm, respectively), in sharp
contrast to the case of urea where only a minor change in
chemical shifts was observed for aromatic protons Hp, Hn
and Hs (0.03, 0.04, 0.04 ppm, respectively). This suggests
a stronger interaction of the receptor with thiourea than
urea. Indeed, the titration experiments for binding thiourea
reveals the association constant of (3.1 1.0) × 104 M−1 in
CDCl3–2%CD3CN, which is more than one order of magni-
tude larger than the value of (6.2 1.9) × 103 M−1 observed
for urea in CDCl3 (vide post). With ethylurea G3, beyond our
expectation, a much larger downfield shift of protons Hv
(1.66 ppm) was observed. However, other interior aromatic
protons (Hp, Hn and Hs) were only marginally influenced by
the binding of this guest. Concomitant with the change of
proton chemical shifts on the receptor, aliphatic protons of
the guest also experience a change of both upfield shifts of
protons H4 and H5. Diethylurea G4, which is a diethylated
derivative of urea, showed a similar downfield shift behav-
iour (1.59 ppm). These results indicate that two amide pro-
tons in 1a should involve the formation of much stronger
H-bonding interactions with G3 and G4 than with G1 and
G2. This drives us to propose a unique ‘threading mode’
for these two guests, as compared to the ‘contact mode’
with G1 and G2 as the interacting guest species (also see
Computational simulations).
The information of the binding stoichiometry of G1–G4
was retrieved from Job’s plot and mole ratio method. In
all cases, results from NMR titration experiments indicate
a 1:1 stoichiometry for each host–guest pair. It is worth
noting that both interior aromatic protons (Hp, Hn, Hs)
experience a significant change of chemical shifts upon
stepwise addition of a guest, For example, addition of 2.0
equiv of G2 to a solution of 1a led to the downfield shift-
ing of signals of protons Hp, Hn and Hs on 1a by 0.20, 0.30
and 0.57 ppm in CDCl3–2%CD3CN (Figure 6). The mixed
solvent is chosen for increasing the complex solubility.
Beyond 1.0 equiv. of the guest, these protons are sub-
jected to a small change, indicating the relatively stronger
binding of G2 by the macrocycle 1a. In the meanwhile,
there are only one set of signals for the protons of the
host and the guest with increasing concentrations of the
2.2. Host–guest complexation
With two predisposed amide functionalities as H-bond
donor and carbonyl oxygen atoms as H-bond acceptor,
1a is expected to bind urea and its derivatives. Control
compound 2, which bears the same number of carbonyl
oxygens but whose oxygen atoms are all pointing inwards,
serves as a control to see if there is any difference in com-
plexation as compared to partially H-bonded cyclo[6]ara-
mide 1a.
Urea (G1) has high affinity for water and is insoluble
in chloroform (34); however, upon adding 0.2 equiv. of
1
G1 to a 1.0 mM solution of cyclo[6]aramide 1a, the H
NMR spectra of the mixture containing 1a and urea in
CDCl3 showed an appreciable change of chemical shifts
associated mainly with the amide protons Hv of the host
(Figure 4). Protons H1 of G1 were identified to appear at
5.5 ppm. Further addition of G1 up to 1.0 equiv. led to
Table 1. hydrogen bonds in the crystal structure of 1b.
D-H⋯A
Bond angle/°
Bond length/Å
N1a–h1a⋯o1a
N1a–h1a⋯o5a
N1B–h1B⋯o3B
N1B–h1B⋯o6a
N2a–h2a⋯o2a
N2a–h2a⋯o4c
N2B–h2B⋯o4B
N2B–h2B⋯o5B
N2c–h2c⋯N4c
N1c–h1c⋯N4c
91.410
132.783
97.395
135.767
107.929
138.509
106.737
139.227
105.931
106.653
2.5070
2.0709
2.3848
2.0106
2.1960
2.1960
2.2310
1.9300
2.3267
2.3807

SUPRAMOLECULAR CHEMISTRY
5
Figure 3. X-ray crystal structure of pyridine-incorporated cyclo[6]aramide 1b: (a) top view with crystallographic numbering, (b) side
view, illustrating a chair conformation with dihedral angles, (c) molecular stacking viewed along the axis with the dashed blue lines
drawn passing through the cavities of the macrocycles. only hydrogen atoms involved in h-bonds are shown for clarity.
1
guest. All these results, taken in concert, suggest a fast
exchange in the complexation process on NMR time scale.
The resulting Job’s plot from NMR and UV–vis experiments
also corroborates the 1:1 stoichiometry. For example, the
maximum value which is obtained through mole fraction
multiplying by ∆δ is observed at 0.5 for G1, indicating a
host–guest ratio of 1:1 in the complex (Figure 7). In line
with the results above, HRMS of an equimolar mixture
of 1a and guest G1 (or G2) also showed the presence
of the 1:1 complex at m/z = 1634.0743, corresponding
to [1a + G1 + H]+ (Figure S5), and at m/z = 1650.0201,
corresponding to [1a + G2 + H]+ (Figure S6), respectively.
On the basis of 1:1 stoichiometry and H NMR titra-
tions data (Figure S9–S22), the association constants of
1a for G1-G4 are obtained using nonlinear curve fitting
method (Table 2). The binding affinities of these guest
by 1a increase in the order of G2 > G1 > G3 > G4. This
indicates that the binding event is favourable for G2, and
thus 1a shows better selectivity towards thiourea in the
recognition process.
To evaluate the importance of preorganised amide NH
protons in the binding event, compound 2 (Figure 2) was
used as a control for comparing its binding affinity with
urea. The association constant with 2 for binding G1 was

6
K. KANG ET AL.
Figure 4. partial 1h Nmr spectra (400 mhz, cDcl3, 298 K) showing chemical shift changes after host–guest complexation in chloroform:
(a) 1.0 mm cyclo[6]aramide 1a, (b) 1.0 mm 1a and 0.2 equiv. urea, (c) 1.0 mm 1a and 1.0 equiv. urea.
Figure 5. partial 1h Nmr (400 mhz, cDcl3, 298 K) spectra of (a) 1a (2.5 × 10−3 m), (b) complex of 1a with urea, (c) complex of 1a with
thiourea, (d) complex of 1a with ethylurea, (e) complex of 1a with diethylurea.
found to be considerably reduced to (4.2 3.4) × 102 M−1
in CDCl3 (Figure S22) as compared to the Ka value of
(6.2 1.9) × 103 M−1 with 1a. This result is significant
because it demonstrates the importance of the pyridyl ring
in directing carbonyl groups to point inwards for efficient
guest binding.
2.3. Binding modes aided by computational
simulations
To gain insight into the binding site, two-dimensional
NOESY experiments were performed in CDCl3/CD3CN (9:1,
v/v) with 1a and G2. G1 is only sparsely soluble in the

SUPRAMOLECULAR CHEMISTRY
7
Table 2. association constants (Ka/m−1)a for the complexation of
guests by 1a and 2 at 298 K.
the signals attributable to the interior aromatic protons
of 1a (denoted as Hp, Hn and Hs) and protons of thiourea
(denoted as H2) are observed (Figure S8); meanwhile, no
cross-peaks associated with the contact between periph-
eral alkyl protons and protons H2 appear. This strongly
implicates that the complexation of the neutral guest
species should most likely occur in the macrocyclic cavity.
To further clarify the observed binding properties, a
series of molecular modelling simulations based on den-
sity functional theory (DFT) method were performed for
the host–guest system comprising pyridine-incorporated
cyclo[6]aramide 1a and guests G1–G4. The computational
Host
Guest
Solvent
Association constant
1a
2
1a
1a
1a
G1
G1
G2
G3
G4
cDcl3
cDcl3
cDcl3–2%cD3cN
cDcl3
(6.2 1.9) × 103
(4.2 3.4) × 102
(3.1 1.0) × 104
(3.4 0.9) × 102
(8.8 4.4) × 10
cDcl3
athis association constants values were obtained by 1h Nmr titration experi-
ments. For full details, see the Supporting information.
chosen solvent system at higher concentrations, and thus
G2 was used for the experiments. Correlations between
Figure 6. Stacked partial 1h Nmr (400 mhz, 298 K) titration spectra of 1a (1.0 mm) with G2 in cDcl3–2%cD3cN.
Figure 7. Job’s plot for the determination of stoichiometry in the complex formed by 1a and G1 from 1h Nmr experiments in cDcl3.

8
K. KANG ET AL.
Figure 8. the complex structure of (a) 1a·urea, (b) 1a·thiourea, (c) 1a·ethylurea, (d) 1a·diethylurea optimised by the DFt method.
results based on the calculated binding energies reveal
that each guest resides in the cavity of the macrocycle
via multiple hydrogen bonding interactions (Figure 8). In
general, the macrocycle in each complex shows a chair-
like geometry (Figure S24–S27), which is very similar to the
conformation of the parent framework of cyclo[6]aramides
as observed in the single crystal structure. In the presence of
G1, the guest urea engages in five intermolecular hydrogen
bonds (Figure 8(a)), among which one NH2 group of urea is
bound to two carbonyl oxygens, and the other NH2 group
forms a single hydrogen bond with one carbonyl oxygen at
2.43 Å. The amide NH2 protons of macrocycle 1a are bound
by a carbonyl oxygen of urea (2.43 and 2.37 Å). It should be
noted that the urea molecule looks slightly protruding out
of the macrocyclic plane. The complex involving G2 is sta-
bilised by six hydrogen bonds with the optimised structure
of the complex 1a·G2 in inclusive conformation (Figures
8(b), and S25). The inter-H bonding distance for each hydro-
gen bond which is formed between four carbonyl oxygen
groups of 1a and NH2 of urea is less than 2.20 Å. As for the
sulphur atom, it binds two amide protons through hydro-
gen bonds at 2.77 and 2.79 Å, each of which is more than
2.70 Å, suggesting that the H-bonding interaction between
sulphur atom and amides is relatively less stronger. So, we
presume that carbonyl oxygens play a more important role
in binding urea and thiourea rather than amide protons. The

SUPRAMOLECULAR CHEMISTRY
9
superior binding affinity with G2 over G1 is supported by
the Gibbs free energy difference of −61.0 kJ/mol of complex
1a·G2 being smaller compared to that of −39.7 kJ/mol of
complex 1a·G1 (Table S2). With G3, which bears additional
ethyl group, the complex is stabilised by only four inter-H
bonds. Different from G1 and G2, the optimised structure
of the complex 1a·G3 clearly shows that G3 threads the
cavity of the macrocycle because of steric repulsion from
the substitution of an ethyl group on urea. Interestingly,
when two ethyl groups are installed on urea, the binding
mode of 1a with G4, is very similar to that of G3 in terms
of both the number of hydrogen bonds and the length of
bonds. Furthermore, this guest also penetrates threads the
cavity to form a pseudo[2]rotaxane-like complex. However,
this host–guest complex (ΔG = −26.1 kJ/mol) is less stable
than complex 1a·G3 (ΔG = −27.5 kJ/mol) as a result of larger
steric effect. These computational results are consistent
with the observations from NMR experiments (vide ante).
Based on all these results above, we propose two different
binding modes that may operate in the binding of urea
and its derivatives, i.e., ‘contact mode’ for G1 and G2, and
‘threading mode’ for G3 and G4. The ‘threading mode’ is
more intriguing in terms of the possibility of using cyclo[6]
aramide-based host–guest system for constructing pesu-
dorotaxanes and rotaxanes.
experiments without further drying. Dichloromethane,
chloroform and methanol were purchased from Chengdu
Kelong Chemical Factory. CH2Cl2 was dried over CaH2.
Column chromatography was carried out using silica gel
(300–400 mesh). All other solvents and chemicals used for
the synthesis were of reagent grade and used as received.
The complex samples for ESI-MS determination were pre-
pared by mixing a MeOH solution.
4.2. Synthese
Receptor 1a was synthesised according to Figure 2.
Pentamer 5a (400 mg, 0.27 mmol) was hydrogenated in
the presence of 20% Pd/C (80 mg) in CHCl3/CH3OH (70 mL,
v/v = 7:1) for 14 h at 45 °C. The solution was filtered in dark-
ness as fast as possible followed by immediate removal
of the solvent. The reduced diamine was used for the
immediate coupling reaction. DMF (5 μL) was added to
a suspension of compound 6a (82 mg, 0.28 mmol) and
oxalyl chloride (105 mg, 0.84 mmol) in CH2Cl2. The mix-
ture was stirred for 40 min at room temperature. The sol-
vent was evaporated and the resulting acid chloride was
dried in vacuum at room temperature for 30 min to get
compound 6a′. Compound 6a′ was dissolved in CH2Cl2
(60 mL) and added dropwise to a mixture of the above 5a′
and Et3 N (162 mg, 1.60 mmol) in CH2Cl2 (20 mL) at 0 °C.
The solution was stirred under N2 for 10 min. The organic
layer was washed with water (20 mL × 3). The crude prod-
uct was purified by chromatography on silica gel (CH2Cl2/
MeOH = 30:1) to provide the product 1a as a white solid.
1a: yield 44.2%. 1H NMR (400 MHz, CDCl3, 298 K): δ = 10.67
(s, 2H), 10.16 (s, 2H), 9.27 (s, 2H), 9.12 (s, 1H), 9.02 (s, 2H),
8.51 (d, J = 7.74 Hz, 2H), 8.29 (s, 1H), 8.19 (d, J = 9.06 Hz, 2H),
8.10 (t, J = 7.74 Hz 1H), 7.05 (d, J = 9.06 Hz, 2H), 6.52 (s, 2H),
6.50 (s, 1H), 4.10 (m, 10H), 3.90 (m, 15H), 2.82 (m, 15H), 1.99
(m, 5H), 1.56–1.28 (m, 85H), 0.94–0.85 (m, 31H); 13C NMR
(100 MHz, CDCl3, 298 K): δ 163.50, 163.10, 162.58, 159.97,
153.85, 149.69, 147.10, 146.24, 138.33, 138.00, 131.60,
127.46, 125.59, 122.03, 121.00, 119.34, 117.90, 116.15,
112.54, 96.33, 94.91, 72.55, 72.27, 55.89, 55.79, 38.58, 37.89,
31.88, 31.86, 30.99, 30.05, 29.88, 29.71, 29.62, 29.52, 29.34,
28.72, 26.70, 26.66, 23.28, 23.06, 22.83, 22.67, 14.11, 14.10,
14.05, 10.47. HRESI-MS m/z: [M + Na]+ Calcd for C93H133N7
O14Na 1594.9803, found 1594.9811.
3. Conclusions
In summary, we have shown that a novel pyridine-incor-
porated cyclo[6]aramide 1a binds strongly and selectively
urea and its derivatives in 1:1 stoichiometry. Among four
guests examined, the thiourea offers the highest binding
affinity in a mixed solution of chloroform-2% acetonitrile
(Ka = 3.1 × 104 M−1) in forming the host–guest complex.
The single crystal structure of 1a evidences the presence
of introverted amide groups that are supposed to play an
important role in enhancing the binding ability for urea-re-
lated compounds. The interplay of multiple H-bonds and
guest size should be responsible for the stability of the
complex as compared to classical fully H-bonded cyclo[6]
aramide. Importantly, NMR experiments reveal two dif-
ferent binding modes, i.e., ‘contact mode’ and ‘threading
mode’, that are operative in the recognition process, which
is further corroborated by computational modelling. The
finding of‘threading mode’holds promise for applications
in constructing mechanically interlocked structures.
4.3. Instruments and apparatus
1H and 13C NMR spectra were recorded on Bruker AVANCE
AV II-400 MHz (1H: 400 MHz; 13C: 100 MHz). High resolu-
tion mass data were collected by WATERS Q-TOF Premier.
Chemical shifts are reported in δ values in ppm using
tetramethylsilane. The geometry optimisations were
carried out in gas phase by employing the Gaussian09
4. Experimental section
4.1. Materials and reagents
Compound 1a was synthesised following the reported
procedure (22). CDCl3 and CD3CN were purchased from
Cambridge Isotope Laboratories, used for the titration

10
K. KANG ET AL.
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Disclosure statement
No potential conflict of interest was reported by the authors.
Funding
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This work was supported by the National Natural Science
Foundation of China [grant number 21572143], the Doctoral
Programme of the Ministry of Education of China [grant num-
ber 20130181110023] and Open Project of State Key Labora-
tory of Supramolecular Structure and Materials [grant number
SKLSSM201629]. Comprehensive Training Platform of Special-
ized Laboratory, College of Chemistry, Sichuan University, is
acknowledged for NMR analyses.
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