Calix[3]amide-based anion receptors: High affinity for fluoride ions and a twisted binding model

Article abstract of DOI:10.1080/10610278.2010.514909

Tris-phenylurea-substituted calix[3]amides (3a, 3b) and tris-phenylthiourea-substituted calix[3]amides (4a, 4b) were synthesised by the reaction of amine with isocyanates and thioisocyanate, respectively. Single crystal X-ray analysis revealed that the cyclic trimers adopt a syn conformation with all of the urea groups on the same side. The binding affinities of these compounds towards anions were measured using 1H NMR titrations in DMF-d7, DMSO-d6 or CDCl3. Each receptor was observed to bind halogen anions in a 1:1 stoichiometry, exclusively through hydrogen bonding, and the anion selectivity was in the order F- > Cl- ? Br- > I- . DFT calculations revealed that the fluoride anion is anchored in the centre of the six N-H hydrogen atoms of 3a through H...F interactions.

Full text of DOI:10.1080/10610278.2010.514909

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Calix[3]amide-based anion receptors: high affinity for
fluoride ions and a twisted binding model
Kosuke Katagiri a , Taniyuki Furuyama b , Hyuma Masu a , Takako Kato a , Mio Matsumura c
, Masanobu Uchiyama b d , Aya Tanatani c , Masahide Tominaga a , Hiroyuki Kagechika e ,
Kentaro Yamaguchi a & Isao Azumaya a
a Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University ,
1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
b Advanced Elements Chemistry Laboratory, The Institute of Physical and Chemical
Research , RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
c Department of Chemistry, Faculty of Science , Ochanomizu University , 2-1-1 Otsuka,
Bunkyo-ku, Tokyo, 112-8610, Japan
d Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo,
Bunkyo-ku, Tokyo, 113-0033, Japan
e Graduate School of Biomedical Science, Tokyo Medical and Dental University , 2-3-10
Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
Published online: 22 Feb 2011.
To cite this article: Kosuke Katagiri , Taniyuki Furuyama , Hyuma Masu , Takako Kato , Mio Matsumura , Masanobu Uchiyama ,
Aya Tanatani , Masahide Tominaga , Hiroyuki Kagechika , Kentaro Yamaguchi & Isao Azumaya (2011) Calix[3]amide-based anion
receptors: high affinity for fluoride ions and a twisted binding model, Supramolecular Chemistry, 23:01-02, 125-130, DOI:
10.1080/10610278.2010.514909
To link to this article: http://dx.doi.org/10.1080/10610278.2010.514909
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Supramolecular Chemistry
Vol. 23, Nos. 1–2, January–February 2011, 125–130
Calix[3]amide-based anion receptors: high affinity for fluoride ions and a twisted binding model
Kosuke Katagiria, Taniyuki Furuyamab, Hyuma Masua, Takako Katoa, Mio Matsumurac, Masanobu Uchiyamabd,
Aya Tanatanic, Masahide Tominagaa, Hiroyuki Kagechikae, Kentaro Yamaguchia and Isao Azumayaa*
aFaculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan;
bAdvanced Elements Chemistry Laboratory, The Institute of Physical and Chemical Research, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama
c
351-0198, Japan; Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610,
Japan; dGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
eGraduate School of Biomedical Science, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku,
Tokyo 101-0062, Japan
(Received 4 June 2010; final version received 27 July 2010)
Tris-phenylurea-substituted calix[3]amides (3a, 3b) and tris-phenylthiourea-substituted calix[3]amides (4a, 4b) were
synthesised by the reaction of amine with isocyanates and thioisocyanate, respectively. Single crystal X-ray analysis
revealed that the cyclic trimers adopt a syn conformation with all of the urea groups on the same side. The binding affinities
of these compounds towards anions were measured using 1H NMR titrations in DMF-d7, DMSO-d6 or CDCl3. Each receptor
was observed to bind halogen anions in a 1:1 stoichiometry, exclusively through hydrogen bonding, and the anion selectivity
was in the order F2 . Cl2 q Br2 . I2. DFT calculations revealed that the fluoride anion is anchored in the centre of the
six NZH hydrogen atoms of 3a through H···F interactions.
Keywords: calix[3]amide; anion receptor; DFT calculations
Introduction
groups are present. In a previous paper, we reported the
synthesis and the crystal structures of calix[3]amides with
nitro or amino groups. The structures of these calix[3]-
amides were dimers, in which the cavity of one molecule
was filled with the functional group of the other molecule
(9), suggesting that the cavity would act as a binding site
for guest molecules. Herein we report the synthesis of
tris-urea/thiourea-substituted calix[3]amides (3a, 3b, 4a
and 4b) which function as anion receptors. Furthermore,
a binding model of 3a-F2 was determined by DFT
calculations.
In recent years, the development of anion receptors has
become a major area of supramolecular chemistry because
anion receptors serve as models of biological processes
and have potential uses in the design of sensors for medical
applications (1). In the design of anion receptors,
macrocyclic structures were utilised because they provide
a well-defined host environment for guest inclusion (2).
During the last two decades, calixarenes have been widely
used in the field of host–guest chemistry as building
blocks or molecular scaffolds for the construction of
various receptors (3–5). Anion receptors that are based on
the calixarenes have recognition sites such as amides (6),
urea/thiourea (7) and pyrroles (8), which establish
hydrogen-bonding (H-bonding) interactions with anions
that bind these receptors. In particular, urea and thiourea
are promising functional groups for designing anion
receptors because they have two NZH fragments, which
can bind a single atom anion with a six-membered chelate
ring (7). In the course of our studies on cyclic aromatic
amides (calixamides), we found that the calix[3]amides
were obtained with larger ring sizes by macrocyclisation
reactions of 3-N-alkylaminobenzoic acids (9). Moreover,
these produced calix[3]amides have a small bowl-shaped
cavity which should bind anions if appropriate functional
Results and discussion
Synthesis
The syntheses of tris-phenylurea-substituted calix[3]a-
mide 3 and tris-phenylthiourea-substituted calix[3]amide 4
are shown in Scheme 1. Details of calix[3]amides (1a, 1b)
syntheses were reported previously. The reaction of 2a and
2b with phenyl isocyanate in CHCl3 at 808C led to the tris-
phenylurea-substituted calix[3]amide 3a and 3b in 94%
and 88% yields, respectively. Similarly, the tris-phe-
nylthioura-substituted calix[3]amides 4a and 4b were
obtained by the reaction of phenyl thioisocyanate with 2a
and 2b, respectively.
*Corresponding author. Email: azumayai@kph.bunri-u.ac.jp
ISSN 1061-0278 print/ISSN 1029-0478 online
q 2011 Taylor & Francis
DOI: 10.1080/10610278.2010.514909
http://www.informaworld.com

126
K. Katagiri et al.
Scheme 1. Syntheses of ureido and thioureidocalix[3]amides 3, 4. (i) H2SO4, EtOH, 808C, 6 h, 98%; (ii) EtI, HMPA, 808C, 6 h, 85%;
(iii) 4 M NaOHaq., EtOH, 908C, 6 h, 94%; (iv) C10H21I, HMPA, 1208C; 6 h, 52%; (v) Ph3PCl2; 1,1,2,2-tetrachloroethane, 1208C, 6 h;
(vi) Pd/C, H2, EtOH, rt, 18 h and (vii) PhNCX, CHCl3, 508C, 7 h.
X-ray analysis
NMR spectra, indicating the formation of NZH···X
(X ¼ F2, Cl2, Br2, I2) H bonds and also the fast
equilibrium between the complexed and free forms of the
hosts. Increasing the concentration of the chloride anion in
the host–guest mixture solution induced a , 1 ppm
downfield shift of the NH peak (Figure 2). Typical titration
curves are shown in Figure 3(a). Binding constants
calculated by curve-fitting 1:1 binding isotherms to these
data are presented in Table 1. The host molecules bind
strongly to F2 and high selectivity between Cl2 and Br2.
The Job plots of the 3a-X2, 3b-X2, 4a-X2 and 4b-X2
interactions displayed maxima of mole fraction x of 0.5,
which is consistent with 1:1 binding stoichiometries
(Figure 3(b)) (10). The electro-spray ionisation mass
spectrometry provided additional support for the for-
mation of 1:1 stoichiometric complexes ([3a þ F]2 (m/z
862.4), [3a þ Cl]2 (m/z 878.4), [3a þ Br]2 (m/z 922.4 and
924.4) and [3a þ I]2 (m/z 970.3); see the Supporting
Information). The syn conformation is a requirement for
this type of very strong complexation through H-bonding
interactions. Although the calix[3]amides show confor-
mational conversion through the sequence syn-anti-anti-
syn ring inversion (9), the major conformation of 3a is syn
in DMF-d7 (Figure S14). The selectivity for halogen
anions can be understood on the basis of the guest basicity
and the anion size (7, 11). In our system, the binding
constants of F2 and Cl2 were much higher than those of
X-Ray crystallography was performed on a single crystal
of ureidocalix[3]amide 3a, which was obtained from a
mixture of chloroform, methanol and toluene by slow
evaporation of the solvent.1 Single crystals of 3a crys-
tallised in a monoclinic system, space group P21/n, and
included four molecules of 3a, four molecules of toluene
and four molecules of water in the unit cell (Figure 1).
The cyclic trimer 3a exists in the syn conformation in the
solid state with three terminal phenyl groups located in the
same direction. Based on the direction of the amide bonds,
3a adopts a syn conformation. The unit cell has the same
number of enantiomeric conformers, which results in
the crystal having no chiral property (Figure 1(b)). These
enantiomeric conformers exist as dimers in the crystal,
where the cavity of one 3a molecule was filled with the
backside of an enantiomeric molecule of 3a through H
bonds between the nitrogen atoms of urea and the oxygen
atom of the carbonyl group in the neighbouring molecule
˚
(the distances of N···O are 2.800(2) and 2.938(3)A).
Complexation abilities
The addition of anions, in the form of tetrabutylammo-
nium (TBA) salts, to the DMF-d7, DMSO-d6 and CDCl3
solutions of each calix[3]amide, 3 or 4, caused significant
1
downfield shifts of the ZNHZ (urea) signals in the H

Supramolecular Chemistry
127
(a)
F
CI
Br
I
11
BF4
PF6
10.5
10
9.5
9
8.5
1
2
3
4
5
Equivalent of guest molecules
1.4
(b)
1.2
1
0.8
0.6
0.4
0.2
0
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Mole fraction χ
Figure 3. (a) 1H NMR titration curves of 3a with various
anions; F2, Cl2, Br2, I2, BF42 and PF26 . (b) Job plot for the
binding of 3a to F2 in DMF-d7.
Figure 1. (a) Thermal ellipsoid models of the crystal structure
of 3a. (b) Enantiomeric dimer of 3a in a ball-and-stick model.
The enantiomeric conformers are shown in cyan and magenta. H
bonds are indicated by black dashed lines. The solvent molecules
are omitted for clarity.
Br2 and I2. These results suggest that F2 and Cl2 have the
proper size for the binding site surrounded by the three
urea/thiourea groups. On the other hand, the fact that the
binding constant of F2 was higher than that of Cl2 would
be attributed to the basicity of anions.
Theoretical calculations
A binding mode of 3a with a fluoride anion (3a-F2) was
calculated using a DFT calculation. The initial model
structure was constructed by combining a fluoride anion
and the host molecule 3a with all NZH protons directed
towards the centre of the cavity, which was based on the
coordinate data of cyclic triamide 3a determined by X-ray
crystallography. The DFT calculation was performed on
the model structure to obtain an accurate position of F2
in the binding site and the stable conformation of host
molecule when the F2 anion is bound. An optimised
structure of the 3a-F2 complex is shown in Figure 4. The
fluoride anion was anchored in the centre of the six NZH
Figure 2. 1H NMR spectral changes observed for the NH protons
of 3a upon the addition of TBACl (0–2.0 equiv.) to a DMF-d7
solution.

128
K. Katagiri et al.
Table 1. Binding constants of 3a, 3b, 4a and 4b with TBAþX2 (298 K).
3a (in DMF-d7)
Ka [M21 a
3b (in CDCl3)
Ka [M21 a
4a (in DMSO-d6)
Ka [M21 a
4b (in DMSO-d6)
Ka [M21 a
X2
]
]
]
]
F2
29,800
9,550
920
49,660
15,910
1,540
280
,100
,100
23,840
7,600
700
25,700
9,720
1,080
,100
Cl2
Br2
I2
170
,100
b
BF24
PF26
–
,100
a (Ddmax–Dd)Ka ¼ DdDdmax/(Ddmax[H]0–Dd [G]0) (10)
b Cannot be estimated from the titration curve.
hydrogen atoms through H···F interactions. Remarkably,
the terminal phenyl groups of 3a are shown to adopt a
twisted structure.
Conclusion
Calix[3]amide-based anion receptors that bind halogen
anions have been synthesised. Tris-phenylurea-substituted
calix[3]amide and tris-phenylthiourea-substituted
calix[3]amide were observed to recognise halogen anions
in a 1:1 stoichiometry, exclusively through H-bonding
interactions. The anion selectivity was in the order of F2
. Cl2 q Br2 . I2. Using a DFT calculation, the F2
anion was found to be anchored in the centre of the six
NZH hydrogen atoms through H···F interactions which
formed a helical structure. Due to their distinct selectivity,
the substituted calix[3]amides hold significant potential
for use in a number of applications, including anion
sensors and anion selective switching devices.
Experimental
General procedures
Melting points were determined using AS ONE (ATM-
1
01). H NMR and 13C NMR spectra were obtained on a
Bruker AV-700 spectrometer (700 MHz) or Bruker AV-
400 spectrometer (400 MHz) at 298 K. High- and low-
mass spectra were obtained on a JEOL MStation JMS-700
spectrometer or JEOL AccuTOF JMS-T100LC spec-
trometer. IR spectra were determined using a JASCO FT-
IR-6300 spectrometer with ATR PR0410-S. X-ray data
were collected on a Bruker SMART Apex II CCD
detector. The crystal structures were solved by direct
methods SHELXS-97 (Sheldrick 1996) and refined by
full-matrix least-squares SHELXL-97 (Sheldrick 1997)
(12). All non-hydrogen atoms were refined anisotropically.
All hydrogen atoms were included at their calculated
positions. Column chromatography was performed using
Wakogel C200, and thin-layer chromatography was
carried out on 0.25 mm Merck precoated silica gel glass
Figure 4. (a) The calculated structure of 3a-F2 in the ball-and-
stick model (side view). The fluoride anion is located in the centre
of the six NZH hydrogen atoms of all the urea groups. H-bonds
are indicated by red dashed lines. (b) The calculated structure of
3a-F2 in the space-filling model (top view). The terminal phenyl
groups are shown to adopt a twisted structure.

Supramolecular Chemistry
129
plates. Elemental analyses were within ^ 0.3% of the
theoretical values.
3.48 mmol) was added. The mixture was heated under
reflux for 5 h. After cooling to room temperature the
solvent was evaporated in vacuo. The residue was
dissolved in CHCl3 (5 ml) and the white powder was
filtered. The filtrate was purified by GPC to give tris-
phenylthiourea-substituted calix[3]amide 4a (0.52 g,
Tris-phenylurea-substituted calix[3]amide 3a
To a suspension of cyclic trimer 2a (0.338 g, 0.70 mmol) in
CHCl3 (7 ml), phenyl isocyanate (0.38 ml, 3.48 mmol) was
added. The mixture was heated under reflux for 5 h. After
cooling to room temperature, the solvent was evaporated in
vacuo. The residue was dissolved in CHCl3 (5 ml) and the
white powder was filtered. The filtrate was purified by gel
permeation chromatography (GPC) to give tris-phenylurea-
substituted calix[3]amide 3a (0.56 g, 0.63 mmol) as a white
0.58 mmol) as
a
white powder. Yield: 83%;
mp . 3008C; 1H NMR (DMSO-d6, 400 MHz, 258C) d
10.03 (s, 1H), 9.94 (s, 1H), 7.47 (d, 2H, J ¼ 8.0 Hz), 7.39
(s, 1H), 7.25–7.20 (m, 3H), 7.11 (s, 1H), 6.96 (s, 1H), 3.70
(br, 2H,) and 1.11 (t, 3H, J ¼ 7.2 Hz); 13C NMR (DMSO-
d6, 100 MHz, 258C) d 188.39, 140.27, 139.95, 142.07,
135.64, 135.35, 132.15, 130.29, 129.28, 128.88, 128.50,
126.43, 124.78, 123.95, 116.11, 13.21 and 13.09; FAB-MS
([M þ H]þ): m/z 892; HRMS: m/z ([M þ H]þ) Calcd for
C48H46N9O3S3: 891.2807. Found 891.2711; Elemental
Analysis Calcd for C48H45N9O3S3: C, 64.62; H, 5.08; N,
14.13; S, 10.78. Found: C, 64.28; H, 5.21; N, 14.00; S,
10.74.
1
powder. Yield: 94%; mp . 3008C; H NMR (DMF-d7,
400 MHz, 258C) d 8.86 (s, 1H), 8.60 (s, 1H), 7.47 (d, 2H,
J ¼ 7.7 Hz), 7.36 (s, 1H), 7.35 (s, 1H), 7.25 (t, 2H,
J ¼ 7.7 Hz), 6.98 (s, 1H), 6.97 (t, 1H, J ¼ 7.0 Hz) 3.76 (q,
2H, J ¼ 7.7 Hz) and 1.15 (t, 3H, J ¼ 7.0 Hz); 13C NMR
(DMF-d7, 100 MHz, 258C) d 169.69, 152.65, 142.69,
140.91, 140.08, 139.85, 128.75, 122.18, 121.26, 118.90,
118.79, 115.52, 44.33 and 12.43; IR (ATR, in DMF) 3648,
3524, 1698 and 1628 cm21; FAB-MS: m/z 845 ([M þ H]þ);
HRMS: m/z ([M þ Na]þ) Calcd for C48H25N9O6Na:
866.33905. Found 866.33477; Elemental Analysis Calcd
for C48H45N9O6·1/2C7H8: C, 69.50; H, 5.55; N, 14.16.
Found: C, 69.48; H, 5.55; N, 14.15.
Tris-phenylthiourea-substituted calix[3]amide 4b
To a suspension of cyclic trimer 2b (0.576 g, 0.70 mmol)
in CHCl3 (7 ml), phenyl thioisocyanate (0.41 ml,
3.48 mmol) was added. The mixture was heated under
reflux for 5 h. After cooling to room temperature, the
solvent was evaporated in vacuo. The residue was
dissolved in CHCl3 (5 ml) and the white powder was
filtered. The filtrate was purified by GPC to give
tris-phenylthiourea-substituted calix[3]amide 4b (0.71 g,
0.60 mmol) as a white powder. Yield: 86%; mp . 3008C;
1H NMR (DMSO-d6, 400 MHz, 258C) d 9.89 (s, 1H), 9.69
(s, 1H), 7.46 (d, 2H, J ¼ 8.0 Hz), 7.30 (br, 2H), 7.20 (s,
1H), 7.14–7.09 (m, 2H), 6.96 (brs, 1H), 3.70 (br, 2H,),
1.51 (br, 3H), 1.24 (br, 10H) and 0.84 (brt, 6H,
J ¼ 6.4 Hz); 13C NMR (DMSO-d6, 100 MHz, 258C) d
169.61, 150.71, 143.99, 142.07, 139.60, 130.23, 129.01,
128.90, 123.93, 123.83, 121.60, 119.61, 47.73, 31.76,
29.45, 29.17, 27.48, 26.70, 22.56, 17.30, 14.41 and 13.63;
FAB-MS ([M þ H]þ): m/z 1229; HRMS: m/z ([M þ H]þ)
Calcd for C48H46N9O3S3: 1227.6563. Found 1227.6521;
Elemental Analysis Calcd for C72H93N9O3S3: C, 70.38;
H, 7.63; N, 10.26; S, 7.83. Found: C, 70.44; H, 7.66; N,
10.40; S, 7.99.
Tris-phenylurea-substituted calix[3]amide 3b
To a suspension of cyclic trimer 2b (0.576 g, 0.70 mmol)
in CHCl3 (7 ml), phenyl isocyanate (0.38 ml, 3.48 mmol)
was added. The mixture was heated under reflux for 5 h.
After cooling to room temperature, the solvent was
evaporated in vacuo. The residue was dissolved in CHCl3
(5 ml) and the white powder was filtered. The filtrate was
purified by GPC to give tris-phenylurea-substituted
calix[3]amide 3b (0.726 g, 0.62 mmol) as a white powder.
Yield: 88%; mp . 3008C; 1H NMR (DMSO-d6, 400 MHz,
258C) d 8.72 (s, 1H), 8.60 (s, 1H), 7.42 (d, 2H, J ¼ 7.7 Hz),
7.37 (s, 1H), 7.35–7.19 (m, 3H), 7.02–6.92 (m, 2H), 3.63
(t, 2H, J ¼ 6.8 Hz), 1.51 (br, 3H), 1.24 (br, 10H) and 0.84
(br, 6H); 13C NMR (DMSO-d6, 100 MHz, 258C) d 169.86,
152.62, 142.79, 140.59, 139.82, 129.23, 129.15, 128.97,
122.44, 118.79, 116.06, 114.31, 49.47, 31.77, 29.46,
29.28, 29.18, 27.56, 26.68, 22.56, 14.40 and 10.36; IR
(ATR, in CDCl3) 2926, 2855, 1709, 1648 and 1593 cm21
;
FAB-MS: m/z 1181 ([M þ H]þ); HRMS: m/z ([M þ H]þ)
Calcd for C72H94N9O6: 1180.7249. Found 1180.7235.;
Elemental Analysis Calcd for C72H93N9O6: C, 73.25; H,
7.94; N, 10.68. Found: C, 73.22; H, 7.93; N, 10.70.
Note
1. Crystal data for 3a: C55H55N9O7; M ¼ 954.08 gmol21
,
Monoclinic, P21/n, colourless prismatic, measuring
0.10 £ 0.10 £ 0.05 mm3, T ¼ 90 K, a ¼ 13.8775(13),
˚
b ¼ 23.609(2), c ¼ 15.5704(15) A, a ¼ 90, b ¼
3
˚
˚
109.216(2), g ¼ 90, V ¼ 4817.1(8) A , Z ¼ 4, Dc ¼
1.316 Mg m23, m ¼ 0.089 mm21, Tmax ¼ 0.9956, Tmin
¼
Tris-phenylthiourea-substituted calix[3]amide 4a
0.9912, GOF on F 2 ¼ 1.050, R1 ¼ 0.0553, wR2 ¼ 0.1416
([I . 2s(I)]), R1 ¼ 0.0986, and wR2 ¼ 0.1787 (all data).
CCDC 2 678149
To a suspension of cyclic trimer 2a (0.338 g, 0.70 mmol)
in CHCl3 (7 ml), phenyl thioisocyanate (0.41 ml,

130
K. Katagiri et al.
Lhotak, P.; Stibor, I.; Lang, K.; Proskova, P. Org. Lett. 2003,
´
´
Acknowledgement
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R.K.; Rebek, Jr., J. J. Am. Chem. Soc. 1998, 120,
This work was supported by a Grant-in-Aid for Young Scientists
(Start-up), Japan (No. 18890226) (K. K.).
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