Synthesis, structure, and conformation of ortho-linked oxacalix[n]arene[n]hetarenes

Article abstract of DOI:10.1016/j.tet.2008.10.083

ortho-Linked oxacalix[n]arene[n]hetarenes (n=2, 3) were prepared by one-step cyclooligomerization of catechol and meta-dichlorinated nitrogen containing heterocycles or via a two-step reaction process. Solid state structure of the ortho-linked oxacalix[n]

Full text of DOI:10.1016/j.tet.2008.10.083

Tetrahedron 65 (2009) 300–304
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Synthesis, structure, and conformation of ortho-linked
oxacalix[n]arene[n]hetarenes
*
Mingliang Ma, Hongxiu Wang, Xiaoyan Li, Longqing Liu, Haishan Jin, Ke Wen
Division of Supramolecular Chemistry and Medicinal Chemistry, Key Laboratory of Brain Functional Genomics, MOE & STCSM, Shanghai Institute of Brain Functional Genomics,
East China Normal University, Shanghai 200062, China
a r t i c l e i n f o
a b s t r a c t
Article history:
ortho-Linked oxacalix[n]arene[n]hetarenes (n¼2, 3) were prepared by one-step cyclooligomerization of
catechol and meta-dichlorinated nitrogen containing heterocycles or via a two-step reaction process.
Solid state structure of the ortho-linked oxacalix[n]arene[n]hetarenes (n¼2, 3) has been determined by
X-ray crystallography. 1,3-Alternate and 1,3,5-alternate conformations were found for ortho-linked oxa-
calix[2]arene[2]pyrazine (1) and oxacalix[3]arene[3]pyrazine (2), respectively. However, a core con-
formation with C3 symmetry was found for ortho-linked oxacalix[3]arene[3]pyrimidine (4), which is
completely different from that of its isomer, compound 2.
Received 12 September 2008
Received in revised form 15 October 2008
Accepted 17 October 2008
Available online 30 October 2008
Ó 2008 Elsevier Ltd. All rights reserved.
1. Introduction
Recently, we became interested in the synthesis of heteroatom-
bridged calixaromatics with novel macrocyclic backbones and their
Calixarenes1 are macrocyclic compounds with interesting con-
formational and cavity structures. They have been widely used in
studying host–guest chemistry,2 molecular encapsulation,3 as
scaffolds for the synthesis of multivalent ligands.4 Heteroatom-
bridged calixaromatics, structural isomers of calixarenes, have
recently attracted considerable attention in the area of supramo-
lecular chemistry.5 Extensive work have been done on the synthesis
and applications of tetrathiacalix[4]arene.6 Much of the work on
the construction of oxa- and aza-calixarene derivatives have been
done by Katz and co-workers,7 Wang and co-workers,8 and others.9
Due to the electron donating nature of the heteroatoms, the het-
eroatom-bridged calixaromatics could offer unique coordinating
and recognition properties,10,11 which would ultimately bring to
their practical applications, for example, ionic sensors.12,13 As far as
we aware all the above-mentioned heteroatom-bridged calix-
aromatics are composed of meta-linked phenyls or heterocycles.
ortho-Linked heteroatom-bridged calixaromatics are rare. Only one
report appeared very recently on the synthesis and structure of
ortho-linked oxacyclophane generated from 2,7-dichloro-1,8-
naphthyridine and naphthalene-2,3-diol. Due to the large arene
space of naphthyridine, the two naphthalene units are separated by
7.0 Å and defined a tweezer cavity, which could incorporate
a CH3CN molecule in the solid state. This compound was also found
to selectively bind ortho-salicylic acid.7d
applications in supramolecular chemistry. We envisioned that if
catechol is employed in the construction of oxacalix[n]arene-
[n]hetarenes instead of resorcinol, the close proximity of the two
oxygen atoms in catechol would result in oxacalix[n]arene-
[n]hetarenes with less molecular flexibilities and smaller cavities
than those known oxacalix[n]arene[n]hetarenes formed from res-
orcinol. Consequently, the new macrocyclic compounds generated
from the condensation of catechol and meta-dihalogenated aza-
heterocyclic aromatics might offer unique scaffolds for special
guest recognition and metal coordination. Herein we describe the
first synthesis, structure, and conformation of ortho-linked
oxacalix[2]arene[2]hetarenes and oxacalix[3]arene[3]hetarenes
generated from the cyclooligomerization of catechol with meta-
dichlorinated nitrogen containing heterocycles (pyridine, pyrazine,
and pyrimidine).
2. Results and discussion
Previous work done by Katz and co-workers has shown that
cyclocondensation of resorcinols with electrophilic meta-dihalo-
genated azaheterocyclic aromatics (2,6-dichloropyrazine, 2,6-
dichloropyridine, and 4,6-dichloropyrimidine) resulted in the
formation of oxacalix[2]arene[2]hetarenes in high yields.7c We
surmise that ortho-linked oxacalix[2]arene[2]hetarenes could be
formed by condensing those same azaheterocyclic electrophiles
employed in Katz’s work with catechol. By slightly modifying Katz’s
reaction condition, catechol reacted with 2,6-dichloropyrazine in
the presence of Cs2CO3 in DMSO at room temperature for 8 h
and then at 120 ꢀC for 16 h resulted in the formation of expected
* Corresponding author. Tel.: þ86 21 62237102; fax: þ86 21 62601953.
E-mail address: kwen@brain.ecnu.edu.cn (K. Wen).
0040-4020/$ – see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tet.2008.10.083

M. Ma et al. / Tetrahedron 65 (2009) 300–304
301
ortho-linked oxacalix[2]arene[2]pyrazine (1) and oxacalix[3]-
arene[3]pyrazine (2) in the yields of 47% and 14%, respectively
(Scheme 1). Byproducts, possibly larger cyclooligomers and poly-
meric species, were also formed, but were difficult to separate from
the reaction mixture. In order to improve the yield of compound 1,
a fragment coupling strategy was examined (in Scheme 1). To our
surprise, compound 1 was formed in an overall yield of only 45%
and compound 2, unexpectedly in a 17% yield. The formation of
compound 2 was a result of the C–O bond breaking and reformation
in the reaction process. This was also evidenced in the following
experiment shown in Scheme 2, in which compound 2 could be
converted to 1 at 120 ꢀC in the presence of Cs2CO3, while the re-
verse process was not found to take place under this condition. This
result demonstrates that compound 1 was thermodynamically
more stable than compound 2. During the investigation of ortho-
linked oxacalix[2]arene[2]pyrazine (1) synthesis, other bases
(Na2CO3, K2CO3, NaH, di(isopropyl)ethylamine (DIPEA), and pyri-
dine) and solvents (DMF, THF, and CH3CN) with different combi-
nation were screened for better reaction system in the synthesis of
compound 1, however, the results showed that the Cs2CO3/DMSO
system was superior to other combinations.
the reaction mixture. However, the coupling reaction of 4,6-
dichloropyrimidine with catechol in the presence of Cs2CO3 in
DMSO, both at room temperature and at 120 ꢀC, provided
only ortho-linked oxacalix[3]arene[3]pyrimidine (4), with no
expected ortho-linked oxacalix[2]arene[2]pyrimidine. In order to
synthesize ortho-linked oxacalix[2]arene[2]pyrimidine, we also
tried the two-step reaction sequence similar as in Scheme 1, by
replacing 2,6-dichloropyrazine with 4,6-dichloropyrimidine, and
found compound 4 was the sole isolated product in both room
temperature and 120 ꢀC in this two-step reaction. The results
demonstrated that compound 4 is both kinetically and thermody-
namically favored product in this reaction.
Calix[4]arenes can adopt cone, partial cone, 1,2-alternate, and
1,3-alternate conformations.1 Oxacalix[4]arenes reported so far all
adopt 1,3-alternate conformation.8a,9h,9k In order to analyze the
structures and conformations of the synthesized compounds, sin-
gle crystals of 1, 2, and 4 with X-ray diffraction quality were grown
by slow evaporation from ethyl acetate. As expected, the crystal
structure of 1 adopts a 1,3-alternate conformation (Fig. 1).14 The
four bridging oxygen atoms are located nearly in the same
plane with a deviation of less than 0.18 Å. The pair of the opposite
O
N
O
O
N
O
N
N
Cs2CO3, DMSO
1, n = 1 (47%)
2, n = 2 (14%)
N
N
+
1. rt, 8h
2. 120 °C, 16h
Cl
Cl
HO
OH
O
N
O
+
N
N
N
HO
OH
Cl Cl
Scheme 1. Synthesis of ortho-linked oxacalix[n]arene[n]pyrazines (n¼2, 3).
pyrazine rings are arranged eclipsing, with a dihedral angle of 27.2ꢀ,
creating transannular N/N distances of 4.199 Å between the two
upper rim nitrogen atoms and 2.865 Å of the two lower rim ni-
trogen atoms, respectively. The two phenyl rings are placed in
a face-to-face orientation with a dihedral angle of 28.6ꢀ, and
a centroid–centroid distance of 5.371 Å. Due to the narrow space
created by this conformation, no guest molecules (solvent mole-
cules) were found to be included in the solid states (Fig. 1). There
are two bridge oxygen atoms were found to conjugate with pyr-
azine rings (average C–O length 1.35 Å), while the other two bridge
atoms are partially conjugated to the pyrazine rings (average C–O
length 1.37 Å), and no conjugation existing between the bridging
oxygen atoms and the phenyl rings (average C–O length 1.39 Å).
Oxacalix[n]arenes (n>4) appeared to be more difficult to synthe-
size,9b,h–j and the structural information of this class of compounds
remains unavailable. Fortunately, ortho-linked oxacalix[3]ar-
ene[3]pyrazine (2) was also isolated in this reaction. The crystal
structure of 2 revealed that it adopts a 1,3,5-alternate conformation
O
N
O
O
N
O
O
N
O
O
N
O
Cs2CO3, DMSO
120 °C, 24h
N
N
N
N
2
1
Scheme 2. Conversion of compound 2 to compound 1 under heating.
Similarly, ortho-linked oxacalix[2]arene[2]pyridine (3) has been
obtained in 38% yield by the reaction of 2,6-dichloropyridine and
catechol in the presence of Cs2CO3 in DMSO at room temperature
for 8 h and then at 120 ꢀC for 16 h. Other products including ortho-
linked oxacalix[3]arene[3]pyridine have not been separated from

302
M. Ma et al. / Tetrahedron 65 (2009) 300–304
Figure 1. X-ray single crystal structure and molecular packing of compound 1.
in the solid state (Fig. 2).15 The structure shows that a pair of pyr-
azine rings (two out of three) is arranged eclipsing with a dihedral
angle of 29.2ꢀ and a centroid–centroid distance of 3.949 Å. Two
phenyl rings (two out of three) are positioned almost parallel with
a dihedral angle of only 9.6ꢀ and a centroid–centroid distance of
4.310 Å. The remaining pyrazine ring and the phenyl ring are
pointed in an opposite direction with a dihedral angle of 21.7ꢀ. The
molecule revealed an unsymmetrical rectangular geometry and
Figure 2. X-ray single crystal structure of compound 2, side view (top left), top view (top right), and molecular packing (bottom).

M. Ma et al. / Tetrahedron 65 (2009) 300–304
303
thus generated a narrow space, which is hardly hosting any guest
molecules (such as solvent molecules, Fig. 2).
diffractometer equipped with a normal focus Mo-target X-ray tube
¼0.71073 Å).
(l
The crystal structure of ortho-linked oxacalix[3]arene[3]pyr-
imidine (4),16 however, adopts a complete different conformation
from its isomer, compound 2. Compound 4 revealed a core con-
formation with C3 symmetry in the solid state (Fig. 3). The position
of the nitrogen atoms in the heterocyclic rings is believed to be
responsible for this difference, yet the mechanistic details remain
to be known. In this structure, the six rings are arranged in a tri-
angular shape, in which the three phenyl segments are located at
the angle positions of the triangle and the three pyrimidine rings
are placed at the line segments of the triangle. The three pyrimidine
rings are oriented almost perpendicular to the triangular plane
with a slight bent toward the triangular core while the three phenyl
rings are bent away from the triangular core. This conformation
thus created no cavity space for taking up guest molecules (Fig. 3).
4.2. Synthesis of ortho-linked oxacalix[2]arene[2]pyrazine (1)
and ortho-linked oxacalix[3]arene[3]pyrazine (2)
Cesium carbonate (7.16 g, 22 mmol) was dissolved in 250 mL
DMSO, catechol (1.1 g, 10 mmol), and 2,6-dichloropyrazine (1.49 g,
10 mmol) were added to the DMSO solution. The reaction mixture
was stirred at room temperature for 8 h, then heated at 120 ꢀC for
additional 16 h. The reaction mixture was poured into 500 mL
water and extracted with ethyl acetate for three times. The com-
bined organic layer was washed with water and brine, dried over
Na2SO4. The solvent was evaporated and the crude products 1 and 2
were purified by FC (PE/AcOEt 8:1).
4.2.1. ortho-Linked oxacalix[2]arene[2]pyrazine (1)
Yield: 0.87 g (47%). White powder. 1H NMR (500 MHz, CDCl3):
3. Conclusions
d
7.92 (s, 4H), 7.05–7.02 (m, 4H), 6.96–6.94 (m, 4H); 13C NMR
(500 MHz, CDCl3):
d 157.04, 145.16, 126.24, 125.97, 124.12; HRMS:
In summary, new types of ortho-linked oxacalix[2]ar-
ene[2]hetarenes and oxacalix[3]arene[3]hetarenes have been
prepared by condensation of catechol and meta-dichlorinated ni-
trogen containing heterocycles. Crystal structure analyses revealed
1,3-alternate and 1,3,5-alternate conformations for ortho-linked
oxacalix[2]arene[2]pyrazine (1) and ortho-linked oxacalix[3]arene-
[3]pyrazine (2), respectively. ortho-Linked oxacalix[3]arene[3]pyr-
imidine (4), an isomer of 2, however, was found to adopt a core
conformation with C3 symmetry. No cavity spaces were formed
under those conformations adopted, and consequently no guest
species were found being taken up by these molecules in the solid
state.
C20H13N4Oþ4 m/z calcd 373.0931, found 373.0939.
4.2.2. ortho-Linked oxacalix[3]arene[3]pyrazine (2)
Yield: 0.26 g (14%). White powder. 1H NMR (500 MHz, CDCl3):
d
d
7.80 (s, 6H), 7.24–7.19 (m, 12H); 13C NMR (500 MHz, CDCl3):
156.88, 144.40, 126.66, 125.15, 123.13; HRMS: C30H19N6Oþ6 m/z
calcd 559.1366, found 559.1353.
4.3. Synthesis of ortho-linked oxacalix[2]arene[2]pyrazine (1)
and ortho-linked oxacalix[3]arene[3]pyrazine (2) by the two-
step reaction protocol
2,6-dichloropyrazine (4.47 g, 60 mmol) and potassium carbon-
ate (6.10 g, 44 mmol) were dissolved in 50 mL DMF and stirred
for 15 min. Catechol (2.0 g, 20 mmol) in 100 mL DMF was added
dropwise to the above reaction mixture. The reaction was moni-
tored by TLC. After the reaction was complete, the reaction mixture
was poured to 500 mL ice-water and extracted with ethyl acetate
for three times. The combined organic layer was washed with water
and brine, dried over Na2SO4. The solvent was evaporated and the
crude product 1,2-bis(6-chloropyrazin-2-ybxy)benzene was puri-
fied by FC (PE/AcOEt 9:1).
4. Experimental
4.1. General
All chemicals were used as received without further purifica-
tion. Chemical reactions were performed in oven-dried glassware
under an atmosphere of nitrogen. Classic column chromatography
was performed using Merck 60 (70–230 mesh) silica gel. 1H and 13
C
NMR spectra were recorded at Bruker Avance 500 spectrometer in
CDCl3. Chemical shifts are reported in parts per million versus
tetramethylsilane. Mass spectra were recorded on
micrOTOF-Q spectrometer (LC/MS). Single crystal X-ray diffraction
data were collected on Bruker SMART APEX X-ray
a
Bruker
4.3.1. 1,2-bis(6-chloropyrazin-2-yloxy)benzene
Yield: 5.38 g (80%). White powder. 1H NMR (500 MHz, CDCl3):
a
2
d
8.28 (s, 2H), 8.20 (s, 2H), 7.35–7.40 (m, 4H); 13C NMR (500 MHz,
Figure 3. X-ray single crystal structure and molecular packing of compound 4.

304
M. Ma et al. / Tetrahedron 65 (2009) 300–304
CDCl3):
d
157.90, 145.71, 144.06, 137.98, 132.13, 126.95, 123.47;
CDCl3): d 170.59, 157.66, 144.29, 126.90, 123.70, 91.68; HRMS:
HRMS: C14H9Cl2N4Oþ2 m/z calcd 335.0097, found 335.0098.
Cesium carbonate (3.10 g, 9.2 mmol) was dissolved in 100 mL
DMSO and slowly heated to 120 ꢀC. Under vigorous stirring, cate-
chol (0.46 g, 4.2 mmol) in 100 mL DMSO and 1,2-Bis(6-chloropyr-
azin-2-ybxy)benzene (1.41 g, 4.2 mmol) in 100 mL DMSO were
slowly added to the reaction mixture dropwise in a same rate. After
complete addition, the reaction mixture was maintained at this
temperature until the completion of the reaction (based on TLC).
The work-up was the same as that in Section 4.2. Compound 1
(0.87 g) was obtained in 56% yield (overall 45%) and compound 2
(0.40 g) was obtained in 17% yield. The analytical data for 1 and 2
were seen in Section 4.2.
C30H19N6Oþ6 m/z calcd 559.1366, found 559.1371.
Acknowledgements
This work was supported by grants from Shanghai Commission
for Science and Technology (06Pj14034, 06DZ19002), Ministry of
Education (106078), and Ministry of Science and Technology
of China (973 Project, 2003CB716600). We thank Dr. Xiao-Li Zhao of
Shanghai Key Laboratory of Green Chemistry and Chemical Pro-
cesses and Department of Chemistry of East China Normal Uni-
versity for performing the X-ray crystallographic study.
References and notes
4.4. Conversion of ortho-linked oxacalix[3]arene[3]pyrazine
(2) to ortho-linked oxacalix[2]arene[2]pyrazine (1)
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Anda, H. J.; Rebek, J. J. Am. Chem. Soc. 2007, 129, 13464.
ortho-Linkedoxacalix[3]arene[3]pyrazine (2) (5.6 mg 0.01 mmol)
and cesium carbonate (6.5 mg, 0.02 mmol) were dissolved in 5 mL
DMSO and heated at 120 ꢀC, the reaction process was monitored by
TLC. After 24 h, over 95% of compound 2 were transformed to ortho-
linked oxacalix[2]arene[2]pyrazine (1) (based on TLC).
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DMSO, catechol (1.1 g, 10 mmol) and 2,6-dicholoropyridine (1.48 g,
10 mmol) were added to the DMSO solution. The following pro-
cedure was the same as that of the synthesis of ortho-linked oxa-
calix[2]arene[2]pyrazine (1).
8. (a) Wang, M.-X.; Yang, H.-B. J. Am. Chem. Soc. 2004, 126, 15412; (b) Wang, M.-X.;
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4.5.1. ortho-Linked oxacalix[2]arene[2]pyridine (3)
Yield: 0.71 g (38.3%). White powder. 1H NMR (500 MHz,
CDCl3):
d
7.45 (t, 2H, J¼8), 6.99–6.94 (m, 8H), 6.43 (d, 4H, J¼8);
13C NMR (500 MHz, CDCl3):
d 161.11, 146.07, 141.66, 124.94,
124.27, 102.75; HRMS: C22H15N4Oþ4 m/z calcd 371.1032, found
371.1012.
4.6. Synthesis of ortho-linked oxacalix[3]arene[3]-
pyrimidine (4)
(a) Cesium carbonate (7.16 g, 22 mmol) was dissolved in 250 mL
DMSO, catechol (1.1 g, 10 mmol) and 4,6-dichloropyrimidine
(1.48 g, 10 mmol) were added to the DMSO solution and re-
action mixture was stirred at room temperature for 48 h. The
work-up was the same as that of compound 1. ortho-Linked
oxacalix[3]arene[3]pyrimidine (4, 0.65 g) was obtained in 35%
yield.
(b) Cesium carbonate (7.16 g, 22 mmol) was dissolved in 250 mL
DMSO, catechol (1.1 g, 10 mmol) and 4,6-dichloropyrimidine
(1.48 g, 10 mmol) were added to the DMSO solution and re-
action mixture was stirred at room temperature for 8 h, then
heated at 120 ꢀC for 16 h. After the work-up, ortho-linked
oxacalix[3]arene[3]pyrimidine (4, 0.76 g) was obtained in 41%
yield.
14. Crystallographic data for ortho-linked oxacalix[2]arene[2]pyrazine (1):
[C20H12N4O4]; Mr¼372.34; triclinic; space group P1; a¼7.15620(10); b¼10.
0339(2); c¼12.7082(2) Å;
a¼97.4090(10);
b¼94.1430(10);
g
¼109.3420(10)ꢀ;
V¼847.352 Å3; rcalcd¼1.459 g cmꢁ3; T¼296(2) K; 11,617 independent measured
reflections; F2 refinement; R1¼0.0540; wR2¼0.1355.
15. Crystallographic data for ortho-linked oxacalix[3]arene[3]pyrazine (2):
[C30H18N6O6]; Mr¼558.50; triclinic; space group P1; a¼8.730(3); b¼9.001(3);
c¼17.867(6) Å;
a
¼77.598(5);
b
¼87.461(6);
g
¼72.300(6)ꢀ; V¼1305.9(7) Å3;
rcalcd¼1.420 g cmꢁ3; T¼293(2) K; 6775 independent measured reflections; F2
refinement; R1¼0.0828; wR2¼0.2148.
16. Crystallographic data for ortho-linked oxacalix[3]arene[3]pyrimidine (4):
[C15H9N3O3]; Mr¼279.25; orthorhombic; space group pnma; a¼17.3767(6);
4.6.1. ortho-Linked oxacalix[3]arene[3]pyrimidine (4)
b¼21.4937(7);
c¼6.8235(2) Å;
V¼2548.51(14) Å3;
rcalcd¼1.456 g cmꢁ1
;
White powder. 1H NMR (500 MHz, CDCl3):
d
8.25 (s, 3H), 7.37–
T¼296(2) K; 27,886 independent measured reflections; F2 refinement; R1¼0.
0299; wR2¼0.0753.
7.35 (m, 6H), 7.29–7.20 (m, 6H), 6.28 (s, 3H); 13C NMR (500 MHz,