Organic crystals bearing both channels and cavities formed from tripodal adamantane molecules

Article abstract of DOI:10.1016/j.molstruc.2013.03.033

Three adamantane-based tripodal molecules bearing either a benzene, pyridine, or toluene unit (1-3) form molecular organic networks (1a-3a) with internal spaces, via intermolecular non-covalent interactions such as CH/π, CH/N, and CH/O interactions in the solid state. Crystals of 1a and 2a formed both one-dimensional channels and cavities, where guest molecules were encapsulated. The channels were derived from the alignment of the hexagonal cavities formed from six component molecules, while cavities formed between the 2D layers. In contrast, 3a contained only cavities built from the six component molecules, which correspond to the spaces which connected to form channels in 1a and 2a.

Full text of DOI:10.1016/j.molstruc.2013.03.033

Journal of Molecular Structure 1046 (2013) 52–56
Contents lists available at SciVerse ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Organic crystals bearing both channels and cavities formed from tripodal
adamantane molecules
⇑
Masahide Tominaga , Akitaka Iekushi, Kosuke Katagiri, Kazuaki Ohara, Kentaro Yamaguchi,
Isao Azumaya
⇑
Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
g r a p h i c a l a b s t r a c t
h i g h l i g h t s
ꢀ
ꢀ
Three adamantane-cored tripodal
molecules were synthesized.
X-ray crystallographic analyses were
performed on single-crystals of
tripodal molecules.
ꢀ
Three tripodal molecules afforded
molecular organic networks bearing
internal spaces.
ꢀ
ꢀ
Two crystals exhibited the formation
of both 1D channels and cavities.
One crystal showed the generation of
only cavities in the crystalline
lattices.
a r t i c l e i n f o
a b s t r a c t
Article history:
Three adamantane-based tripodal molecules bearing either a benzene, pyridine, or toluene unit (1–3)
form molecular organic networks (1a–3a) with internal spaces, via intermolecular non-covalent interac-
tions such as CH/p, CH/N, and CH/O interactions in the solid state. Crystals of 1a and 2a formed both one-
dimensional channels and cavities, where guest molecules were encapsulated. The channels were derived
from the alignment of the hexagonal cavities formed from six component molecules, while cavities
formed between the 2D layers. In contrast, 3a contained only cavities built from the six component mol-
ecules, which correspond to the spaces which connected to form channels in 1a and 2a.
Ó 2013 Elsevier B.V. All rights reserved.
Received 26 October 2012
Received in revised form 11 March 2013
Accepted 18 March 2013
Available online 26 March 2013
Keywords:
Adamantane
Tripodal molecule
Channel structure
Cavity
Crystal packing
1. Introduction
molecules with rigid frameworks are useful building blocks for the
production of organic crystals with channels or cavities [16–19].
The construction of channels and cavities in molecular organic
networks are important subjects in the fields of crystal engineering
and materials science [1–4]. Organic materials which have inner
spaces are of considerable interest due to their ability to recognize
molecules selectively, stabilize unstable guest species, and perform
chemical transformations [5–15]. Especially, C3-symmetric organic
For example, tris(o-phenylenedioxy)cyclotriphosphazene forms a
porous crystal with a permanent one-dimensional channel, where
gases, linear
p–conjugated molecules, and polymers can be
encapsulated [20–22]. Substituted 1,3,5-triazine molecules provide
channel-type structures, and can accommodate large molecules
such as fullerenes in addition to small aromatic molecules
[23,24]. However, examples of molecular organic networks
containing both channels and cavities are quite limited. The
generation of these higher orders of network structures containing
inner spaces is an intrinsically important task for the development
⇑
Corresponding authors. Tel.: +81 87 894 5111; fax: +81 87 894 0181.
E-mail addresses: tominagam@kph.bunri-u.ac.jp (M. Tominaga), azumayai@
kph.bunri-u.ac.jp (I. Azumaya).
0022-2860/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.molstruc.2013.03.033

M. Tominaga et al. / Journal of Molecular Structure 1046 (2013) 52–56
53
of host-guest systems for the molecular recognition of gasses, or-
ganic molecules, and others [25–36]. Thus, we envisioned mole-
(d, 6H, J = 7.6 Hz), 7.60 (t, 3H, J = 7.2 Hz), 7.48 (t, 6H, J = 8.0 Hz),
6.75 (s, 6H), 3.84 (s, 18H), 2.59 (s, 1H), 2.20–2.06 (m, 12H). 13C
NMR (100 MHz, CDCl3, 27 °C) d 164.60, 152.01, 148.25, 133.24,
130.29, 129.33, 128.33, 127.18, 102.24, 56.25, 48.27, 41.42, 38.83,
30.06. MS (FAB, m/z) calcd for C55H53O12 (M+H+) 905.35, found
905.1. Anal. Calcd for C55H52O12Á0.1H2O: C, 72.85; H, 5.80. Found:
C, 72.56; H, 5.78.
cules with non-planar C3v
, to bent planar C3 symmetric
compounds would be appropriate for the preparation of crystalline
materials which have both channels and cavities. This is because
these molecules may form a cavity separate from the channels
due to their three-dimensional shape, whilst maintaining the chan-
nel structures. Tri-substituted adamantane is a suitable skeleton
for the design of C3v-symmetric molecules. Recently, we presented
hydrogen-bonded organic networks with channels that were built
from adamantane-based tripodal molecules containing dime-
thoxyphenol moieties [37]. Herein we report three different ada-
mantane-centered tripodal molecules bearing either a benzene,
pyridine, or toluene moiety and the molecular organic networks
they form through intermolecular non-covalent interactions such
2.2.2. 1,3,5-Tris(4-isonicotinoyloxy-3,5-dimethoxyphenyl)
adamantane (2)
To
a
solution
of
1,3,5-tris(4-hydroxy-3,5-dimethoxy-
phenyl)adamantane (0.59 g, 1.00 mmol) in dry THF (20 mL), isoni-
cotinoyl chloride hydrochloride (0.59 g, 3.30 mmol) was added
under an argon atmosphere at 0 °C. After 10 min, triethylamine
(2.5 mL) was added into the solution, and stirred for 3 d at room
temperature. After evaporation to dryness, the residue was dis-
solved in CHCl3, and washed with a saturated aqueous NaHCO3
solution, then H2O, and finally brine. The organic layer was dried
over anhydrous Na2SO4 and filtered. Evaporation of the solvent fol-
lowed by silica gel column chromatography (eluent: CHCl3:-
MeOH = 50:1) and gel permeation chromatography (JAIGEL
1H+2H, CHCl3) afforded 2 as a white solid (0.58 g, 0.64 mmol) in
64% yield. m.p. 232–233 °C. FT-IR (ATR, cmÀ1): 2931, 2847, 1748,
1587, 1508, 1451, 1413, 1324, 1248, 1212, 1124, 847, 687. 1H
as CH/p, CH/N, and CH/O interactions.
2. Experimental
2.1. General
All the reagents and solvents used were commercially avail-
able and employed as received without further purification.
The 1H NMR and 13C NMR spectra were recorded on a Bruker
AV-400M spectrometer at 27 °C using CDCl3 as the solvent and
TMS as an internal reference. Melting points were determined
on an ASONE ATM-01 melting point apparatus and were uncor-
rected. FAB mass was performed on a JEOL JMS-700 using an
m-nitrobenzylalcohol (NBA) matrix. Elemental analyses were
NMR (400 MHz, CDCl3, 27 °C)
d 8.85 (s, 6H), 8.05 (d, 6H,
J = 5.6 Hz), 6.75 (s, 6H), 3.86 (s, 18H), 2.62 (s, 1H), 2.22–2.08 (m,
12H). 13C NMR (100 MHz, CDCl3, 27 °C) d 163.22, 151.75, 150.55,
148.63, 136.54, 126.61, 123.40, 102.02, 56.16, 48.20, 41.33, 38.87,
29.98. MS (FAB, m/z) calcd for C52H50N3O12 (M+H+) 908.33, found
908.9. Anal. Calcd for C52H49N3O12Á1H2O: C, 67.45; H, 5.55; N,
4.54. Found: C, 67.14; H, 5.41; N, 4.53.
performed with
a Perkin-Elmer 2400 elemental analyzer. IR
spectra were recorded with a Jasco FT/IR-6300 instrument. X-
ray data for the crystals 1a–3a were collected on a CCD diffrac-
tometer with graphite monochromated Mo K
a (k = 0.71073 Å)
radiation. Data collection was carried out at 100 K using a Japan
Thermal Eng. Col., Ltd. Cryostat system equipped with a liquid
nitrogen generator. The crystal structures were solved by direct
methods (SHELXS 97, Sheldrick, 1997) [38]. Refinements were
carried out by full-matrix least squares on F2, with anisotropic
temperature factors for non-H atoms. In all structures, H atoms
were included as their calculated positions. SHELXTL was used
for refinement of the structure and structure analysis. Column
chromatography was performed using a Wakogel C200, and
thin-layer chromatography was carried out on 0.25 mm Merck
precoated silica gel glass plates. Gel permeation Chromatography
(GPC) was performed using a recycling preparative HPLC system
(LC-9204, Japan Analytical Industry Co., Ltd.) fitted with a JAIGEL
H series column (Japan Analytical Industry Co., Ltd.).
2.2.3. 1,3,5-Tris(4-(4-methylbenzoyloxy)-3,5-dimethoxyphenyl)
adamantane (3)
To
a
solution
of
1,3,5-tris(4-hydroxy-3,5-dimethoxy-
phenyl)adamantane (0.59 g, 1.00 mmol) in dry THF (20 mL), p-tol-
uoyl chloride (0.51 g, 3.30 mmol) was added under an argon
atmosphere at 0 °C. After 10 min, triethylamine (1.5 mL) was
added into the solution, and stirred for 2 d at room temperature.
After evaporation to dryness, the residue was dissolved in CHCl3,
and washed with a saturated aqueous NaHCO3 solution, then
H2O, and finally brine. The organic layer was dried over anhydrous
Na2SO4 and filtered. Evaporation of the solvent followed by silica
gel column chromatography (eluent: CHCl3) and gel permeation
chromatography (JAIGEL 1H+2H, CHCl3) afforded 3 as a white solid
(0.67 g, 0.71 mmol) in 71% yield. m.p. 163–165 °C. FT-IR (ATR,
cmÀ1): 2933, 2849, 1733, 1598, 1515, 1452, 1411, 1325, 1263,
1211, 1128, 1061, 816, 746. 1H NMR (400 MHz, CDCl3, 27 °C) d
8.13 (d, 6H, J = 8.0 Hz), 7.29 (d, 6H, J = 8.4 Hz), 6.73 (s, 6H), 3.83
(s, 18H), 2.59 (s, 1H), 2.43 (s, 9H), 2.18–2.05 (m, 12H). 13C NMR
(100 MHz, CDCl3, 27 °C) d 164.69, 152.09, 148.20, 144.02, 130.40,
129.07, 127.30, 126.63, 102.32, 56.31, 48.31, 41.48, 38.86, 30.11,
21.65. MS (FAB, m/z) calcd for C58H59O12 (M+H+) 947.39, found
946.8. Anal. Calcd for C58H58O12Á0.1H2O: C, 73.42; H, 6.18. Found:
C, 73.08; H, 6.10.
2.2. Synthesis
2.2.1. 1,3,5-Tris(4-benzoyloxy-3,5-dimethoxyphenyl)adamantane (1)
To
a
solution
of
1,3,5-tris(4-hydroxy-3,5-dimethoxy-
phenyl)adamantane (0.59 g, 1.00 mmol) in dry THF (20 mL), ben-
zoyl chloride (0.46 g, 3.30 mmol) was added under an argon
atmosphere at 0 °C. After 10 min, triethylamine (1.5 mL) was
added into the solution, and stirred for 2 d at room temperature.
After evaporation to dryness, the residue was dissolved in CHCl3,
and washed with a saturated aqueous NaHCO3 solution, then
H2O, and finally brine. The organic layer was dried over anhydrous
Na2SO4 and filtered. Evaporation of the solvent followed by silica
gel column chromatography (eluent: CHCl3) and gel permeation
chromatography (JAIGEL 1H+2H, CHCl3) afforded 1 as a white solid
(0.74 g, 0.82 mmol) in 82% yield. m.p. 170–172 °C. FT-IR (ATR,
cmÀ1): 2932, 2850, 1739, 1599, 1514, 1450, 1412, 1327, 1262,
1212, 1125, 1059, 704. 1H NMR (400 MHz, CDCl3, 27 °C) d 8.24
2.3. Crystallization
The appropriate tripodal molecule (0.02 mmol) was stirred in
tetrahydrofuran (10.0 mL) for 1 or acetonitrile (10.0 mL) for 2
and 3 at room temperature for 1 h. Colorless single crystals of
1a–3a were obtained by slow evaporation of the solvent after a
few days.

54
M. Tominaga et al. / Journal of Molecular Structure 1046 (2013) 52–56
and cavities were observed in the crystalline lattices, with solvent
3. Results and discussion
molecules included in both the channels and cavities.
2a Crystallized in the trigonal system in the centrosymmetric
space group PÀ3c1, and included one molecule of 2, one molecule
of water, and two molecules of acetonitrile in the asymmetric unit.
The organic networks (1a–3a) were formed from an adaman-
tane-cored tripodal molecule (1–3), in which either benzene, pyri-
dine, or toluene units were linked through ester groups to a
triaryladamantane derivative (Fig. 1). The esterification of 1,3,
5-tris(4-hydroxy-3,5-dimethoxyphenyl)adamantane with the cor-
responding acid chloride compounds in the presence of triethyl-
amine gave the desired adamantane-cored tripodal molecules
bearing arylester groups. Colorless single crystals of 1a were
obtained by slow evaporation of a tetrahydrofuran solution of 1.
Crystals 2a and 3a were isolated by the slow evaporation of an ace-
tonitrile solution of the compounds 2 and 3, respectively. X-ray
crystallographic analyses were carried out on single-crystals of
1a–3a (Table 1).
1a Crystallized in the trigonal system, in the centrosymmetric
space group PÀ3c1, and included one molecule of 1 and three mol-
ecules of tetrahydrofuran in the asymmetric unit. In the structure,
the tripodal molecules were assembled into two-dimensional (2D)
layers via CH/p interactions [39] between the phenyl groups (the
distance between the carbon atom and the ring center of the phe-
nyl ring was 4.07 Å) (Fig. 2a) [40,41]. These layers were further or-
ganized as three-dimensional networks via CH/O interactions
between the methylene protons of the adamantane units and the
oxygen atoms of carbonyl groups at a distance of 3.45 Å, measured
between the methylene carbon and the carbonyl oxygen atoms
(Fig. 2b). An isolated cavity A was formed between the individual
2D layers, where disordered tetrahydrofuran molecules were enc-
lathrated. A hexagonal cavity B formed from the cyclic hexamers of
the tripodal molecule 1, and these cavities formed the channel
framework (Fig. 2c). Disordered tetrahydrofuran molecules were
accommodated within the hexagonal cavity. Thus, both channels
Fig. 1. The three adamantane-centered tripodal molecules 1–3.
Table 1
Crystallographic data for the adamantane-centered tripodal molecules 1a–3a.
Crystal
1a
2a
3a
Formula
Crystal system
Space group
a (Å)
b (Å)
c (Å)
C
66.99H75.99O15
C56H49N5O13.5
Trigonal
P3c1
15.425 (2)
15.425 (2)
25.083 (5)
90
C36H29N3.5O6.25
Trigonal
R3
18.3248 (18)
18.3248 (18)
35.862 (3)
90
Trigonal
P3c1
15.7084 (10)
15.7084 (10)
25.9732 (18)
90
ꢀ
ꢀ
ꢀ
a
(°)
b (°)
90
90
90
c
(°)
120
5550.3 (6)
1.342
120
5168.3 (16)
1.295
120
10429.0 (17)
1.167
V (Å3)
Dc (Mg mÀ3
)
Z
4
100
0.0789, 0.2398
903301
4
100
0.0552, 0.1660
903302
12
100
0.1004, 0.3152
903303
Fig. 2. Crystal structure of 1a. (a) The 2D layer structure, (b) the 3D network
structure viewed from the side, along the b axis, and (c) a space-filling model of the
3D network structure viewed from the top. The guest molecules were omitted for
T (K)
R1, wR2 [I > 2
CCDC number
r
(I)]
clarity. The red dotted lines show the CH/p interactions.

M. Tominaga et al. / Journal of Molecular Structure 1046 (2013) 52–56
55
Fig. 3. Crystal structure of 2a. (a) The 2D layer structure, (b) the 3D network
structure viewed from the side, along the b axis, and (c) a space-filling model of the
3D network structure viewed from the top. The guest molecules were omitted for
clarity. The red dotted lines show the CH/O interactions.
Fig. 4. Crystal structure of 3a. (a) The 2D layer structure, (b) the 3D network
structure viewed from the side, along the b axis, and (c) a space-filling model of the
3D network structure viewed from the top. The guest molecules were omitted for
clarity. The red dotted lines show the CH/p interactions.
In 2a, the tripodal molecules assembled into 2D layers via CH/O
interactions between the methylene protons of the adamantane
units and the oxygen atoms of carbonyl groups. The distance be-
tween the carbon atom and the oxygen atom was 3.45 Å
(Fig. 3a). These layers were further organized into 3D networks
via CH/O interactions between the carbon atom of one methoxy
groups and the oxygen atom of another at a distance of 3.39 Å
(Fig. 3b). Similarly, a cavity A was generated between the 2D lay-
ers, where acetonitrile molecules were enclathrated via CH/N
interactions between the phenyl protons and the nitrogen atoms
of acetonitrile where the distance between the carbon atom and
the nitrogen atom was 3.58 Å. A hexagonal cavity B was produced
from the cyclic hexamers of the tripodal molecule 2, and forms a
channel framework (Fig. 3c). Acetonitrile and water molecules
were encapsulated within the hexagonal cavity and disordered
over two identical sites.
3a Crystallized in the trigonal system in the centrosymmetric
space group RÀ3, and included one molecule of 3, one molecule
of water, and three molecules of acetonitrile in the asymmetric
unit. In 3a, the tripodal molecules were arranged into 2D layers

56
M. Tominaga et al. / Journal of Molecular Structure 1046 (2013) 52–56
via CH/
p
interactions between the methylene protons of the ada-
associated with this article can be found in the online version, at
doi:http://dx.doi.org/10.1016/j.molstruc.2013.03.033.
mantane units and the phenyl groups, with a distance between
the carbon atom and the ring center of the phenyl ring of 4.14 Å,
and between the methyl protons of the methoxy groups and the
phenyl groups with a distance between the carbon atom and the
ring center of the phenyl ring of 4.18 Å (Fig. 4a). These layers were
Acknowledgment
This work was supported by a Grant-in-Aid for Young Scientists
(B) from the Ministry of Education, Culture, Sports, Science, and
Technology of Japan (No. 22750113).
extended into 3D networks via CH/
p interactions between the
methyl protons of the methoxy groups and the phenyl groups, with
a distance between the carbon atom and the ring center of the phe-
nyl ring of 3.66 and 4.35 Å (Fig. 4b). A hexagonal cavity A arose
from the cyclic hexamers of the tripodal molecule 3 (Fig. 4c), where
multiple acetonitrile molecules were enclathrated due to CH/N
interactions between the phenyl protons and the nitrogen atoms
of nitrile groups with distances between the carbon atoms and
the nitrogen atoms from 3.55 to 3.47 Å. The 2D layers were assem-
bled into 3D networks with a half molecule shift along the c axis.
This means the hexagonal cavity could not produce channels along
the c axis. Thus, in 3a, only cavities were formed in the organic net-
works, where acetonitrile and water molecules were included.
Each organic crystal had different types of internal spaces in the
crystalline lattices, where multiple guest molecules were accom-
modated. In 1a and 2a, both channels and cavities were generated.
The channels were built from the arrangement, directly along c
axis, of the hexagonal cavities consisting of six component mole-
cules, while the cavities were formed between the individual 2D
layers. In contrast, only cavities were produced in the crystal 3a.
This relatively large cavity was derived from six component mole-
cules, which correspond to the cavities inducing into channels ob-
served for 1a and 2a. The cavity observed between the 2D layers in
1a and 2a was not found in 3a. These differences were probably
due to the influence of steric methyl groups in the tripodal mole-
cule 3 influencing the crystal packing. Namely, the nature of the
arylester units was crucial for the formation of organic networks
bearing both channels and cavities.
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Additional material comprised of the full X-ray data collection
details and final refinement parameters, including anisotropic
thermal parameters and full list of the bond lengths and angles,
have been deposited with the Cambridge Crystallographic Data
Centre in the CIF format as CCDC-903301, 903302, and 903303.
Copies of the data can be obtained free of charge on the application
to CCDC, 12 Union Road, Cambridge CB21EZ, UK, (Fax: +44 1233
336 033; e-mail: deposit@ccdc.cam.ac.uk). Supplementary data