Hydrogen-bonded porous solid derived from trimesic amide

Article abstract of DOI:10.1039/a705339h

N,N′,N″-Tris(3-pyridyl)trimesic amide, 1, forms a unique P3 symmetrical crystal containing pores with a mean diameter of 8.26 A.

Full text of DOI:10.1039/a705339h

View Article Online / Journal Homepage / Table of Contents for this issue
Hydrogen-bonded porous solid derived from trimesic amide
Anja R. A. Palmans,a Jef A. J. M. Vekemans,*a Huub Kooijman,b Anton L. Spekb† and E. W. Meijera
a Laboratory of Organic Chemistry, University of Technology, PO Box 513, 5600MB Eindhoven, The Netherlands
b Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, University of Utrecht, Padualaan 8, 3584 CH
Utrecht, The Netherlands
N,NA,NB-Tris(3-pyridyl)trimesic amide, 1, forms a unique
The infinite bilayer sheets themselves belong to a three
dimensional super structure in which all the sheets are in fact
repeating units placed exactly on top of each other. This results
in the formation of a real porous structure with channels of
¯
P3 symmetrical crystal containing pores with a mean
diameter of 8.26 Å.
Supramolecular assembly and crystal engineering are fruitful
concepts to use in the design and development of structures with
a desired shape. Recently these concepts evolved to be used in
the construction of tubular superstructures1 and porous solids.2
Hydrogen bonding is one of the major tools which can be used
to achieve the desired order.3
Here we report on the highly ordered infinite bilayer crystal
structure of triamide 1,‡ derived from trimesic acid (benzene-
1,3,5-triacarboxylic acid) and 3-pyridylamine.§ In contrast to
recently designed structures,4 our result was entirely serendipi-
tous. Structure 1 served just as a model for comparison with
intramolecularly hydrogen-bonded structure 2, a precursor for
extended core discotic liquid crystals of enhanced thermal
a
b
stability.5
NH2
c 0
N
N
N
H
H
O
N
O
N
N
N
N
H
O
N
H
O
N
H2N
N
H
N
H
N
O
N
O
N
NH2
1
2
Fig. 1 Infinite rosette structure of 1
The transparent, hexagon-shaped crystals of 1, obtained upon
crystallization from methanol, suggested hexagonal symmetry
and prompted us to investigate a single crystal by X-ray
diffraction. As indicated in Fig. 1 the asymmetric cell comprises
only one third of a molecule while the unit cell is populated by
two molecules.‡ Intermolecular hydrogen bonding between the
pyridyl nitrogens and the amide NHs of adjacent molecules
provides the basis for a macrocyclic organization in a rosette-
like structure. A 30-membered macrocycle is formed with
participation of six molecules and the 3-aminopyridyl units
constitute the walls of a cavity with a mean diameter of 8.26 Å
(Fig. 2).
The C3-symmetry of the molecule then allows for the creation
of an infinite two-dimensional honeycomb grid with repeating
units at 13.87 Å in six directions and with a thickness of
approximately 8.40 Å. According to Etter’s6 graph set analysis
the nitrogen hydrogen bond donors and acceptors are involved
6
in a R6 (30) pattern. Closer inspection reveals the bilayer
structure of an ensemble of molecules in one sheet (Fig. 3). The
benzene units occupy alternating up and down positions. All the
amide carbonyls point outwards, while the pyridyl units
orientate their nitrogens inwards in the bilayer structure. This
implies that although the crystal is achiral, the structure is a
combination of trimesic units of P-helicity with units of
M-helicity.
Fig. 2 Cavity in 1 as a result of six-fold intermolecular hydrogen bonding
Chem. Commun., 1997
2247

View Article Online
Footnotes and References
* E-mail: tgtojv@chem.tue.nl
† Correspondence address for crystallographic data.
‡ Crystal structure data for 1: C24H18N6O3, Mr = 438.45, colourless,
¯
block-shaped crystal (0.3 3 0.5 3 0.5 mm), trigonal, space group P3 (no.
147) with a = 13.8762(10), c = 8.4005(5) Å, V = 1400.80(17) Å3, Z = 2,
Dc
reflections measured, 2135 independent, Rint = 0.0288, 1.7° < q < 27.5°,
scan, 150 K, Mo-Ka radiation, graphite monochromator,
= = 456, m(Mo-Ka) =
1.039 g cm23, F(000) 0.7 cm21, 4819
w
T =
l = 0.71073 Å on an Enraf-Nonius CAD4 Turbo diffractometer on rotating
mode. Data were corrected for Lp effects and for a linear instability of 1%
of the reference reflections, but not for absorption. The structure was solved
by automated direct methods (SHELXS96). Refinement on F2 was carried
out by full-matrix least-squares techniques (SHELXL96); no observance
criterion was applied during refinement. Electron density in a disordered
solvent area (the unit cell contains a channel parallel to the c-axis, through
the origin, with a volume of 450 Å3 and containing 111 electrons per
c-translation period, suggesting the presence of approximately six mole-
cules of methanol) was taken into account in the refinement via PLATON/
SQUEEZE. Where relevant, data cited above are given without disordered
solvent contribution. Positional parameters for hydrogen atoms were
included in the refinement; initial values were obtained from a difference
Fourier map. Refinement converged at a final wR2 value of 0.0973
R1 = 0.0376 [for 1727 reflections with Fo > 4 s(Fo)], S = 1.071, for 118
parameters. A final difference Fourier showed no residual density outside
20.20 and 0.24 e Å23. CCDC 182/632.
§ Synthesis of 1: Standard reaction of trimesic chloride (0.90 g, 3.39 mmol)
with 3-pyridylamine (1.00 g, 10.6 mmol) in THF (20 ml) in the presence of
triethylamine (1.6 ml, 1.13 g, 11.2 mmol) afforded a precipitate which after
washing with water and diethyl ether and drying in vacuo gave 1 (1.18 g,
79%) as a white solid. Recrystallization from methanol (200 ml) afforded
large, transparent hexagonal crystals, mp 287–289 °C; dH([2H6]DMSO)
10.87 (s, NH), 9.01 (d, H-2A), 8.82 (s, H-2, 4, 6), 8.39 (dd, H-6A), 8.26 (ddd,
H-4A), 7.47 (dd, H-5A), 4.15 (s, OH), 3.18 (s, CH3); m/z (ES) (MeOH +
HCO2H) Calc. for C24H18N6O3 438.142. Found: 439.1 (M + H)+ and 219.9
(M + 2 H)2+. Analysis (after exhaustive removal of methanol at 150 °C)
Calc. C, 65.75; H, 4.14; N, 19.17. Found: C, 64.80; H, 4.17; N, 18.78%.
¶ Crystals of 1·(MeOH)x were unloaded from exterior MeOH by repetitive
immersion in pentane. Crystals were kept in CD3OD for four days. The
crystals remained intact and were then filtered and washed with pentane.
The 1H NMR spectrum in [2H6]DMSO indicated the complete replacement
of MeOH by CD3OD.
Fig. 3 Superimposed bilayer structure of 1 creating channels
nanometer scale diameter and millimeter scale length. The
formation of this 3D structure may rest simply on optimal
packing. Alternatively it is rationalized by cooperative C–H···O
interactions7 (total length 3.39 Å) between each amide oxygen
and a pyridyl C–H belonging to an adjacent bilayer.
Methanol is essential to guarantee the stability of the crystals,
undoubtedly due to its role as a template and guest filling some
of the void space in the interior of the channels, more
specifically in the cavity surrounded by the six pyridyl units.
The X-ray determination does not allow accurate localization of
methanol in 1 but a molar ratio of 3:1 is estimated. According
1
to the H NMR spectrum in [2H6]DMSO the molar content of
methanol ranges from 1.5 to 3.0, depending on sample
preparation. Elemental analysis of the crystals is irreproducible
due to partial loss of methanol during analysis while analysis
after removal of methanol at high temperature shows a
deviation, presumably due to uptake of atmospheric (water)
vapours. Upon heating between glass the crystals undergo, far
below the melting point, a phase transition at 190 °C, suggesting
loss of methanol. In air or in solvents like toluene the crystals
become opaque and disintegrate. In pentane, by contrast, the
crystals are stable.
To provide evidence for the accessibility of the channels for
external molecules, a methanol–CD3OD exchange experiment
1
was conducted¶ and the H NMR spectrum in [2H6]DMSO
1 E. Weber, R. Pollex and M. Czugler, J. Org. Chem., 1992, 57, 4068;
D. Venkataraman, S. Lee, J. Zhang and J. S. Moore, Nature, 1994, 371,
591; M. R. Ghadiri, Adv. Mater., 1995, 7, 675.
2 G. B. Gardner, D. Venkataraman, J. S. Moore and S. Lee, Nature, 1995,
374, 792; P. Brunet, M. Simard and J. D. Wuest, J. Am. Chem. Soc.,
1997, 119, 2737.
3 V. A. Russell and M. D. Ward, Chem. Mater., 1996, 8, 1654; E. Fan,
C. Vicent, S. J. Geib and A. D. Hamilton, Chem. Mater., 1994, 6,
1113.
4 N. Khazanovich, J. R. Granja, D. E. McCree, R. E. Milligan and
M. R. Ghadiri, J. Am. Chem. Soc., 1994, 116, 6011; M. D. Ward, Nature,
1995, 374, 764; R. E. Melendez, C. V. Krishnamohan Sharma,
M. J. Zarawotko, C. Bauer and R. D. Rogers, Angew. Chem., Int. Ed.
Engl., 1996, 35, 2213; M. Mascal, N. M. Hext, R. Warmuth,
M. H. Moore and J. P. Turkenburg, Angew. Chem., Int. Ed. Engl., 1996,
35, 2204; R. Bishop, Chem. Soc. Rev., 1996, 311.
5 A. R. A. Palmans, J. A. J. M. Vekemans, H. Fischer, R. A. Hikmet and
E. W. Meijer, Chem. Eur. J., 1997, 3, 300.
6 M. C. Etter, Acc. Chem. Res., 1990, 23, 120.
7 Z. Berkovich-Yellin and L. Leiserowitz, Acta Crystallogr., Sect. B,
1984, 40, 1596; G. R. Desiraju, Acc. Chem. Res., 1996, 29, 441.
8 (a) A. Mahdyarfar and K. D. M. Harris, J. Chem. Soc., Chem. Commun.,
1993, 51; (b) X. Wang, M. Simard and J. D. Wuest, J. Am. Chem. Soc.,
1994, 116, 12119; (c) O. M. Yaghi, G. Li and H. Li, Nature, 1995, 378,
704.
unambiguously demonstrates the complete disappearance of
non-deuteriated methanol from the crystals. Analogous experi-
ments have been conducted in other trimesic acid derivatives
and in other tectonic molecules.8 The calculated density of 1
without guests amounts to 1.0395 g cm23 and of 1·3 MeOH to
1.267 g cm23. This relatively low density contrasts with the
higher density of many trimesic derivatives including the parent
acid (1.449 g cm23).9
The presence of C3-symmetry tends to induce void space in
crystals, which Nature may compensate for by producing
concatenated or interpenetrated structures or by incorporation
of appropriate guest molecules. To our surprise, up to now no
X-ray data are available on symmetrical secondary trimesic
amides. In trimesic acid three-fold interpenetration of two-
dimensional layers composed of three parallel molecules is
observed,9 unless guests like pyrene and ethanol are built in.10
A pattern such as the one found in compound 1 is, to the best of
our knowledge, unprecedented. It seems that in this particular
molecule an acceptable compromise is found between void
space, concatenation of molecules and inclusion of guests. The
formation of a bilayer structure in compound 1 is reminiscent of
the Piedfort units observed in other C3-symmetric systems like
2,4,6-tris[4-(2-phenylpropan-2-yl)phenoxy]-1,3,5-triazine,11 in
which two p-stacked molecules are mutually rotating by 60° to
resemble a spatially filled hexagonal system.
9 D. J. Duchamp and R. E. Marsh, Acta Crystallogr., Sect. B, 1969, 25,
5.
10 S. V. Kolotuchin, E. E. Fenlon, S. R. Wilson, C. J. Loweth and
S. C. Zimmerman, Angew. Chem., Int. Ed. Engl., 1995, 34, 2654.
11 A. S. Jessiman, D. D. MacNicol, P. R. Mallinson and I. Vallance,
J. Chem. Soc., Chem. Commun., 1990, 1619.
This work was supported in part by the Netherlands
Foundation of Chemical Research (SON) with financial aid
from the Netherlands Organization for Scientific Research
(NWO). DSM Research is gratefully acknowledged for an
unrestricted grant.
Received in Bath, UK, 23rd July 1997; 7/05339H
2248
Chem. Commun., 1997