Assembly of a Porous Supramolecular Polyknot from Rigid Trigonal Prismatic Building Blocks

Article abstract of DOI:10.1021/jacs.9b06445

Herein we report a hydrogen-bonded three-dimensional porous supramolecular polyknot assembled from a rigid trigonal prismatic triptycene building block with six extended peripheral aryl-carboxyl groups. Within this superstructure, three arrays of undulate

Full text of DOI:10.1021/jacs.9b06445

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Communication
Assembly of a Porous Supramolecular Polyknot
from Rigid Trigonal Prismatic Building Blocks
Penghao Li, Zhijie Chen, Matthew R. Ryder, Charlotte L. Stern, Qing-
Hui Guo, Xingjie Wang, Omar K. Farha, and J. Fraser Stoddart
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.9b06445 • Publication Date (Web): 21 Jul 2019
Downloaded from pubs.acs.org on July 21, 2019
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Assembly of a Porous Supramolecular Polyknot from Rigid
Trigonal Prismatic Building Blocks
Penghao Li,† Zhijie Chen,† Matthew R. Ryder,‡ Charlotte L. Stern,† Qing-Hui Guo,† Xingjie
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Wang,† Omar K. Farha† and J. Fraser Stoddart*†║#
†Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
‡Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
║Institute for Molecular Design and Synthesis, Tianjin University, 92 Weijin Road, Tianjin 300072, China
#School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
Supporting Information Placeholder
Self-assembly of discrete organic molecules relying upon
noncovalent bonding interactions (hydrogen, halogen, etc.)
has led to the construction of supramolecular architectures
with, not only exotic topologies, but also exceptional
material properties.7 Nevertheless, pure organic 2D and 3D
supramolecular frameworks,8 compared to MOFs, still lack
the diversity and complexity in terms of network topology,9 a
deficiency which hinders the understanding of the
underlying assembly principles. Thus, uncovering new
network topologies, which can be accessed using simple
supramolecular synthons, is of great importance since they
broaden the scope of supramolecular chemistry and
stimulate the rational design of functional supramolecular
materials. Herein, we report the assembly of a hydrogen-
ABSTRACT: Herein we report a hydrogen-bonded three-
dimensional porous supramolecular polyknot assembled
from a rigid trigonal prismatic triptycene building block with
six extended peripheral aryl-carboxyl groups. Within this
superstructure, three arrays of undulated 2D rhombic
subnets, which display an inclined polycatenation, are
interconnected to give an unprecedented uninodal six-
connected net with a point symbol of (3.44.610). Such an
entanglement results in a trefoil knot motif, which, as the
basic repeating unit, is fused and interlocked with itself
three-dimensionally to afford a supramolecular polyknot.
This example highlights the ability of supramolecular
systems to form topologically complex architectures using
geometrically simple building blocks.
bonded supramolecular polyknot (PETHOF-3) using
a
simple trigonal prismatic building block H6PET-1. This
polyknot10 displays a complicated 3D architecture with
periodically fused and interlocked knot moieties, as well as
an unprecedented uninodal self-entangled six-connected
topology with a point symbol of (3.44.610).
Mechanically interlocked emblems, such as Borromean
Rings and Solomon Knots, have captivated humankind for
millennia, showing their presence as symbols of art, culture
and spiritual life.1 Catenanes,2 rotaxanes3 and molecular
knots4 represent interlocked and entangled species at the
molecular level. Research1 on these mechanically interlocked
molecules (MIMs) has been gaining momentum in recent
decades because of their aesthetic beauty1a and practical
applications1b,c,d in nanotechnology. Mechanical interlocking
also exists in extended two-dimensional (2D) and three-
dimensional (3D) networks in the form5 of interpenetration,
polycatenation, polythreading, and self-entanglement. These
topologically complex networks, which can be considered as
the polymeric equivalent of MIMs, are well represented5b in
metal-organic frameworks (MOFs) and coordination
polymers (CPs), which are composed of metal cations and
organic linkers. Such structural diversity of MOFs, enabled
by versatile modularity of the building components, makes
them attractive candidates6 for applications in catalysis,
electronics, and gas storage and separation.
Installation of six 4-(4-phenylethynyl)phenylene carboxyl
groups on the periphery of the triptycene backbone creates
(Figure 1a and Scheme S2) a rigid trigonal prismatic building
block H6PET-1 for the assembly of 3D networks. Slow
evaporation of a THF and PhMe solution of H6PET-1
afforded faint yellow crystalline blocks (PETHOF-3) suitable
for single-crystal X-ray crystallographic investigation, which
revealed
a hexagonal lattice with space group P-62c.
PETHOF-3 exhibits a complex entangled network topology,
which, according to ToposPro,11 is identified with an
unprecedented uninodal six-connected net with a point
symbol of (3.44.610). In the crystal superstructure, each
molecule engages four of its six aryl-carboxyl arms in
building (Figure 1b,e) a 44-net which shows12 a puckered 2D
geometry with large distorted rhombic windows (dimensions
×
of 33
39 Å). The remaining two aryl-carboxyl arms, which
participate in a hydrogen-bonded triangle motif (Figure 1c),
are oriented perpendicular to the 2D layers (Figure 1f).
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Overall, there are three independent arrays of the 2D layers
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stacked in an alternating AB manner along the [210], [120]
and [110] directions, leading (Figure 1g) to a 2D → 3D
inclined polycatenation in which the 2D sheets are
interlocked (Figure S9) through the Hopf-links of the
rhombic circuits. The polycatenated 2D layers are further
interconnected (Figure 1d and Figure S10) into a singular
network through the hydrogen bonding of the appended
aryl-carboxyl arms. Therefore, PETHOF-3, which is
topologically categorized as
a self-entangled network,
9
represents a rare example of a supramolecular assembly held
together solely by hydrogen bonding. It is noteworthy to
point out that PETHOF-3 is constructed from a single
molecular component that is rigid and highly symmetrical,
properties
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Figure 1. (a) The trigonal prismatic building block H6PET-1. (b) The hydrogen-bonded rhombic circuit motif (depicted in blue).
(c) The hydrogen-bonded triangle motif (depicted in red). (d) The extended superstructure of PETHOF-3 viewed along the c
axis. (e-f) Views of the rhombic 2D subnet (depicted in blue) with appended carboxyl groups (depicted in red) in different
directions. (g) The 2D → 3D inclined polycatenation of three independent arrays of the 2D subnets (depicted in green, magenta
and cyan). The appended carboxyl groups are omitted for the sake of clarity.
which distinguish it from self-entangled MOFs that are
built13 of either asymmetric metal nodes or flexible organic
bridges. Moreover, it is well documented14 that trigonal
prismatic building blocks tend to form extended structures
based on the edge-transitive six-connected acs net. We
reported15 previously that an analogous triptycene building
block, with peripheral p-phenylene carboxyl groups,
assembles into PETHOF-1 and PETHOF-2 with, respectively,
acs-2c and acs-5c topologies. Here, PETHOF-3, a rare
exception, broadens the scope of the complex
supramolecular architectures that can be accessed using
simple molecular building blocks.
Figure 2. The supramolecular knot (a) in PETHOF-3 is
composed of two enantiomeric trefoil knots with positive (+)
(b) and negative () (c) crossings. The three rhombic circuits
in the supramolecular knot are colored blue, green and
magenta. Irrelevant molecular components are omitted for
the sake of clarity.
Upon close examination, we identify (Figure 2a)
a
supramolecular knot, which, as the basic repeating unit, is
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fused and interlocked periodically with one another three-
푑H···O =
2.50 Å. If we
CH•••O hydrogen bonds with mean
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dimensionally to form the whole network. In this regard,
PETHOF-3 can best be described as a supramolecular
polyknot. The knot moiety consists of three rhombic circuits
that are connected cyclically at the opposing vertices with
the linking bridges threading through each rhombic cavity,
creating (Figure 2b,c) a pair of fused trefoil knots with
opposite chirality. In this supramolecular knot, 12 molecules
of H6PET-1 participate as the corners, along with 15 of their
hydrogen-bonded carboxyl dimers as the edges. Each
H6PET-1 molecule is involved in the formation of four
supramolecular knots. Along the c axis, the supramolecular
knots are aligned linearly by sharing three vertices with each
neighbor to form (Figure 3a) a 1D columnar superstructure.
Two of these 1D columns are entangled in such a way that
each supramolecular knot is triply interlocked through the
rhombic windows (Figure 3b) with two knots in a different
column, which gives (Figure 3d) rise to a 1D channel with a
diameter of about 10 Å running parallel to the c axis. In the
ab plane, the supramolecular knots are arranged (Figure 3c)
consider this supramolecular cluster as a 12-connected node,
the superstructure (Figure 4c) of the polyknot can be
simplified14a to a 12-connected hcp (hexagonal close packing)
net with the transitivity of [1232]. This hcp net contains two
types of tiles, which correlate with the disordered tetrahedral
and octahedral cages (Figure 4d,e) of this superstructure,
with effectively accessible diameters of 1.6 and 3.0 nm,
respectively, taking into account vdW radii. In this sense, the
tris-molecular cluster is reminiscent16 of the multinuclear
metal clusters in MOFs, diversifying the network topologies
that can be accessed by trigonal prismatic building blocks.
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into
a 2D triangular tessellation where each knot is
interlocked with six neighboring knots with which it shares
vertices.
Figure 4. (a-b) The tris-molecular cluster viewed as a 12-
connected node in a cuboctahedral geometry. The triptycene
cores are shown in red. The connecting bridges composed of
a single and two paralleled carboxyl dimers are shown in
green and blue, respectively. Irrelevant molecular
components are omitted for the sake of clarity. (c) The hcp
topology (the red spheres, as the vertices, correspond to the
tris-triptycene cores; the green and blue sticks, as the edges,
correspond to the single and two paralleled carboxyl dimer
linkages, respectively). (d-e) Depictions of the tetrahedral
(with magenta faces) and the octahedral (with yellow faces)
cages with the tris-molecular clusters as the vertices.
Figure 3. The representations of (a) the 1D supramolecular
column (depicted in green) showing two knots with shared
vertices, (b) the entangled superstructure containing two 1D
columns (depicted in green and blue), (c) the 2D triangular
tessellation pattern showing the entanglement of one knot
with two of its six neighbors in the ab plane (three knots are
colored green, red and blue), and (d) the 1D channel viewed
along the c axis. Irrelevant molecular components are
omitted for the sake of clarity.
PETHOF-3 possesses an extraordinarily large gust-
accessible volume17 of about 85%, which, to the best of our
knowledge, is
a record for hydrogen-bonded organic
The supramolecular polyknot is sustained by
a
frameworks (HOFs). It showcases the ability of the
peripherally functionalized triptycenes to assemble into
frameworks with large cavities, which are useful for guest
encapsulation and low-κ dielectric response.8g In fact,
density functional theory (DFT) calculations, performed on
the optimized single-crystal structure of PETHOF-3, predict
the static dielectric constant to be as low as 1.29 along the a
and b crystallographic axes. The averaged values are also
consistent with the reported18 trend in the low-κ dielectric
response and framework porosity. Thus, PETHOF-3
represents the lowest predicted value (Table 1) of the static
dielectric constant so far reported15 for framework materials,
a status, until now, held by PETHOF-1. The voids, however,
are filled with highly disordered solvent molecules, which
could not be refined by crystallography and hence were
omitted from the computational optimization. The
combination of intermolecular CH•••π and CH•••O
interactions, in addition to the hydrogen bonding of the
푑O···O
=
carboxyl dimers (mean
2.63 Å). These cooperative
noncovalent intermolecular forces (vide infra), along with the
interactions between H6PET-1 and solvent molecules, might
well be responsible for dictating the formation of the
polyknot, instead of the acs net, during crystallization. The
푑
H···C
=
CH•••π interactions (mean
2.89 Å) occur exclusively
in a tris-molecular cluster that exhibits (Figure S11) C3
symmetry. Each cluster is connected (Figure 4a,b) with 12
neighboring clusters in a cuboctahedral geometry, where six
coplanar neighbors in the ab plane are linked with the center
cluster through
a single aryl-carboxyl dimer, and the
remaining six neighbors through two paralleled aryl-carboxyl
dimers which are also associated (Figure S12) by means of the
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experimental dielectric constants would, therefore, be
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expected to be higher than those predicted on account of the
presence of residual solvent molecules. Supercritical CO2
activation of PETHOF-3 gave a microporous material with a
type-I N2 isotherm at 77 K (Figure S14a) and an apparent
Brunauer-Emmett-Teller (BET) surface area of about 600
m2/g. The main pore width was estimated (Figure S14b) to be
about 1.3 nm, which is slightly smaller than the diameter of
the tetrahedral cavities in the crystalline superstructure. We
did not observe the mesopores that correspond to the
octahedral cavities in the calculated pore distribution,
indicating partial collapse of the pore system upon
activation. This superstructural change is also evidenced
(Figure S13) by the disappearance of the well-resolved peaks
in the powder X-ray diffraction patterns (PXRD) of
PETHOF-3 after activation. Overall, these observations
suggest that the disordered solvent guests also play a crucial
role in supporting the superstructural integrity of PETHOF-
3.
Notes
The authors declare no competing financial interests.
ACKNOWLEDGMENT
This research is part of the Joint Center of Excellence in
Integrated Nano-Systems (JCIN) at King Abdul-Aziz City for
Science and Technology (KACST) and Northwestern
University (NU). The authors thank both KACST and NU for
their continued support of this research. P.L. would like to
thank Dr. Peng Li and Dr. Minh T. Nguyen for helpful
discussions. M.R.R. acknowledges the U.S. Department of
Energy Office of Science (Basic Energy Sciences) for research
funding and the National Energy Research Scientific
Computing Center (NERSC), a U.S. Department of Energy
Office of Science User Facility operated under Contract No.
DE-AC02-05CH11231 for access to supercomputing resources.
O.K.F. gratefully acknowledges the support from the Defense
Threat Reduction Agency (HDTRA1-19-1-0010).
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Table 1. Comparison of the Crystallographic Averaged
Electronic and Dielectric Properties of PETHOF-3 with
PETHOF-1
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Polarizability /  (Å3)
Dielectric Tensor / κ
Refractive Index / n
7,334
1.33
1.15
1.14
Electric Susceptibility /

0.329
80%
0.304
85%
Guest-Accessible
Volume
In summary, PETHOF-3, assembled from a rigid trigonal
prismatic building block, constitutes ubiquitous
a
supramolecular polyknot with a complex 3D architecture
composed of periodically fused and interlocked
supramolecular knots. This polyknot, which also possesses a
uninodal self-entangled six-connected framework with a
point symbol of (3.44.610), represents
a new topology,
accessible by trigonal prismatic building blocks other than
the acs net. Most noteworthy of all is that such
superstructural complexity is realized using geometrically
simple molecular building blocks. We anticipate that this
communication will inspire new design strategies for
supramolecular materials with tailored architectures for
customized applications.
ASSOCIATED CONTENT
Supporting Information
The Supporting Information is available free of charge on
ACS Publication website.
Experimental and computational details, including synthesis,
NMR, PXRD, gas-sorption studies and density functional
theory (DFT) calculations (PDF).
X-ray crystallographic data for PETHOF-3 (CIF)
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Corresponding Author
*stoddart@northwestern.edu.
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Tohnai, N.; Sakurai, H. A Hydrogen-Bonded Hexagonal Buckybowl
Framework. Angew. Chem. Int. Ed. 2017, 56, 15294; (f) Lewandowska,
U.; Zajaczkowski, W.; Corra, S.; Tanabe, J.; Borrmann, R.; Benetti, E.
M.; Stappert, S.; Watanabe, K.; Ochs, N. A. K.; Schaeublin, R.; Li, C.;
Yashima, E.; Pisula, W.; Müllen, K.; Wennemers, H., A Triaxial
Supramolecular Weave. Nat. Chem. 2017, 9, 1068; (g) Yamagishi, H.;
Sato, H.; Hori, A.; Sato, Y.; Matsuda, R.; Kato, K.; Aida, T. Self-
Assembly of Lattices with High Structural Complexity from a
Geometrically Simple Molecule. Science 2018, 361, 1242.
(10) In network topology, “polyknotting” is equivalent to “self-
entangled” (“self-penetrating” and “self-catenating”), which is used
to describe single nets with “the peculiar feature of containing rings
through which pass other components of the same network”. See
Ref.5. In this report, “polyknot” refers specifically to the self-
entangled networks (PETHOF-3) that possess prime knot subunit
with a circuit smaller than a 10-membered ring. (The trefoil knot in
PETHOF-3 is a nine-membered ring. See Figure 2).
(11) (a) Blatov, V. A.; Shevchenko, A. P.; Proserpio, D. M. Applied
Topological Analysis of Crystal Structures with the Program Package
ToposPro. Cryst. Growth & Des. 2014, 14, 3576; (b) Bonneau, C.;
O’Keeffe, M.; Proserpio, D. M.; Blatov, V. A.; Batten, S. R.; Bourne, S.
A.; Lah, M. S.; Eon, J.-G.; Hyde, S. T.; Wiggin, S. B.; Öhrström, L.
Deconstruction of Crystalline Networks into Underlying Nets:
Relevance for Terminology Guidelines and Crystallographic
Databases. Cryst. Growth & Des. 2018, 18, 3411.
(12) The network topology of PETHOF-3 has been analyzed
following a subnet tecton approach reported in: Hill, R. J.; Long, D.-
L.; Champness, N. R.; Hubberstey, P.; Schröder, M. New Approaches
to the Analysis of High Connectivity Materials: Design Frameworks
Based upon 44- and 63-Subnet Tectons. Acc. Chem. Res. 2005, 38,
335.
(13) Ke, X.-J.; Li, D.-S.; Miao, D. Design and Construction of Self-
Penetrating Coordination Frameworks. Inorg. Chem. Commun. 2011,
14, 788.
(14) (a) Li, M.; Li, D.; O’Keeffe, M.; Yaghi, O. M. Topological
Analysis of Metal–Organic Frameworks with Polytopic Linkers
and/or Multiple Building Units and the Minimal Transitivity
Principle. Chem. Rev. 2014, 114, 1343; (b) Chen, Z.; Li, P.; Zhang, X.; Li,
P.; Wasson, M. C.; Islamoglu, T.; Stoddart, J. F.; Farha, O. K.
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Figure 1. (a) The trigonal prismatic building block H6PET-1. (b) The hydrogen-bonded rhombic circuit motif
(depicted in blue). (c) The hydrogen-bonded triangle motif (depicted in red). (d) The extended
superstructure of PETHOF-3 viewed along the c axis. (e-f) Views of the rhombic 2D subnet (depicted in blue)
with appended carboxyl groups (depicted in red) in different directions. (g) The 2D → 3D inclined
polycatenation of three independent arrays of the 2D subnets (depicted in green, magenta and cyan). The
appended carboxyl groups are omitted for the sake of clarity.
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Figure 2. The supramolecular knot (a) in PETHOF-3 is composed of two enantiomeric trefoil knots with
positive (+) (b) and negative (-) (c) crossings. The three rhombic circuits in the supramolecular knot are
colored blue, green and magenta. Irrelevant molecular components are omitted for the sake of clarity.
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Figure 3. The representations of (a) the 1D supramolecular column (depicted in green) showing two knots
with shared ver-tices, (b) the entangled superstructure containing two 1D columns (depicted in green and
blue), (c) the 2D triangular tessellation pattern showing the entanglement of one knot with two of its six
neighbors in the ab plane (three knots are colored green, red and blue), and (d) the 1D channel viewed
along the c axis. Irrelevant molecular components are omitted for the sake of clarity.
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Figure 4. (a-b) The tris-molecular cluster viewed as a 12-connected node in a cuboctahedral geometry. The
triptycene cores are shown in red. The connecting bridges composed of a single and two paralleled carboxyl
dimers are shown in green and blue, respectively. Irrelevant molecular components are omitted for the sake
of clarity. (c) The hcp topology (the red spheres, as the vertices, correspond to the tris-triptycene cores; the
green and blue sticks, as the edges, correspond to the single and two paralleled carboxyl dimer linkages,
respectively). (d-e) Depictions of the tetrahedral (with magenta faces) and the octahedral (with yellow
faces) cages with the tris-molecular clusters as the vertices.
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