Hydrogen and halogen bonding drive the orthogonal self-assembly of an organic framework possessing 2D channels

Article abstract of DOI:10.1039/c2cc33682k

Orthogonal self-assembly of an open organic framework showing 2D channels has been obtained by combining hydrogen and halogen bonding. The framework is able to host various guest molecules with a diverse set of steric demands and substitution patterns, and survives single-crystal-to-single-crystal guest exchanges from liquid and gas phases.

Full text of DOI:10.1039/c2cc33682k

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COMMUNICATION
Hydrogen and halogen bonding drive the orthogonal self-assembly of an
organic framework possessing 2D channelsw
Javier Martı
´ ¨
-Rujas,a Luca Colombo,a Jian Lu,b Archan Dey,b Giancarlo Terraneo,ab
Pierangelo Metrangolo,*ab Tullio Pilatib and Giuseppe Resnati*ab
Received 22nd May 2012, Accepted 25th June 2012
DOI: 10.1039/c2cc33682k
Orthogonal self-assembly of an open organic framework showing
2D channels has been obtained by combining hydrogen and halogen
bonding. The framework is able to host various guest molecules
with a diverse set of steric demands and substitution patterns, and
survives single-crystal-to-single-crystal guest exchanges from liquid
and gas phases.
Orthogonal self-assembly relying on different, noninterfering
intermolecular interactions is attracting considerable interest
as a strategy to obtain ‘‘smarter’’ stimuli-responsive materials.1
The combination of two or more orthogonal supramolecular
synthons resulted, in fact, in a range of novel materials like
switchable supramolecular copolymers,2 chiral bimetallic self-
supported hydrogenation catalysts,3 voltage-responsive vesicles,4
and self-assembled fibrillar networks.5 Orthogonal self-assembly
has also yielded functional monolayer architectures,6 as well as
the improvement of bulk material properties.7 Ionic interactions,
metal–ligand complexation, and hydrogen bonds are most
frequently combined in driving orthogonal self-assembly
processes. Different complementary hydrogen bonding motifs
have also been explored for this purpose.8
Fig. 1 Top: synthesis of ligand 3. Bottom: cartoon showing the self-
assembly of 3 (linker) with Iꢀ and H+ ions (nodes) through XB and
HB, respectively, and the formation of the supramolecular open
framework 4x(G1) (G1 = dioxane; x = 2.5).
The ligand 4,40-[1,2-bis(2,3,5,6-tetrafluoro-4-iodophenoxy)-
ethane-1,2-diyl]dipyridine (3) (Fig. 1, top) has two pairs of
sites for potentially orthogonal binding processes and is thus a
potential candidate to be engaged in simultaneous HB and
XB, in a chemically and geometrically orthogonal manner. In
fact, iodotetrafluorophenyl moieties are prototypical XB-donor
groups, while pyridyl residues can behave as both HB- and XB-
acceptor sites. Indeed, pure ligand 3 in the crystal self-assembles
by pairing the two couples of complementary binding sites,
which are saturated via multiple XBs.13
In this communication, we demonstrate that hydrogen
bonding (HB) and halogen bonding (XB),9 which most often
are seen in competition, can cooperate orthogonally in building
up open organic frameworks, provided that self-assembling
units with optimized geometries are chosen. Organic open
frameworks have found applications in, e.g., gas adsorption,10
conductivity,11 and molecular transport.12 Here, we report that
the obtained open framework is able to host various guest
molecules with a diverse set of steric demands and substitution
patterns, and survives single-crystal-to-single-crystal (SCSC)
guest exchanges from liquid and gas phases.
In order to disrupt the tendency of ligand 3 to self-assemble
via XB and to elicit its orthogonal HB/XB potential, a suitable
partner has to be identified, which is able to involve the two
pairs of complementary binding sites in two noninterfering
interactions. To this purpose we selected hydrogen iodide
(HI), as a source of both a strong HB-donor (H+), for the
binding of pyridine, and a strong XB-acceptor (Iꢀ), for
the binding of the iodotetrafluorophenyl ring, no more bound
to the pyridine (Fig. 1).14 An iodide anion was preferred over
other halide anions due to the particular reliability of the C–IꢁꢁꢁIꢀ
supramolecular synthon.15 A straightforward formation of the
hydroiodide salt of 3 from pure starting compounds was expected
a Center for Nano Science and Technology@Polimi, Istituto Italiano
di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy.
E-mail: pierangelo.metrangolo@polimi.it, giuseppe.resnati@polimi.it
b NFMLab, Department of Chemistry, Materials, and Chemical
Engineering, Politecnico di Milano, via Mancinelli 7, 20131 Milan,
Italy
w Electronic supplementary information (ESI) available: Experimental
details, crystal structure description, additional figures. CCDC 866 321
(3), 866 318 (4 ꢂ 2.5(G1)), 866 320 (4 ꢂ 2(G2)), 866 319 (4 ꢂ 2(G3)). For
ESI and crystallographic data in CIF or other electronic format see
DOI: 10.1039/c2cc33682k
c
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Chem. Commun., 2012, 48, 8207–8209 8207

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and it was anticipated that the organization of the formed salt
in the crystal was driven by the pairing of the two Lewis base
sites (pyridine nitrogen and iodide anion) with the two Lewis
acid sites (iodine of the iodotetrafluorophenyl ring and the
proton) after the hard and soft acid–base theory (HSAB).16
A poorly crystalline yellow precipitate was obtained by rapid
mixing of a methanol/toluene solution of 3 and excess HI dissolved
in methanol. Recrystallization from methanol with slow diffusion
of dioxane (G1) gave large pristine pale yellow crystals.13 Single
crystal X-ray diffraction analysis showed that the open organic
framework 4x(G1) (G1 = dioxane; x = 2.5) was obtained.z The
crystal packing of 4x(G1) is governed mainly by HB, XB, and p–p
stacking. As expected, the ion pair in HI is fully dissociated
(the shortest H+/Iꢀ distance is 7.10 A). The H+ ion functions
as a linear bidentate HB-donor (Nꢁ ꢁ ꢁH+ꢁ ꢁ ꢁN distances and
angles are 2.657(8) A and 172(7)1) and bridges two pyridines
of two distinct and adjacent ligand 3 molecules. Analogously,
the Iꢀ ion behaves as a quasi linear bidentate XB-acceptor
(Iꢁ ꢁ ꢁIꢀꢁ ꢁ ꢁI angle is 146.07(1)1) and bridges the iodine atoms of
other two distinct and following ligands. The Iꢁ ꢁ ꢁIꢀ XB shows
the standard geometric features.17 In the network, ligand 3
adopts a cruciform shape with the four arms fully extended
two-by-two to opposite sides. The above discussed HB and XB
linearity translates this molecular geometry into the topology
of the network which comprises a quasi-rectangular 2D grid
(sides B22 A and 11 A, Fig. 2a).
Fig. 3 Voids in 4x(G1) observed after in silico removal of guest
molecules. Contact surface (yellow) and solvent accessible surface
(blue) calculated using a 1.2 A probe radius. (a) View along the
a-axis showing channels A and B. (b) The different arrangement of
dioxane molecules in channels A and B denotes the biporous nature of
the network. (c) View along the c-axis of channel C which intersects
A and B channels to yield an overall 2D open framework. (d) View of
the network along the b-axis showing the intersection of the channels.
The 2D grid networks described above stack through p–p
interactions between antiparallel tetrafluorophenyl rings [distance
between centroids (C19–C24)ꢁꢁꢁ(C19–C24)1ꢀx,1ꢀy,1ꢀz = 3.725 A]
and residual crystal packing interactions. However, between two
adjacent layers there is an offset of ca. 11 A (Fig. 2b), which, upon
superimposition of n layers, gives rise to a biporous18 network
consisting of two channels (A and B) running along the crystallo-
graphic a-axis and having similar dimensions (ca. 7 ꢂ 4 A2) but
different shape and chemical environment (Fig. 3a). The channels
are filled with dioxane molecules, which adopt a different
arrangement in the channels as a likely consequence of their
different shape and chemical environment (Fig. 3b).13
Fig. 4 Guest exchange in 4x(G1) (x = 2.5) for G2 to yield 4x(G2)
(x = 2). The new G2 guest molecules are considerably well localized.
Only one of the two crystallographically independent G2 molecules is
disordered. For clarity purposes the disordered G2 is not shown.
The robustness of 4x(G1) is demonstrated by its ability to
survive the introduction of halogenated guests which can give
rise to polar host–guest interactions between the halogen atoms
and the ionic 2D sheets. Immersion of a single crystal of 4x(G1)
in 0.5 mL of 1,3-dibromobenzene (G2) at 300 K for ca. 2 h
yielded a good quality crystal, which, upon single crystal X-ray
diffraction analysis, revealed to be the open framework 4x(G2)
(G2 = 1,3-dibromobenzene; x = 2) (Fig. 4). Thus, G1 (dioxane)
was neatly exchanged by G2 (1,3-dibromobenzene) without
disrupting the framework topology.
Interestingly, the packing of ligand 3 in 4x(G1) also originates
channels (C) extending along the c-axis (Fig. 3c) having similar
size but different shape from channels A and B. The two sets of
channels intersect each other resulting in a 2D channel network
structure (Fig. 3d), with a total solvent accessible volume of ca.
376 A3 per unit cell volume (1977 A3), which represents ca. 19%
of the overall crystal lattice upon guest removal.19
The two crystallographically independent 1,3-dibromobenzene
molecules present in 4x(G2) are involved in several contacts with
the framework walls and between them.13 Nevertheless, the
framework 4x(G2) is isoreticular with 4x(G1) and shows similar
geometric features for HB and XB (Fig. 4).20 The total solvent
accessible volume is ca. 17.1% of the unit cell volume.
Finally, we tested the ability of 4x(G1) to guest exchange in
a gas/solid reaction by exposing a single crystal of 4x(G1) to
vapours of G2. After exposure for ca. 20 h at room temperature
in a closed jar, the crystal was still suitable for X-ray diffraction
analysis, revealing new unit cell parameters matching those of
4x(G2), indicating that guest exchange took place.
Fig. 2 Single crystal X-ray structure of 4x(G1) (G1 = dioxane; x = 2.5).
(a) The self-assembly of ligand 3 and HI via orthogonal HB and XB
yields a 2D grid with dimensions ca. 22 ꢂ 11 A2. The Iꢀ and H+ ions are
shown as spheres. (b) Two adjacent layers (red and green) stack along the
a-axis resulting in the partitioning of the void in the rectangular grids.
Dioxane molecules have been omitted for clarity.
In conclusion, XB, due to its strength and directionality, is
revealing to be a promising new tool for the design of open
framework materials.21 In this communication we demonstrated
c
8208 Chem. Commun., 2012, 48, 8207–8209
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that HB and XB can successfully be combined in an orthogonal
manner to drive the self-assembly of a complex and functional
supramolecular network. The reported results pave the way for a
new design concept in orthogonal self-assembly and may also
have implications for, e.g., drug design.22 The combination of
pyridines and iodotetrafluorophenyl rings in the same scaffold,
along with the coordination of HI may develop as a general
strategy for the orthogonal self-assembly of new supramolecular
co-polymers that can be tuned by various external stimuli
through addressing HB and XB separately (e.g. pH change, or
anion exchange, respectively). Current studies in our laboratory
are addressing this issue as well as the synthesis of a permanently
porous framework.
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This research was supported by Fondazione Cariplo under
projects 2009-2550 and 2010-1351.
´
Notes and references
´
´
-
z Single crystal X-ray diffraction data for (3), (4 ꢂ 2.5(G1)), (4 ꢂ
2(G2)), (4 ꢂ 2(G3)) were recorded using Mo-Ka radiation in Bruker
KAPPA APEX II diffractometer. Data were collected with o and j
scan with the scan width 0.5. The data were reduced with empirical
absorption correction. Structures were solved by a direct method using
SHELXL9723 present in the program suite WinGX (version 1.80.04).24
The molecular diagrams were generated using Mercury.25 The non-
hydrogen atoms are refined anisotropically and hydrogen atoms were
positioned geometrically. All crystallographic details are listed in
Table S1 and intermolecular interactions are listed in Tables S1.1
and S1.2 in the ESI.w Single crystal X-ray diffraction data for 4 ꢂ
2.5(G1): C24H11N2O2F8I2+, 2.5(C4H8O2), Iꢀ, Mr = 1112.31, triclinic,
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13 See the ESIw for further details.
14 A survey of the Cambridge Structure Database (CSD version 5.33,
November 2011) shows that the Nꢁ ꢁ ꢁH supramolecular synthon
(HB) occurs when a hydrogen halide is in the presence of a pyridine
ring. The simultaneous presence of a halocarbon moiety further
favours the ion pair separation in thus formed pyridineꢁ ꢁ ꢁHX
adduct via formation of the C–Xꢁ ꢁ ꢁXꢀ supramolecular synthon
(XB): G. M. Espallargas, L. Brammer and P. Sherwood, Angew.
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%
space group P1, a = 9.3334(16) A, b = 11.853(2) A, c = 18.412(3) A,
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a = 96.076(12)1, b = 96.664(12)1, g = 99.784(13)1, V = 1977.2(6) A3,
T = 173 K, Z = 2, rcalcd = 1.868 g cmꢀ3, 5278 unique reflections out
of 7669 with I > 2s(I), 490 parameters, 2.25 o y o 26.0, final R
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16 We note that H+ is the hardest acid and an iodocarbon is a soft
acid; pyridine is a borderline base and Iꢀ a quite soft base:
Tse-Lok, Hard and Soft Acids and Bases Principle in Organic
Chemistry, Academic Press, New York, 1977.
%
1363.87, triclinic, space group P1, a = 9.2497(4) A, b = 11.8502(6) A,
17 The C3–I1ꢁ ꢁ ꢁI3ꢀ distance is 3.3601(8) A and C22–I2ꢁ ꢁ ꢁI3ꢀ distance
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sum of vdW and Pauling ionic radii for I and Iꢀ, respectively. The
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c = 19.1570(10) A, a = 92.354(3)1, b = 94.750(3)1, g = 98.469(3)1,
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y o 32.65, final R factors R1 = 0.0561 and wR2 = 0.1559.
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