An interdigitated functionally rigid [2]rotaxane

Article abstract of DOI:10.1039/b808005d

The synthesis of a functionally rigid [2]rotaxane incorporating π-electron rich 1,5-disubstituted naphthalene (NP) ring systems, encircled by the π-electron deficient tetracationic cyclophane, cyclobis(paraquat-p- phenylene), is described; in the solid state, the molecules of this donor-acceptor [2]rotaxane line themselves up in parallel π-π stacks of alternating NP ring systems and bipyridinium units, affording an interdigitated superstructure. The Royal Society of Chemistry.

Full text of DOI:10.1039/b808005d

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An interdigitated functionally rigid [2]rotaxanew
a
a
a
a
´
´
Il Yoon, Ognjen S. Miljanic, Diego Benıtez, Saeed I. Khan and
J. Fraser Stoddart*b
Received (in Austin, TX, USA) 12th May 2008, Accepted 11th August 2008
First published as an Advance Article on the web 13th August 2008
DOI: 10.1039/b808005d
The synthesis of a functionally rigid [2]rotaxane incorporating
p-electron rich 1,5-disubstituted naphthalene (NP) ring systems,
encircled by the p-electron deficient tetracationic cyclophane,
cyclobis(paraquat-p-phenylene), is described; in the solid state,
the molecules of this donor–acceptor [2]rotaxane line themselves
up in parallel p–p stacks of alternating NP ring systems and
bipyridinium units, affording an interdigitated superstructure.
Combining equimolar amounts of 23 and CBPQTꢀ4PF6 in
MeCN produced the red [2]pseudorotaxane [2 C CBPQT]ꢀ
4PF6. Treatment of this mixture with 6 equiv. of Cu(OAc)2ꢀ
H2O at 25 1C for 24 h, followed by column chromatography
(SiO2: 1% solution of NH4PF6 in Me2CO), afforded the
functionally rigid [2]rotaxane 1ꢀ4PF6 as a red solid in 18%
yield—a sizable improvement over the 8% yield previously3
reported. However, the free dumbbell 3 was isolated as the
major product (60%) of the coupling reaction.
7
The absence of covalent bonds between the components of
mechanically interlocked molecules known as rotaxanes makes
this class of compounds potentially applicable as switchable
components in functioning molecular devices.1 In order to
understand (and, in the future, predict) the related mechanical
motions of the components in rotaxanes in a device context, it
is advantageous to operate with rigid systems that have a
decreased number of degrees of freedom.2 With this notion in
mind, we have developed3 recently a functionally rigid and
degenerate molecular shuttle4 1ꢀ4PF6 (Scheme 1), in which the
tetracationic cyclophane, cyclobis(paraquat-p-phenylene)
(CBPQT4+), travels back and forth between two identical
naphthalene-based stations (NP) located on the dumbbell
component. The study of degenerate functionally rigid
dynamic [2]rotaxanes, such as 1ꢀ4PF6, may provide valuable
information in the design, synthesis, and characterization of
more complex molecular shuttles and switches. Specifically,
the dynamic properties that rigid linkers and recognition
stations exhibit may be studied with more detail in degenerate
model systems as the one described herein. Using dynamic
1H NMR spectroscopy, we calculated the barrier to be
9.6 kcal molꢁ1 for the movement of the CBPQT4+ ring along
the rigid butadiyne spacer between the two NP stations.3
Herein, we complement these initial studies with (a) a crystal-
lographic analysis of the solid-state structures of 1ꢀ4PF6 and
its dumbbell component 3, and (b) an improved template-
directed5 synthesis of 1ꢀ4PF6 using the threading approach and
Cu2+-mediated Eglinton6 coupling of two half dumbbells via
their terminal alkyne functions.
Scheme 1 Synthesis of functionally rigid [2]rotaxane 1ꢀ4PF6.
In order to explain the reasons leading to the isolation of a
high proportion of undesired free dumbbell 3, we estimated
the binding constant of the [2]pseudorotaxane [2 C CBPQT]ꢀ
1
4PF6 using H NMR spectroscopy by successive dilutions of
an equimolar solution and found it to be B15 Mꢁ1 in MeCN
at 298 K. At the specific coupling reaction initial concentra-
tions (12 mM) in MeCN at 298 K, we calculated that only
B14% of [2 C CBPQT]ꢀ4PF6 is formed. This is consistent
with the high yield of 3 and the low yield of 1ꢀ4PF6.
a California NanoSystems Institute and Department of Chemistry and
Biochemistry, University of California, Los Angeles, 405 Hilgard
Avenue, Los Angeles, California 90095, USA
b Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, USA.
E-mail: stoddart@northwestern.edu; Fax: +1 (847) 491 1009;
Tel: +1 (847) 491 3793
w Electronic supplementary information (ESI) available: Synthesis
and characterization data, further crystal structures and crystal data.
CCDC reference numbers 661694–661695. For ESI and crystallo-
graphic data in CIF or other electronic format see DOI: 10.1039/
b808005d
Fig. 1 A ball-and-stick representation of the solid-state structure of
3. Colours are as used in Scheme 1.
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Slow evaporation of a CH2Cl2–C6H14–iPr2O solution of 3
yielded single crystals suitable for X-ray crystallography.z In
the solid state, 3 adopts (Fig. 1) a centrosymmetric conforma-
tion. The total length of the molecule is 31.0 A and the
distance covered by the butadiyne unit as the spacer between
two NP units is 3.8 A, with an S-shaped fully rigid NP–buta-
diyne–NP unit in which stabilization within and beyond
the molecule is achieved by (a) intramolecular [C–Hꢀ ꢀ ꢀO]
interactions8 between the oxygen atoms (O2) in the di(ethylene
glycol) chains and the protons on the isopropyl groups
associated with the stoppers, and (b) intermolecular
[C–Hꢀ ꢀ ꢀO] interactions between the oxygen atoms (O1) in
the di(ethylene glycol) chains and the protons (see ESIw) on
the NP unit in the neighboring molecule.
Fig. 3 A ball-and-stick representation of the interdigitated super-
structure (packing diagram) of 14+. Colours are as used in Scheme 1.
The pale pink stripes highlight p–p stacks involving the NP ring systems
in the dumbbells and the BIPY2+ units of the CBPQT4+ ring as the
[2]rotaxane molecules line up to form parallel donor–acceptor arrays.
Red-colored single crystals of 1ꢀ4PF6, suitable for X-ray
crystallographic analysis,z were obtained upon slow vapor
diffusion of iPr2O into an MeCN–Me2CO solution of 1ꢀ4PF6.
The solid-state structure (Fig. 2) of 14+ confirms that the
CBPQT4+ ring encircles one of the two NP units on the rod
section of the dumbbell and establishes that the compound is a
[2]rotaxane, not a [3]rotaxane! The functionally rigid [2]rotaxane
is stabilized by a combination of (a) [C–Hꢀ ꢀ ꢀO] interactions8
between the oxygen atoms (O5 and O6) in the dumbbell and an
a-bipyridinium (BIPY2+) proton and a proton on the p-xylylene
link in the CBPQT4+ ring, (b) [C–Hꢀ ꢀ ꢀp] interactions9 between
the two peri protons (H64 and H67, see ESIw) of the NP units and
the two p-xylylene links, and (c) p–p stacking interactions10
between the NP and BIPY2+ units (see ESIw). Interestingly, the
environments of the two half dumbbells are significantly
different. The side of the half dumbbell with the encircled
CBPQT4+ ring is folded to stabilize the [2]rotaxane formation
through the [C–Hꢀ ꢀ ꢀO] interactions, while the side without the
CBPQT4+ ring is fully extended, resulting in different lengths of
half dumbbells of 15.3 A when the NP unit is encircled by the
CBPQT4+ ring and 17.4 A when the NP unit is free.
each other, perhaps in the solid state itself employing photo-
chemical dimerization11 of olefinic units attached to the stop-
pers, we could produce the prototypes of two-dimensional
actuators based on extended donor–acceptor stacks con-
structed of interacting molecular shuttles.
In summary, we have adapted the Eglinton coupling protocol,
previously utilized6c,12 in the preparation of donor–acceptor
catenanes, to the synthesis of a symmetric donor–acceptor
Fig. 2 A ball-and-stick representation of the solid-state structure of
4+. Colours are as used in Scheme 1.
1
Fig. 3 illustrates the superstructure (packing diagram) for 14+
.
Parallel p–p stacks (shaded pink) of alternating NP and BIPY2+
units are aligned along the b-axis in the crystal wherein four half
molecules occupy the unit cell. The distances associated with the
intercomponent (intramolecular) and intermolecular p–p stacking
interactions between the alternating mean planes of the encircled
and free NP ring systems in the dumbbells and the centroids of
the BIPY2+ units span the range from 3.26 to 3.44 A.
We have never ceased to be amazed at how a solid-state
structure or superstructure can open up a new vista in
supramolecular chemistry and beyond. The solid-state super-
structure illustrated in Fig. 3 has been interpreted in a
graphical form in Fig. 4. This representation suggests that, if
we were to use stoppers which could be linked covalently to
Fig. 4 A graphical representation of how a solid-state (X-ray crystal)
superstructure might be transformed by post-covalent assembly into
an integrated two-dimensional prototype of a device.
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[2]rotaxane. Characterization of this system by X-ray crystal-
lography revealed a non-centrosymmetric [2]rotaxane forma-
tion in the solid state. Interestingly, this functionally rigid
[2]rotaxane forms a superstructure wherein parallel p–p stacks
of alternating NP ring systems and BIPY2+ units line up in a
continuous manner. The rigidity of the central linker in the
rotaxane molecules is likely the key to this very organized
supramolecular assembly in the crystal. This observation could
be useful in the design and synthesis of mechanically inter-
locked molecules, as well as for the development of devices
based on more rigid molecular systems.
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This work was supported by the Microelectronics Advanced
Research Corporation (MARCO) and its focus center on
Functional Engineered NanoArchitectonics (FENA) and the
Defense Advanced Research Projects Agency (DARPA), and
the Center for Nanoscale Innovation for Defense (CNID), and
NSF (ECS-0609128).
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