Donor-acceptor oligorotaxanes made to order

Article abstract of DOI:10.1002/chem.201001822

Five donor-acceptor oligorotaxanes made up of dumbbells composed of tetraethylene glycol chains, interspersed with three and five 1,5-dioxynaphthalene units, and terminated by 2,6-diisopropylphenoxy stoppers, have been prepared by the threading of discrete numbers of cyclobis(paraquat-p- phenylene) rings, followed by a kinetically controlled stoppering protocol that relies on click chemistry. The well-known copper(I)-catalyzed alkyne-azide cycloaddition between azide functions placed at the ends of the polyether chains and alkyne-bearing stopper precursors was employed during the final kinetically controlled template-directed synthesis of the five oligorotaxanes, which were characterized subsequently by ¹HaNMR spectroscopy at low temperature (233aK) in deuterated acetonitrile. The secondary structures, as well as the conformations, of the five oligorotaxanes were unraveled by spectroscopic comparison with the dumbbell and ring components. By focusing attention on the changes in chemical shifts of some key probe protons, obtained from a wide range of low-temperature spectra, a picture emerges of a high degree of folding within the thread protons of the dumbbells of four of the five oligorotaxanesa the fifth oligorotaxane represents a control compound in effecta brought about by a combination of Ci-H···O and π-π stacking interactions between the π-electron-deficient bipyridinium units in the rings and the π-electron-rich 1,5-dioxynaphthalene units and polyether chains in the dumbbells. The secondary structures of a foldamer-like nature have received further support from a solid-state superstructure of a related [3]pseudorotaxane and density functional calculations performed thereon.

Full text of DOI:10.1002/chem.201001822

FULL PAPER
DOI: 10.1002/chem.201001822
Donor–Acceptor Oligorotaxanes Made to Order
Subhadeep Basu,[a] Ali Coskun,[a] Douglas C. Friedman,[a] Mark A. Olson,[a]
Diego Benꢀtez,[b] Ekaterina Tkatchouk,[b] Gokhan Barin,[a] Jeffrey Yang,[a]
Albert C. Fahrenbach,[a] William A. Goddard, III,[b] and J. Fraser Stoddart*[a]
Abstract: Five donor–acceptor oligoro-
taxanes made up of dumbbells com-
posed of tetraethylene glycol chains, in-
terspersed with three and five 1,5-
oligorotaxanes, which were character-
ized subsequently by 1H NMR spec-
troscopy at low temperature (233 K) in
deuterated acetonitrile. The secondary
structures, as well as the conformations,
of the five oligorotaxanes were unrav-
eled by spectroscopic comparison with
the dumbbell and ring components. By
focusing attention on the changes in
chemical shifts of some key probe pro-
tons, obtained from a wide range of
emerges of a high degree of folding
within the thread protons of the dumb-
bells of four of the five oligorotax-
anes—the fifth oligorotaxane repre-
sents a control compound in effect—
brought about by a combination of
dioxyACHTUNGTRENNUNGnaphthalene units, and terminated
by 2,6-diisopropylphenoxy stoppers,
have been prepared by the threading
of discrete numbers of cyclobis(para-
quat-p-phenylene) rings, followed by a
kinetically controlled stoppering proto-
col that relies on click chemistry.
The well-known copper(I)-catalyzed
alkyne–azide cycloaddition between
azide functions placed at the ends of
the polyether chains and alkyne-bear-
ing stopper precursors was employed
during the final kinetically controlled
template-directed synthesis of the five
ꢀ
C H···O and p–p stacking interactions
between the p-electron-deficient bipyr-
idinium units in the rings and the
p-electron-rich 1,5-dioxynaphthalene
units and polyether chains in the
dumbbells. The secondary structures of
a foldamer-like nature have received
further support from a solid-state su-
perstructure of a related [3]pseudoro-
taxane and density functional calcula-
tions performed thereon.
low-temperature spectra,
a
picture
Keywords: folding noncovalent
·
bonding interactions · oligomers ·
rotaxanes · template-directed syn-
theses
Introduction
The advent of mechanically interlocked molecules
(MIMs),[1] such as catenanes,[2] rotaxanes,[3] daisy chains,[4]
Borromean rings,[5] and trefoil knots,[6] that rely upon tem-
plate-directed protocols[7] for their efficient synthesis have
already impacted nanotechnology from molecular electronic
devices[8] to stimuli-responsive therapeutic materials.[9]
A
[a] Dr. S. Basu, Dr. A. Coskun, D. C. Friedman, M. A. Olson, G. Barin,
J. Yang, A. C. Fahrenbach, Prof. J. F. Stoddart
Department of Chemistry, Northwestern University
2145 Sheridan Road, Evanston, IL 60208 (USA)
Fax : (+1)-847-491-1009
common theme running through templation is the fact that
the noncovalent bonding interactions, which are expressed
through acts of molecular recognition and self-assembly
during the synthesis, “live on” inside the molecules after-
wards. This prevailing characteristic of template-directed
syntheses[7] means that although MIMs belong to the molec-
ular world, weak noncovalent bonding interactions charac-
teristic of the supramolecular world are retained. The ques-
tion arises as to whether this footprint can be expressed in
synthetic polymers at the level of secondary structure and, if
so, can this additional level of structure be harnessed in a
materials setting?
E-mail: stoddart@northwestern.edu
Homepage: http://stoddart.northwestern.edu
[b] Dr. D. Benꢀtez, Dr. E. Tkatchouk, Prof. W. A. Goddard, III
Materials and Process Simulation Center
California Institute of Technology
1200 E. California Blvd MC 139-74
Pasadena CA 91125 (USA)
Fax : (+1)626-585-0918
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/chem201001822.
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While small molecule[2–6] donor–acceptor (DA) MIMs
have had these footprints exposed and expressed,[8–10] the
larger oligomeric[11–13] and polymeric[14] ones remain some-
thing of an enigma. The time is ripe to probe the nature of
the noncovalent bonding interactions that dictate the secon-
dary structures of DA-MIMs. From a physical organic chem-
istꢂs perspective, not to mention the applications that could
be envisaged, the template-directed syntheses[7] of a homol-
ogous series of monodisperse donor–acceptor oligocate-
nanes[11] and oligorotaxanes[12] of well-defined constitutions
is alluring from the viewpoint
none (HQ) or three 1,5-dioxynaphthalene (DNP) units sepa-
rated by tetraethyleneglycol (TEG) chains and terminated
by benzyloxy groups form [2]pseudorotaxanes with a cyclo-
bis(paraquat-p-phenylene) (CBPQT4+) ring, such that the
central p-donating HQ/DNP unit resides in a p–p stacking
mode with the inner surfaces of the p-accepting bipyridini-
um (BIPY2+) units in the middle of the tetracationic cyclo-
phane, leaving the two terminal p-donating HQ/DNP units
to enter into alongside p–p stacking interactions with the
exterior surfaces of the BIPY2+ units of the CBPQT4+ ring.
of elucidating the intricate and
intimate details of the noncova-
lent bonding interactions that
are repeated in oligomers. Spe-
cifically, what are the roles
ꢀ
played by p–p, C H··O and
[15]
ꢀ
C H···p interactions
in solu-
tion as well as in the solid
state? How important are these
relatively weak interactions in
the stabilization of the secon-
dary structures of oligomeric
DA-MIMs? Both quantitative
and qualitative answers to these
questions would, not only pres-
ent
a fundamentally well-re-
searched opportunity for mate-
rials scientists to forge new ma-
terials with elastic-style proper-
ties, but might also provide a
better understanding about the
nature of folding (secondary
structure) in biopolymers, such
as proteins and nucleic acids.
Noncovalent bonding interac-
tions in nature play a crucial
role in determining the func-
tions and operations of these
biomolecular machines. Finding
out how to control these inter-
actions in wholly synthetic sys-
tems and utilizing them to
define secondary structures
could pave the way to the
design and synthesis of a new
generation of synthetic poly-
mers with tunable properties.
We selected our starting
point for the investigation of
donor–acceptor oligorotaxanes,
the observation—made[16] in the
Scheme 1. The structural formulas of the three rotaxanes [2]3NPR·4PF6, [3]3NPR·8PF6, and [4]3NPR·12PF6
obtained by template-directed synthesis from 3NP (7), CBPQT·4PF6, and the precursor 5 of the stoppers. The
corresponding free dumbbell 3NPD was also synthesized from 3NP (7) and 5 for comparison (Table 1) with
the 1H NMR spectra of the three rotaxanes. We have labeled the central constitutionally symmetrical DNP
unit 2/6, 3/7, and 4/8, and, for the other two equivalent, but constitutionally unsymmetrical, DNP units, 2, 3, 4,
6, 7, and 8. Protons on DNP units included inside CBPQT4+ rings have been designated as i2/6, i3/7, and i4/8
when the DNP unit is constitutionally symmetrical, and i2, i3, i4, i6, i7, and i8 when they are constitutionally un-
symmetrical. Protons on DNP units not included inside CBPQT4+ rings and positioned so that they can inter-
act in a p–p stacking manner with one BIPY2+ unit are designated as o2, o3, o4, o6, o7, and o8. Protons on DNP
units not included inside the CBPQT4+ ring and positioned so that they can interact in a p–p stacking manner
with two BIPY2+ units are designated a2/6, a3/7, and a4/8. Likewise, the descriptors o and a are employed to iden-
tify the a and b protons on BIPY2+ units that are interacting with one and two DNP units, respectively, by
1
1990s by H NMR spectroscopy
in solution and by X-ray crys-
tallography in the solid state—
that threadlike molecules con-
taining either three hydroqui- virtue of p–p stacking interactions.
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Donor–Acceptor Oligorotaxanes
FULL PAPER
Scheme 2. The structural formulas of the two rotaxanes [3]5NPR·8PF6 and [4]5NPR·12PF6 obtained by template-directed synthesis form 5NP (10),
CBPQT·4PF6, and the precursor 5 of the stoppers. The corresponding free dumbbell 5NPD was also synthesized from 5NP (10) and 5 for comparison
(Table 1) with the 1H NMR spectra of the two rotaxanes. For the notations that have been employed to identify the protons on the DNP and BIPY2+
units, see the caption to Scheme 1.
The foldamer-like[17] superstructure is further ordered and
2,6-diisopropylphenoxy stoppers, appended by triazole rings
to the terminal TEG chains and 2) one, two or three
CBPQT4+ rings corresponding, in turn, to the rotaxanes
[2]1NPR·4PF6 and [2]3NPR·4PF6, [3]3NPR·8PF6, and
[4]3NPR·12PF6 and [4]5NPR·12PF6. Three of the rotaxanes,
namely, [2]3NPR·4PF6, [3]3NPR·8PF6, and [4]3NPR·12PF6,
ꢀ
stabilized by weak orthogonal C H···p interactions, involv-
ing the central HQ/DNP unit and the two p-xylylene struts
linking the two BIPY2+ links together, and much stronger
ꢀ
C H···O interactions between some of the methine H atoms
a to the (formally) positively charged N atoms on the two
BIPY2+ units of the CBPQT4+ ring, and the three centrally
located O atoms in the two TEG chains.
We decided at the outset, however, to employ only the
larger DNP p-donating system and to make a couple of im-
portant constitutional modifications to these foldamer-like,
donor–acceptor superstructures, namely, to add 1) terminal
ꢀ
TEG chains in recognition of the known importance of C
H···O interactions in the stabilization of such complexes,[15]
and also 2) bulky stoppers to turn the pseudorotaxanes into
rotaxanes, thus removing the additional complication pres-
ent in the former, wherein complexes are constantly equili-
brating with each other and also with uncomplexed species
in solution. These important modifications were designed to
dampen the dynamics between the rings and their dumbbells
and introduce mechanical bonds, which effectively take us
from the erratic supramolecular regime to a much tamer
molecular world.[18]
Scheme 3. The structural formula of the model rotaxane [2]1NPR·4PF6
obtained by template-directed synthesis from 1NP (2), CBPQT·4PF6, and
the precursor 5 of the stoppers. The corresponding free dumbbell 1NPD
was also synthesized from 1NP (2) and 5 for comparison (Table 1) with
the 1H NMR spectrum of the model rotaxane. For the notations that
have been employed to identify the protons on the DNP and BIPY2+
units, see the caption to Scheme 1.
Herein, we report the synthesis and characterization of
five donor–acceptor oligorotaxanes (Schemes 1–3) made up
of 1) dumbbells composed of TEG chains interspersed with
three (3NP) and five (5NP) DNP units and terminated by
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J. Fraser Stoddart et al.
were obtained starting from the DNP trimer (3NP), while
another two, namely, [3]5NPR·8PF6 and [4]5NPR·12PF6,
were assembled from the DNP pentamer (5NP). To be able
to compare the folding properties of these oligorotaxanes,
(ESI-HRMS), following its separation and purification by
reverse-phase high-performance liquid chromatography
(RP-HPLC). The trimeric 3NP was obtained (Scheme 5) by
the monotosylation of 2 (1NP) to give 6, which was then
used to alkylate 1,5-dihydroxynaphthalene (DNP), yielding
1
particularly at low temperature, by H NMR spectroscopy,
[2]1NPR·4PF6 (Scheme 3) was also synthesized as a small-
molecule monomeric reference compound. The co-confor-
mational behavior of the oligor-
the diol
7
(3NP). The rotaxanes [2]3NPR·4PF6,
[3]3NPR·8PF6, and [4]3NPR·12PF6 (Scheme 1) were all pro-
otaxanes was investigated by
comparison with the individual
dumbbell and ring control com-
pounds, calling on the changes
in chemical shifts of some key
probe protons obtained from a
wide range of low-temperature
1H NMR spectra. The overall
picture of folding that emerges
is substantiated by an X-ray
crystal
superstructure
of
3NPꢁ(CBPQT·4PF6)2,
along
with a detailed analysis of its
(intracomplex) bonding interac-
tions.
Scheme 4. Synthesis of the [2]rotaxane [2]1NPR·4PF6.
Results and Discussion
A template-directed threading-
followed-by-stoppering
proach[19] was employed to gen-
erate the (oligo)rotaxanes
ap-
(Schemes 1–3) in the wake of
the more conventional synthesis
(Schemes 4–6) of the diols[20]
1NP (2), 3NP (7), and 5NP
(10).
[2]1NPR·4PF6 was obtained
(Scheme 4) by converting
The
[2]rotaxane
2
(1NP)[21] to the ditosylate[22] 3,
which was then treated with
NaN3 in DMF to afford the dia-
zide[22] 4, before subjecting it to
copper-catalyzed azide–alkyne
cycloaddition[23] (CuAAC) in
the presence of CBPQT·4PF6
and the propargyl derivative[14]
5, the precursor to the stoppers.
This template-directed protocol
involves the mixing of the dia-
zide 4 with the CBPQT·4PF6
and the alkyne 5 at room tem-
perature in Me2CO in the pres-
ence of the copper catalyst. The
[2]rotaxane, which was obtained
in 56% yield was characterized
by electrospray ionization high-
Scheme 5. Synthesis of the p-electron rich trimer 3NP (7) and the subsequent formation of the rotaxanes
resolution mass spectrometry [2]3NPR·4PF6, [3]3NPR·8PF6 and [4]3NPR·12PF6.
2110
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Donor–Acceptor Oligorotaxanes
FULL PAPER
Scheme 6. Synthesis of the p-electron rich pentamer 5NP (10) and the subsequent formation of the rotaxanes [3]5NPR·8PF6 and [4]5NPR·12PF6.
duced (Scheme 5) after converting the terminal OH groups
of 3NP (7) to azide functions in two steps: tosylation, fol-
lowed by displacement of both tosyl groups in 8 by NaN3 to
afford the diazide 11, which was subjected to CuAAC[23] in
the presence of CBPQT·4PF6 and the propargyl derivative
5. The use of 3.0 equivalents of CBPQT·4PF6 led to the
[2]rotaxane [2]3NPR·4PF6 (20%) and the [3]rotaxane
with the alkyne 5 in the presence of 2.5 equivalents of
CBPQT·4PF6. Separation and purification by RP-HPLC af-
forded [3]5NPR·8PF6 (50%) and [4]5NPR·12PF6 (20%)
(see the Experimental Section), the constitutions of which
were confirmed by ESI-HRMS. Neither the [5]- nor [6]ro-
taxane was isolated.
To probe the solution-state structures of the six (oligo)ro-
taxanes (Schemes 1, 2, and 3) with respect to both their con-
formations and co-conformations, we were obliged to
[3]3NPR·8PF6
(52%).
When
6.0 equivalents
of
CBPQT·4PF6 were employed (Scheme 5), the [4]rotaxane
[4]3NPR·8PF6 was obtained, albeit in low (3%) yield, along
with 10% of [2]3NPR·4PF6 and 45% of [3]3NPR·8PF6. All
of these oligorotaxanes were characterized (see the Experi-
mental Section) by ESI-HRMS following their separation
and purification by RP-HPLC. It appears that adding on the
donor oligomers (1NP/3NP/5NP) leads to an increase in the
binding of the CBPQT4+ rings to the outer DNP units on
1
employ high-field (600 MHz) H NMR spectroscopy. It tran-
spired that we had to record spectra at low temperature
(233 K) and utilize multidimensional techniques to aid the
assignments of resonances to protons. Since our analysis of
the different spectra relies heavily on chemical shift changes
ꢀ
account of their providing yet another source of C H···O in-
teractions, hence leading to [3]3NPR·8PF6 as the major
product. The formation of the [4]rotaxane [4]3NPR·12PF6
in small amounts indicates that the overall recognition motif
is prepared to give up some p–p stacking, external to the
CBPQT4+ ring, to gain the maximum recognition internally.
Perhaps as a result of ion pairing, Coulombic repulsion be-
tween the CBPQT4+ rings does not seem to be a deal break-
er. Finally, what about the oligorotaxanes templated by
5NP? In the first instance, the ditosylate 8 (Scheme 5) of
3NP (7) was used (Scheme 6) to alkylate preferentially the
phenolic hydroxyl group of the phenol 9 to afford the pen-
tamer 5NP (10). The [3]- and [4]rotaxanes [3]5NPR·8PF6
and [4]5NPR·12PF6 were obtained (Scheme 6) from 5NP
(10), following tosylation to give 12, from which the diazide
13 was prepared prior to the CuAAC-based click reaction[23]
Figure 1. Full 1H NMR assignment of [2]1NPR·4PF6 in CD3CN at 233 K.
The H4/8 of the DNP protons are shifted to d=2.2 ppm as a consequence
ꢀ
of the strong C H···p edge-to-face interactions with the face of the p-xy-
lylene units in the CBPQT4+ ring.
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J. Fraser Stoddart et al.
and NOE correlations, which occur on the rotaxana-
tion of the relevant dumbbells (1NP, 3NP, and 5NP)
by CBPQT4+ rings, it became necessary for us to
devise a method for identifying heterotopic protons
on both the donor (DNP) and acceptor (BIPY2+
)
units in the dumbbell and the ring components, re-
spectively. This method is summarized in the cap-
tions to Schemes 1, 2, and 3.
1
At the outset, we compared the H NMR spectrum
(Figure 1) of the [2]rotaxane [2]1NPR·4PF6 with that
of the dumbbell compound 1NPD. Table 1 lists the
differences in chemical shifts, expressed as Dd values,
between probe protons on the DNP (i2/6, i3/7, and i4/8)
and the BIPY2+ (oaa, oab, oba, and obb) units in
[2]1NPR·4PF6 with those in 1NP and CBPQT·4PF6.
The proton assignments for [2]1NPR·4PF6 and
1NPD (Scheme 3 and Figure 1) were confirmed by
2D COSY and NOESY experiments (see the Sup-
porting Information). Let us first consider the reso-
nances associated with CBPQT4+ ring in the [2]ro-
taxane. They appear as two sets of doublets (oaa&b
and oba&b), as expected on account of the local C2
symmetry imposed on the CBPQT4+ ring by the
DNP unit. The oba, oab, and obb protons experienced
substantial upfield shifts (Dd values ranging from
ꢀ0.37 to ꢀ1.03 ppm) with reference to the equivalent
protons in CBPQT·4PF6, while the three resonances
(i2/6, i3/7, i4/8) for the DNP protons have Dd values
ranging from ꢀ0.58 to ꢀ5.44 ppm, in comparison
with the equivalent protons in 1NP. The magnitude
of these upfield shifts in both cases reflects the posi-
tioning of the DNP unit inside the CBPQT4+ ring of
the [2]1NPR4+, a geometry that leads to mutual
shielding—arising from a combination of p–p stack-
ꢀ
ing and C H···p interactions—of all of the aforemen-
tioned aromatic protons.
Next let us now examine the H NMR spectra of
1
the [2]-, [3]-, and [4]rotaxanes, derived from 3NP (7)
and draw comparisons (Dd values listed in Table 1)
1
with the H NMR spectrum for the dumbbell com-
1
pound 3NPD. The H NMR spectrum (Figure 2c) of
[4]3NPR·12PF6 exhibits overlapping signals (d=
6.15–6.22, 5.85–5.95, and 2.22–2.25 ppm) for the reso-
nances associated with the protons identified as i2/i6/
i2/6, i3/i7/i3/7, and i4/i8/i4/8, respectively, arising from the
two constitutionally different DNP units. The includ-
ed DNP unit in [4]3NPR12+ exhibits Dd values
(Table 1) that are on par with those for [2]1NPR4+
.
This observation reflects the fact that all three DNP
units in [4]3NPR12+ are encircled by CBPQT4+ rings.
Since [4]3NPR12+ carries a total of 12 positive charg-
es, spread out across three contiguous DNP units, all
encircled by CBPQT4+ rings and hence without any
p-donating systems inserted between them to help
shield the tetracationic cyclophanes from each other,
this [4]rotaxane ends up being a considerably elon-
gated molecule as a result of significant charge–
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Donor–Acceptor Oligorotaxanes
FULL PAPER
(Scheme 1 and Figure 2b) are
not too dissimilar from the Dd
values for the protons i2/i6/i2/6
associated with the included
terminal DNP units. Moreover,
if we discount the significant
ꢀ
C H···p shielding effect provid-
ed by the bridging p-xylylene in
relation to the i3/i7/i3/7 and i4/i8/
i4/8 protons, then we are able to
compare (Table 1) the magni-
tudes of the Dd values of the
protons a3/7 and a4/8 in
[3]3NPR8+ with those of i2/i6/i2/6
which are essentially unaffected
of the shielding influence of the
p-xylylene units. Finally, in the
3NP series, the 1H NMR
spectrum
(Figure 2a)
of
[2]3NPR·4PF6 reveals the pres-
ence of two co-conformations
with the major one (90%)
being that in which the central
DNP ring system is included
inside the CBPQT4+ ring. The
Dd values associated with the
terminal free DNP units in this
[2]rotaxane are a little less dra-
matic on account of their inter-
action with only
a
single
BIPY2+ unit. In addition to this
analysis of the Dd values for
DNP protons in the [2]-, [3]-,
and [4]rotaxanes, a similar eval-
uation of the Dd values for the
BIPY2+ protons was performed
and is summarized in Table 1.
An in-depth analysis of the Dd
1
Figure 2. Full H NMR assignment of a) [2]3NPR·4PF6, b) [3]3NPR·8PF6, and c) [4]3NPR·12PF6 in CD3CN at values for the a and b protons
233 K. The protons a to the nitrogen in the CBPQT4+ ring show two, four, and six (merged) signals for the
[2]-, [3]-, and [4]rotaxanes. For the DNP units, [2]3NPR·4PF6 and [3]3NPR·8PF6 display two types of H NMR
signals, corresponding to the p-electron-donating units being inside or outside the cavity of the p-electron-defi-
cient ring. [4]3NPR·12PF6 reveals signals that correspond only to the DNP protons included inside the cavity
of the BIPY2+ units supports
1
the existence of an ordered sec-
ondary structure stabilized by
p–p stacking interactions. This
analysis reveals the anticipated
of the tetracationic cyclophane.
trends (upfield chemical shifts)
in Dd values from p–p stacking
charge (Coulombic) repulsion. By contrast, a similar analy-
sis, carried out on the 1H NMR spectrum (Figure 2b) of
[3]3NPR·8PF6, points to the asymmetrical location of the
two CBPQT4+ rings on the terminal DNP units, leaving the
central DNP ring system in an alongside relationship with
both CBPQT4+ rings. First of all, it is noteworthy that the
Dd values for all the alongside DNP protons exhibit upfield
chemical shifts (Dd values in the range of ꢀ0.38 to
ꢀ0.86 ppm) relative to those of the dumbbell compound
3NPD. The magnitudes of the Dd values for the protons on
the alongside DNP unit in the middle in [3]3NPR8+
of the donor and acceptor units where the latter are divided
into “outside” BIPY2+ units which interact with only one in-
cluded DNP unit and “alongside” BIPY2+ units where they
are sandwiched between two DNP ring systems. It is impor-
tant to note that the Dd values associated with the alongside
BIPY2+ protons are larger and more negative (Dd values in
the range of ꢀ0.13 to ꢀ1.83 ppm) than those (Dd values in
the range of +0.03 to ꢀ1.21 ppm) for the outside BIPY2+
units. Clearly, two p–p stacking charge-transfer (CT) inter-
actions have a greater influence on chemical shift move-
ments than does one p–p stacking CT interaction.
Chem. Eur. J. 2011, 17, 2107 – 2119
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J. Fraser Stoddart et al.
In addition to the magnitude of the chemical shift changes
observed in the H NMR spectrum, NOESY was employed
to gain further evidence for the secondary structure of the
3NP-based oligorotaxanes. Analysis of 2D NOESY spectra
(Figure 3a and b) of [2]3NPR·4PF6 and [3]3NPR·8PF6, re-
corded in CD3COCD3 at 233 K, revealed correlations be-
tween the aa and ab protons on the CBPQT4+ ring and
their outside or alongside DNP protons. The presence of
these NOEs—taken in conjunction with the chemical shift
data presented in Table 1—present a clear picture of the
“folded” solution-state structure of oligorotaxanes
[2]3NPR·4PF6 and [3]3NPR·8PF6.
1
The co-conformation of [3]3NPR8+
, deduced from
1H NMR spectroscopy performed in solution was given ad-
ditional credence from a solid-state superstructure (Fig-
ure 4a and c) of the [3]pseudorotaxane formed between
3NP and two CBPQT4+ rings. Slow vapor diffusion of iPr2O
into a solution of CBPQT·4PF6 and 3NP (4:1 equiv) in
MeCN afforded deep purple single crystals suitable for
X-ray crystallographic analysis. A close examination of
3NPꢁ[CBPQT·4PF6]2 reveals that the 3NP component of
the [3]pseudorotaxane assumes a folded conformation to
ꢀ
ꢀ
maximize its p–p, C H···p, and C H···O interactions with
Figure 3. Partial 1H–1H NOESY of a) [2]3NPR·4PF6, b) [3]3NPR·8PF6,
and c) [4]5NPR·12PF6 recorded in CD3COCD3 at 233 K, demonstrating
the folded conformation of the oligorotaxanes in solution. a) An NOE
signal is observed between o2/6 of the terminal DNP unit of
[2]3NPR·4PF6 with the alongside b proton of the CBPQT4+ ring encir-
cling the middle DNP unit of the dumbbell. b) An NOE signal observed
between the protons of the middle DNP unit (a2/6 and a3/7), with the b
protons of the terminal CBPQT4+ ring in [3]3NPR·8PF6. c) Similar NOE
signals were observed between the alongside protons from the free DNP
Figure 4. X-ray crystal superstructure of the [3]pseudorotaxane
3NPꢁ(CBPQT·4PF6)2 in a) space-filling and c) ball-and-stick representa-
tions. X-ray crystal superstructure of the analogous [2]pseudorotaxane re-
ported previously[24] in b) space-filling and d) ball-and-stick representa-
tions. e) Space-filling and f) ball-and-stick representations of the energy-
minimized superstructure of the [3]pseudorotaxane 3NPꢁ(CBPQT
·4PF6)2 obtained by using DFT.
units and the
b
protons of the p-electron-deficient ring in
[4]5NPR·12PF6. d) Partial structural formula of a rotaxane showing the
key NOE interactions observed in a) to c).
2114
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Chem. Eur. J. 2011, 17, 2107 – 2119

Donor–Acceptor Oligorotaxanes
FULL PAPER
two CBPQT4+ rings, which encircle the two terminal DNP
units, leaving the central DNP unit between them. The p–p
interplanar separations (Figure S11a in the Supporting Infor-
mation) between the encircled DNP units and the outside
and inside BIPY2+ units of the CBPQT4+ ring are 3.30 and
3.28 ꢃ, respectively; the interplanar distances between the
inside BIPY2+ units and the central (encircled) DNP unit
stacking of alternating p-electron-rich (DNP units) and p-
electron-deficient (BIPY2+ units) systems similar to the one
present in the [3]pseudorotaxane. By contrast, the super-
structure in which the CBPQT4+ ring is encircling one of
the two terminal DNP units allows for only one of the three
DNP units to be present without p–p interactions, affording
it the opportunity to reside adjacent to the available, slightly
acidic, methylene of the CBPQT4+ ring and stabilized by a
ꢀ
are both 3.36 ꢃ as a result of symmetry. The C H···p distan-
ꢀ
ces, which characterize the encircled DNP units and the p-
xylylene struts of the CBPQT4+ rings, are 3.41 and 3.44 ꢃ
and clearly help to stabilize the 2:1 complex between the
weak C H···p interaction. The M06-2X/6-311++GG**
level of theory predicts a relative energy difference of about
11 kcalmolꢀ1 in MeCN favoring the co-conformation (i) with
the CBPQT4+ ring on the central DNP unit over co-confor-
mation (ii) in which the CBPQT4+ ring encircles one of the
terminal DNP units. This preference for a superstructure in
which p–p stacking interactions are maximized[26] is in good
agreement with the solid-state superstructure of
3NPꢁ[CBPQT·4PF6]2 and the numerous 1D and 2D NMR
spectroscopic techniques applied to the [3]rotaxane in
CD3CN.
two CBPQT4+ rings and 3NP. There are also eight C H···O
ꢀ
interactions ranging from 2.35 to 2.59 ꢃ between the H
atoms on the carbon atoms a to the nitrogen atoms in the
BIPY2+ units contributing to the foldamer-like superstruc-
ture of 3NPꢁ[CBPQT·4PF6]2. The solid-state packing (Fig-
ure S12 in the Supporting Information) of the 2:1 complex
constituting the [3]pseudorotaxane 3NPꢁ[CBPQT·4PF6]2 is
mediated by noncovalent p–p interactions between the p-xy-
lylenes of the CBPQT4+ rings and the included DNP units
of the 3NP threads. Previously, we obtained[24] the solid-
state superstructure of the [2]pseudorotaxane shown in Fig-
ure 4b and d, which exhibits many of the same features, for
example, folding of the polyether chain to maximize both
Although it did not prove possible at this juncture to
1
carry out a detailed H NMR spectroscopic investigation on
the [3]rotaxane [3]5NPR·8PF6 at 233 K, we were able to
complete a detailed examination of [4]5NPR·12PF6 using
multidimensional techniques to assign the resonances in the
1H NMR spectrum (Figure 5) of the [4]rotaxane. Analysis of
the spectrum indicates an alternating distribution of
CBPQT4+ rings on the DNP subunits leave two, symmetric,
alongside DNP units sandwiched between the BIPY2+ func-
tions of the CBPQT4+ rings. Close inspection of the Dd
values for [4]5NPR4+ (Table 1) reveals negative chemical
shift changes, for both DNP and BIPY2+ protons, which are
comparable (see above) to the series of 3NP oligorotaxanes.
Moreover, close examination of the 2D NOESY spectrum
(Figure 3c) of [4]5NPR·12PF6 shows clear NOE signals
ꢀ
p–p and C H···O interactions in the 1:1 complex.
We have also invoked DFT calculations[25] to compare
and contrast the preferential binding of CBPQT4+ rings to
the two constitutionally unsymmetrical outer DNP units in
3NP (7), which are separated by TEG chains from the one
inner constitutionally symmetric DNP unit. We began by op-
timizing the geometry of 3NPꢁ[CBPQT·4PF6]2 at the
M06L/6-31G** level.[26] We observed (Figure 4e) in the ex-
pected superstructure for the [3]pseudorotaxane that the in-
termolecular p–p stacking interactions between the p-elec-
tron-rich DNP units and the p-
electron-deficient BIPY2+ units
are comparable with the X-ray
superstructure
(Figure 4a).
Moreover, we believe that the
calculated superstructure is a
good model for a supramolec-
ular solvate in a medium polari-
ty solvent (e. g., MeCN) where
tight ion pairs are preserved. To
evaluate the interactions pres-
ent in the secondary structures
of
complexes
like
3NPꢁ[CBPQT·4PF6]2, we gen-
erated, based on the minimized
superstructure of this [3]pseu-
dorotaxane, superstructures for
the analogous [2]pseudoro-
taxane
3NPꢁ[CBPQT·4PF6],
Figure 5. Full 1H NMR assignment of [4]5NPR·12PF6 in CD3CN at 233 K. The spectrum reveals the presence
of both bound and unbound DNP units with respect to the CBPQT4+ ring. The changes in chemical shift of
the alongside DNP protons, as described in Table 1, reveals that the molecule exists in a folded conformation
in solution (at 233 K), interacting strongly with the outer p surface of the BIPY2+ unit of the p-electron-defi-
wherein the CBPQT4+ ring en-
circles the central (i) and one of
the terminal DNP units (ii).
The former exhibits “tight” cient CBPQT4+ ring.
Chem. Eur. J. 2011, 17, 2107 – 2119
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2115

J. Fraser Stoddart et al.
Figure 6. The Dd values, averaged from those values listed in Table 1, for the alongside (light green) and included (dark green) protons in the rotaxanes
a) [3]3NPR·8PF6 and b) [4]5NPR·12PF6. The data further reveals that the average Dd values of the alongside protons are 67 and 75% (shown in black)
of the corresponding included protons for their respective [3]- and [4]rotaxane, indicating a higher influence of the p–p stacking interactions in the more
extended structures of the two.
stemming from through space interactions of the outside
ed [3]pseudorotaxane and theoretical calculations thereon
(Figure 4). We envision that a fundamental understanding
and a careful tuning of the noncovalent bonding forces in
these well-defined oligomeric molecules, inspired by na-
tureꢂs elegant use of similar kinds of noncovalent bonding
interactions, has the potential to help in the design of the
next generation of functional polymeric materials.
1
BIPY2+ and alongside DNP protons. H NMR spectroscopic
evidence reveals, as expected, that four of the five oligoro-
taxane structures exist in solution as a p–p stacked donor–
acceptor array. In contrast, the [4]3NPR·12PF6, on account
of its strong electrostatic repulsion between the CBPQT4+
rings, does not exhibit a secondary structure.
Conclusion
Experimental Section
3NP-rotaxanes: Compound 6 (80 mg, 0.062 mmol) was dissolved in dry
Me2CO under an N2 atmosphere. CBPQT·4PF6 (22 mg, 0.20 mmol), tris
The chemical shift changes (Dd) that are observed for the
dioxynaphthalene ring protons in dumbbells with one, three,
and five DNP units, after they have been converted to [2]-,
[3]-, and [4]rotaxanes by using template-directed protocols,
have been averaged for all the included and alongside diox-
ynaphthalene ring protons. These average Dd values are pre-
sented in bold in Table 1. When comparing (Figure 6) the
six averaged Dd values, those arising from i2 and i6 in the in-
cluded dioxynaphthalene ring systems, which are least influ-
enced by the bridging p-xylylene units in the tetracationic
cyclophane, are the most reliable probe protons to have
their Dd values compared with those of a2 and a6 in the
alongside dioxynaphthalene units. The average Dd values
for the H-2 and H-6 protons in the alongside DNP units in
the [3]- and [4]rotaxanes are 67 and 75%, respectively, of
the corresponding averaged Dd values for the equivalent
protons in the included DNP units. This observation points
to a secondary structure in which p–p noncovalent bonding
interactions help to stabilize the folded conformations of
these [2]-, [3]-, and [4]rotaxanes at ꢀ408C in acetonitrile.
The increase in percentage terms from 67 to 75% of the
averaged Dd values on going from [3]- to [4]rotaxane sug-
gests that the secondary structure becomes more stable as
the homologous series (chain length) grows. This conclusion
is in agreement with the solid-state superstructure of a relat-
(benzyltriazolylmethyl)amine (TBTA) (23 mg, 0.003 mmol), and
7
(29 mg, 0.14 mmol) were added and the solution was stirred for 1 h
during which time it became deep purple, indicating the formation of the
pseudorotaxanes. Finally, [CuACHTNUGTRNEUNG(MeCN)4]PF6 (20 mg, 0.003 mmol) was
added and the reaction mixture was stirred for 24 h at RT. The solvent
was then evaporated and the resulting purple solid was purified by RP-
HPLC (C18 column: H2O/MeCN: 0!100% in 55 min, l=254 nm). Three
different fractions [2]3NPR·4PF6 (20 mg, 10%), [3]3NPR·8PF6 (55 mg,
45%), and [4]3NPR·12PF6 (15 mg, 3%)] were collected.
[2]3NPR·4PF6: 1H NMR (600 MHz, CD3CN, 233 K): d=8.74 (d, J=
6.8 Hz, 4H), 8.13 (d, J=6.6 Hz, 4H), 8.02 (s, 2H), 7.85–7.83 (br, 4H),
7.75–7.73 (br, 4H), 7.20 (br, 1H), 7.19 (br, 1H), 7.17 (d, J=2.05 Hz, 2H),
7.16 (br, 2H), 7.14–7.16 (br, 3H), 7.05–6.98 (m, 6H), 6.57–6.54 (br, 4H),
6.52 (d, J=7.3 Hz, 2H), 6.47–6.44 (br, 4H), 6.33 (d, J=7.7 Hz, 2H), 5.84
(d, J=8.5 Hz, 2H), 5.71 (d, J=13.7 Hz, 4H), 5.58 (d, J=8.5 Hz, 2H),
5.53 (d, J=14.7 Hz, 4H), 4.80 (s, 4H), 4.52 (t, J=4.7 Hz, 4H), 4.04–3.94
(br, 18H), 3.90–3.86 (br, 4H), 3.83–3.78 (br, 14H), 3.69–3.62 (br, 12H),
3.59–3.54 (br, 8H), 3.54–3.50 (br, 5H), 3.50–3.46 (br, 5H), 3.46–3.42 (br,
5H), 3.41 (m, 4H), 1. 17 ppm (d, J=7.0 Hz, 24H); 13C NMR (150 MHz,
CD3CN, 233 K): d=154.2, 153.3, 141.7, 129.6, 126.2, 125.4, 124.3, 117.5,
114.0, 105.3, 72.6, 70.6, 70.4, 70.3, 70.1, 69.4, 67.6, 60.8, 26.2, 23.8 ppm;
HRMS (ESI): m/z calcd for [MꢀPF6]+: 2587.0296; found: 2587.0289;
calcd for [Mꢀ2PF6]2+
:
1221.5343; found: 1221.5356; calcd for
[Mꢀ3PF6]3+: 765.7004; found: 765.7013.
[3]3NPR·8PF6:1H NMR (600 MHz, CD3CN, 233 K): d=8.89 (d, J=
7.6 Hz, 4H), 8.78 (d, J=7.5 Hz, 4H), 8.41 (d, J=7.5 Hz, 4H), 8.13 (d, J=
7.5 Hz, 4H) 7.89 (s, 2H), 7.88 (br, 8H), 7.73 (d, J=11.5, 8H), 7.19 (m,
2H), 7.18 (s, 2H), 7.16–7.13 (m, 2H), 7.03–7.00 (br, 4H), 7.00–6.95 (br,
2116
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Chem. Eur. J. 2011, 17, 2107 – 2119

Donor–Acceptor Oligorotaxanes
FULL PAPER
8H), 6.92–6.84 (m, 4H), 6.84–6.80 (br, 4H), 6.25 (d, J=7.5 Hz, 2H), 6.05
(d, J=8.0, 2H), 6.00 (d, J=7.5 Hz, 2H), 5.76 (d, J=8.6 Hz, 2H), 5.70 (d,
J=8.6 Hz, 2H), 5.65 (d, J=13.8 Hz, 4H), 5.57–5.52 (m, 8H), 5.46 (d, J=
14.4 Hz, 4H), 4.76 (s, 4H), 4.19 (t, J=5.2 Hz, 18H), 4.15–4.05 (br, 16H),
3.99–3.96 (br, 4H), 3.95–3.91 (br, 4H), 3.89–3.85 (br, 4H), 3.80–3.75 (br,
8H), 3.68–3.61 (br, 12H), 3.57–3.52 (br, 4H), 3.51–3.48 (br, 4H), 3.45–
3.38 (m, 8H), 1.18 ppm (d, J=7.0 Hz, 26H); 13C NMR (150 MHz,
CD3CN, 233 K): d=153.0, 152.3, 150.6, 144.2, 144.0, 143.3, 141.5, 136.1,
130.8, 127.6, 125.4, 124.8, 123.8, 117.0, 113.4, 107.7, 105.5, 103.7, 70.6,
70.2, 70.0, 69.6, 69.2, 69.1, 68.8, 68.3, 67.8, 67.4, 64.5, 49.2, 29.5, 25.9,
23.0 ppm; HRMS (ESI): m/z calcd for [Mꢀ2PF6]2+: 1771.5939; found:
1771.5950; calcd for [Mꢀ3PF6]3+: 1132.4068; found: 1132.4081; calcd for
[Mꢀ4PF6]4+: 813.0641; found: 813.0647; calcd for [Mꢀ5PF6]5+: 621.4584;
found: 621.4595.
3.37–3.33 (br, 4H), 2.01 (d, J=7.8 Hz, 2H), 1.86 (d, J=7.8 Hz, 2H),
1.18 ppm (d, J=6.8 Hz, 24H); 13C NMR (150 MHz, CD3CN, 233 K): d=
156.1, 152.2, 148.1, 145.9, 144.8, 144.3, 143.8, 138.4, 131.9, 131.3, 130.7,
130.4, 128.9, 128.1, 125.6, 124.5, 113.6, 70.0, 69.6, 67.6, 64.7, 63.1, 35.3,
32.4, 29.2, 24.5 ppm; HRMS (ESI): m/z calcd for [Mꢀ3PF6]3+: 1710.8763;
found: 1710.8693; calcd for [Mꢀ4PF6]4+: 1246.9161; found: 1246.8966.
X-ray crystal superstructure of 3NPꢁ[CBPQT·4PF6]2: Deep purple
single crystals, suitable for X-ray crystallography (Figures S11 and S12 in
the Supporting Information) were obtained by slow vapor diffusion of
iPr2O into a solution of the pseudorotaxane in MeCN at 298 K.
CCDC-769519 contains the supplementary crystallographic data for this
paper. These data can be obtained free of charge from The Cambridge
Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
[4]3NPR·12PF6: 1H NMR (600 MHz, CD3CN, 233 K): d=8.97 (d, J=
7.1 Hz, 4H), 8.94–8.91 (br, 8H), 8.64 (t, J=7.4 Hz, 8H), 8.53 (d, J=
7.1 Hz, 4H) 7.96–7.92 (m, 14H), 7.91–7.89 (br, 8H), 7.79–7.77 (br, 8H),
7.42–7.38 (m, 8H), 7.34–7.32 (m, 4H), 7.22–7.19 (br, 4H), 7.18–7.12 (br,
14H), 6.22–6.14 (m, 6H), 5.95–5.88 (m, 4H), 5.88–5.84 (m, 2H), 5.73–
5.60 (m, 22H), 5.58–5.52 (d, J=13.7, 4H), 4.78 (s, 4H), 4.26–4.12 (br,
28H), 4.06–3.96 (br, 22H), 3.81–3.77 (br, 4H), 3.71–3.68 (br, 4H), 3.53–
3.49 (br, 4H), 3.49–3.42 (m, 4H), 3.37–3.32 (br, 4H), 2.28–2.22 (br, 6H),
1.20 ppm (d, J=7.0 Hz, 24H); 13C NMR (150 MHz, CD3CN, 233 K): d=
156.9, 140.5, 132.1, 130.0, 125.0, 120.9, 118.1, 79.2, 43.7, 30.7, 28.4, 26.8,
24.4 ppm; HRMS (ESI): m/z calcd for [Mꢀ2PF6]2+: 2321.6558; found:
2321.6443; calcd for [Mꢀ3PF6]3+: 1499.4492; found: 1499.4440; calcd for
Acknowledgements
This research was supported in the beginning by the National Science
Foundation (NSF) under grant CHE-0924620 and subsequently by the
Non-Equilibrium Energy Research Center (NERC), which is an Energy
Frontier Research Center (EFRC) funded by the US Department of
Energy (DOE) of Basic Energy Sciences under Award Number DE-
SC0000989. G.B. thanks the International Center for Diffraction Data for
the award of a 2011 Ludo Frevel Crystallography Scholarship.
[Mꢀ4PF6]4+
:
1088.3459; found: 1088.3445; calcd for [Mꢀ5PF6]5+
:
841.6839; found: 841.6828; calcd for [Mꢀ6PF6]6+
: 677.2426; found:
677.2426.
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5NP-rotaxanes: Compound 11 (250 mg, 0.014 mmol) was dissolved in dry
Me2CO (50 mL) under an N2 atmosphere. CBPQT·4PF6 (39 mg,
0.035 mmol), TBTA (2 mg, 0.007 mmol), and 7 (76 mg, 0.035 mmol) were
added and the solution was stirred for 1 h during which time it became
deep purple, indicating the formation of the pseudorotaxanes. Finally,
[CuACHTUNGTRENNUNG(MeCN)4]PF6 (3 mg, 0.007 mmol) was added and the reaction mixture
was stirred for 24 h at RT. The solvent was then evaporated and the re-
sulting purple solid was purified by RP-HPLC (C18 column: H2O/MeCN:
0!100% in 55 min, l=254 nm). Two fractions [3]5NPR·8PF6 (15 mg,
50%) and [4]5NPR·12PF6 (20 mg, 20%)] were collected.
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[3]5NPR·8PF6: 1H NMR (600 MHz, CD3CN, 233 K): d=8.94 (d, J=
7.1 Hz, 1H), 8.76–8.65 (br, 6H), 8.42 (d, J=7.1 Hz, 1H), 8.23 (d, J=
7.2 Hz, 1H), 8.13–8.08 (br, 4H), 8.06 (d, J=7.2 Hz, 1H), 8.01 (d, J=
5.9 Hz, 1H), 7.94–7.89 (br, 2H), 7.85–7.79 (br, 6H), 7.79–7.76 (br, 1H),
7.74–7.69 (br, 5H), 7.67–7.65 (br, 1H), 7.25–7.19 (m, 2H), 7.19–7.10 (br,
8H), 7.08–6.99 (br, 6H), 6.99–6.94 (br, 2H), 6.91–6.88 (br, 1H), 6.82–6.74
(br, 2H), 6.72–6.69 (br, 1H), 6.66–6.46 (br, 10H), 6.46–6.43 (br, 1H), 6.38
(d, J=8.2 Hz, 1H), 6.34 (d, J=8.2 Hz, 1H), 6.31 (t, J=8.2 Hz, 1H), 6.15
(d, J=7.9 Hz, 1H), 6.04 (d, J=7.9 Hz, 1H), 5.98 (d, J=7.9 Hz, 1H),
5.87–5.81 (br, 2H), 5.72–5.41 (br, 18H), 4.78 (d, J=5.8 Hz, 2H), 4.73 (s,
2H), 4.54–4.49 (m, 2H), 4.19–3.74 (br, 54H), 3.69–3.37 (br, 41H), 3.38–
3.34 (m, 2H), 1.20–1.12 ppm (m, 24H); 13C NMR (150 MHz, CD3CN,
233 K): d=153.5, 150.9, 148.1, 145.9, 144.8, 144.3, 143.8, 139.6, 137, 131.9,
131.3, 130.7, 130.4, 128.9, 128.1, 125.6, 124.5, 113.6, 70.0, 69.6, 67.6, 64.7,
63.1, 34.1, 33.4, 30.8, 23.6, 13.7 ppm; HRMS (ESI): m/z calcd for
ˇ
´
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[Mꢀ2PF6]2+
:
2088.7371; found: 2088.7172; calcd for [Mꢀ3PF6]3+
:
1344.1698; found: 1344.1646; calcd for [Mꢀ4PF6]4+: 971.8862; found:
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6.2 Hz, 4H), 8.25 (d, J=6.4 Hz, 4H), 8.08 (d, J=6.2 Hz, 4H), 7.90 (s,
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Donor–Acceptor Oligorotaxanes
FULL PAPER
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the M06-2X functional.
Received: September 6, 2010
Published online: January 27, 2011
Chem. Eur. J. 2011, 17, 2107 – 2119
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