Template-directed syntheses of rigid oligorotaxanes under thermodynamic control

Article abstract of DOI:10.1002/anie.201004304

Strategically placing secondary dialkyl-ammonium recognition sites at the magic distance of 3.5 A apart in the dumbbell components of a series of oligorotaxanes (see picture) renders otherwise conformationally floppy [n]rotaxanes rigid and rodlike. These oligorotaxanes form with near-quantitative conversion under thermodynamic control using dynamic covalent chemistry.

Full text of DOI:10.1002/anie.201004304

Communications
DOI: 10.1002/anie.201004304
Dynamic Chemistry
Template-Directed Syntheses of Rigid Oligorotaxanes under
Thermodynamic Control**
Matthew E. Belowich, Cory Valente, and J. Fraser Stoddart*
The application of mechanically interlocked molecules
(MIMs) as molecular switches for nanoelectronics,[1] as
molecular actuators for constructing artificial muscles,[2] and
in controlling the release of molecules stored in mesoporous
silica nanoparticles[3] remains an area of intense activity in
research. Dynamic covalent chemistry[4] (DCC), a process
whereby covalent bonds are formed reversibly under thermo-
dynamic control, hence possessing an element of “proof-
reading” or “error-checking”, has emerged as a valuable tool
in the construction of MIMs, such as rotaxanes,[5] catenanes,[6]
suitanes,[7] trefoil knots,[8] Borromean rings,[9] and Solomon
knots.[10] The main attribute of DCC is that it operates under
equilibrium such that the formation of undesired, kinetically
competitive intermediates will eventually make their way
back to the thermodynamically most stable product.
subsequently. This approach suffers from the fact that it
does not provide complete control over the number of
threaded rings—which often do not encircle every recognition
unit—and, moreover, stoppering conditions must be mild and
chosen carefully. Alternatively, the “clipping” approach[12]
(Figure 1, Strategy B) takes advantage of noncovalent bond-
ing interactions to control ring formation by templation,
starting from acyclic precursors and using every single
recognition site. With adequate system design, equilibrating
reactions including olefin metathesis,[13] disulfide[5c,14] and
imine bond formation[5b,15] have all been utilized extensively
in the syntheses of MIMs. For example, it has been
demonstrated[12f] that this “clipping” approach is effective in
the near quantitative synthesis of oligorotaxanes in a one-pot,
multicomponent self-assembly process from 1) a dumbbell
+
Oligorotaxanes are commonly prepared employing a
“threading-followed-by-stoppering” approach[11] (Figure 1,
Strategy A), wherein preformed rings locate around well-
chosen recognition units in a thread that is stoppered
component containing n -CH2NH2 CH2- recognition sites and
2) n equivalents each of 2,6-pyridinedicarboxaldehyde (5)
and tetraethyleneglycol bis(2-aminophenyl)ether (6). The
[2]rotaxane 1R·PF6 composed of bis(3,5-dimethoxybenzyl)-
ammonium hexafluorophosphate and the [24]crown-8 deriv-
ative (red ring in Figure 2) is the quantitative outcome of (1)
plus (2) in CD3CN within 5 min of mixing the starting
materials. In this self-assembly process, involving
+
-CH2NH2 CH2- activation/recognition sites, the clipping reac-
tion is driven by a combination of DCC and noncovalent
bonding interactions[15b] including [N H···X] hydrogen
+
À
+
À À
bonds and [N C H···X] (X = O or N) interactions, as well
as [p···p] stacking interactions between the dumbbell and the
encircling rings.
Whereas much research has been devoted to the syntheses
and applications of such MIMs, very little research has been
dedicated to controlling their overall conformations. From
computational investigations,[16] the above-mentioned oligor-
otaxanes were predicted to assume flexible conformations.
We suspected that [p···p] interactions between adjacent
encircling rings would not only provide added stability to
the oligorotaxanes, but would also lend linearity and rigidity
Figure 1. Two different strategies employed in the template-directed
synthesis of oligorotaxanes. Strategy A: the kinetically controlled (usu-
ally) “threading-followed-by-stoppering” approach. Strategy B: the ther-
modynamically controlled “clipping” approach. Strong hydrogen-bond-
donor recognition sites are indicated in blue, while the complementary
acceptor sites are associated with red rings.
[*] M. E. Belowich, Dr. C. Valente, Prof. J. F. Stoddart
Department of Chemistry, Northwestern University
2145 Sheridan Road, Evanston, IL 60208 (USA)
Fax: (+1)847-491-1009
E-mail: stoddart@northwestern.edu
Homepage: http://stoddart.northwestern.edu
[**] The research described here was supported by the National Science
Foundation (NSF) in the United States under award CHE0924620.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201004304.
Figure 2. Design of rigid rodlike oligorotaxanes based on [p···p] stack-
ing interactions between aromatic rings separated by 3.5 ꢀ.
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to the molecules, rendering (Figure 2) them rodlike. Specif-
+
ically, we rationalized that by placing -CH2NH2 CH2- recog-
nition sites approximately 3.5 ꢀ apart from one another in the
dumbbells, the macrocycles would be situated so as to
optimize inter-ring [p···p] stacking interactions. We report,
herein, the design, the synthesis, and characterization of some
rigid [3]-, [4]-, [5]-, and [8]rotaxanes—namely 2R·2PF6,
3R·3PF6, 4R·4PF6, and 7R·7PF6.
The synthesis of the [3]rotaxane 2R·2PF6 is summarized
in Figure 3a. The dialdehyde 5 and the diamine 6 were added
to a solution of bisammonium salt 2D·2PF6 in CD3CN. Within
5 min, 2R·2PF6 was formed in quantitative conversion
according to 1H NMR spectroscopy. The chemical shifts
(Figure 3b) for the imine (Hc), pyridyl (Ha and Hb), and
ortho-aryl (Hd–Hg) protons are in good agreement with those
observed previously[15b] for a not dissimilar [2]rotaxane
1R·PF6. As expected, a single set of resonances in the
1H NMR spectrum is observed for the two homotopic rings
encircling the dumbbell.
Figure 4. a) Stick and b) space-filling representations of the solid-state
+
structure of 2R2+. The [N H···N] distances range from 2.03 to 2.14 ꢀ
À
+
À
and have [N H···N] angles of 172 and 1748. c) Stick and d) space-
filling representations[21] of the solid-state structure of 3R3+. Hydrogen
atoms and counterions have been omitted and discounted for clarity.
imposes[19] a linear, rigid conformation on the [3]rotaxane.
This observation begs the question—do these noncovalent
bonding interactions carry through to higher-order rotax-
anes?
The [4]rotaxane 3R·3PF6 was prepared[20] (Figure 5a) in
near quantitative conversion by adding 3D·3PF6 to 3 equiv-
alents each of 5 and 6. While the two outer rings are
homotopic, they are constitutionally heterotopic with respect
to the central ring, consistent with the 2:1 relative intensities
in the 1H NMR spectrum (Figure 5b) for the resonances
arising from the heterotopic rings. The presence of sharp
peaks at m/z 2149.8608 ([3R·2PF6]+), 1002.4507 ([3R·PF6]2+),
and 619.9806 ([3R]3+) in the ESI mass spectrum confirms the
constitution of the rotaxane. Single crystals of the [4]rotaxane,
suitable for X-ray crystallography, were grown by vapor
diffusion of tert-butyl methyl ether into a solution of 3R·3PF6
Figure 3. a) The template-directed synthesis of the [3]rotaxane
2R·2PF6, starting from 2D·2PF6, 5 and 6 employing Strategy B. b) The
1H NMR spectrum (500 MHz, CD3CN, 298 K) of the [3]rotaxane. The
assignment of the resonances is assisted by partitioning the structural
formula of 2R2+ into its separate dumbbell and ring components.
Electrospray ionization (ESI) mass spectrometry con-
firmed the constitution of the [3]rotaxane by the presence of
an intense base peak at m/z 1471.6220, corresponding to
[2R·PF6]+. Single crystals of the [3]rotaxane, suitable for X-
ray crystallography, were grown by liquid–liquid diffusion of
iPr2O into a solution of 2R·2PF6 in CH2Cl2. The solid-state
structure of 2R·2PF6 (Figure 4a,b) reveals[17] that the three
arenes in each of the two rings are in register with one another
and that their average mean planes are separated by the
[p···p] stacking distance of 3.5 ꢀ. In addition, the conforma-
Figure 5. a) The template-directed synthesis of the [4]rotaxane 3R·3PF6
starting from 3D·3PF6, 5, and 6, and employing strategy B. b) The
partial 1H NMR spectrum (500 MHz, CD3CN, 298 K) of the [4]rotaxane.
The assignment of the resonances is assisted by partitioning the
structural formula of 3R3+ into its separate dumbbell and ring—two
outer and one inner—components.
+
tion of 2R·2PF6 is stabilized[18] by four [N H···N] hydrogen
À
bonds and additional [p···p] stacking interactions between
one of the terminal 3,5-dimethoxyphenyl rings on the dumb-
bell with one of the pyridyl rings in one of the macrocycles.
This combination of noncovalent bonding interactions
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in MeOH. In this case, the solid-state structure (Figure 4c,d)
of 3R3+ reveals[22] that the arenes in two of the macrocycles
(RA and RB) are in register with one another—their average
mean planes are separated by a distance of 3.5 ꢀ—while the
third macrocycle (RC) is out of register with the other two by
ca. 528. This observation[23] is probably an artifact of crystal
packing and does not change the rigid and rodlike conforma-
tion of the molecule. The [5]rotaxane, 4R·4PF6, was also
1
prepared in a similar fashion and characterized by H NMR
spectroscopy as well as by ESI mass spectrometry (see the
Supporting Information). The spectroscopic evidence (see
below) is consistent with this rotaxane having a rigid rodlike
conformation.
In order to prepare higher-order rotaxanes, it has been
necessary to develop syntheses of their dumbbell components
using iterative reaction sequences. We illustrate this chemistry
by outlining (Figure 6a) the synthesis of the dumbbell
7D·7PF6 employing a single iteration beginning with the
reductive amination of 3,5-dimethoxybenzaldehyde (8) and
the diamine 9 to provide 10 which was subsequently Boc
protected, affording the alcohol 11. Swern oxidation afforded
the aldehyde 12, which was subjected to reductive amination
with bis(3-aminopropyl)amine (13), followed by acid-medi-
ated global deprotection of the amino groups and counterion
exchange providing 7D·7PF6. When this dumbbell was added
to 7 equivalents each of 5 and 6, the [8]rotaxane 7R·7PF6 was
obtained with near quantitative conversion. ESI mass spec-
Figure 7. The partial 1H NMR spectra (500 MHz, CD3CN, 298 K),
showing how the resonances for the imine and aromatic protons move
to higher fields and—in the case of the dibenzo ring—fan out as more
rings are added on going from the [2]- to the [3]- to the [4]- to the [5]-
to the [8]rotaxane. This pattern of behavior is indicative of multiple
[p···p] stacking interactions.
trometry confirmed the constitutional identity of 7R·7PF6 on
account of the intense peaks at m/z 1524.2985 ([7R·4PF6]3+),
1106.9836 ([7R·3PF6]4+), and 856.5903 ([7R·2PF6]5+). In the
1H NMR spectrum (Figure 6b), there are four resonances in a
2:2:2:1 ratio, corresponding to the imine protons present in
1) the three homotopic pairs of heterotopic rings and 2) the
central constitutionally heterotopic ring. The chemical shifts
of the imine resonances move upfield as they become more
shielded toward the center of the [8]rotaxane, i.e., the imine
protons corresponding to ring RA appear the furthest down-
field while the imine protons corresponding to ring RD appear
the furthest upfield.
Conformational insight can be deduced from 1H NMR
spectroscopic data, in line with literature precedence[24] for
other systems with efficient [p···p] stacking. In this present
case, there is strong evidence (Figure 7) that the higher-order
rotaxanes 4R·4PF6 and 7R·7PF6 are rodlike in solution. In
moving from the [2]rotaxane to the higher-order rotaxanes,
the resonances for the ring(s) that are nearest to the stoppers
of the dumbbell relocate progressively upfield. For example,
the imine proton in the [2]rotaxane, which resonates at d =
8.42 ppm, moves upfield by d = 0.12, 0.28, 0.35, and 0.45 ppm,
in turn, upon the addition of one (i.e., 2R·2PF6), two (i.e.,
3R·3PF6), three (i.e., 4R·4PF6), and six (i.e., 7R·7PF6) rings.
This upfield trend in chemical shifts is also observed for the
pyridyl (Ha and Hb) and aryl (Hd–Hi) protons. These 1H NMR
shifts shed light on the overall conformation of these
oligorotaxanes, in so far that as the number of macrocycles
increases, the amount of [p···p] interactions (shielding)
between the aromatic rings is more pronounced, accounting
for the upfield shifts observed in the spectra. This observation
is consistent with the stacking of aromatic rings, and strongly
suggests that the conformation of these oligorotaxanes is rod-
like in solution. Most importantly, this trend is not observ-
ed[12f] in the previously synthesized [3]-, [4]-, [5]-, [7]-, and
[11]rotaxanes where [p···p] interactions between adjacent
macrocycles are not possible.
Figure 6. a) The synthesis of the dumbbell 7D·7PF6 containing seven
secondary dialkylammonium recognition sites which are employed
under templation subsequently to assemble the [8]rotaxane under
thermodynamic control leading into the template-directed synthesis of
the [8]rotaxane 7R·7PF6, starting from 7D·7PF6, 5, and 6. b) The partial
1H NMR spectrum (500 MHz, CD3CN, 298 K) of the [8]rotaxane. The
assignment of the resonances follows the practice established previ-
ously for the [3]- and [4]rotaxanes.
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C225H275F18N28O39P3 [7R·3PF6]4+: 1106.9825, found 1106.9836; Calcd.
In this research program, aimed at producing readily
soluble, polycationic, monodisperse, rigid-rodlike polyrot-
axanes for single-molecule investigations on surfaces and
rheological studies in polar solvents, we have established
proof-of-principle in terms of efficient, high-yielding, tem-
plate-directed syntheses under thermodynamic control for
[n]rotaxanes up to n = 8. The challenge, which we are tackling
presently, is to extend the highly successful synthetic protocol,
based on DCC and employing iterative reaction sequences, to
make dumbbells with (nÀ1) recognition sites from whence
[n]rotaxanes, where n lies in the range 20–50, can be self-
assembled by templation of multiple rings around each and
every recognition site along the lengths of the dumbbells.
for C225H275F12N28O39P2 [7R·2PF6]5+: 856.5930, found 856.5903.
Received: July 14, 2010
Published online: August 30, 2010
Keywords: dynamic covalent chemistry ·
.
mechanically interlocked molecules · molecular recognition ·
noncovalent bonding interactions · self-assembly
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In a typical procedure, the appropriate oligoammonium dumbbell
compound (0.05 mmol, 1 equiv) was added to a solution of 2,6-
pyridine-dicarboxaldehyde (5) (n equiv, n = number of ammonium
recognition sites) and tetraethyleneglycol bis(2-aminophenyl)ether
(6) (n equiv) in MeCN (1 mL) and stirred for 24 h at room temper-
ature. Neat iPr2O was added dropwise to the reaction mixture until
precipitation of the oligorotaxane was complete. The precipitate was
collected by filtration, washed with iPr2O, and air-dried to afford the
oligorotaxane as a typically bright yellow powder.
2R·2PF6: Yield 93%. 1H NMR (CD3CN, 500 mhz): d = 9.40 (br.
s, 4H), 8.30 (s, 4H), 7.75 (t, J = 7.8 Hz, 2H), 7.59 (d, J = 7.8 Hz, 4H),
7.20 (t, J = 8.0 Hz, 4H), 6.99 (d, J = 2 Hz, 4H), 6.72 (t, J = 8.0 Hz,
4H), 6.70 (d, J = 8.0 Hz, 4H), 6.19 (d, J = 2.2 Hz, 4H), 5.97 (t, J =
2.2 Hz, 2H), 4.37 (t, J = 6.8 Hz, 4H), 4.24–4.21 (m, 8H), 3.82–3.78 (m,
4H), 3.74–3.70 (m, 4H), 3.58–3.37 (m, 20H), 3.25 (s, 12H), 1.9 ppm
(br. s, 2H). 13C NMR (CD3CN, 125 mhz): d = 161.3, 160.0, 151.3,
151.1, 139.6, 138.8, 134.2, 129.6, 128.4, 121.0, 120.4, 112.1, 106.4, 100.2,
69.7, 69.6, 68.4, 67.8, 54.2, 50.8, 44.7, 23.1 ppm. HR-MS (ESI): m/z
Calcd for C75H90F6N8O14P [2R·PF6]+: 1471.6217, found 1471.6220.
3R·3PF6: Yield 90%. 1H NMR (CD3CN, 500 mhz): d = 9.29 (br.
s, 4H), 8.99 (br. s, 2H), 8.23 (s, 4H), 8.14 (s, 2H), 7.72 (t, J = 7.7 Hz,
2H), 7.54 (d, J = 7.7 Hz, 4H), 7.47 (d, J = 7.7 Hz, 2H), 7.36, (t, J =
7.7 Hz, 1H), 7.14–7.08 (m, 6H), 6.92 (d, J = 8.3 Hz, 4H), 6.78 (d, J =
8.3 Hz, 2H), 6.61 (d, J = 8.3 Hz, 4H), 6.56 (t, J = 8.3 Hz, 4H), 6.48 (d,
J = 8.3 Hz, 2H), 6.39 (t, J = 8.3 Hz, 2H), 6.15 (d, J = 2.3 Hz, 4H), 5.94
(t, J = 2.3 Hz, 2H), 4.22 (t, J = 7.0 Hz, 4H), 4.15–4.13 (m, 8H), 3.89 (t,
J = 3.9 Hz, 4H), 3.76–3.32 (m, 36H), 3.33 (br. s, 4H), 3.18 (br. s, 4H),
3.26 (s, 12H), 1.72 ppm (br. s, 4H). 13C NMR: see SI. HR-MS (ESI):
m/z Calcd for C105H127F12N12O19P2 [3R·2PF6]+: 2149.8622, found
2149.8608; Calcd for C105H127F6N12O19P1 [3R·PF6]2+: 1002.4490, found
1002.4507; Calcd for C105H127N12O19 [3R]3+: 619.9780, found 619.9806.
4R·4PF6: Yield 88%. 1H NMR (CD3CN, 500 mhz): d = 9.25 (br.
s, 4H), 8.90 (br. s, 4H), 8.20 (s, 4H), 8.07 (s, 4H), 7.69 (t, J = 7.7 Hz,
2H), 7.52 (d, J = 7.7 Hz, 4H), 7.42 (d, J = 7.7 Hz, 4H), 7.32 (t, J =
7.7 Hz, 2H), 7.10 (t, J = 8.4 Hz, 4H), 7.04 (t, J = 8.4 Hz, 4H), 6.92 (d,
J = 8.4 Hz, 4H), 6.70 (d, J = 8.4 Hz, 4H), 6.56 (d, J = 7.3 Hz, 4H), 6.51
(t, J = 7.3 Hz, 4H), 6.36 (t, J = 7.3 Hz, 4H), 6.29 (t, J = 7.3 Hz, 4H),
6.12 (d, J = 1.9 Hz, 4H), 5.91 (t, J = 1.9 Hz, 2H), 4.18–4.08 (m, 12H),
3.81–3.72 (m, 8H), 3.67 (br. s, 8H), 3.55–3.52 (m, 15H), 3.42–3.32 (m,
30H), 3.27 (s, 12H), 3.10–3.05 (m, 7H), 1.65 (br. s, 4H), 1.47 ppm (br.
s, 2H). 13C NMR: see SI. HR-MS (ESI): m/z Calcd for
C135H164F12N16O24P2 [4R·2PF6]2+: 1341.5689, found 1341.5625; Calcd
for C135H164F6N16O24P1 [4R·PF6]3+: 846.0577, found 846.0558.
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spectroscopic data. HR-MS (ESI): m/z Calcd for C225H275F24N28O39P4
[7R·4PF6]3+
1524.2982, found 1524.2985; Calcd for
C
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[17] Crystal data for 2R·2PF6. C75H90F12N8O14P2·CH2Cl2·(C3H7)2O.
M = 1804.59, space group P1, triclinic, a = 13.4795(5), b =
14.5068(4), c = 24.8176(7) ꢀ, a = 85.849(2)8, b = 88.703(2)8, g =
62.846(2)8, V= 4306.4(2) ꢀ3, Z = 2, Calculated density =
1.392 gcmÀ3
,
m = 1.839 mmÀ1
,
13912 reflections collected,
13912 observed independent reflections (Rint = 0.0000) gave
R = 0.0601 for I > 2s(I) and wR2 was 0.1616.
À
[18] There are intramolecular [C H···p] interactions in the crystal
lattice between the 3,5-dimethoxyphenyl unit of one molecule
and the 3,5-dimethoxyphenyl unit of the adjacent molecule.
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dissociation from 3R·3PF6 because it can be removed by further
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+
[21] The [N H···N] distances are not provided in the case of 3R3+ as
À
a result of the dumbbell component being disordered in the
crystal lattice.
´
Org. Lett. 2003, 5, 1887 – 1890; d) J. D. Badjic, S. J. Cantrill, R. H.
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c = 22.7396(5) ꢀ, a = 90.000(2)8, b = 95.673(2)8, g = 90.000(2)8,
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1.320 mmÀ1, 78337 reflections collected, 18089 observed inde-
pendent reflections (Rint = 0.0765) gave R = 0.0840 for I > 2s(I)
and wR-2 was 0.2296.
[23] RC is twisted by approximately 528 with respect to the other two
macrocycles (RA and RB) thus forming only two sets of [p···p]
interactions with RB. This phenomenon is most likely a result of
[p···p] interactions between one arene of RC with a 3,5-
dimethoxyphenyl ring of the adjacent molecule in the crystal
lattice.
Grubbs, E. N. Guidry, R. Orenes, J. F. Stoddart, Angew. Chem.
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7212
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