Rotaxanes synthesized through sodium-ion-templated clipping of macrocycles around nonconjugated amide and urea functionalities

Article abstract of DOI:10.1002/chem.201400323

A single urea or amide functionality in a dumbbell-shaped guest can be clipped by a macrocycle generated from a diamine and a dialdehyde through the templating effect of a Na⁺ ion (see scheme). The resulting imine-containing rotaxanes can then be reduced to allow isolation of stable amine-based rotaxanes. A single urea or amide functionality in a dumbbell-shaped guest can be clipped by a macrocycle generated from a diamine and a dialdehyde through the templating effect of a Na⁺ ion (see scheme). The resulting imine-containing rotaxanes can then be reduced to allow isolation of stable amine-based rotaxanes.

Full text of DOI:10.1002/chem.201400323

DOI: 10.1002/chem.201400323
Communication
&
Macrocycles
Rotaxanes Synthesized Through Sodium-Ion-Templated Clipping
of Macrocycles Around Nonconjugated Amide and Urea
Functionalities
Tsung-Hsien Ho,[a] Chien-Chen Lai,[b] Yi-Hung Liu,[a] Shie-Ming Peng,[a] and Sheng-
Hsien Chiu*[a]
which sodium ions template the threading of linear molecules,
featuring non-conjugated urea and amide functionalities,
through the cavity of bis-p-xylyl[26]crown-6 (BPX26C6) to form
pseudorotaxanes and indicated its potential for application in
the formation of (pseudo)rotaxane structures from peptide
and nylon units.[6] For this present study, we wished to develop
a “clipping” version of this recognition system to extend the
capability and flexibility of introducing interlocked structures
into important artificial and biological (macro)molecules.
Herein, we report that a macrocycle generated from a diamine
and a dialdehyde can be “clipped” around a single urea or
amide functionality in a dumbbell-shaped guest through the
templating effect of a Na+ ion, with subsequent reduction of
the imine-containing rotaxane allowing isolation of a stable
amine-based rotaxane.
Abstract: A single urea or amide functionality in a dumb-
bell-shaped guest can be “clipped” by a macrocycle gen-
erated from a diamine and a dialdehyde through the tem-
plating effect of a Na+ ion (see scheme). The resulting
imine-containing rotaxanes can then be reduced to allow
isolation of stable amine-based rotaxanes.
Because rotaxanes have potential applications in many re-
search fields (e.g., molecular electronics;[1] gelation;[2] molecular
preservation and transportation[3]), several synthetic ap-
proaches have been developed to facilitate their syntheses
using different molecular designs and employing various syn-
thetic conditions.[4] Among them, the “clipping” approach pro-
vides high synthetic flexibility: the interlocked macrocycle is
generated in situ and, therefore, the reaction conditions, the
selection of suitable stoppering groups, and the assembly of
the dumbbell-shaped component are less restricted than in
other approaches (Figure 1). Many elegant interlocked mole-
To realize the concept, we synthesized the dumbbell-shaped
urea 1, diamine 2, and dialdehyde 3 (Scheme 1) and mixed
them with sodium tetrakis(3,5-trifluoromethylphenyl)borate
Figure 1. Cartoon representation of the “clipping” approach in rotaxane syn-
thesis.
cules have been synthesized using this approach, through
both kinetic (irreversible) and thermodynamic (reversible) reac-
tions.[5] Previously, we reported a new recognition system in
[a] T.-H. Ho, Y.-H. Liu, Prof. S.-M. Peng, Prof. S.-H. Chiu
Department of Chemistry and Center for Emerging
Material and Advanced Devices
Scheme 1. “Clipping” synthesis of the [2]rotaxane 5 from a conjugated urea-
containing dumbbell-shaped component.
National Taiwan University
No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, 10617, (R.O.C.)
Fax: (+886)2-33661677
(NaTFPB)[7] as an equimolar (10 mm) solution in CDCl3. The
rapid appearance and disappearance of the signals for the
imine and aldehyde groups, respectively, in the region d 8.0–
E-mail: shchiu@ntu.edu.tw
1
[b] Prof. C.-C. Lai
10.0 in the H NMR spectra suggested that imine bond forma-
Institute of Molecular Biology, National Chung Hsing University and Depart-
ment of Medical Genetics, China Medical University Hospital,
Taichung, Taiwan (R.O.C.)
tion between the diamine 2 and the dialdehyde 3 was favored
under these conditions (Figure 2b). To accelerate the reaction
toward equilibrium, we heated the solution at 323 K, resulting
in a gradual increase in the set of signals for the corresponding
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/chem.201400323.
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Although we had successfully isolated the [2]rotaxane 5
after using Na+ ions to template the synthesis of a macrocycle
around a single conjugated urea functionality, the low efficien-
cy of this reaction, most likely related to the originally low
complexation ratio in the formation of the imine-containing
[2]rotaxane [4·Na][TFPB], certainly required improvement. We
suspected that the proximity of the bulky 3,5-di-tert-butyl
group to the urea functionality in the dumbbell-shaped mole-
cule 1 might have disturbed the formation of the imine-con-
taining macrocycle and/or the p-stacking of its aromatic rings
with those of 1, thereby decreasing the efficiency of the forma-
tion of the imine-containing [2]rotaxane. Moreover, because
imine-containing oligomers and/or polymers would presuma-
bly be generated in solution prior to the formation of such
[2]rotaxanes, we wished to increase their solubility in less-polar
solvents to avoid the formation of precipitates or gels. Thus,
we synthesized the dumbbell-shaped threadlike molecules 6
and 7 (which have their urea functionalities conjugated and
non-conjugated to aromatic rings, respectively) and dialdehyde
8, all presenting hexyl groups (Scheme 2).
1
Figure 2. Partial H NMR spectra (400 MHz, CDCl3, 298 K) of a) the dumbbell-
shaped urea 1 and b, c) an equimolar mixture of 1, the diamine 2, the di-
aldehyde 3, and NaTFPB (10 mm) after heating at 323 K for b) 0 and c) 33 h.
Because BPX26C6 can encircle a single urea functionality
through the templating effect of a Na+ ion,[6a] we suspected
that diamine 9, which mimics part of the structure of BPX26C6
(one diethylene glycol chain linked to two xylyl groups), would
be a possible clipping component. As revealed in Figure 4, an
imine-containing [2]rotaxane [4·Na][TFPB].[8] We estimated the
yield of [4·Na][TFPB] generated at equilibrium under these con-
ditions after 33 h to be 24%, based on integration of the
signal at d 6.80–6.90, which we assign to the shielded aromatic
protons of the xylyl unit in the imine-containing [2]rotaxane.
Subsequent NaBH4-mediated reduction of the imino bonds of
[4·Na][TFPB] provided the [2]rotaxane 5 in 11% yield (in two
steps) after column chromatography.[9]
We obtained single crystals suitable for X-ray crystallography
after vapor diffusion of hexanes into a CH2Cl2 solution of the
[2]rotaxane 5. The solid state structure reveals[10,11] the expect-
ed [2]rotaxane geometry (Figure 3), in which the urea unit is
encircled by the aza-macrocycle, with the urea C=O and NH
units hydrogen bonded to the secondary amino groups and
one of the oxygen atoms of the macrocycle, respectively.
Figure 3. Ball-and-stick representation of the solid state structure of the
[2]rotaxane 5.
Scheme 2. “Clipping” syntheses of [2]rotaxanes from two dumbbell-shaped
molecules, each containing a single urea functionality.
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of the various imine-containing [2]rotaxanes prepared in this
study as well as those of their corresponding amine-containing
[2]rotaxanes.
Equimolar (10 mm) mixtures of the dumbbell-shaped urea
derivative 6 or 7, the dialdehyde 8, the diamine 2, and NaTFPB
in CDCl3 reached equilibrium after being heated at 323 K for 8
and 24 h, respectively; we estimated the yields of the corre-
sponding imine-containing [2]rotaxanes to be 69 and 28%, re-
spectively, based on integration of various signals in the
1H NMR spectra (see Supporting Information). Using NaBH4 to
reduce the imino bonds, we isolated the [2]rotaxanes 12 (53%
yield) and 13 (21% yield) in which the aza-macrocyclic compo-
nents encircled the conjugated and non-conjugated urea sta-
tions, respectively. This result suggested that the 2,6-
dihydroxymethylpyridine and the diethylene glycol motifs
present in the diamines 2 and 9, respectively, were structurally
similar components when constructing urea-based rotaxanes
through such a “clipping” approach.
1
Figure 4. Partial H NMR spectra (400 MHz, CDCl3, 298 K) of a) the dumbbell-
shaped urea 6 and b–d) an equimolar mixture of 6, the dialdehyde 8, the di-
amine 9, and NaTFPB (10 mm) heated at 323 K for b) 0, c) 1, and d) 8 h.
Having proven that “clipping” could be applied to both con-
jugated and non-conjugated urea derivatives, we wished to
equimolar (10 mm) mixture of the dumbbell-shaped
urea derivative 6, dialdehyde 8, diamine 9, and
Table 1. Efficiencies of the “clipping” syntheses of imine-containing [2]rotaxanes and
NaTFPB in CDCl3 reached equilibrium after heating at
323 K for 8 h. The gradual growth of two sets of sig-
nals for the benzylic and para-disubstituted phenyl
protons—at d=4.35/4.55 and 6.70/7.20, respectively,
representing the complexed imine-containing macro-
cyclic and the dumbbell-shaped components, respec-
yields of corresponding amine-containing [2]rotaxanes.[a]
[2]Rotaxane
Diamine
Dumbbell
Imine[2]rotaxane
[%][b]
Amine[2]rotaxane
[%][c]
t
[h][d]
10
11
12
13
15
16
18
19
9
9
2
2
9
2
9
2
6
7
6
82
27
69
28
23
9
40
17
53
21
10
2
8
22
8
24
28
36
24
28
1
tively—in the H NMR spectra suggested that the de-
7
sired imine-containing [2]rotaxane was generated
over time. Based on integration of the signals in the
1H NMR spectra, the yield of the imine-containing
[2]rotaxane generated under these conditions
reached 82% at equilibrium.[12] The significantly
higher yield of the imine-containing [2]rotaxane gen-
erated in solution when using 6 as the dumbbell-
shaped urea derivative instead of 1 supported our
hypothesis that the proximity of the bulky 3,5-di-tert-
butyl groups to the urea station in 1 was a factor af-
fecting the efficiency of the clipping process. The re-
14
14
17
17
65
58
36
34
[a] Experiments performed using an equimolar mixture of the dialdehyde 8, NaTFPB,
a diamine, and a dumbbell-shaped guest (10 mm) at 323 K. [b] Determined from inte-
gration of signals in the 1H NMR spectra. [c] Isolated yield from the NaBH4-mediated
reduction of the imine precursor. [d] Time required for the reaction to reach equilibri-
um.
action of an equimolar (10 mm) mixture of the dumbbell-
shaped urea 7 (containing a non-conjugated and less-acidic
NH urea unit), the dialdehyde 8, the diamine 9, and NaTFPB in
CDCl3 at 323 K also produced a corresponding imine-contain-
ing [2]rotaxane, but with relatively low efficiency (27%) and
a longer time (22 h) required to reach equilibrium. The relative-
ly low yield at equilibrium for the formation of the imine-con-
taining [2]rotaxane incorporating the dumbbell-shaped urea 7,
relative to that incorporating 6, was likely due to the urea
functionality in the former not being conjugated to aromatic
rings; that is, its less-acidic NH units formed weaker hydrogen
bonds to the oxygen and/or nitrogen atoms of the encircling
imine-containing macrocycle. Reduction of these two imine-
containing [2]rotaxanes gave the amine-containing [2]rotax-
anes 10 (40% yield) and 11 (17% yield), in which the dumb-
bell-shaped components featured conjugated and non-conju-
gated urea functionalities, respectively. Table 1 lists the yields
demonstrate that such an approach could also be used to
form a macrocycle around a dumbbell-shaped component fea-
turing a single non-conjugated amide unit. Therefore, we
heated an equimolar (10 mm) mixture of the dumbbell-shaped
amide 14, the dialdehyde 8, the diamine 9 (2), and NaTFPB in
CDCl3 at 323 K for 28 (36) h and then performed NaBH4-medi-
ated reduction to afford the [2]rotaxane 15 (16) in 10% (2%)
yield after column chromatography (Scheme 3). Because the
corresponding intermediate imine-containing [2]rotaxanes
were generated in approximately 23 and 9% yields at equilibri-
um (see the Supporting Information), we suspect that the low
efficiencies of the syntheses of the amine-containing [2]rotax-
anes 15 and 16 arose from relatively weak interactions be-
tween the templating Na+ ion, the imine-containing macrocy-
cle, and the dumbbell-shaped amides.
Although the use of Na+ ions to template the clipping of
imine-containing macrocycles around a dumbbell-shaped com-
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Scheme 3. “Clipping” syntheses of [2]rotaxanes from a dumbbell-shaped
component containing a single non-conjugated amide functionality.
ponent featuring a single non-conjugated amide unit appeared
to be less efficient than those reactions involving urea-contain-
ing counterparts, presumably because of weaker noncovalent
interactions, we suspected that the situation could be im-
proved significantly if the dumbbell-shaped component pre-
sented two proximal amide units. Therefore, we synthesized
the dumbbell-shaped molecule 17 (Scheme 4), which contains
a glycine residue amidated at both its N- and C-termini to
mimic the linking of amino acids in common peptides, and
mixed it with the diamine 2 (9), the dialdehyde 8, and NaTFPB
Scheme 4. “Clipping” syntheses of two [2]rotaxanes from a dumbbell-
shaped component containing two peptide-like amido groups.
1
(each 10 mm) in CDCl3. The H NMR spectra of the solutions
containing the diamines 2 (Figure 5b and c) and 9 (Figure 5d
and e) both displayed the growth of new sets of signals after
mixing. The intensities of these sets of signals reached their
maxima (i.e., equilibria were established) after heating at 323 K
for 28 and 24 h, respectively; we estimated the yields for the
corresponding rotaxanes to be 58 and 65%, respectively,
1
based on integration of pertinent signals in the H NMR spec-
tra.[13] Using NaBH4 to reduce the imine-containing macrocyclic
components, we isolated, after column chromatography, the
[2]rotaxanes 18 (36% yield) and 19 (34% yield), incorporating
2,6-dihydroxypyridine and diethylene glycol units, respectively,
in their interlocked macrocyclic components. The significantly
higher yields of the [2]rotaxanes 18 and 19 (and of their imine-
containing precursors) relative to that of the [2]rotaxanes 15
and 16 indicated that, although such a “clipping” approach
might not be particularly efficient for the recognition of
a single non-conjugated amide functionality, its application to
1
Figure 5. Partial H NMR spectra (400 MHz, CDCl3, 298 K) of a) the dumbbell-
shaped diamide 17; b, c) an equimolar (10 mm) mixture of 17, the dialde-
hyde 8, the diamine 2, and NaTFPB after heating at 323 K for b) 0 and c)
28 h; and d, e) an equimolar (10 mm) mixture of 17, the dialdehyde 8, the
diamine 9, and NaTFPB after heating at 323 K for d) 0 and e) 24 h.
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macrocycles onto dibenzylammonium or pyridinium ion-containing
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the syntheses of interlocked structures from dumbbell-shaped
molecules presenting multiple amide bonds (e.g., peptides)
has the potential to be reasonably efficient. These results sug-
gest that such a clipping approach has potential for applica-
tion in the construction of interlocked molecules from pep-
tides containing multiple C- and N-terminal amidated amino
acid residues, especially glycine residues.[14]
We have demonstrated that Na+ ions are capable of tem-
plating the formation of imine-containing macrocycles around
single non-conjugated urea or amide functionalities in dumb-
bell-shaped guests (yields of up to 82%), with subsequent
NaBH4-mediated reductions affording corresponding thermo-
dynamically stable amine-containing [2]rotaxanes (yields of up
to 53%). We have also demonstrated that such a “clipping” ap-
proach has high potential for application in the construction of
rotaxanes from guests having peptide-like structures. We be-
lieve that the requirement of only a single common urea or
amide functionality in the dumbbell-shaped component and
the ease of formation of the macrocyclic components from
linear species will make this synthetic approach and recogni-
tion system practically useful for introducing interlocked struc-
tures into artificial or biological (macro)molecules, a direction
that we are current investigating.
Acknowledgements
We thank the National Science Council (Taiwan) (NSC-102-2119
M-002-007) and National Taiwan University (NTU-102-R890913)
for financial support.
Keywords: amide
·
clipping
·
molecular recognition
·
rotaxane · template · urea
[9] Using selenophenol (PhSeH) as the reductant in the same reaction, we
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tography.
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paper. These data can be obtained free of charge from The Cambridge
Crystallographic Data Centre via www.ccdc.cam.ac.uk/data request/cif.
[11] Crystal data for 5: [C59H76O3N6]; Mr =917.26; orthorhombic; space group
P2(1)2(1)2(1); a=10.4439(2); b=13.3308(4); c=39.3404(9) ꢂ.; V=
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5477.2(2) ꢂ3; 1calcd =1.112 gcmÀ3
; ; T=200(2) K.;
m(CuKa)=0.533 mmÀ1
colorless plate; 9955 independent measured reflections; F2 refinement;
R1 =0.0768; wR2 =0.2108.
[12] When we replaced NaTFPB with LiTFPB or KTFPB and performed the
synthesis of the [2]rotaxane 10 under similar conditions, the yields of
the imine-containing [2]rotaxane generated in solution, based on inte-
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“clipping” reaction.
[13] Possibly because of stronger solvation of the templating Na+ ion in
more-polar solvents, a similar “clipping” reaction performed in CD3CN
provided no observable signals belonging to the corresponding [2]ro-
1
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Received: January 26, 2014
Published online on March 13, 2014
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