Squaraine rotaxanes with boat conformation macrocycles

Article abstract of DOI:10.1021/jo901298n

(Chemical Equation Presented) Mechanical encapsulation of fluorescent, deep-red bis(anilino)squaraine dyes inside Leigh-type tetralactam macrocycles produces interlocked squaraine rotaxanes. The surrounding macrocycles are flexible and undergo rapid excha

Full text of DOI:10.1021/jo901298n

pubs.acs.org/joc
Squaraine Rotaxanes with Boat Conformation Macrocycles
Na Fu, Jeffrey M. Baumes, Easwaran Arunkumar, Bruce C. Noll, and Bradley D. Smith*
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46545
smith.115@nd.edu
Received June 17, 2009
Mechanical encapsulation of fluorescent, deep-red bis(anilino)squaraine dyes inside Leigh-type
tetralactam macrocycles produces interlocked squaraine rotaxanes. The surrounding macrocycles
are flexible and undergo rapid exchange of chair and boat conformations in solution. A series of
X-ray crystal structures show how the rotaxane co-conformational exchange process involves
simultaneous lateral oscillation of the macrocycle about the center of the encapsulated squaraine
thread. Rotaxane macrocycles with 1,4-phenylene sidewalls and 2,6-pyridine dicarboxamide brid-
ging units are more likely to adopt boat conformations in the solid state than analogous squaraine
rotaxane systems with isophthalamide-containing macrocycles. A truncated squaraine dye, with a
secondary amine attached directly to the central C4O2 core, is less electrophilic than the extended
bis(anilino)squaraine analogue, but it is still susceptible to chemical and photochemical bleaching. Its
stability is greatly enhanced when it is encapsulated as an interlocked squaraine rotaxane. An X-ray
crystal structure of this truncated squaraine rotaxane shows the macrocycle in a boat conformation,
and NMR studies indicate that the boat is maintained in solution. Encapsulation as a rotaxane
increases the dye’s brightness by a factor of 6. The encapsulation process appears to constrain the dye
and reduce deformation of the chromophore from planarity. This study shows how mechanical
encapsulation as a rotaxane can be used as a rational design parameter to fine-tune the chemical and
photochemical properties of squaraine dyes.
Introduction
namics of the mechanically bonded components.2-4 More than
a decade ago, the group of Leigh and co-workers developed a
versatile rotaxane synthesis method based on a templated
clipping reaction that wraps a tetralactam macrocycle around
Interest in mechanically interlocked molecules, especially
catenanes and rotaxanes, is increasing as advances in templated
synthesis allow chemists to design more complicated molecular
systems with programmable functions.1 A requirement for
rational design of functional rotaxanes is a quantitative under-
standing of the factors that control the conformational dy-
(2) (a) Yoon, I.; Miljanic, O. S.; Benitez, D.; Khan, S. I.; Stoddart, J. F.
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Published on Web 07/29/2009
DOI: 10.1021/jo901298n
r
2009 American Chemical Society

Fu et al.
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FIGURE 1. Squaraine dyes and squaraine rotaxanes.
an appropriate dumbbell-shaped thread component.5,6 On-
going work by this group and by others has produced a
spectacular array of Leigh-type rotaxanes and demonstrated
sophisticated molecular functions such as shuttling, solar en-
ergy capture, and chemical sensing.7-9 The published papers
include quite a few rotaxane X-ray crystal structures, and the
vast majority show the surrounding macrocycle in a chair or
distorted-chair conformation.5-7 Examples of Leigh-type ro-
taxanes with the tetralactam macrocycle in an obvious boat
conformation are very rare.6 However, several recent papers
from different laboratories report UV and IR spectral evidence
suggesting, but not proving definitively, that the boat confor-
mation can become favored under shuttling conditions that
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A.; Slawin, A. M. Z.; Teat, S. J.; Wong, J. K. Y. J. Am. Chem. Soc. 2001, 123,
5983–5989. (c) Lane, A. S.; Leigh, D. A.; Murphy, A. J. Am. Chem. Soc. 1997,
119, 11092–11093. (d) Clegg, W.; Gimenez-Saiz, C.; Leigh, D. A.; Murphy, A.;
Slawin, A. M. Z.; Teat, S. J. J. Am. Chem. Soc. 1999, 121, 4124–4129.
(6) Brancato, G.; Coutrot, F.; Leigh, D. A.; Murphy, A.; Wong, J. K. Y.;
Zerbetto, F. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4967–4971.
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J. Am. Chem. Soc. 2008, 130, 1836–1838. (b) Barrell, M. J.; Leigh, D. A.;
Lusby, P. J.; Slawin, A. M. Z. Angew. Chem., Int. Ed. 2008, 47, 8036–8039.
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(d) Marlin, D. S.; Cabrera, D. G.; Leigh, D. A.; Slawin, A. M. Z. Angew.
Chem., Int. Ed. 2006, 45, 77–83. (e) Biscarini, F.; Cavallini, M.; Leigh, D. A.;
Leon, S.; Teat, S. J.; Wong, J. K. Y.; Zerbetto, F. J. Am. Chem. Soc. 2002,
124, 225–233. (f ) Asakawa, M.; Brancato, G.; Fanti, M.; Leigh, D. A.;
Shimizu, T.; Slawin, A. M. Z.; Wong, J. K. Y.; Zerbetto, F.; Zhang, S. W.
J. Am. Chem. Soc. 2002, 124, 2939–2950. (g) Brouwer, A. M.; Frochot, C.;
Gatti, F. G.; Leigh, D. A.; Mottier, L.; Paolucci, F.; Roffia, S.; Wurpel,
G. W. H. Science 2001, 291, 2124–2128.
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Soc. 2008, 130, 1534–1535. (b) Jagesar, D. C.; Hartl, F.; Buma, W. J.; Brouwer, A.
M. Chem.;Eur. J. 2008, 14, 1935–1946. (c) Mateo-Alonso, A.; Guldi, D. M.;
Paolucci, F.; Prato, M. Angew. Chem., Int. Ed. 2007, 46, 8120–8126. (d)
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FIGURE 2. X-ray crystal structures of bis(anilino)squaraine ro-
taxanes 2a-e.
provide stabilizing noncovalent interactions such as aromatic
stacking and hydrogen bonding.9,10
(10) For other examples of macrocycle conformational equilibria, see: (a)
Abbenante, G.; Fairlie, D. P.; Gahan, L. R.; Hanson, G. R.; Pierens, G. K.; van
den Brenk, A. L. J. Am. Chem. Soc. 1996, 118, 10384–10388. (b) Kumar, S.;
Hundal, M. S.; Hundal, G.; Kaur, N.; Singh, H. Tetrahedron 1997, 53, 10841–
10850. (c) Loeb, S. J.; Tiburcio, J.; Vella, S. J. Chem. Commun. 2006, 1598–1600.
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TABLE 1. Diagnostic Crystallographic Distances and Angles for Rotaxanes 2a-e and 5
distance or anglea
2a
2b
2c
2d
2e
5
˚
amide NH O (A)
3 3 3
2.02/2.01
2.01/2.01
157.8/156.8
156.8/157.8
6.61
2.13/2.03
2.12/2.12
156.3/152.6
151.6/151.7
6.63
2.41/2.38
3.24/3.32
13.15
2.39/2.39
2.14/2.29
146.5/158.2
158.7/160.5
6.78
2.36/2.53
3.50/3.21
13.09
2.22/2.18
2.25/2.04
156.3/153.9
156.1/150.1
6.66
2.39/2.48
3.35/3.28
13.16
1.95/2.07
2.13/2.17
169.4/179.4
163.2/146.4
7.16
2.16/2.18
2.15/2.17
163.9/164.0
164.0/163.9
7.18
amide N
H
O (deg)
3 3 3 3 3 3
b
Centr.-to-Centr. (A)
˚
2.41/2.41c
3.15/3.15
13.29
˚
Nc-Ha and Nd-Hb (A)
˚
Nc-Oa and Nd-Ob (A)
Na-Nb (A)
˚
13.25
a Atom labels are in Figure 3. b Centroid-to-centroid distance between the two parallel 1,4-phenylene sidewalls in the macrocycle. c Nc-Ha and Nd-Hd
distances because of chair conformation.
In 2005, we reported that the Leigh clipping methodology
can be used to convert squaraine dyes 1 into squaraine
rotaxanes 2 (Figure 1), and we are developing squaraine
rotaxanes as a new class of highly stable and very bright,
deep-red fluorescent dyes.11 We have demonstrated that the
surrounding tetralactam macrocycle sterically protects the
dye and greatly increases chemical stability. A more subtle
question is whether the macrocycle can be used to fine-tune
the squaraine photophysical properties in a controllable
manner. This requires an intimate understanding of rotaxane
FIGURE 3. Atom labels for squaraine rotaxanes.
structure and macrocycle dynamic motion. X-ray crystal
structures of the first few squaraine rotaxanes that we
and the solved structures are illustrated in Figure 2, with the
key crystallographic distances in Table 1 and associated
atom labeling in Figure 3. It is worth noting that the
ORTEPs of these solid-state structures show no evidence
of conformational disorder (see Supporting Information).
The structural discussion starts with the four squaraine
rotaxanes 2a-d that each have a pyridyl-containing macro-
cycle. The previously reported solid-state structure of 2a,11a
with R = H on the four terminal benzyl stopper groups,
shows the macrocycle in a chair conformation (C2h
symmetry) that is commonly observed with Leigh-type
rotaxanes. In striking contrast, the new crystal structures
of squaraine rotaxanes 2b-d, where R=Br, I, and CH3, each
have the surrounding pyridyl-containing macrocycle in a
boat conformation (C2ν symmetry). Another difference is the
location of the macrocycle relative to the encapsulated dye.
The chair macrocycle in 2a is located centrally and symme-
trically over the core of its encapsulated squaraine, whereas
the boat macrocycles in 2b-d are translocated to one side.
This co-conformation reduces the degree of cofacial overlap
of the macrocycle’s electron-rich 1,4-phenylene sidewalls
with the electron-deficient C4O2 core of the squaraine.12
In an effort to rationalize this difference in solid-state
conformations, we looked for diagnostic intramolecular
distances that were conformation-dependent. In each struc-
ture, the macrocyclic NH residues are engaged in bifurcated
hydrogen bonds with the encapsulated squaraine oxygens,
but there is little difference in the apparent strength of the
prepared all showed the phenylene-containing tetralactam
macrocycle located centrally over the squaraine dye and in a
chair conformation. Here, we report a comparative study of
the homologous squaraine rotaxane series 2a-e and our
finding of a much richer array of solid-state structures,
including several examples with the surrounding macrocycle
in a boat conformation. We also report the structure of a new
type of truncated squaraine rotaxane, 5, with green fluores-
cence and a surrounding macrocycle that adopts a rigid boat
conformation in the solid and solution state. The reduced
structural flexibility of rotaxane 5 appears to be the reason
why it exhibits a significantly higher fluorescence quantum
yield than its parent squaraine dye. This work expands our
understanding of squaraine rotaxane dynamic structure and
how it affects the photophysical properties of the encapsu-
lated dye.
Results and Discussion
Bis(anilino)squaraine Rotaxanes. The bis(anilino)squaraine
dyes 1a-d were made by condensing the appropriate aniline
precursors with squaric acid using standard literature condi-
tions.11 The squaraine rotaxanes 2a-e were subsequently
prepared by a common procedure that simultaneously added
separate solutions of the appropriate diacid dichloride and 1,4-
xylylenediamine to a solution of squaraine dye. The isolated
yields for this five-component assembly process were between
26 and 40% and quite reproducible.
All of the rotaxane tetralactam macrocycles in this report
are comprised of two 1,4-phenylene side-walls that are
connected by two identical bridging units that are either
2,6-pyridinedicarboxamide (hereafter referred to as the
pyridyl-containing macrocycle) in the case of 2a-d or iso-
phthalamide units in 2e. Single crystals of these five bis(anil-
ino)squaraine rotaxanes were analyzed by X-ray diffraction,
hydrogen bonding as judged by the N O distances and
NH O angles that are listed in Table 1. Similarly, the
centroid-to-centroid distance between the phenylene side-
3 3 3
3 3 3
˚
walls in chair conformer 2a is 6.60 A and quite close to the
(12) In this paper, we use the term “conformation” when we refer to the
macrocycle as an isolated structural entity, and we use the term “co-
conformation” when we refer to the entire rotaxane. Co-conformation refers
to the relative positions and orientations of the mechanically interlocked
components with respect to each other. Fyfe, M. C. T.; Glink, P. T.; Menzer,
S.; Stoddart, J. F.; White, A. J. P.; Williams, D. J. Angew. Chem., Int. Ed.
1997, 36, 2068–2069.
(11) (a) Arunkumar, E.; Forbes, C. C.; Noll, B. C.; Smith, B. D. J. Am.
Chem. Soc. 2005, 127, 3288–3289. (b) Arunkumar, E.; Fu, N.; Smith, B. D.
Chem.;Eur. J. 2006, 12, 4684–4690. (c) Arunkumar, E.; Sudeep, P. K.;
Kamat, P. V.; Noll, B. C.; Smith, B. D. New J. Chem. 2007, 31, 677–683.
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FIGURE 4. Partial 1H NMR spectra at 22 °C in CDCl3 showing
the macrocycle methylene signals for squaraine rotaxanes: (a) 2d
with J=5.8 Hz in a 300 MHz spectrum; (b) 5 with J1=8.2 Hz, J2=
14.4 Hz (left) and J1=1.5 Hz, J2=14.4 Hz (right) in a 600 MHz
spectrum.
FIGURE 5. Co-conformational exchange in squaraine rotaxanes
2a-e induces linear oscillation of the macrocycle about the center of
the squaraine thread. For clarity, not all possible conformational
exchange pathways are shown.
˚
range of 6.63-6.78 A for boat conformers 2b-d. As
expected, the two pyridyl nitrogens Nc and Nd in each
macrocycle form internal hydrogen bonds with the adjacent
macrocycle amide NH residues.13 In addition, the same
pyridyl nitrogen atoms have short contacts with the proxi-
mal squaraine hydrogens Ha and Hb (or Hd in the case of
chair-conformer rotaxane 2a). These short, cross-component
distances are indicative of an attractive interaction between dye
and macrocycle, but the distances are very similar for chair and
boat conformations. There is a conformation-dependent dif-
ference in the cross-component distances between the pyridyl
nitrogens Nc and Nd and squaraine oxygens Oa and Ob; the two
macrocycle adopts a flattened chair conformation, and the
macrocycle is translocated from the center of the encapsu-
lated squaraine. Indeed, the macrocycle conformation in 2e
is intermediate between the chair in 2a and the boat in 2d. It
appears, from the crystal structures in hand, that squaraine
rotaxanes with pyridyl-containing macrocycles are more likely
to adopt macrocyclic boat conformations than rotaxanes with
isophthalamide-containing macrocycles, but the solid-state
conformations are influenced by crystal-packing forces. In
the solution state, there is no evidence that the macrocyclic boat
conformation is predominant for any of the bis(anilino)-
˚
equal distances of 3.15 A in symmetric chair conformation 2a
˚
1
squaraine rotaxanes 2a-e. In each case, the H NMR spectra
are significantly shorter than the range of 3.21-3.50 A for boat
indicate that the rotaxane structure is symmetrical on the NMR
time scale, and the spectral pattern is essentially unchanged at low
temperatures. Specifically, the spectra for 2b and 2c in CD2Cl2
were monitored to -90 °C, where there was slight peak broad-
ening but little change in chemical shifts. The macrocycles in these
symmetrical squaraine rotaxanes are predominantly in either a
chair conformation or a rapidly exchanging chair/boat equilibri-
um. Evidence for the latter stems from the signal pattern for the
four equivalent sets of macrocycle methylene protons. The two
methylene protons would be diastereotopic if the macrocycle was
rigidly fixed in a chair or boat conformation (this feature is
observed below with rotaxane 5); however, both protons have
the same chemical shift, and they are equally coupled (J=5.8 Hz)
to the adjacent NH residue (Figure 4a). This spectral pattern
suggests that the rotaxane macrocycles are rapidly exchanging
between different conformations and that the exchange barrier is
quite low. The X-ray structures provide snapshots of the likely
intermediates in the co-conformational exchange process.12 As the
macrocycle flips between the two degenerate chair and two boat
conformations, its linear position relative to the center of the
squaraine thread undergoes harmonic oscillation (Figure 5).
Overall, it appears that the conformational energy landscape
for the phenylene-containing tetralactam in these symmetrical
squaraine rotaxanes is quite flat and the different macrocyclic
conformations are energetically similar.
conformers 2b-d. By sliding away from the center of the dye,
the boat-conformation macrocycles lower both of these cross-
component N O repulsions.14 Another conformation-de-
3 3 3
pendent structural difference is the shape of the encapsulated
squaraine chromophore. It is planar in symmetric chair con-
former 2a but slightly twisted and bent in boat conformations
2b-d. A comparative measure of this dye bending is the
distance between squaraine nitrogen atoms Na and Nb. It is
˚
13.29 A for the chair conformer 2a, which is longer than the
˚
range of 13.09-13.16 A for boat conformers 2b-d. It appears
that the encapsulated squaraines in boat conformers 2b-d are
less planar because this minimizes steric strain and maximizes
attractive cross-component attractions. In some of the X-ray
structures there are close intra- and intermolecular distances
between certain atoms in the surrounding macrocycle and the
terminal stopper groups on the encapsulated dye, but there
does not appear to be any systematic set of close interactions
that explain the switch of solid-state conformations from chair
to boat.
To test the empirical hypothesis that pyridyl-containing
macrocycles are more likely to adopt a solid-state boat
conformation, we prepared and investigated rotaxane 2e,
which has an isophthalamide-containing macrocycle and
thus is an analogue of pyridyl-containing 2d. The X-ray
crystal structure of 2e is shown in Figure 2. The surrounding
The photophysical properties of symmetrical squaraine
dyes 1a-d and their corresponding squaraine rotaxanes 2a-
e are listed in Table 2. Compared to the precursor squaraines,
the absorption/emission maxima for rotaxanes 2a-d with
pyridyl-containing macrocycles are red-shifted by about
10 nm while maintaining similar fluorescence quantum
(13) (a) Schalley, C. A. J. Phys. Org. Chem. 2004, 17, 967–972. (b) Affeld,
A.; H€ubner, G. M.; Seel C.; Schalley, C. A. Eur. J. Org. Chem. 2001, 25, 2877-
2890 and references therein.
(14) The repulsive effect of the pyridyl nitrogen with oxygen-containing
guests has been noted before; see: Chang, S.-Y.; Kim, H. S.; Chang, K.-J.;
Jeong, K.-S. Org. Lett. 2004, 6, 181–184.
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TABLE 2. Photophysical Properties in THF
compd
λabs (nm)
λema (nm)
Φfb
1a
1b
1c
1d
2a
2b
2c
2d
2e
631
630
629
632
640
638
636
641
650
647
647
648
651
658
657
659
662
674
0.70
0.72
0.70
0.65
0.70
0.74
0.67
0.65
0.26
a Symmtrical dyes 1a-d and rotaxanes 2a-e were excited at 580 nm,
and emission was monitored in the 600-750 nm region for estimating
Φf. b Fluorescence quantum yields (error limit ( 5%) were determined
for using 4,4-[bis(N,N-dimethylamino)phenyl]squaraine dye as the stan-
dard (Φf=0.70 in CHCl3). Molar absorptivities were typical of squaraine
dyes 1a-d having log ε=5.4 and squaraine rotaxanes 2a-e having log
ε=5.6.
FIGURE 6. X-ray crystal structure of truncated squaraine rotax-
ane 5.
squaraine rotaxane 5 with shorter absorption/emission wa-
velengths that match the Cy-2 filter set (also known as the
FITC filter set, approximately 450-490 nm excitation, 500-
550 nm emission).
The synthesis of 5 started with the semisquaraine 3
(Scheme 1), a literature compound that was prepared from
squaric acid.17 Condensation of 3 with N,N-dibenzylamine
resulted in 1,3-substitution and produced the truncated
squaraine dye 4 in 45% yield.18 Conversion to the truncated
squaraine rotaxane 5 was achieved in 25% yield by reacting
isophthaloyl chloride with 1,4-xylylenediamine in the pre-
sence of template 4. Recrystallization of 5 gave single crystals
that were suitable for analysis by X-ray diffraction, and the
refined solid-state structure is shown in Figure 6. The
unsymmetrical squaraine dye is encapsulated inside a boat-
conformation macrocycle that has its two bridging isophtha-
lamide units pointing toward the N,N-dibenzyl stopper
group at the more distant end of the dye. The intramolecular
distances listed for 5 in Table 1 show that the bifurcated
hydrogen bonds between the macrocyclic NH residues and
the encapsulated squaraine oxygens have normal distances
and angles, and the centroid-to-centroid distance between
the phenylene sidewalls is also typical for an isophthalamide-
containing macrocycle. Like the other boat-conformer struc-
tures described above, the macrocycle is offset from the
squaraine C4O2 core.
In CHCl3, the truncated squaraine rotaxane 5 rigidly
maintains its solid-state macrocyclic boat conformation.
This conclusion is based on variable-temperature 1H NMR
data. In contrast to the single macrocycle methylene peak for
rotaxane 2d (Figure 4a), the methylene protons in 5 are
diastereotopic and they have significantly different chemical
shifts (Figure 4b). The two inequivalent CH signals exhibit
strong geminal coupling (J=14.4 Hz) and unequal vicinal
coupling with the adjacent NH residue (J=8.2 Hz versus
SCHEME 1. Synthesis of truncated rotaxane 5.
yields (0.65-0.72). The isophthalamide-containing macro-
cycle in squaraine rotaxane 2e induces a 20 nm red-shift of
the absorption/emission maxima and significantly decreases
the fluorescence quantum yield to 0.26. The decreased
quantum yield seems to be related to the fact that the
isophthalamide-containing macrocycle is not wrapped as
tightly around the encapsulated squaraine as the pyridyl-
containing macrocycle (as listed in Table 1, the centroid-to-
centroid distance between the phenylene sidewalls is 7.16 A
˚
for 2e, which is substantially longer than the 6.66 A for
analogue 2d). Squaraine rotaxane 2e is less rigid and able to
undergo dynamic motions that allow radiationless loss of
excited state energy.15
Truncated Squaraine Rotaxane . The absorption/emission
maxima of the symmetrical bis(anilino)squaraine rotaxanes
2a-e match the Cy-5 filter set (approximately 590-635 nm
excitation, 650-720 nm emission) that is commonly em-
ployed on microscopes and related photonic devices. We
have previously shown that these symmetrical squaraine
rotaxanes exhibit greatly enhanced stability, and they have
tremendous potential as substitutes for the problematic Cy-5
fluorophore in various imaging applications.16 This success
has motivated us to develop other classes of squaraine
rotaxanes with altered chromophores that emit at different
wavelengths, and here we describe the novel truncated
˚
(17) (a) Gassensmith, J. J.; Arunkumar, E.; Barr, L.; Baumes, J. M.;
DiVittorio, K. M.; Johnson, J. R.; Noll, B. C.; Smith, B. D. J. Am. Chem. Soc.
2007, 129, 15054–15059. (b) Keil, D.; Hartmann, H. Dyes Pigm. 2001, 49,
161–179.
(18) Nucleophilic substitution of squaric acid, or its corresponding
diesters, with amines can potentially give 1,2- or 1,3-bis(squaramide) isomers
as products. The isomer ratio is dependent on the reaction conditions. For
discussions of this synthetic chemistry, see: (a) Neuse, E. W.; Green, B. R. J.
Org. Chem. 1974, 39, 3881–3887. (b) Ramalingam, V.; Bhagirath, N.;
Muthyala, R. S. J. Org. Chem. 2007, 72, 3976–3979.
(19) The unequal vicinal coupling indicates that the macrocycle is not
flipping rapidly on the NMR time-scale between conformations that ex-
change psuedoaxial and psuedoequatorial CH positions. A fixed macrocyclic
chair conformation in 5 can be ruled out because it would exhibit four
diastereotopic methylene CH signals, corresponding to two sets of inequi-
valent psuedoequatorial protons and two sets of inequivalent psuedoaxial
protons.
(15) Jacquemin, D; Perpete, E. A.; Laurent, A. D.; Assfeld, X.; Adamo,
C. Phys. Chem. Chem. Phys. 2009, 11, 1258–1262.
(16) Johnson, J. R.; Fu, N.; Arunkumar, E.; Leevy, W. M.; Gammon,
S. T.; Worms, W. P.; Smith, B. D. Angew. Chem., Int. Ed. 2007, 46, 5528–5531.
6466 J. Org. Chem. Vol. 74, No. 17, 2009

Fu et al.
JOCFeatured Article
TABLE 3. Photophysical Properties in CHCl3
compd
λabs (nm)
λema (nm)
log ε
Φfb
rel brightnessc
4
5
456
475
483
503
4.8
4.9
0.11
0.50
1
6
a Short-conjugated squaraine dye 4 and rotaxane 5 were excited at 420
nm, and emission was monitored in the 440-650 nm region for
b
estimating Φf. Using coumarin-6 dye as a standard (Φf = 0.78 in
ethanol). c Brightness was determined as molar absorptivity ꢀ quantum
yield.
FIGURE 7. Absorption spectra of 4 (black - -) and 5 (red - -)
and fluorescence emission spectra of 4 (black ;) and 5 (red ;) in
CHCl3 (5 μM).
1.5 Hz). Furthermore, the splitting pattern does not change
over the temperature range þ50 °C to -50 °C (see the
Supporting Information), which indicates that the macro-
cycle conformation is fixed as the boat structure shown in
Figure 619,20 It is worth noting that the four aromatic protons
on each of the phenylene sidewalls are chemical shift equiva-
lent, even at -50 °C, indicting that both 1,4-phenylene rings
are spinning rapidly on the NMR time frame.
FIGURE 8. Change in absorption of 4 (O) and 5 (ꢀ) in CHCl3
(10 μM) upon exposure to an unfiltered xenon arc lamp (150 W) at
25 °C.
The absorption/emission spectra for truncated squaraine
dye 4 and squaraine rotaxane 5 in CHCl3 are shown in
Figure 7, and the numerical data are listed in Table 3. As
expected for yellow compounds, the dye 4 and rotaxane 5
absorb at 456 and 475 nm, respectively, with the rotaxane
having a slightly higher molar absorptivity. The emission
spectra exhibit a remarkable difference in that the fluores-
cence quantum yield of 0.50 for rotaxane 5 is more than four
times higher than the value of 0.11 for parent dye 4. Indeed,
squaraine rotaxane 5 is about six times brighter than the
parent squaraine 4 (brightness is defined in Table 3). This
result is notable and pleasing since one of our major research
goals is to develop dye encapsulation strategies that improve
the brightness of fluorescent dyes. We propose that the
encapsulated squaraine dye in 5 is sterically constrained
and that encapsulation decreases out-of-plane deformations
of the N,N-dibenzyl nitrogen atom that is attached directly to
the squaraine chromophore and inhibits rotation around the
corresponding C-N bond.15 These effects combine to en-
hance molar absorptivity and also decrease radiationless
decay of the squaraine excited state.
FIGURE 9. Change in absorption upon addition of 2-mercap-
toethanol (50 mM) to 4 (b), 5 (O), and 1a (ꢀ) in CHCl3 (10 μM) at
25 °C.
indicating that the latter undergoes a much slower photo-
bleaching process. The photoprotection is similar in magni-
tude to that observed with previous squaraine rotaxanes.12a
To determine ground-state chemical stability, three separate
cuvettes containing the symmetrical bis(anilino)squaraine 1a,
the truncated squaraine 4, and truncated squaraine rotaxane 5
in CHCl3 (each 10 μM) were treated with a large excess of the
2-mercaptoethanol (50 mM). As shown in Figure 9, the color
of the symmetrical squaraine 1a was lost within 10 min due to
attack of the thiol nucleophile at the electrophilic C4O2 core.21
In strong contrast, the truncated squaraine 4 and truncated
squaraine rotaxane 5 resisted thiol attack and there was no
The next characterization step was to determine the relative
stabilities of truncated squaraine dye 4 and squaraine rotax-
ane 5. To determine photostability, separate cuvettes contain-
ing the squaraine 4 or rotaxane 5 in CHCl3 were continuously
irradiated using a 150 W xenon arc lamp located 15 cm away,
and the absorption was monitored over time. As shown in
Figure 8, the absorption decay half-life was approximately
100 s for squaraine 4 and around 1100 s for rotaxane 5,
(20) Because of the planar symmetry in 5 it is not possible to determine by
NMR if the surrounding boat conformation macrocycle is pirouetting
around the encapsulated squaraine thread. Indeed, it is not trivial to
experimentally characterize macrocycle pirouetting for any type of squaraine
rotaxane. The squaraine C4O2 core has no protons to allow NMR studies,
and any NMR observable group that is directly attached to the core (e.g., an
anilino ring) can undergo rapid spinning about the connecting single bond.
(21) Ros-Lis, J. V.; Garcia, B.; Jimenez, D.; Martinez-Manez, R.;
Sancenon, F.; Soto, J.; Gonzalvo, F.; Valldecabres, M. C. J. Am. Chem.
Soc. 2004, 126, 4064–4065.
J. Org. Chem. Vol. 74, No. 17, 2009 6467

Fu et al.
JOCFeatured Article
loss of color after 30 min. However, the treated cuvette
containing dye 4 lost its color over the much longer time
frame of one month, whereas the treated cuvette containing 5
was essentially unchanged. We conclude that the C4O2 core of
truncated squaraine dye 4 is much less electrophilic than the
core of bis(anilino)squaraine 1a because the electron-releasing
effect of the directly attached nitrogen atom in 4 is much
stronger than the aromatic aniline in 1a. Nonetheless, 4 is still
susceptible to eventual nucleophilic attack by thiols and it also
undergoes photobleaching. Both of these dye degradation
processes can be strongly inhibited by permanent encapsula-
tion of the dye as rotaxane 5.
reduced pressure and the crude product precipitated by washing
with hexanes (40 mL). Thiscrude product was purified by column
chromatography using a column of silica gel with MeOH/CHCl3
(1:19) as the eluent to give the squaraine dye as a green solid in
30-50% yield. Spectral data for squaraine 1c: 1H NMR (300MHz,
CDCl3) δ 4.70 (s, 8H), 6.83 (d, J=9.0 Hz, 4H), 7.05 (d, J=8.7 Hz,
8H), 7.48 (d, J=9.0 Hz, 8H), 8.38 (d, J=9.0 Hz, 4H); 13C NMR
(150 MHz, CDCl3) δ 53.8, 113.3, 121.4, 122.0, 128.4, 132.5, 134.0,
134.9, 155.0, 182.9, 192.0; MS (FAB) [M]þ 939.9.
Procedure To Synthesize Truncated Squaraine Dye 4 . To a
solution of N,N-dibenzylsemisquaraine 3 (400 mg, 1.1 mmol)17
in isopropyl alcohol (30 mL) was added N,N-dibenzylamine
(210 mg, 1.1 mmol). After addition of tri-n-butyl orthoformate
(1 mL), the reaction was heated to reflux for 12 h. The solvent
was removed by rotary evaporation and the crude product
purified by column chromatography using a column of silica
gel with CH2Cl2 as eluent to give 4 as a yellow solid in 45% yield:
1H NMR (300 MHz, CDCl3) δ 4.73 (s, 4H), 4.95 (s, 4H), 6.78 (d,
J=9.0 Hz, 2H), 7.20-7.34 (m, 20H), 8.20 (d, J=9.0 Hz, 2H); 13C
NMR data was not acquired because of poor solubility; HRMS
(FAB) calcd for C38H32N2O2 [M þ H]þ 549.2542, found
549.2569.
Conclusions
Permanent encapsulation of bis(anilino)squaraine dyes
1a-d inside Leigh-type tetralactam macrocycles produces
squaraine rotaxanes 2a-e that have slightly red-shifted
absorption/emission wavelengths, similar or decreased
brightness, and substantially enhanced chemical and photo-
chemical stabilities. The surrounding macrocycles are flex-
ible and undergo rapid chair/boat conformational exchange
in solution. A series of X-ray crystal structures provide
snapshots of several intermediates in the coconformational
exchange process, which involves lateral oscillation of the
macrocycle relative to the center of the encapsulated squar-
aine thread (Figure 5). Pyridyl-containing macrocycles are
more likely to adopt boat conformations in the solid-state
than analogous squaraine rotaxane systems with isophthal-
amide-containing macrocycles. The truncated squaraine
dye 4 is less electrophilic than the bis(anilino)squaraine
family 1, but it is still susceptible to chemical and photo-
chemical degradation. Its stability is greatly enhanced
when it is converted into truncated squaraine rotaxane 5.
An X-ray crystal structure of 5 shows the macrocycle in
a boat conformation (Figure 6) and NMR studies indi-
cate that the boat is maintained in solution. Most notably,
mechanical encapsulation of 4 as rotaxane 5 increases
the dye’s brightness by a factor of 6 (Table 3). The encapsu-
lation process appears to constrain the dye and reduce
deformation of the chromophore from planarity. This study
expands our basic understanding of squaraine rotaxane
dynamic structure and improves our ability to use mecha-
nical encapsulation as a rational design parameter to
fine-tune the chemical and photochemical properties of
encapsulated dyes.
General Procedure To Synthesize Squaraine Rotaxanes 2a-e
and 5 . Clear solutions of the corresponding diacid chloride
(0.31 mmol) and 1,4-xylylenediamine (42 mg, 0.31 mmol) in
anhydrous chloroform (5 mL) were drawn into two separate
10 mL syringes. Over 5 h, these solutions were added dropwise,
using a mechanical syringe pump, to a stirred solution contain-
ing the corresponding squaraine dye (0.07 mmol) and triethyla-
mine (71 mg, 0.72 mmol) in anhydrous chloroform (40 mL).
After being stirred overnight, the reaction mixture was filtered
through a pad of Celite to remove any polymeric material. The
solvent was removed by rotary evaporation and the crude
product purified by column chromatography using a column
of silica gel with MeOH/CHCl3 (1:19) as the eluent to give
squaraine rotaxane in 26-40% yield. Spectral data for rotaxane
2c: 1H NMR (500 MHz, CDCl3) δ 4.50 (d, J=6.0 Hz, 8H), 4.58
(s, 8H), 6.21 (d, J=9.0 Hz, 4H), 6.54 (s, 8H), 6.97 (d, J=7.8 Hz,
8H), 7.53 (d, J=7.8 Hz, 8H), 7.98 (t, J=7.6 Hz, 2H), 8.10 (d, J=
8.4 Hz, 4H), 8.39 (d, J=10.5 Hz, 4H), 9.83 (t, J=5.1 Hz, 4H); 13
C
NMR (125 MHz, CDCl3) δ 43.4, 54.0, 112.6, 120.4, 122.4, 125.4,
128.3, 129.1, 132.6, 134.1, 134.5, 137.0, 138.8, 149.5, 155.0,
163.6, 184.8, 188.0; MS (FAB) [M]þ 1472.2.
Acknowledgment. We are grateful for funding support
from the NIH and the University of Notre Dame. We thank
Dr. A. Oliver and Professor K. Henderson for enlightening
conversations.
Supporting Information Available: Synthesis and spectral
characterization of all new compounds as well as detailed
crystallographic information and thermal ellipsoid plots. This
material is available free of charge via the Internet at http://
pubs.acs.org. Crystallographic data are available from the Cam-
bridge Crystallographic Data Centre as publication nos.
CCDC-736492 (2b), CCDC-736496 (2c), CCDC-736494 (2d),
CCDC-736493 (2e), and CCDC-736495 (5). Copies of the data
can be obtained free of charge on application to CCDC via the
Internet at http://www.ccdc.cam.ac.uk.
Experimental Section
General Procedure to Synthesize Squaraine Dyes 1a-d . The
appropriate N,N-dibenzylaniline derivative (1.2 mmol) was
added to a solution of 3,4-dihydroxy-3-cyclobutene-1,2-dione
(67 mg, 0.59 mmol) in a mixture of benzene (30 mL) and
n-butanol (15 mL) contained in a 100 mL round-bottom flask.
The flask was equipped with a Dean-Stark apparatus and
refluxed for 16 h. After cooling, the solvent was removed under
6468 J. Org. Chem. Vol. 74, No. 17, 2009