Squaraine [2]catenanes: Synthesis, structure and molecular dynamics

Article abstract of DOI:10.1039/c1cc10946d

Three squaraine [2]catenanes are synthesized and found to have bright, deep-red fluorescence and high chemical stability. The interlocked molecules undergo two large-amplitude dynamic processes, twisting of the squaraine macrocycle and skipping over the p

Full text of DOI:10.1039/c1cc10946d

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Squaraine [2]catenanes: synthesis, structure and molecular dynamicswz
Jung-Jae Lee, Jeffrey M. Baumes, Richard D. Connell, Allen G. Oliver and
Bradley D. Smith*
Received 17th February 2011, Accepted 2nd May 2011
DOI: 10.1039/c1cc10946d
Three squaraine [2]catenanes are synthesized and found to have
bright, deep-red fluorescence and high chemical stability. The
interlocked molecules undergo two large-amplitude dynamic
processes, twisting of the squaraine macrocycle and skipping
over the partner tetralactam.
red-shifts upon conversion to catenanes 1–3 are very similar
qto the optical changes previously observed with analogous
squaraine rotaxanes having anthracene-containing tetralactam
macrocycles.8 The insensitivity of the squaraine optical
properties to interlocked topology is notable and suggests that
we can confidently design increasingly complicated mechanically-
linked molecular architectures with predictable photophysics.
Another attractive feature with squaraine encapsulation
is enhanced chemical stability. The electrophilic cores of
squaraine dyes are readily attacked by strong nucleophiles
and previously we have shown that squaraine rotaxanes such
as 6 exhibit high levels of steric protection from thiols in
weakly polar solvents such as chloroform.1,13 However, the
rotaxane protection effect is much weaker in more polar
organic solvents that disrupt non-covalent association of
encapsulated squaraine dye with the surrounding tetralactam
In 2005 we reported that highly fluorescent squaraine dyes can
be permanently encapsulated inside tetralactam macrocycles
to make interlocked [2]rotaxane molecules.1 These compounds
exhibit a range of favorable chemical and photophysical
properties that make them attractive candidates as high
performance fluorescence imaging probes,2 chemiluminescent
dyes,3 photosensitizers,4 and chemosensors.5 Structural
modifications of the rotaxane building blocks have lead to
rationalizable changes in molecular dynamics,6 chemical
reactivity,7 and photophysical properties.8,9 Utilizing this
expanding knowledge base we are beginning to design next-
generation molecules with different interlocked topologies and
here we report compounds 1–3 as the first examples of highly
fluorescent and extremely stable squaraine [2]catenanes.10 In
addition to the synthetic methods and optical properties, we
describe a solid-state catenane structure and characterize the
solution-state molecular dynamics.
The [2]catenane synthesis starts with the bisalkene squaraine
4 which was converted into squaraine macrocycle 5 in 28%
yield under ring closing metathesis conditions (Scheme 1).11
Consistent with literature precedence, the macrocycle alkene
unit in 5 is a 25 : 75 mixture of cis : trans isomers. Conversion
of this squaraine macrocycle into squaraine catenanes 1–3 was
achieved in the yield range of 18–35% by conducting
Leigh-type clipping reactions using the appropriate diacid
chloride and 9,10-bis(aminomethyl)anthracene.12 Listed
in Table 1 are the standard photophysical properties for
compounds 1–5. The two unencapsulated dyes 4 and 5 exhibit
typical squaraine absorption and emission maxima. The large
Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, IN 46556, USA.
E-mail: smith.115@nd.edu; Fax: 1 574 631 6652; Tel: 1 574 631 8632
w This article is part of a ChemComm ‘Supramolecular Chemistry’
web-based themed issue marking the International Year of Chemistry
2011.
z Electronic supplementary information (ESI) available: Synthesis and
spectral data and summary of X-ray analysis. CCDC 813692. For ESI
and crystallographic data in CIF or other electronic format see DOI:
10.1039/c1cc10946d
Scheme 1 Synthesis of squaraine [2]catenanes 1–3 and chemical
structure of squaraine rotaxane 6.
c
7188 Chem. Commun., 2011, 47, 7188–7190
This journal is The Royal Society of Chemistry 2011

Table 1 Absorption and emission values in CHCl3 (5.0 mM)
Compound
labs (nm)
lem (nm)
log10
e
Ffa
1
2
3
4
5
663
663
667
632
633
699
699
700
650
652
5.08
5.14
5.16
5.18
5.22
0.42
0.43
0.42
0.51
0.51
a
Fluorescence quantum yields determined using 4,4-[bis-(N,N-
dimethylamino)phenyl]squaraine as a standard (Ff) 0.70 in CHCl3,
error limit (ꢀ5%).
Fig. 2 X-Ray crystal structure of squaraine [2]catenane 3. For clarity,
only amide and alkene hydrogens are shown and intramolecular
hydrogen bonds are indicated as light blue lines.
and expose the reactive squaraine core.8a This solvent
enhanced reactivity is reflected by the plot in Fig. 1 showing
a rapid decrease in squaraine absorption band for rotaxane 6
due to attack by excess 2-mercaptoethanol in DMF. In
contrast, the plot for catenane 1 under identical conditions
shows a half-life that is approximately 100-fold longer,
indicating a substantially higher degree of steric protection.
Apparently, it is much harder for the encapsulated squaraine
in catenane 1 to be displaced from the surrounding tetralactam
by the DMF solvent. We conclude that squaraine catenanes
retain the impressive deep-red fluorescent properties of squaraine
rotaxanes but exhibit significantly enhanced resistance to
nucleophilic attack in polar organic solvents.14
Catenane 3, with its novel tetralactam macrocycle containing
two bridging pyridine 2,4-dicarboxamide units, is relatively
insoluble and was readily obtained as single crystals. Analysis
by X-ray diffraction was possible even though the compound
exists as a mixture of four stereoisomers—in addition to the
squaraine macrocycle alkene stereochemistry, the tetralactam
component in 3 can have planar or axial symmetry depending
on the relative positions of the two pyridyl nitrogen atoms.
Shown in Fig. 2 is the solid-state molecular structure with a
trans alkene geometry and the tetralactam having planar
symmetry because the two pyridyl nitrogens have a syn
relationship. The structure shows no major distortions from
expected bond angles and bond distances. The squaraine
chromophore is essentially planar which agrees with the
unperturbed absorption data in Table 1.15 As discussed below,
there is hindered rotation about the two aniline C–N bonds
at each end of the squaraine chromophore, such that the
macrocycle can be twisted to adopt either syn or anti
conformations with essentially identical energies (Fig. 3A).
The catenane chemical structure that is drawn in Scheme 1
depicts the squaraine macrocycle in a syn conformation with
respect to these two C–N bonds, but the X-ray crystal
Fig. 3 Squaraine [2]catenane molecular dynamics showing; (A) slow
squaraine macrocycle twisting between syn and anti conformations,
and (B) fast squaraine macrocycle skipping over the tetralactam.
structure shows that the anti macrocycle conformation is
preferred in the solid state, a bias that is attributed to crystal
packing forces. This anti conformation constrains the alkene
unit in the squaraine macrocycle to be directly over the face
of the adjacent anthracene unit in the partner tetralactam
component. The tetralactam adopts a flattened macrocyclic
chair conformation that is very similar to that observed with
analogous squaraine rotaxanes.8a The catenane and rotaxane
co-conformations are also similar in that both anthracene
units in the tetralactam encapsulate the C4O2 core of the
squaraine chromophore. The distance between the centers of
the two anthracene units in catenane 3 is 6.95 A and each
amide residue in the tetralactam is hydrogen bonded to a
squaraine oxygen atom with NH–O distances of 2.10–2.16 A.7
Compared to squaraine catenane 3, catenanes 1 and 2 are
more soluble and thus they were chosen for detailed study by
variable temperature NMR. Both molecular systems exhibit
similar temperature dependent changes in spectral patterns,
suggesting that they undergo the same dynamic processes. The
large anisotropic shielding of the squaraine chemical shifts
indicates that the solid-state structure is firmly maintained in
solution with the tetralactam encapsulating the squaraine
chromophore. This helps explain why the catenane exhibits
such high steric protection of the electrophilic squaraine core
(Fig. 1). Further inspection of the NMR spectra indicates that
the catenanes undergo two large-amplitude dynamic motions
due to conformational exchange.16 One motion, with a relatively
low activation energy, is skipping of the hydrocarbon chain of
the squaraine macrocycle over a bridging isophthalamide unit
in the partner tetralactam component. (Fig. 3B). At room
temperature, the process is sufficiently rapid to produce a
Fig. 1 Normalized changes in squaraine (5.0 mM) absorption for: 6 in
DMF ( ), mixtures of 2-mercaptoethanol (50 mM) with either 1 ( ), 6
(
), or 5 (’) in DMF. All samples at room temperature and in the
dark.
c
This journal is The Royal Society of Chemistry 2011
Chem. Commun., 2011, 47, 7188–7190 7189

Notes and references
y The co-conformational exchange in Fig. 3B can also be acheived by
tetralactam circumrotation, but this is a less favored pathway because
it must break four hydrogen bonds. For further discussion, see ref. 16
and 18.
z The Leigh group has reported that energy barriers for tetralactam
circumrotation in [2]catenanes are quite sensitive to tetralactam
molecular structure and solvent. For tetralactams with isophthalamide
units, the steric bulk at the 5-position has a large influence on
circumrotation rates. For further discussion, see ref. 18.
1
Fig. 4 Partial H NMR spectra (500 MHz) of catenane 2 in CD2Cl2
1 (a) E. Arunkumar, C. C. Forbes, B. C. Noll and B. D. Smith,
J. Am. Chem. Soc., 2005, 127, 3288; (b) J. J. Gassensmith,
J. M. Baumes and B. D. Smith, Chem. Commun., 2009, 6329.
2 (a) J.-J. Lee, A. G. White, J. M. Baumes and B. D. Smith, Chem.
Commun., 2010, 46, 1068; (b) A. G. White, N. Fu, W. M. Leevy,
J.-J. Lee, M. A. Blasco and B. D. Smith, Bioconjugate Chem., 2010,
21, 1297; (c) J. R. Johnson, N. Fu, E. Arunkumar, W. M. Leevy,
S. T. Gammon, D. Piwnica-Worms and B. D. Smith, Angew.
Chem., Int. Ed., 2007, 46, 5528.
3 J. M. Baumes, J. J. Gassensmith, J. Giblin, J.-J. Lee, A. G. White,
W. J. Culligan, W. M. Leevy, M. Kuno and B. D. Smith,
Nat. Chem., 2010, 2, 1025.
4 E. Arunkumar, P. K. Sudeep, K. V. Kamat, B. C. Noll and
B. D. Smith, New J. Chem., 2007, 31, 677.
5 J. J. Gassensmith, S. Matthys, J.-J. Lee, A. Wojcik, P. V. Kamat
and B. D. Smith, Chem.–Eur. J., 2010, 16, 2916.
6 N. Fu, J. M. Baumes, E. Arunkumar, B. C. Noll and B. D. Smith,
J. Org. Chem., 2009, 74, 6462.
7 (a) J. M. Baumes, I. Murgu, A. Oliver and B. D. Smith, Org. Lett.,
2010, 12, 4980; (b) E. Arunkumar, N. Fu and B. D. Smith,
Chem.–Eur. J., 2006, 12, 4684.
8 (a) J. J. Gassensmith, E. Arunkumar, L. Barr, J. M. Baumes,
K. M. DiVittorio, J. R. Johnson, B. C. Noll and B. D. Smith,
J. Am. Chem. Soc., 2007, 129, 15054; (b) D. Jacquemin,
E. A. Perpete, A. D. Laurent, X. Assfeld and C. Adam, Phys.
Chem. Chem. Phys., 2009, 11, 1258.
9 (a) S.-Y. Hsueh, C.-C. Lai, Y.-H. Liu, S.-M. Peng and S.-H. Chiu,
Angew. Chem., Int. Ed., 2007, 46, 2013; (b) S.-Y. Hsueh, C.-C. Lai
and S.-H. Chiu, Chem.–Eur. J., 2010, 16, 2997; (c) M. Xue,
Y.-S. Su and C.-F. Chen, Chem.–Eur. J., 2010, 16, 8537.
10 (a) D. B. Amabilino and F. Stoddart, Chem. Rev., 1995, 95, 2725;
(b) J.-P. Sauvage and C. Dietrich-Buchecker, in Molecular Catenanes,
Rotaxanes and Knots, ed. Wiley-VCH, Weinheim, Germany, 1999.
11 (a) M. Weck, B. Mohr, J.-P. Sauvage and R. H. Grubbs, J. Org.
Chem., 1999, 64, 5463; (b) M. D. Lankshear and P. D. Beer, Acc.
Chem. Res., 2007, 40, 657; (c) S. T. Caldwell, G. Cooke,
B. Fitzpatrick, D. Long, G. Rabani and V. M. Rotello, Chem.
Commun., 2008, 5912.
12 D. A. Leigh, A. Murphy, J. P. Smart and A. M. Z. Slawain, Angew.
Chem., Int. Ed. Engl., 1997, 36, 728.
13 J. V. Ros-Lis, B. Garcia, D. Jimenez, R. Martinez-Manez,
F. Sancenon, J. Soto, F. Gonzalvo and M. C. Valldecabres,
J. Am. Chem. Soc., 2004, 126, 4064.
14 (a) E. Arunkumar, C. C. Forbes and B. D. Smith, Eur. J. Org. Chem.,
2005, 19, 4051; (b) K.-Y. Law, in Organic Photochemistry,
ed. V. Ramamurthy and K. S. Schanze, Marcel Dekker, New York,
1997, ch. 12, pp. 519–584; (c) S. Das, K. G. Thomas and
M. V. George, in Organic Photochemistry, ed. V. Ramamurthy and
K. S. Schanze, Marcel Dekker, New York, 1997, ch. 11, pp. 467–517;
(d) J. J. McEwen and K. J. Wallace, Chem. Commun., 2009, 6339.
15 J. J. Gassensmith, L. Barr, J. M. Baumes, A. Paek, A. Nguyen and
B. D. Smith, Org. Lett., 2008, 10, 3343.
16 (a) M. Pons and O. Millet, Prog. Nucl. Magn. Reson. Spectrosc.,
2001, 38, 267; (b) M. S. Deleuze, D. A. Leigh and F. Zerbetto,
J. Am. Chem. Soc., 1999, 121, 2364.
17 N. Fu, J. J. Gassensmith and B. D. Smith, Aust. J. Chem., 2010, 63,
792.
showing the squaraine macrocycle cis and trans alkene signals. The
spectra indicate two-site exchange of equally populated syn and anti
conformations.
single set of exchange-averaged signals for the tetralactam’s
two anthracene units.y In other words, NMR cannot distinguish
the anthracene unit inside the tetralactam from the anthracene
that is outside. Even at low temperatures it is not apparent
that squaraine macrocycle skipping becomes slow relative to
the NMR time scale. For example, the four sets of tetralactam
benzylic protons remain chemical shift equivalent at ꢁ90 1C.
The second, large-amplitude motion is twisting of the
squaraine macrocycle due to hindered rotation about the
squaraine aniline C–N bonds which exhibit partial double
bond order due to strong delocalization with the squaraine
chromophore (Fig. 3A). In this case, the activation barrier is
sufficiently high that signal coalescence is observed at around
ꢁ40 1C and slow exchange spectra are obtained at lower
temperatures. The key evidence that unambiguously identifies
this dynamic process is the two-site exchange phenomena
exhibited by the squaraine macrocycle alkene signals
(Fig. 4). Measurements of the coalescence temperatures and
limiting chemical shifts for these signals (see ESI) allowed
determination of the free energy of activation to be 11.6 ꢀ 0.3
and 11.4 ꢀ 0.2 kcal molꢁ1 for 1 and 2, respectively. Thus, the
dynamic process is independent of the size of the group at the
5-position of the two isophthalamide units in the tetralactam,
suggesting that this motion does not involve the tetralactam.z
Moreover, the energy barrier is quite similar to the value of
13 kcal molꢁ1 for squaraine aniline C–N bond rotation in a
related squaraine rotaxane system.17 Additional broadening of
some catenane signals is observed at ꢁ90 1C (see ESI), and
most likely this is due to slowing of low energy dynamic
processes such as squaraine macrocycle skipping and tetra-
lactam macrocyclic chair/boat flips.6,18
In summary, squaraine catenanes 1–3 are the first examples
of a new class of interlocked squaraine-derived molecular
architecture. The catenane topology exhibits unique dynamic
processes as summarized in Fig. 3. Recently, we reported that
squaraine rotaxanes with anthracene-containing tetralactam
macrocycles can be converted by simple photooxidation into
endoperoxide derivatives that undergo a chemiluminescent
cycloreversion reaction.3 Preliminary studies indicate that
squaraine catenanes exhibit the same phenomenon and
work is ongoing to determine how the chemiluminescence
intensity is altered by the changes in structural topology. This
study was supported by the NSF and the University of
Notre Dame.
18 (a) D. A. Leigh, A. Murphy, J. P. Smart, M. S. Deleuze and
F. Zerbotto, J. Am. Chem. Soc., 1998, 120, 6458;
(b) A. G. Johnston, D. A. Leigh, L. Nezhat, J. P. Smart and
M. D. Deegan, Angew. Chem., Int. Ed. Engl., 1995, 34, 1212.
c
7190 Chem. Commun., 2011, 47, 7188–7190
This journal is The Royal Society of Chemistry 2011