Synthetic β-Cyclodextrin Dimers for Squaraine Binding: Effect of Host Architecture on Photophysical Properties, Aggregate Formation and Chemical Reactivity

Article abstract of DOI:10.1002/ejoc.201800283

Reported herein is the synthesis and application of three novel β-cyclodextrin dimer hosts for the complexation of near infrared (NIR) squaraine dyes in aqueous solution. A series of eight different N-substituted N-methyl anilino squaraine dyes with variable terminal groups are investigated, with an optimal n-hexyl-substituted squaraine guest demonstrating binding constants orders of magnitude higher than the other squaraine–host combinations and comparable to literature-reported systems. Moreover, hydrophobic complexation of the squaraine dyes with the β-cyclodextrin dimer hosts causes drastic changes in the squaraine's photophysical properties, propensity for aggregation and susceptibility to hydrolytic decay.

Full text of DOI:10.1002/ejoc.201800283

A Journal of
Accepted Article
Title: Synthetic β-cyclodextrin dimers for squaraine binding: Effect
of host architecture on photophysical properties, aggregate
formation and chemical reactivity
Authors: Sauradip Chaudhuri, Molly Verderame, Teresa L. Mako, Y. M.
Nuwan D. Y. Bandara, Ashvin I. Fernando, and Mindy Levine
This manuscript has been accepted after peer review and appears as an
Accepted Article online prior to editing, proofing, and formal publication
of the final Version of Record (VoR). This work is currently citable by
using the Digital Object Identifier (DOI) given below. The VoR will be
published online in Early View as soon as possible and may be different
to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published
to ensure accuracy of information. The authors are responsible for the
content of this Accepted Article.
To be cited as: Eur. J. Org. Chem. 10.1002/ejoc.201800283
Link to VoR: http://dx.doi.org/10.1002/ejoc.201800283
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10.1002/ejoc.201800283
European Journal of Organic Chemistry
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Synthetic β-cyclodextrin dimers for squaraine binding: Effect of
host architecture on photophysical properties, aggregate
formation and chemical reactivity
Sauradip Chaudhuri, Molly Verderame, Teresa L. Mako, Y. M. Nuwan D. Y. Bandara, Ashvin I.
Fernando and Mindy Levine*[a]
Dedicated in memory of the father of biomimetic chemistry, a giant in the field of cyclodextrin chemistry, and the former Ph.D. advisor
of M.L., Professor Ronald Breslow.
Abstract: Reported herein is the synthesis and application of three
novel β-cyclodextrin dimer hosts for the complexation of near infrared
(NIR) squaraine dyes in aqueous solution. A series of eight different
N-substituted N-methyl anilino squaraine dyes with variable terminal
groups are investigated, with an optimal n-hexyl substituted squaraine
guest demonstrating binding constants orders of magnitude higher
than the other squaraine-host combinations and comparable to
literature-reported systems. Moreover, hydrophobic complexation of
the squaraine dyes with the β-cyclodextrin dimer hosts causes drastic
changes in the squaraine’s photophysical properties, propensity for
aggregation and susceptibility to hydrolytic decay.
active but still binds in cyclodextrin and promotes proximity-
induced, analyte-specific changes in the fluorophore emission. No
previous work in our group has reported the use of higher order
cyclodextrin architectures for detection applications, despite the
fact that such architectures have the potential to exhibit
significantly enhanced binding affinities.14
One group of guests that is known to bind well in cyclodextrins is
squaraine fluorophores,15 which contain a common cyclobutene-
dione core.16 The unique electronic structure of the squaraine
fluorophore leads to high extinction coefficients,17 narrow Stokes
shifts, and high quantum yields,18 with absorption and emission
maxima often in the near-infrared spectral region. Squaraine
fluorophores have significant potential in detection applications,
as a result of the limited interference of other analytes in the near-
Introduction
19
infrared spectral region.
Moreover, squaraine binding in
cyclodextrin hosts often results in changes in the absorption and
emission spectra of the squaraine that can be used for sensing
applications.20
The complexation of small molecule guests inside a variety of
supramolecular hosts has been extensively reported in the
literature. Examples of such hosts include cyclodextrins,1 which
bind guests primarily via hydrophobic encapsulation inside the
hydrophobic cavity;2 cucurbiturils (CBs),3 which bind guests via
electrostatic interactions with the highly polarized carbonyl groups
that line the CB rims as well as via hydrophobic association;4 and
synthetic macrocycles5 and cavitands,6 whose structures vary
widely as a result of synthetic manipulations.
Previous work by our group has focused on the use of
cyclodextrin complexation to develop highly sensitive and
selective fluorescence-based detection methods for multiple
classes of toxicants, including polycyclic aromatic hydrocarbons
Reported herein is the rational design and synthesis of dimeric
cyclodextrin architectures, their ability to bind squaraine
fluorophores with extremely high binding constants, and the
effects of such binding on the squaraines’ photophysical
properties, propensity for aggregate formation, and reactivity
towards hydrolysis. Detailed structure-property relationships are
invoked to understand the effects of the structural architectures of
the dimers on squaraine guests with variable-length terminal alkyl
chains.
7
8
(PAHs),
polychlorinated biphenyls (PCBs),
aliphatic alcohols,
11
aromatic
and aromatic oil-spill
These detection methods operate via
9
10
pesticides,
components.
cyclodextrin-promoted fluorescence energy transfer,12 in cases
where the toxicant is photophysically active and a competent
energy donor, or via cyclodextrin-promoted fluorescence
modulation,13 in cases where the toxicant is not photophysically
[a]
S. Chaudhuri, M. Verderame, T. L. Mako, Y. M. N. D. Y. Bandara, A.
I. Fernando, M. Levine
Department of Chemistry
University of Rhode Island
140 Flagg Road, Kingston, RI 02881
E-mail: mindy.levine@gmail.com; mlevine@chm.uri.edu
URL: https://www.chm.uri.edu/levinegroup/webpages/index.html
Supporting information for this article is given via a link at the end of
the document.
Figure 1. Structures of new cyclodextrin dimers 1-3.
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Results and Discussion
Host design and properties
Three novel, covalently linked β-cyclodextrin dimers (compounds
1-3) with aromatic linkers were synthesized via the coupling of
activated amide derivatives with two equivalents of
monofunctionalized β-cyclodextrin. While compound
1
incorporates a rigid 2,6-pyridine diamide linker, compounds 2 and
3 incorporate flexible 1,4-naphthalene and 9,10-anthracene
dipropylamide linkers, respectively (Figure 1). The three linker
architectures were chosen to determine the effect of
a
heteroaromatic moiety (compound 1), increasing sizes of the
aromatic core (compound 2 vs. compound 3), and differences in
the linker flexibility (compound 1 vs. compounds 2 and 3) on the
binding properties of β-cyclodextrin dimers. Such flexibility can be
seen in the energy-minimized structures of compounds 1-3,
obtained via PM3-level computations: whereas compound 1
exhibits an open structure as a result of its limited flexibility,
compounds 2 and 3 are sufficiently flexible to fold in, exhibiting a
closed, sandwich-like structure (Figure 2).
Figure 3. Structures of N-substituted N-methylanilino squaraine dyes 4-11 (note
that the alkyl substituents in compounds 4-9 are all straight chain n-alkanes).
Eight squaraine guests (compounds 4-11, Figure 3) were
synthesized via the condensation of squaric acid and N-
substituted N-methylanilines following
a general procedure
previously reported for the synthesis of similar species.21 Six of
the squaraines reported herein incorporate straight chain alkyl
groups from n-butyl to n-nonyl (compounds 4-9), with a cyclic
substituent (compound 10) and a tert-butyl substituted benzene
(compound 11) included in the other two structures (Figure 3). All
of the cyclodextrins and squaraines were fully characterized via
spectroscopic methods.
Figure 4. Illustration of Donor-Acceptor-Donor (D-A-D) structure of squaraine
dye 10, resulting in the formation of intense H-aggregate (blue-shifted) and J-
aggregate (red-shifted) bands, especially in aqueous solution
Figure 2. Energy minimized semi-empirical PM3-levl calculations of hosts 1-3.
Moreover, dimers 1-3 are photophysically active, as a result of the
incorporation of fluorescent linkers. While the integrated
fluorescence intensities of compounds 2 and 3 increased linearly
with increased dimer concentration, the fluorescence intensity of
compound 1 displayed non-linear behaviour (see ESI for more
details). This is due to the rigid conformation of 1, which facilitates
intermolecular aggregation, especially at elevated concentrations
in aqueous solutions; such aggregation, in turn, results in the
development of different fluorescence profiles with complicated
spectroscopic trends.
Complexation-driven spectroscopic changes
Squaraines can exist in their monomeric form under certain
conditions, but are particularly prone to aggregation (as either H-
aggregates or J-aggregates) due to their highly planar structures
(Figure 4). 22 Cyclodextrin complexation of the squaraines is
reported to affect the equilibrium between the monomeric and
aggregated states, with squaraines in β-cyclodextrin complexes
stabilized in their monomeric states, and squaraines in γ-
cyclodextrin complexes stabilized as dimers.23 In our system, the
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10.1002/ejoc.201800283
European Journal of Organic Chemistry
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monomeric squaraine species (shown in Figure 5 for compound
6) shows a UV-visible absorption peak with a maximum around
650 nm (band II), with the H-aggregate absorbing between 500
and 600 nm (band I), and the J-aggregate showing a strong
absorption in the near-infrared spectral range (band III). These
separate absorption profiles enable quantification of the
prevalence of both H- and J-aggregates for varying squaraine
concentrations in presence of dimers 1-3 (Figure 5).
which gradually diminished with increasing concentrations of the
dye. This spectroscopic behaviour can be explained by the ability
of dimers 2 and 3 to bind two squaraines, forming a stable 1:2
host-guest complex.
Figure 6. Plots of the ratios of H-aggregate (I/II, grey) and J-aggregate (III/II,
orange) to monomeric squaraine vs concentrations of squaraine 6 for (A) control
(no host); (B) compound 1 (8 μM); (C) compound 2 (8 μΜ); and (D) compound
3 (8 μM).
Figure 5. Spectral deconvolution for investigation of H- and J-aggregate
formation with increasing concentrations of squaraine 6. (A) UV-vis spectra of
increasing concentrations of squaraine 6 ([6] = 1.3 μM (red), 2.6 μM (black), 3.9
μM (orange), 5.2 μM (grey), 6.5 μM (yellow), 7.8 μM (light grey), 9.1 μM (green),
10.4 μM (pink), 11.7 μM (brown), 13.0 μM (blue); (B) Representative
deconvoluted spectra of squaraine 6 ([6] = 7.8 μM, H-aggregate (I), Monomeric
state (II), J-aggregate (III)); (C) Plot of H- aggregate prevalence (ratio I/II, blue)
and J- aggregate prevalence (ratio III/II, red) against dye concentration for
squaraine 6.
Of note, among squaraines 4-9, the shorter alkyl chain-
substituted squaraines 4-6 showed predominantly H-aggregate
formation, whereas the longer alkyl chain-substituted squaraines
7-9 showed mostly J-aggregation. Of the two N-substituted
squaraines with cyclic substituents (compounds 10 and 11), H-
aggregation was slightly more dominant than J-aggregation for
compound 10, whereas compound 11 favoured J-aggregation.
Moreover, the cyclodextrin dimers had a substantial effect in
disrupting H-aggregation in the smaller squaraines, whereas
lower effects were observed in the cyclodextrin-induced
disruption of aggregation of the larger squaraines.
While compounds 1 and 2 caused a significant decrease in the H-
band of squaraine 6 (Figure 6A-C), virtually no aggregation was
observed in the presence of compound 3 (Figure 6D). The effect
of host dimer 3 was also very pronounced for guest squaraine 10,
and resulted in a marked decrease in both the H-aggregate and
J-aggregate absorption bands (Figure 7). Squaraines with N-
terminal substituents shorter than n-hexyl (i.e. 4 and 5) showed a
sharp rise in the H-band with flexible dimer hosts 2 (for squaraine
4) and 3 (for squaraines 4 and 5) at low squaraine concentrations,
Figure 7. Bar graphs showing H and J-aggregate formations for various
squaraines in presence of: (A) no cyclodextrin (control); (B) 1 (8 μM); (C) 2 (8
μM); and (D) 3 (8 μM). Downward arrows indicate the significant reduction of
aggregate formation for the squaraines 6 and 10.
Complexation-induced effects on squaraine hydrolysis
The hydrolyses of squaraines 4-11 in aqueous solution at room
temperature were studied in the presence of equimolar amounts
of dimers 1-3. These reactions follow first-order reaction kinetics,
as shown in Equation 1, below:
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A/A0 = e-kt + C
(Equation 1),
that a ratio value of 1 would represent no effect of the host on the
rate or extent of hydrolysis. Notably, squaraines in the presence
of host 1 demonstrated the lowest effects of complexation on
hydrolysis behaviours (as indicated by ratios closest to 1). For
most squaraines, the presence of host 2 led to moderate
protection from hydrolysis, indicated by ratio values slightly higher
than 1, and host 3 conferred substantial hydrolytic protection to
the squaraines.
where A is the integrated area of absorption at a given time, A0 is
the initial integrated area of absorption, k is the exponential decay
constant, and C is the equilibrium concentration of the decaying
squaraine species (Figure 8A).
The linear form of Equation 1 can also be expressed in logarithmic
form, as shown in Equation 2, below:
-Log10 (A/Ao – C) = kt –Log10 (1-C)
(Equation 2),
where the intercept and the slope is given by –Log10 (1-C) and
decay constant k respectively (Figure 8B).
Figure 9. Bar graph plot of the ratio of hydrolytic protection (Tdimer/Tcontrol) of
squaraines in presence of the dimers (1-3). (Τ is defined in Equation 3;
downward arrows indicate the larger extent of hydrolytic decay for the
squaraines 6; errors are calculated from standard deviations of c and k from the
linear plots and error bars are within 10% of the calculated T values).
Figure 8. (A) Plot of A/Ao vs time for first-order exponential hydrolytic decay of
squaraine 6 measured at every half an hour over 5 hours. (B) Linear plot for
first order exponential hydrolytic decay of squaraine 6 for (i) control; (ii)
compound 1; (iii) compound 2; and (iv) compound 3 (slope of the plot is a
measure of the exponential decay constant k; intercept c of the plot is a measure
of the aggregate concentration C)
In Equation 1, the two constants C and k are independent
parameters that indicate the extent of hydrolysis, by providing the
equilibrium squaraine concentration, and the rate of hydrolysis, by
providing the first-order rate constant. They can be related to each
other via the theoretical hydrolytic protection parameter, T,
defined in Equation 3, below:
Figure 10. (A) Generalized representation of the structure of squaraines dyes
(4-11) depicting the relatively hydrophilic (red) and hydrophobic (blue) parts of
the molecule. (B) Schematic representation of the host-guest association in
dimer 1, showing the H-bonding interaction of the two amide linkers to the
oxoanion of the squaraine core.
T = -Log(1-C)/k
(Equation 3)
where -Log(1-C) is the Y-intercept and k is the slope of the line.
Higher T values mean greater degrees of hydrolytic protection,
whereas lower T values indicate increased rates of decay.
We plotted the ratio of T in the presence of cyclodextrin hosts 1-3
(Tdimer) to T in the absence of any host (Tcontrol) (Figure 9), noting
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Notably, squaraine 6 in the presence of host 2 demonstrated an
exception to this general trend, and displayed markedly increase
hydrolysis rates in the presence of the host compared to in its
absence. This aberrant behaviour is a result of the optimal fit
between the squaraine 6 guest and the β-cyclodextrin host
cavities, which enables each β-cyclodextrin unit to activate the
electrophilic squaraine for hydrolysis via hydrogen-bonding
interactions with the oxoanions upon complexation (Figure 10).
Host 2 was particularly effective at increasing the rates of
hydrolysis, as a result of the greater conformational flexibility of
the linker in compound 2, which enables the β-cyclodextrin units
to access the squaraine core and promote hydrolysis. Although
dimer 3 has a relatively similar architecture, the tethering of the
methylene linkers to the 9,10-positions of the anthracene moiety
constrains the conformational flexibility.
A particularly high degree of hydrolytic protection was observed
for squaraines 10 and 11 with host 3, which is a result of the
conformational changes induced by the binding of the bulky
cycloalkyl and aromatic substituents in the cyclodextrin cavities.
These changes further stabilize the dimer-squaraine complex,
resulting in highly effective protection. Both complexes (3 + 10
and 3 + 11) were studied computationally and shown to have
different conformations than the n-alkyl substituted guest 6
(Figure 11).
squaraine) complex. While squaraines 4 and 5 form stable 1:2
host-guest complex with 3, squaraines 6-9 thread into the β-
cyclodextrin cavities and adapt a pseudo-rotaxane geometry.
Moreover, as a result of the closed structures of β-cyclodextrin
dimer hosts 2 and 3, they are more able than host 1 to protect the
electrophilic squaraine core against hydrolysis.
Fluorescence titration of cyclodextrin dimer hosts
The guest-induced fluorescence changes of the dimers 1-3
([dimer] = 5 x 10-7 M) was studied in presence of increasing
concentrations of squaraines 4-11.24 Importantly, the observed
behaviours are intimately dependent on the specific interactions
between each squaraine guest and cyclodextrin host, which
makes general trends challenging to elucidate.
While the fluorescence intensity of dimer 1 decreased with
increasing concentrations of squaraine guests (for all guests
except compounds 4 and 10), the intensities of dimers 2 and 3
increased with increasing amounts of squaraine (except for
guests 9-11 with dimer 3). The smallest squaraine 4 formed stable
1:2 host-guest association complex with all three hosts, while 5
exhibited a 1:2 binding with only 3. In contrast, the bulkier
squaraines (6-11) formed 1:1 host-guest binding model with all
the three dimers (1-3) in all cases (Table 1).
Table 1. Calculated association constant values for β-cyclodextrin dimer
hosts (1-3) with squaraine guests (4-11)
Guest
Host 1
Host 2
Host 3
4
5
[b]7.5 (1.3) x 1014
[a]2.7 (0.5) x 106
[a]3.5 (0.5) x 106
[a]1.5 (0.7) x 106
[a]4.5 (0.8) x 106
[a]6.6 (0.8) x 106
[a]1.7 (0.4) x 105
[a]1.2 (0.2) x 107
[b]8.8 (2.4) x 1013
[a]2.6 (0.4) x 106
[a]3.5 (1.2) x 105
[a]2.1 (0.8) x 105
[a]3.1 (0.1) x 105
[a]2.4 (0.7) x 105
[a]4.2 (1.0) x 105
[a]1.0 (0.1) x 106
[b]2.3 (0.4) x 1013
[b]4.5 (1.0) x 1013
[a]2.3 (0.1) x 108
[a]4.1 (0.5) x 106
[a]3.2 (0.4) x 107
[a]8.1 (0.5) x 105
[a]2.4 (0.6) x 106
[a]3.0 (0.2) x 106
6
7
8
9
Figure 11. Energy minimized (semi-empirical PM3) computational models for
(A) squaraine-dimer combination (3 + 6); and (B) squaraine-dimer combination
(3 + 10), illustrating the different location of the anthracene core with respect to
the electrophilic squaraine core in both the cases.
10
11
[a] Association constant (M-1) values are reported for 1:1 host-guest complex
formation in aqueous phosphate buffered saline (PBS) solution. [b]
Association constant (M-2) values are reported for 1:2 host-guest complex
formation in aqueous PBS solution. All values are calculated as an average
of at least three trials. Error values are included in parentheses.
Another combination of note was squaraine 11 with dimer 3, in
which the hydrolytic decay of the squaraine exhibited zero-order
behaviour. This is likely due to the fact that the complexation-
induced conformational changes minimize complex dissociation,
which in turn limits the availability of free squaraine 11. As a result,
the rate of hydrolysis becomes independent of the overall
squaraine concentration. In fact, all hosts 1-3 when complexed
with squaraine 11 led to near zero-order behaviour as well,
pointing to the likelihood of the interactions between β-
cyclodextrin and the tert-butylphenyl substituent as key for
inducing this kinetic behaviour.
For all squaraines except for 6 and 7, which are particularly easily
hydrolysed in the presence of dimer 2 due to optimal steric
matching, the general trend in the complexation-induced
hydrolytic protection follows the order 3 > 2 > 1. This trend can be
explained based on the conformation of the host-guest (dimer-
The association constant values for 1:2 host-guest complexes of
squaraine 4 (shown in the top row of Table 1) followed the trend
1>2>3, with the association constants of first guest binding events,
K1 (2.8(0.3) x 103 M-1, 1.6(0.4) x 104 M-1, and 3.3(0.4) x 103 M-1,
respectively), being several orders of magnitude lower than that
of the association constants of the second guest binding events,
K2 (2.7(0.4) x 1011 M-1, 5.4(0.8) x 109 M-1, and 7.1(0.9) x 109 M-1,
respectively). This means that the binding of the first squaraine 4
guest renders the host cavity much more receptive to the second
guest. While the association constant values for most of the
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10.1002/ejoc.201800283
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cyclodextrin-squaraine combinations were on the order of 105-107
M-1, squaraine 6 exhibited extraordinary affinity for dimer host 3,
with calculated association constants of 108 M-1. The association
constant values are comparable in magnitude to previously
reported values for host-guest binding with cyclodextrin dimers.25
Among the straight chain alkyl-substituted squaraines,
compounds 5 and 6 have optimal sizes and hydrophobicities to
bind in hosts 2 and 3, respectively. Squaraines with longer alkyl
chain substituents (7-9) exhibited association constants that were
one and two orders of magnitude lower with dimers 2 and 3,
respectively. This trend is likely due to less optimal steric
matching with the host cavity for the larger squaraines.
A comparison of squaraine guests 10 and 11 revealed that
compound 11 exhibited higher association constants because of
the tert-butylphenyl substituent, which has been reported to bind
strongly in β-cyclodextrin (Ka = 1.6 x 104 M-1).25 Despite structural
similarities between hosts 2 and 3, the association constants for
compound 2 are low for most of the squaraines compared to those
observed for compound 3 (Figure 12). This differential behaviour
may be a result of the greater hydrophobicity of the anthracene
unit in compound 3, which in turn contributes to increased
cooperativity of the β-cyclodextrin units in forming a stable 1:1
host-guest complex.
host 3, resulting in the anthracene-containing linker interacting
closely with the electron deficient core of guest 10 and facilitating
excited state energy transfer. This host-guest conformation was
also noted for 11 with bulky tert-butylphenyl substituents. In
contrast, complexation of guest 6 leads to a relatively open
structure, where the anthracene core is displaced from the host
cavity (Figure 11, vide supra).
Computational Modelling
The stabilities of the 1:1 cyclodextrin: squaraine complexes were
calculated using PM3 calculations (with a semi-empirical force
field) for host 3 with guests 6, 10 and 11. Guest 6 complexation
with all hosts 1-3 was also investigated to determine the
oxoanion-amide distances in host-guest complexes (Table 2).
The calculated negative stabilization energies indicate that the
squaraine guests thread inside the host cavity (1-3) to form a
stable host-guest association complex. Interestingly, complexes
of host 3 with guests 10 and 11 were substantially more stable
than the complex formed between host 3 and n-hexyl-substituted
squaraine 6.
Table 2. Calculated stabilization energy values for β-cyclodextrin dimer
hosts (1-3) with squaraine guests 10,11 (with host 3) and 6 (with hosts 1,2,
and 3) assuming 1:1 complexation.
[a]
[b]
[c]
[d]
[e]
Ehost
Eguest
Ecomplex
ΔEcomplex
d2-d1
(KJ/mol)
(KJ/mol)
(KJ/mol)
(KJ/mol)
(Å)
11 = 215.4
10 = -3.4
6 = -42.1
6 = -42.1
6 = -42.1
-11497.7
-11689.2
-11719.5
-11841.3
-11890.9
-53.0
-25.7
-17.3
-63.4
-33.9
4.37
4.31
4.35
0.86
2.31
3 = -11660.1
2 = -11735.8
1 = -11814.9
[a] Energy of formation of the host. [b] Energy of formation of the guest. [c]
Energy of formation of the 1:1 host-guest complex. [d] Stabilization energy
of the 1:1 host-guest complex. [e] Difference in the 1st and 2nd oxoanion-
amide pair bond lengths (Figure 13). Energy minimized models were carried
out using PM3 level calculations with semi-empirical force field. Values of d1
(distance of the 1st oxoanion-amide pair bond) and d2 (distance of the 2nd
oxoanion-amide pair bond) are included in Table S19 in the ESI.
(
Figure 12. Plot of log K (association constants) versus N-substituted anilino
squaraines (4-11) for β-cyclodextrin dimer hosts (1-3). Values for squaraine 4
(for all hosts) and squaraine 5 (for host 3) are for 1:2 host-guest complexes.
(Error bars that are shown represent the error of least three trials).
The distances of the two oxoanion-amide pairs (d1 and d2, Figure
13) were compared to determine the precise position of the
electrophilic squaraine core, and in particular to distinguish
between two possible modes of interaction: (a) interaction in
which the two amide groups of the linker interact closely with one
oxoanion of the squaraine core, resulting in a significant
difference between the two measured distances (option I, Figure
13); or (b) interaction in which the two amide groups of the linkers
interact equally with both oxoanions of the squaraine core,
resulting in approximately equivalent distances (option II, Figure
13). Notably, the dual hydrogen bonding interactions available in
option II are expected to provide substantially more electrophilic
activation than option I. The observed trend in the difference of
the measured distances (d2 - d1) for squaraine 6 for all the
complexes was 3>1>2, and supports option (b) as the more likely
The changes in the fluorescence of the dimer 3 upon addition of
squaraines 6 and 10 were further analysed to understand the
different complexation modes of the squaraine guests. While
compound 6 is an example of the n-alkyl squaraines that caused
an increase in the fluorescence of dimer 3, compound 10 is an
example of the bulky N-substituted squaraines that caused a
decrease in the fluorescence emission of compound 3 with
complex formation. These opposing trends were explained by
computational energy minimized models of host-guest complexes
of host 3 with guest 6 compared to host 3 with guest 10. Unlike
flexible n-alkyl substituents in compound 6, the bulky substituent
in compound 10 causes a significant conformational change of
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10.1002/ejoc.201800283
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mode of interaction (2-SQ, II, Figure 13) This observation explains
the anomalously high rate of hydrolysis of squaraine 6 in presence
of host 2, owing to the enhanced electron deficient nature of the
squaraine core making it susceptible to hydrolytic attack.
as well as investigating its sensitivity for them. The results of these
investigations will be reported in due course.
Figure 14. Visual detection of benzo[a]pyrene via squaraine 10 and dimer 2
combination (Left: aqueous PBS solution of squaraine 10 (24 µM); centre:
solution of squaraine 10 (24 µM) + dimer 2 (120µM); right: squaraine 10 (24 µM)
+ dimer 2 (120 µM) + benzo[a]pyrene (30 µM))
Figure 13. Possible modes of squaraine core-linker interactions resulting in a
significantly large (case I) and minimum (case II) difference in the measured
oxoanion-amide distances (d2 - d1).
Conclusions
In conclusion, we have synthesized a series of three novel β-
cyclodextrin dimers. These three variable architectures have
been synthesized through variation of the linker moieties tethering
the two individual β-cyclodextrin units, which alters their
flexibilities and associated binding properties. The incorporation
of fluorescent anthracene and naphthalene units in these flexible
linkers render the β-cyclodextrin dimer hosts both photophysically
active and conformationally flexible. We also incorporated a rigid
heteroaromatic (pyridyl group) linker to compare the host
properties against the flexible dimer hosts, and observed that the
structural adaptations exhibited by the flexible dimers directly
enables unprecedently high association constant values for
complimentary guest molecules like linear squaraine dyes. A
remarkable control of photophysical properties and chemical
reactivity of squaraine dyes has been shown via hydrophobic
complexation with the dimer hosts in aqueous solution, which can
be utilized in selective and sensitive colorimetric sensing of
environmentally toxic analytes.
Synthetic tetralactam macrocycle-based squaraine rotaxanes
have been reported in the literature with association constants
1000 times greater in aqueous solution compared to organic
solvents.26 Unlike tetralactam macrocycles, where the rational
design of the macrocycles is primarily targeted at hydrogen
bonding-induced stabilization of the squaraine core, the
complexation of squaraines in β-cyclodextrin dimers is entirely
driven by hydrophobicity of the squaraine guests (4-11) in the
aqueous medium, but results in substantial hydrogen bonding
interactions. The hydrophobic nature of the complexation of 3 and
6 was further evident from the two separate spots visible on the
TLC plate after eluting an aqueous solution of 3 and 6 with a
mixture (1:9) of methanol in chloroform (see ESI). These results
mean that the squaraine guest is not bound in the host in the
absence of water, because of the inability to use hydrophobic
binding under such conditions. Previous work on squaraine
encapsulation,26 in contrast, which relies on hydrogen bonding of
the oxoanions by the macrocycles, results in one spot on the TLC
plate after elution in an organic solvent.
Of the three hosts investigated herein, 3 is most efficient, both in
altering the aggregation properties (6 and 10), and in inhibiting the
hydrolytic decay (10 and 11) of the squaraines.
Experimental Section
Preliminary efforts towards developing a colorimetric sensing
system employing the squaraine-dimer complexes resulted in the
discovery of a unique visual response for benzo[a]pyrene via the
combination of squaraine 10 and dimer 2. While the free
squaraine 10 undergoes hydrolysis in aqueous phosphate saline
buffer (PBS) solution, a mixture of squaraine 10 + dimer 2 (1:5
molar ratio) results in a stable solution with an intense purple
coloration (Figure 14). Addition of benzo[a]pyrene results in the
dissipation of the intense purple hue of the solution, which exhibits
a bluish coloration. This could likely be due to the competitive
association of the analyte to the host 2, thereby disrupting the pre-
formed 10 + 2 complex. Current work in our laboratory is focused
on establishing this detection system for selective guest analytes,
General Information. All of the starting materials, reagents, and solvents
were purchased from Sigma Aldrich, Acros Organics, TCI chemicals, Alfa
Aesar, or Fisher Scientific, and were used as received. For air and
moisture-free reactions, oven dried glassware, anhydrous solvent, and
proper Schlenk-line techniques were employed. Reactions were monitored
via analytical thin layer chromatography (TLC) using polyester-backed
TLC plates. Visualization was accomplished with UV light at 254 nm. Flash
column chromatography was performed with SiliaFlash F60 (230-400
mesh) or using automated flash chromatography (Yamazen Smart Flash
AI-580S & AKROS). UV-VIS spectra were recorded on a Shimadzu UV-
3600 Plus spectrophotometer. Fluorescence spectra were recorded on a
Shimazdu RF-6000 spectrophotometer with 3.0 nm excitation slit widths
and 3.0 nm emission slit widths. 1H and 13C NMR spectra were taken on a
Bruker 400 MHz spectrometer and were recorded in D2O, CDCl3 or DMSO-
d6 at room temperature. Chemical shifts (δ) are reported in parts per
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201800283
European Journal of Organic Chemistry
FULL PAPER
million relative to D2O at 4.79 ppm, chloroform at 7.26 ppm, dimethyl
UV/vis analysis of squaraine dyes. In a quartz cuvette, the absorption
spectra of a mixture of increasing concentration of squaraine guests (4-
11), 8 μM solution of host dimers (1-3) added to 2.5 mL of PBS were
recorded. For the absorption spectra, 50 μL of the host solution of the
dimer (1 mg/mL in DI water) and increasing volumes of a 1 mg/mL solution
of squaraine guests (1.5 μL; 3.0 μL; 4.5 μL; 6.0 μL; 7.5 μL; 9.0 μL; 10.5
μL; 12.0 μL; 13.5 μL; 15.0 μL) was added to 2.5 mL of PBS. The solution
was shaken to ensure homogeneity and data was collected. The UV
spectra were subjected to a piecewise linear background subtraction
method. The selection of spectral positions to run the background were
identified by a custom threshold approach. After the background spectral
subtraction, the spectral signal was fitted using “Non-linear Mode Fit”
1
sulfoxide at 2.59 ppm, or to tetramethylsilane (TMS) at 0.00 ppm for H
NMR, and relative to CDCl3 at 77.16 ppm or DMSO at 40.76 ppm for 13
C
NMR spectra. Mass spectra for compounds 1, 2 and 3 were recorded in a
Bruker Omniflex MALDI-TOF instrument (using 2,5- dihydroxybenzoic acid
as a matrix) and in a Waters Q-TOF micro-mass spectrometer at the
Department of Chemistry Instrumentation Facility (DCIF) at the
Massachusetts Institute of Technology (MIT), with samples run by Dr. Li Li.
Mass spectra of compounds 4, 5, 6, 7, 10 and 11 were recorded on a
ThermoScientific LTQ Qrbitral XLTM. For further information of sample
preparation, see ESI.
command in Mathematic
2
) a (method set to “automatic”) with three Gaussian
(
푥−휇
2
Spectroscopic Methods
2휎
functions, 퐴 · 퐸푥푝
, where A, μ, σ and x refer to the amplitude, mean,
standard deviation, and wavelength, respectively.
Methods for fluorescence titration experiments. 6.25 μL of a 0.5 mg/mL
(0.2 mM) aqueous solution of the host dimer (1-3) was added to a cuvette
containing 2.5 mL of aqueous phosphate buffer solution (PBS, buffered at
pH 7.4). The fluorescence spectra of this solution were measured after
being titrated with solutions of the guest dyes (0.2 mg/mL solution in THF)
at the following addition volumes: 0.0, 1.5, 3.0, 4.5, 6.0, 7.5, 9.0, 10.5, 12.0,
13.5, 15.0, 20.0, 30.0, 40.0 and 50.0 μL dye solutions. Each measurement
was repeated for four trials. All fluorescence spectra were integrated vs.
wavenumber on the X-axis using OriginPro Version 9.1. The concentration
range scanned for each dye against the host concentration (approximately
0.5 μM) was further refined based on the association constant values of
the host-guest combination. In particular, for association constant values
greater than 106 M-1, the guest concentration was reduced to a sub-
stoichiometric (i.e. 0-0.5 μΜ) range with respect to the host. This was
achieved by further diluting the stock guest solution to a final concentration
of 0.04 mg/mL and adjusting the volume additions accordingly. See table
S1 for final concentrations of squaraine dyes in solution
Methods for Spectral Deconvolution and Curve Fitting
All spectral analysis was done using custom codes written in Mathematica
11.0.1.0 (Wolfram Research, Champaign, IL).
Deconvolutions. The UV spectra were subjected to a piecewise linear
background subtraction method. The selection of spectral positions to run
the background were identified by a custom threshold approach. After the
background spectral subtraction, the spectral signal was fitted using
“NonlinearModeFit” command (method set to “automatic”) with three
2
(푥−휇)
2
2휎
gaussian functions, 퐴 · 퐸푥푝
, where A, μ, σ and x have their usual
meanings—amplitude, mean, standard deviation, and wavelength
respectively.
Linear Fits. All linear fits were done with “NonlinearModeFit” command
(method set to “automatic”) using the form − log [ 퐴 − 푐] = 푘 · 푥, where c,
퐴
0
Methods for Job’s plot experiments. 0.5 mg/mL of the dimer hosts in DI
water and 0.04 mg/mL of the squaraine dye guests in THF were prepared
separately. The fluorescence spectra of the varying concentrations of the
dimer host solutions were recorded (four trials each) for the sets of
mixtures (decreasing host and increasing guest) seen in Table S2. All
fluorescence spectra were integrated vs. wavenumber on the X-axis using
OriginPro Version 9.1. After diluting each mixture, with 2.5 mL of PBS
solution in a quartz cuvette, the fluorescence spectra were recorded.
A, A0, k and x refer to the integrated absorption at the aggregate
concentration, concentration at time t, concentration at time zero, rate
constant and the independent variable respectively. The value of c is found
from the corresponding exponential fit.
Titration Curve Fits. All fluorescence titration data fits were done with
Solver.xlam using “GRG-Nonlinear” method in Excel 2017 using the 1:1
and 1:2 supramolecular titration equations.
Normalized fluorescence intensity (f
= (F-F0)/F0; where F is the
fluorescence intensity at a particular host concentration, and F0 is the
fluorescence intensity at initial concentration) was measured for each
solution. Difference in f were calculated for solutions A (without squaraine
guests) and B (solutions of varying concentrations of host and guest, with
a fixed overall concentration of 0.5 μM). The product of Δf and mole
fraction of guest (γ*Δf) is plotted against the mole fraction (γ) of guests.
The mole fraction corresponding to the maxima of the plot (γmax) was
recorded.
Synthetic Methods
Synthesis of all cyclodextrin hosts and squaraine guests: The conversion
of β-cyclodextrin to 6-amino-6-monodeoxy-β-cyclodextrin was carried out
following literature-reported procedure.
acid and anthracene-9,10-dipropionic acid (linkers for dimer hosts 2 and
3) were synthesized using literature-reported procedures starting from 1,4-
27
Naphthalene-1,4-dipropionic
28
dimethylnaphthalene and 9,10-dimethylanthracene, respectively.
Bis(sucinimidyl) 2,6-pyridine carboxylate (linker for host 1) was
syntheszied using a literature-reported procedure.29 β-cyclodextrin dimer
hosts 1-3 (Figure 1) were synthesized via activated amide coupling
reactions of 6-amino-6-monodeoxy-β-cyclodextrin and the bis-succinimide
esters of the linkers (see ESI for more details).
Methods for observing hydrolysis behavior of squaraine (4-11). The
absorption spectra of a mixture of 24 μM solution of host dimers (1-3) and
24 μM solution of guest squaraines (4-11) were recorded over a period of
5 hours, with spectra acquired every 30 minutes. For the 1:1 absorption
spectra, 30 μL of a guest solution of squaraine (1 mg/mL in THF, 2.0 mM)
and 150 μL of host solution of dimer (1 mg/mL in DI water, 0.4 mM) was
added to 2.5 mL of PBS. The solution was shaken to ensure homogeneity,
and the data was collected. All linear fits were done with the “Non-linear
Mode Fit” command (method set to “automatic”), using the form
− log [퐴퐴 − 푐] = 푘 · 푥, where c, A, A0, k and x refer to the integrated
1: Bis(succinimidyl) 2,6-pyridine carboxylate (50 mg, 0.14 mmol, 1.00 eq)
and S3 (350 mg, 0.31 mmol, 2.20 eq) were dissolved in 20 mL of
anhydrous N, N-dimethylformamide under N2 and stirred at room
temperature. After 24 hours, the reaction mixture was poured into
approximately one liter of acetone to precipitate all cyclodextrin
compounds. The precipitate was collected and washed with excess
acetone and then dried under vacuum. Purification by recrystallization
(acetone:water 20:80 (vol/vol)) afforded host 1 as an off-white powder (162
0
absorption at the aggregate concentration, concentration at time t,
concentration at time zero, rate constant and the independent variable,
respectively. The value of c was found from the exponential fit.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201800283
European Journal of Organic Chemistry
FULL PAPER
mg, yield = 48%). 1H-NMR (400 MHz, DMSO-d6): δ (ppm) = 3.10-3.45 (m,
overlap with HDO, 29 H), 3.50-3.80 (m, 56 H), 4.23-4.62 (m, 12 H, 6-OH),
4.65-5.03 (m, 14 H, 1-H), 5.60-5.85 (m, 28 H, 2-OH & 3-OH), 8.06-8.26 (m,
3 H, ArH), 9.23–9.36 (br s, 1 H, ArNH); 13C-NMR (100 MHz, DMSO-d6) δ
(ppm) = 33.44, 59.9-60.5, 71.2-73.4, 80.8-81.2, 101.6-102.0, 123.8-124.0,
125.3-125.6, 126.8-126.9, 177.7-177.8; MS (Q-TOF): m/z = 2420.72 [M +
Na]+ (Calculated for C91H143N3O70 + Na = 2420.76).
3: Compound S17 (50 mg, 0.10 mmol, 1.00 eq) and 6-amino-6-
monodeoxy-β-cyclodextrin (250 mg, 0.22 mmol, 2.20 eq) were dissolved
in 20 mL of anhydrous N, N-dimethylformamide under N2 and stirred at
room temperature. After 24 hrs., the reaction mixture was poured into
acetone (1 L) to precipitate the cyclodextrin compounds. The precipitate
was collected and washed with excess acetone and then dried under
vacuum. Purification by recrystallization (acetone/water 20:80) afforded
host 3 as an off-white powder (84 mg, 33% yield). 1H-NMR (400 MHz,
DMSO-d6) δ (ppm) = 2.53-2.58 (s, 4 H), 3.10-3.45 (m, overlap with HDO,
32 H), 3.50-3.80 (m, 56 H), 4.35-4.58 (m, 12 H, 6-OH), 4.75-4.90 (s, 14 H,
1-H), 5.60-5.85 (m, 28 H, 2-OH & 3-OH), 7.25-7.65 (m, 4 H, ArH), 7.65–
8.40 (m, 4 H, ArH); 13C-NMR (100 MHz, DMSO-d6): δ (ppm) = 25.0-25.2,
30.4-30.7, 35.5-35.7, 59.5-59.9, 71.7-72.6, 72.6-73.1, 80.9-81.9, 101.6-
102.0, 124.6-125.5, 128.6-128.8, 162.0-162.2; MS (Q-TOF): m/z =
2575.78 [M + Na]+ (Calculated for C104H156N2O70 + Na = 2575.86).
S11: Bis(succinimidyl) Napthalene-1,4-dipropionic acid. To a solution of
Napthalene-1,4-dipropionic acid (100 mg, 0.37 mmol, 1.00 eq) in
anhydrous N, N-dimethylformamide (2.0 mL) under nitrogen, N-
hydroxysuccinimide (NHS, 157 mg, 1.36 mmol, 3.67 eq), N-(3-
dimethylaminopropyl)-N’-ethylcarbodiimide hydrochloride (EDC, 180 mg,
0.93 mmol, 2.51 eq) and 4-(dimethylamino) pyridine (DMAP, 7.5 mg, 0.06
mmol, 0.16 eq) were added. The reaction mixture was stirred at room
temperature under nitrogen overnight. After the reaction was completed
(ca. 16 hours), the solvent was removed under reduced pressure. The
residue was then dissolved in dichloromethane (20 mL) and this solution
was washed with water (20 mL), dried with anhydrous Na2SO4 and
evaporated to dryness under vacuum. The residue was dissolved in 1 mL
of anhydrous N, N-dimethylformamide and recrystallized at 0 ºC to give
S11 as a white product (120 mg, 70% yield). 1H-NMR (400 MHz, DMSO-
d6): δ (ppm) = 2.72(t, 4 H, J = 7.6 Hz, CH2CH2CO), 2.92 (s, 8 H, Suc-H),
3.35 (t, 4 H, J = 7.6 Hz, CH2CH2CO), 7.30 (s, 2 H, H- 2,3), 7.56–7.61 (m,
2 H, H-6,7), 8.07–8.11 (m, 2 H, H- 5,8), 12.29 (br s, 2 H, CO2H); 13C-NMR
(100 MHz, DMSO-d6): δ (ppm) = 25.5, 27.4, 34.6, 124.2, 125.4, 125.8,
131.5, 135.3, 170.3, 174.5.
Synthesis of squaraine dyes (compounds 4-11, Figure 3). A mixture of
aniline (10-20 mmol, 1.00 eq), 3,4-dihydroxycyclobut-3-ene-1,2-dione (i.e.
squaric acid; 0.50 eq) in 10-20 mL n-butanol/toluene (2:1 vol/vol mixture)
was stirred at refluxing temperature for 1-2h in Dean-Stark apparatus. The
reaction was allowed to cool to room temperature, after which the majority
of the solvent was removed under reduced pressure. The remaining crude
mixture was recrystallized using isopropanol to yield blue, green, purple,
or gold crystalline dyes.
4: 2,4-Bis[4-(N-butyl, N-methylamino)phenyl]squaraine. Yield: 60 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.2
Hz, 4H), 3.48 (t, J = 7.6 Hz, 4H), 3.15 (s, 6H), 1.77 – 1.58 (m, 4H), 1.39 (h,
J = 7.3 Hz, 4H), 0.98 (t, J = 7.3 Hz, 6H). 13C NMR (101 MHz, chloroform-
d) δ 188.24, 183.46, 154.22, 133.25, 119.74, 112.25, 52.60, 38.91, 29.39,
20.21, 13.88. HRMS (ESI+) Calcd. For C26H32N2O2 [M]+: 405.2537;
Found: 405.2516.
2: Compound S11 (50 mg, 0.11 mmol, 1.00 eq) and 6-amino-6-
monodeoxy-β-cyclodextrin (275 mg, 0.24 mmol, 2.20 eq) were dissolved
in 20 mL of anhydrous N, N-dimethylformamide under N2 and stirred at
room temperature. After 24 hrs, the reaction mixture was poured into
acetone (1 L) to precipitate the cyclodextrin compounds. The precipitate
was collected and washed with excess acetone and then dried under
vacuum. Purification by recrystallization (acetone/water 20:80) afforded
5: 2,4-Bis[4-(N-pentyl, N-methylamino)phenyl]squaraine. Yield: 51 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.3
Hz, 4H), 3.48 (t, J = 7.6 Hz, 4H), 3.15 (s, 6H), 1.71-1.63 (m, 4H), 1.40-1.33
(m, 8H), 0.93 (t, J = 7.0 Hz, 6H). 13C NMR (101 MHz, chloroform-d) δ
188.20, 183.47, 154.21, 133.25, 119.74, 112.25, 52.85, 38.90, 29.10,
26.98, 22.49, 14.00. HRMS (ESI+) Calcd. For C28H37N2O2 [M]+:
433.2850; Found: 433.2827.
1
dimer 2 as an off-white powder (110 mg, 40% yield). H-NMR (400 MHz,
DMSO-d6): δ (ppm) = 2.53-2.58 (s, 4 H), 3.10-3.45 (m, overlap with HDO,
34 H), 3.50-3.80 (m, 56 H), 4.35-4.58 (m, 12 H, 6-OH), 4.75-4.90 (s, 14 H,
1-H), 5.60-5.85 (m, 28 H, 2-OH & 3-OH), 7.25-7.30 (s, 1 H, ArH), 7.50–
7.60 (m, 2 H, ArH), 7.69–7.77 (br s, 1 H, ArH), 8.03-8.14 (m, 2 H, ArH);
13C-NMR (100 MHz, DMSO-d6): δ (ppm) = 25.0-25.2, 30.4-30.7, 35.5-35.7,
59.5-59.9, 71.7-73.1, 80.9-81.9, 101.6-102.0, 124.6-125.5, 128.6-128.8,
162.0-162.2; MS (MALDI-TOF): m/z = 2525.95 [M + Na]+ (Calculated for
C100H154N2O70 + Na = 2525.85).
6: 2,4-Bis[4-(N-hexyl, N-methylamino)phenyl]squaraine. Yield: 52 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.2
Hz, 4H), 3.48 (t, J = 7.6 Hz, 4H), 3.15 (s, 6H), 1.65 (q, J = 7.3 Hz, 4H), 1.40
– 1.27 (m, 12H), 0.90 (d, J = 6.7 Hz, 6H). 13C NMR (101 MHz, chloroform-
d) δ 188.27, 183.46, 154.20, 133.25, 119.75, 112.25, 52.87, 38.90, 31.56,
27.23, 26.63, 22.58, 14.00. HRMS (ESI+) Calcd. For C30H40N2O2 [M]+:
461.3163; Found: 461.3155.
S17: Bis(succinimidyl) anthracene-9,10-dipropionic acid. To a solution of
anthracene-9,10-dipropionic acid (100 mg, 0.31 mmol, 1.00 eq) in
anhydrous N, N-dimethylformamide (2.0 mL) under a nitrogen atmosphere,
N-hydroxysuccinimide (NHS, 157 mg, 1.36 mmol, 4.39 eq), N-(3-
dimethylaminopropyl)-N’-ethylcarbodiimide hydrochloride (EDC, 180 mg,
0.93 mmol, 3.00 eq) and 4-(dimethylamino) pyridine (DMAP, 7.5 mg, 0.06
mmol, 0.19 eq) were added. The reaction mixture was stirred at room
temperature under nitrogen overnight. After 16 hours, the solvent was
removed under reduced pressure. The residue was then dissolved in
dichloromethane (20 mL) and this solution was washed with water (20 mL),
dried with anhydrous K2SO4 and evaporated to dryness under vacuum.
The residue was dissolved in 1 mL of anhydrous N, N-dimethylformamide
and recrystallized at 0 ºC to give compound S17 as a dark brown colored
product (105 mg, 65% yield). 1H-NMR (400 MHz, DMSO-d6): δ (ppm) =
2.82 (t, 4 H, J=8.2 Hz, CH2CH2CO), 2.92 (s, 8 H, Suc-H), 3.92 (t, 4 H, J =
8.2 Hz, CH2CH2CO), 7.59 (dd, 4H, Ar–H, J1 = 3.2 Hz, J2 = 7.0 Hz), 8.36
(dd, 4 H, Ar–H, J1 = 3.2 Hz, J2 = 7.0 Hz); 13C-NMR (100 MHz, DMSO-d6):
δ (ppm) = 25.5, 27.4, 34.6, 130.7, 129.2, 126.7, 124.7, 170.3, 174.5.
7: 2,4-Bis[4-(N-heptyl, N-methylamino)phenyl]squaraine. Yield: 42 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.3
Hz, 4H), 3.46 (t, J = 7.7 Hz, 4H), 3.15 (s, 6H), 1.65 (q, J = 7.2 Hz, 4H), 1.38
– 1.25 (m, 16H), 0.89 (t, J = 7.0 Hz, 6H). 13C NMR (101 MHz, chloroform-
d) δ 188.17, 183.48, 154.21, 133.25, 119.74, 112.25, 52.88, 38.90, 31.75,
29.07, 27.29, 26.94, 22.58, 14.06. HRMS (ESI+) Calcd. For C32H45N2O2
[M]+: 489.3476; Found: 489.3452.
8: 2,4-Bis[4-(N-octyl, N-methylamino)phenyl]squaraine. Yield: 45 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.3
Hz, 4H), 3.48 (t, J = 7.6 Hz, 4H), 3.15 (s, 6H), 1.72 – 1.61 (m, 4H), 1.43 –
1.21 (m, 20H), 0.89 (t, J = 7.3 Hz, 6H). 13C NMR (101 MHz, chloroform-d)
δ 188.26, 183.47, 154.20, 133.25, 119.75, 112.25, 52.88, 38.90, 31.77,
29.37, 29.22, 27.28, 26.98, 22.63, 14.09.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201800283
European Journal of Organic Chemistry
FULL PAPER
9: 2,4-Bis[4-(N-nonyl, N-methylamino)phenyl]squaraine. Yield: 50 %. 1H
NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H), 6.75 (d, J = 9.3
Hz, 4H), 3.48 (t, J = 7.3 Hz, 4H), 3.15 (s, 6H), 1.71 – 1.61 (m, 6H), 1.42 –
1.20 (m, 24H), 0.88 (t, J = 7.0 Hz, 6H). 13C NMR (101 MHz, chloroform-d)
δ 188.23, 183.47, 154.20, 133.25, 119.75, 112.25, 52.88, 38.90, 31.83,
29.51, 29.41, 29.23, 27.28, 26.98, 22.66, 14.10.
dynamics simulations. Next, these structures were submitted to MMF94
molecular mechanics methods, and the minimized structure from this was
further optimized and minimized using a PM3-level semi-empirical force
field in a gaseous medium. The energy obtained from these calculations
were used to calculate the stabilization energy of the complex using the
equation below1:
10: 2,4-Bis[4-(N-cyclohexylmethyl, N-methylamino)phenyl]squaraine.
Yield: 44 %. 1H NMR (400 MHz, chloroform-d) δ 8.38 (d, J = 9.2 Hz, 4H),
6.75 (d, J = 9.3 Hz, 4H), 3.33 (d, J = 7.1 Hz, 4H), 3.17 (s, 6H), 1.78 – 1.66
(m, 12H), 1.31 – 1.11 (m, 6H), 1.06 – 0.93 (m, 4H). 13C NMR (101 MHz,
chloroform-d) δ 183.48, 154.51, 133.15, 112.41, 59.44, 40.32, 37.13,
31.08, 26.27, 25.83. HRMS (ESI+) Calcd. For C32H40N2O2 [M]+:
485.3163; Found: 485.3138.
∆퐸푐표푚푝푙푒푥 = 퐸퐶표푚푝푙푒푥 − 퐸퐻표푠푡 − 퐸퐺푢푒푠푡
where ∆퐸푐표푚푝푙푒푥 is the stabilization energy of the host-guest complex,
퐸푐표푚푝푙푒푥 is the energy of formation of the host-guest complex, 퐸퐻표푠푡is
the energy of formation of the β-cyclodextrin dimer hosts, and 퐸퐺푢푒푠푡 is
the energy of formation of the squaraine guest.
11:
2,4-Bis[4-N-(tert-butylphenyl),
N-methylamino)phenyl]squaraine.
Acknowledgements
Yield: 53 %. 1H NMR (400 MHz, chloroform-d) δ 8.39 (d, J = 9.2 Hz, 4H),
7.37 (d, J = 8.4 Hz, 4H), 7.10 (d, J = 8.4 Hz, 4H), 6.84 (d, J = 9.3 Hz, 4H),
4.71 (s, 4H), 3.23 (s, 6H), 1.31 (s, 18H). 13C NMR (101 MHz, chloroform-
d) δ 189.43, 150.79, 133.41, 133.05, 126.18, 125.92, 120.29, 112.66,
55.75, 39.05, 34.55, 31.32. HRMS (ESI+) Calcd. For C40H45N2O2 [M]+:
585.3476 Found: 585.3453.
Funding is acknowledged from the NSF under Award 1453483.
We graciously acknowledge the support of Dr. Li Li
(Massachusetts Institute of Technology) and Aliaksandr
Yeudakimau (University of Rhode Island) for their assistance in
acquiring mass spectral data.
Computational Modelling
Keywords: supramolecular chemistry • macrocycles •
All computational modelling was done using commercially available
Spartan software, version 16. To obtain the molecular models, the
structures were first energy-minimized using multiple runs of molecular
hydrophobic effect • inclusion compounds • host-guest systems
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Entry for the Table of Contents
FULL PAPER
Three newly synthesized β-
S. Chaudhuri, M. Verderame, Y. M. N.
D. Y. Bandara, A. I. Fernando, T. L.
Mako and M. Levine*
cyclodextrin dimers have been found
to complex a variety of squaraine
dyes with high association constants
and interesting geometries.
Page No. – Page No.
Displacement of the squaraine dye
from the cavity by an analyte provides
a promising sensing platform.
Synthetic β-cyclodextrin dimers for
squaraine binding: Effect of host
architecture on photophysical
properties, aggregate formation and
chemical reactivity
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