A squaraine dye with bulky end groups is employed as the thread component in two Leigh-type amide rotaxanes. The rotaxanes are synthesized in a simple two-step process. X-ray crystal structures of the rotaxanes show that the pyridyl-containing macrocycle is more rigid and wraps more tightly around the cyclobutene core of the squaraine thread compared to the isophthalamide-containing macrocycle. The rotaxanes exhibit photophysical properties that are similar to the precursor squaraine. The encapsulating macrocycle greatly increases the chemical stability of the squaraine thread and inhibits aggregation-induced broadening of its absorption spectrum. It should be possible to prepare squaraine-derived rotaxanes with improved properties for a wide range of photophysical, photochemical, and biomedical applications.

Anthracene-containing tetralactam macrocycles are prepared and found to have an extremely high affinity for squaraine dyes in chloroform (log Ka = 5.2). Simply mixing the two components produces highly fluorescent, near-infrared inclusion complexes in quantitative yield. An X-ray crystal structure shows the expected hydrogen bonding between the squaraine oxygens and the macrocycle amide NH residues, and a high degree of cofacial aromatic stacking. The kinetics and thermodynamics of the assembly process are very sensitive to small structural changes in the binding partners. For example, a macrocycle containing two isophthalamide units associates with the squaraine dye in chloroform 400,000 times faster than an analogous macrocycle containing two 2,6-dicarboxamidopyridine units. Squaraine encapsulation also occurs in highly competitive media such as mixed aqueous/organic solutions, vesicle membranes, and the organelles within living cells. The highly fluorescent inclusion complexes possess emergent properties; that is, as compared to the building blocks, the complexes have improved chemical stabilities, red-shifted absorption/emission maxima, and different cell localization propensities. These are useful properties for new classes of near-infrared fluorescent imaging probes.

It's hip to be square: Squaraine rotaxanes have very similar photophysical properties to the commonly used Cy‐5 fluorophore, but are substantially more photostable and resist self‐quenching upon aggregation. Molecular probes containing squaraine rotaxanes (see structure) are shown to be versatile, high‐performance NIR fluorescence stains for in vitro fluorescence imaging of cells (middle) and in vivo whole‐body imaging of living mice (right).

There is a demand for new methods of protecting organic dyes from aggregation effects and photochemical degradation. The purpose of this microreview is to summarize the recent attempts to improve the properties of dyes by molecular encapsulation. Organic dyes have been encapsulated inside inorganic matrices such as molecular sieves, and molecular containers such as cyclodextrins, cucurbiturils, dendrimers, and self-assembled gels. Another strategy is perma- IntroductionOrganic chromophores such as cyanines, squaraines, azo dyes and perylenediimide dyes are widely used as pigments in many commercial products. They are active ingredients in semiconducting materials, [1] textile products, [2] laser materials, [3] optical disks, [4] paints, [5] and probes for biological systems.[6] Modern research on organic dyes includes investigations of building blocks for conjugated polymers, hydrogen bonded assemblies, chromogenic sensors, molecular shuttles, solar energy cells, photonics and various approaches to photodynamic therapy. [7][8][9][10][11] A common limitation with organic dyes, especially those with long-wavelength absorption bands, is their susceptibility to chemical and photochemical degradation. The reason for the enhanced reactivity is the inherently small HOMO-LUMO energy gap, which means that the dyes are potentially reactive with both nucleophiles and electrophiles. Another potential drawback with organic dyes is their tendency to aggregate, which induces multichromophoric interactions that alter the color quality and quench the photoluminescence. In principle, these problems can be attenuated by supramolecular encapsulation strategies that isolate the individual dye molecules and prevent self-aggregation or similar interactions with the chemical environment. The purpose of this microreview is to summarize the recent literature on meth- Germany, 2005) ods to improve the properties of organic dyes by molecular encapsulation. The focus is on relatively "robust" molecular containers and does not include "soft" assemblies like micelles, emulsions or vesicles.

Several squaraine tethered bichromophoric podand systems 1a-d and a monochromophoric analogue 2 were prepared and characterized. Among these, the bichromophore, 1b, containing five oxygen atoms in the flexible podand moiety was found to specifically bind Ca(2+) in the presence of other metal ions such as K(+), Na(+), and Mg(2+). The selective binding of Ca(2+) is clear from the absorption and emission spectral changes as well as by the visual color change of 1b from light-blue to an intense purple-blue. Benesi-Hildebrand and Job plots confirmed a 1:1 binding between 1b and Ca(2+). Signaling of the binding event is achieved by the cation-induced folding of the bichromophore and the resultant exciton coupling between the squaraine chromophores. The monochromophoric squaraine dye 2 failed to give optical signals upon Ca(2+) binding, due to the absence of exciton interaction in the bound complex. Titration of the folded complex 9 with EDTA released the metal ion from the complex, thereby regaining the original absorption and emission properties of the bichromophore. The squaraine foldamer 1b reported here is the first example of a selective chromogenic Ca(2+) sensor, which works on the principle of exciton interaction in the folded Ca(2+) complex of a bichromophore, the optical properties of which are similar to those of the "H"-type aggregates of analogous squaraine dyes.

Squaraines are fluorescent, near-IR dyes with promising photophysical properties for biomedical applications. A limitation with these dyes is their inherent reactivity with nucleophiles, which leads to loss of the chromophore. Another drawback is their tendency to form nonfluorescent aggregates in water. Both problems can be greatly attenuated by encapsulating the dye inside an amide-containing macrocycle. In other words, the squaraine becomes the thread component in a Leigh-type rotaxane, a permanently interlocked molecule. Two new rotaxanes are described: an analogue with four tri(ethyleneoxy) chains on the squaraine to enhance water solubility, and a rotaxane that has an encapsulating macrocycle with transposed carbonyl groups. An X-ray crystal structure of the latter rotaxane shows that the macrocycle provides only partial protection of the electrophilic cyclobutene core of the squaraine thread. The stabilities of each compound in various solvents, including serum, were compared with a commercially available cyanine dye. The squaraine rotaxane architecture is remarkably resistant to chemical and photochemical degradation, and likely to be very useful as a versatile fluorescent scaffold for constructing various types of highly stable, near-IR imaging probes.

Three different squaraine tethered bichromophoric podands 3a-c with one, two, and three oxygen atoms in the podand chain and an analogous monochromophore 4a were synthesized and characterized. Among these, the bichromophores 3a-c showed high selectivity toward alkaline earth metal cations, particularly to Mg(2+) and Ca(2+) ions, whereas they were optically silent toward alkali metal ions. From the absorption and emission changes as well as from the Job plots, it is established that Mg(2+) ions form 1:1 folded complexes with 3a and 3b whereas Ca(2+) ions prefer to form 1:2 sandwich dimers. However, 3c invariably forms weak 1:1 complexes with Mg(2+), Ca(2+), and Sr(2+) ions. The signal output in all of these cases was achieved by the formation of a sharp blue-shifted absorption and strong quenching of the emission of 3a-c. The signal transduction is achieved by the exciton interaction of the face-to-face stacked squaraine chromophores of the cation complex, which is a novel approach of specific cation sensing. The observed cation-induced changes in the optical properties are analogous to those of the "H" aggregates of squaraine dyes. Interestingly, a monochromophore 4a despite its binding, as evident from (1)H NMR studies, remained optically silent toward Mg(2+) and Ca(2+) ions. While the behavior of 4a toward Mg(2+) ion is understood, its optical silence toward Ca(2+) ion is rationalized to the preferential formation of a "Head-Tail-Tail-Head" arrangement in which exciton coupling is not possible. The present study is different from other known reports on chemosensors in the sense that cation-specific supramolecular host-guest complexation has been exploited for controlling chromophore interaction via cation-steered exciton coupling as the mode of signaling.

The goal of this study was to assess the ability of squaraine-rotaxanes to generate singlet oxygen for potential application in photodynamic therapy (PDT). Specifically, we compare the aggregation and photophysical properties of an iodinated squaraine dye and an iodinated squaraine-rotaxane. Even under strongly aggregating conditions, the absorption spectra of both remain relatively sharp. An X-ray crystal structure of the iodinated squaraine dye shows that it adopts perpendicular, end-to-face orientations in the solid state. Singlet oxygen generation efficiency was measured by trapping with 1,3-diphenylisobenzofuran. The triplet state of the rotaxane was characterized using laser flash photolysis. The results of this study suggest that heavily halogenated squaraine-rotaxanes have potential as singlet oxygen photosensitizers for PDT.