Cyanine aggregates

Figure 10.15). Catalytic stability was enhanced by the encapsulation within the dendritic structure due to the catalytic activity of metallophthalocyanines being influenced by phthalo-cyanine aggregation resulting from strong intermolecular stacking. 

Cyanine aggregation in an electronically inert substrate is exemplified in Figure 25, where several diffuse-reflectance spectra of thiacyanines are shown, namely 3,3 -diethylthiacarbocyanine (TCC) and 3,3 -diethyl-9-methylthiacarbo-cyanine (9-MeTCC) entrapped within the polymer chains of microcrystalline cellulose. 

Optical properties of cyanines can be usefiil for both chiral substituents/environments and also third-order nonlinear optical properties in polymer films. Methine-chain substituted die arbo cyanines have been prepared from a chiral dialdehyde (S)-(+)-2-j -butylmalonaldehyde [127473-57-8] (79), where the chiral properties are introduced via the chiral j -butyl group on the central methine carbon of the pentamethine (die arbo cyanine) chromophore. For a nonchiral oxadicarbocyanine, the dimeric aggregate form of the dye shows circular dichroism when trapped in y-cyclodextrin (80). Attempts to prepare polymers with carbocyanine repeat units (linked by flexible chains) gave oligomers with only two or three repeat units (81). However, these materials... 

A wide variety of stmetures exist in the cyanine, merocyanine, and oxonol classes of dyes. Properties that may affect toxicity vary widely also. These include solubihty, propensity to be oxidized or reduced, aggregation tendency, and diffusion through membranes. Specific acute toxicity data are Hsted in Table 2, and the LD q data vary widely with the test used. 

Figure 11.3 Hierarchical pattern of cyanine-dye J-aggregates. Dye molecules form strongly fluorescent nanoscale J-aggregates J-aggregates arrange at the rim of the micrometer-sized polymer droplet droplets arrange in a regular mm-sized two-dimensional array (adapted from Ref 39).

Karthaus, O., Okamoto, K., Chiba, R. and Kaga, K (2002) Size effect of cyanine dye J-aggregates in micrometer-sized polymer Domes . Int. J. Nanosci., 1, 461—464. 

Araki K, Yoshikawa I (2005) Nucleobase-Containing Gelators. 256 133-165 Armitage BA (2005) Cyanine Dye-DNA Interactions Intercalation, Groove Binding and Aggregation. 253 55-76... 

Figure 6.17. Absorption spectra of l,r-diethyI-2,2 -cyanine bromide in ethylene glycol water (1 1) at room temperature and at 173°K, showing the //-aggregate states.(84> Reprinted by permission of Chemical Physics Letters.

Table 6.8. Spectral Shifts of Aggregated States of 1,1 -Diethyl-2,2 -cyanine Bromide in Ethylene Glycol-Water Matrix at 173°Ka...

Reference [33] describes recent progress on cyanine probes that bind noncova-lently to DNA, with a special emphasis on the relationship between the dye structure and the DNA binding mode. Some of the featured dyes form well-defined helical aggregates using DNA as a template. This reference also includes spectroscopic data for characterizing these supramolecular assemblies as well as the monomeric complexes. 

Kirstein, S. and Daehne, S. (2006). J-aggregates of amphiphilic cyanine dyes self-organization of artificial light harvesting complexes. Int. J. Photoenergy 5, 1-21. 

This model has been successfully applied to J aggregates of cyanine dyes in a brick stonework arrangement [47,48]. However, this model cannot explain the spectral shift of chromophores having transition moments in two or more directions as shown in Figure 8 for long-axis and short-axis transition dipoles of carbazolyl chromophores, nor it can predict the orientation of chromophores with respect to the substrate. In order to explain such spectral shifts and molecular orientation of alloxazine and carbazolyl chromophores as mentioned above, we proposed a three-dimensional extended dipole model which takes a three-dimensional... 

Fig. 7 Structures of the dyes forming aggregates on DNA (a) l-methyI-4-[[3-methyl-2(3//)-benzothiazolylidene]methyl]-quinolinium (Thiazole Orange, TO), (b) 3,3 -diethyIthiadicarbo-cyanine (DiSC2(5)), (c) 3,3 -trimethylammoniopropylthiadicarbocyanine (DiSC3+(5)), (d) 2- [(Z)-2-(2,5-dihydro-2-thienyl)-3 - [3 -methyl-2(3/f)-benzothiazolylidene] -1 -propenyl] -3 -methyl -benzothiazol-3-ium (L-21), (e) 2-[( )-3-[3,7-diethyT6-[( ,2 )-3-(l-ethyl-3,3-dimethyl-3/7-indo-lium-2-yl)-2-propenylidene]-6,7-dihydrothiazolo[5,4-/]benzothiazol-2(3//)-ylidene]-l-propenyl]-l-ethyl-3,3-dimethyl-3//-indolium (BCD), (f) 3-methyl-2-[( )-3-methyl-2-[[3-methyl-2(3/f)-ben-zothiazolylidene]methyl]-l-butenyl]-benzothiazol-3-ium (Cyan ]3iPr)...

Summarizing, some of the organic dyes, particularly cyanines, are able to form fluorescent aggregates on DNA. Comparing with the dye monomers bound to DNA, the J-aggregates are more sensitive to the concentrations ratio and to DNA nucleotides content. Though these structures can hardly be applied for the routine DNA detection assays, they are rather interesting systems for special studies. 

Presently, the only commercially available dyes that are applied because of then-ability to form fluorescent aggregates are trimethine cyanines JC-1 and JC-9 (Fig. 11) [25], the first one being studied much more extensively than the second one. The dye JC-1 is known to form red-fluorescent (emission maximum at 590 nm) J-aggregates in mitochondria possessing strong intramitochondrial negative potential, while upon depolarization of the mitochondrial membrane, the dye monomer green emission (maximum at 527 nm) is observed [25]. JC-9 demonstrates similar properties [25]. Such properties permit the application of these dyes for, e.g., detection of apoptotic electrical depolarization of mitochondria [25]. 

Ogul chansky TYu, Yashchuk VM, Losytskyy MYu, Kocheshev IO, Yarmoluk SM (2000) Interaction of cyanine dyes with nucleic acids. XVII. Towards an aggregation of cyanine dyes in solutions as a factor facilitating nucleic acid detection. Spectrochim Acta A 56 805-814... 

Ogul chansky TYu, Losytskyy MYu, Kovalska VB, Yashchuk VM, Yarmoluk SM (2001) Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra. Spectrochim Acta A Mol Biomol Spectrosc 57 1525-1532... 

---