Cyanine dye structures

Figure 4 shows the photocurrent action spectra of three typical cells under short circuit conditions [20]. Three different dyes were used to sensitize the heterojunction. In all three cases the action spectrum matches closely the absorptivity spectrum of the sensitizing dye. Solid-state heterojunctions sensitized with the mero-cyanine dyes (structure see Fig. 4) used in this study showed higher peak IPCE values when compared to Ru(lI)L2(SCN)2-sensitized junctions. Strongly improved... 

Effect of Cyanine Dye Structure on Primary and Secondary Splittings in H-Aggregates... 

In the first chapter, devoted to thiazole itself, specific emphasis has been given to the structure and mechanistic aspects of the reactivity of the molecule most of the theoretical methods and physical techniques available to date have been applied in the study of thiazole and its derivatives, and the results are discussed in detail The chapter devoted to methods of synthesis is especially detailed and traces the way for the preparation of any monocyclic thiazole derivative. Three chapters concern the non-tautomeric functional derivatives, and two are devoted to amino-, hydroxy- and mercaptothiazoles these chapters constitute the core of the book. All discussion of chemical properties is complemented by tables in which all the known derivatives are inventoried and characterized by their usual physical properties. This information should be of particular value to organic chemists in identifying natural or Synthetic thiazoles. Two brief chapters concern mesoionic thiazoles and selenazoles. Finally, an important chapter is devoted to cyanine dyes derived from thiazolium salts, completing some classical reviews on the subject and discussing recent developments in the studies of the reaction mechanisms involved in their synthesis. 

Methylation of 2- or 4-methylquinazoline is reported to proceed with difficultyj" but 4-methylquinazoline has been quaternized with methyl iodide. The product was very hygroscopic and, although not purified, was shown to consist mostly of 1,4-dimethylquinazolinium iodide, since it gave the same cyanine dye (11) with 2-methylthio-benzthiazole metho-toluene-p-sulfonate as did l-methyl-4-methyl-thioquinazolinium iodide (of unambiguous structure) with 2-methyl-benzthiazole methiodide. ... 

Cyanine dyes have been prepared from the salts obtained by the quatemization of 4,6-dimethyl-2-phenylpyrimidine and 2-alkyl- or 2-aryl-4,6-dimethylthiopyrimidines, but there can be no ambiguity in the structure of these quaternary salts. 

Structural hybrid, in resonance theory. 69 Structures, of dyes, in relation with elecuo-chemical potential. 75 extreme of cyanine dyes, 69 Styryl compounds, nomenclature of, 29 Styryl dyes, in basicity scale, 71 with dialkylamino group, 77 as models in relation with pKa, 50 and role of anhvdrobases. 50 as sensitizers, in photography. 79 stereo aspect of condensation. 50 synthesis of, 49... 

Symmetrical cyanine dyes, because of the resonance shown in Figure 6.4 (in which the two contributing structures are exactly equivalent), are completely symmetrical molecules. X-ray crystal structure determinations and NMR spectroscopic analysis have demonstrated that the dyes are essentially planar and that the carbon-carbon bond lengths in the polymethine chain are uniform. The colour of cyanine dyes depends mainly on the nature of the terminal groups and on the length of the polymethine chain. The bathochromicity of the dyes is found to increase... 

The valence-bond (resonance) description of the triphenylmethine dye Malachite Green (125) is illustrated in Figure 6.5. Comparison with Figure 6.4 reveals their structural similarity compared with cyanine dyes. Formally, the dye contains a carbonium ion centre, as a result of a contribution from resonance form II. The molecule is stabilised by resonance that involves delocalisation of the positive charge on to the p-amino... 

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. 

Compared to oxo-squaraines or other ring-substituted squaraines, amino-squaraines 39 [45, 52, 112] have ionic character, similar to open-chain cyanine dyes, and due to the positive net charge, these dyes are to some extend water-soluble. Amino-squaraines absorb and emit at longer wavelength than the corresponding oxo-squaraines the absorption maxima are between 650-710 nm (eM = 85,000-300,000 M-1cm-1) [45, 112], The increase in solvent polarity is accompanied by a hypsochromic shift of the absorption. Amino-squaraine dyes are potentially used as fluorescent probes but because their photostability is inferior to those of oxo-squaraines and other ring substituted squaraines of similar structure, their applications are rather limited. 

The nonreactive base structures of cyanine dyes (or carbocyanines) have been used for many years as components in photographic emulsions to increase the range and sensitivity of film and also in CD-R and DVD-R optical disks to record digital information. A major innovation came when Ernst et al. (1989) and Waggoner et al. (1993) recognized that cyanine dyes would make excellent labels for fluorescence detection, and for this reason, they synthesized reactive dye derivatives, which then could be covalently attached to proteins and other molecules. 

Cyanine dyes also are used as labels for oligonucleotide probes. Unlike the hydrophilic cyanine dyes valuable for protein labeling, the use of dye-phosphoramidite compounds to synthesize DNA or RNA probes typically requires the use of more hydrophobic dye structures to make them compatible with the solvents and reactions of oligonucleotide synthesis. Thus, indol cyanines containing few or no sulfonates are used in these applications to label oligos for applications such as array detection, hybridization assays, and RT-PCR. 

Most companies selling cyanine dyes do not reveal their exact structures. This likely is due to each company keeping proprietary the small synthetic tweaks that create unique fluorescence properties for their dyes. However, some structures are available through published documents, such as patents and early publications (Leung et al., 2005). Figure 9.45 illustrates some of these structures, which may not reflect precisely what any one company actually offers today, but it gives an idea of the types of modifications that can be done to add water solubility and reactivity. 

The molecular structure of a complex formed between cyanine dye 27 (n = 1) with K2[Ni(CN)4] has been shown by X-ray diffraction to consist of two organic cations and a centrosymmetric inorganic dianion [Ni(CN)4]2, and it is apparently only the second cyanine molecular complex whose structure has been reported to date <2006MIml03>. 

Cations other than Li+ can be introduced into the film by a simple ion-exchange procedure, and this may be a simple method for obtaining multilayered structures with any cation. Organic cations, e.g., cyanine dyes, can also be introduced into the film by this procedure. Perhaps this approach for the application of highly ordered thin LB films onto the surface of electrodes could yield some new results, such an improvement in response time, as was discussed in Section 7.3.7. 

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