Cyanine dyes chemical structures

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. 

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... 

It has been stated that the method using HPLC as an analytical tool can be applied for the study of the adsorption of dyes, furthermore, it can be employed for the optimization of adsorption efficacy in environmental protection studies [146], New precursors for cyanine dyes were synthesized and the purity of the end products was checked by RP-HPLC. The chemical structures and UIPAC names of the intermediates are listed in Fig. 3.84. Purity control and the identification of the intermediates was performed in an ODS column... 

The synthesis of a new near-infrared cyanine dye was monitored by CE and fluorescence detection. The chemicals structure of the dye and its synthetic precursor are depicted in Fig. 3.165. The analysis of the dye was realized in fused-silica capillaries of 75 and 100 /an i.d. The total and effective lengths of capillaries were 75 and 60 cm, respectively. The separation voltage was 30 kV and separations were carried out at ambient temperature. The running buffer was 2.5 mM Na2B407 (pH = 9.2). A near-infrared laser-induced fluorescence detector was applied. Electropherograms illustrating the separation of the dye are shown in Fig. 3.166. 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

Abstract Construction of chemical libraries is a useful approach to the discovery of better fluorescent materials, and several types, such as styryl dyes and cyanine dyes, have been reported. In this chapter, we focus on construction of a library of chemicals having a coumarin skeleton as the core structure. Coumarin and its derivatives are key structures in various bioactive or fluorescent molecules, and their fluorescence properties are dependent on the precise structure, including the positions of substituents. 

Fig. 2.7. Chemical structures of cyanine dyes that may form J-type aggregates...

Fig. 4.1 The chemical representation (hydrogen atoms are omitted) of cyanine dyes (by resonating structures) and a polyene.

In 1928, at Grangemouth, Scotland, at the works of Messrs. Scottish Dyes Ltd., traces of a dark blue insoluble complex were noticed in the iron vessels used to prepare phthalimide from phthalic anhydride and ammonia (65, 221). This product was subsequently shown to be ferrous phthalo-cyanine. Since then literally thousands of patents and publications concerning the phthalocyanines have appeared. It is probable that the phthalocyanines have been the subject of more physical studies than any other single class of compound, partly as a result of their unique structure and partly because of their high thermal and chemical stability. 

Porphyrin-like structures received considerable attention because of their interesting chemical and physical behaviors, and because of nature s ubiquitous use of porphyrins in electron-transfer processes. The phthalocyanine (hereafter referred to as Pc) is a porphyrin-like dye that has been known for many years. The word phthalocyanine, from the Creek for naphtha (rock oil) and cyanine (blue), was first used by Linstead in 1933 to describe a new class of organic compounds.Phthalocyanine was probably discovered by accident in 1907. as a by-product during the synthesis of o-cyanobenzamide, but it was not until almost 20 years later that a patent was filed describing a manufacturing process. Linstead and coworkers showed that a vast range of phthalocyanines, the metal (M)-substituted forms of the molecules (hereafter referred to as MPcs), were all based on the structure depicted in Fig. 1. In a classic series of papers, starting in 1935, Robertson and coworkers showed that the enviromnent of the metal atom in MPcs was square planar and coordinated with four pyrrolic N atoms, and moreover, that the entire Pc-molecule was flat within the limits of uncertainty. ... 

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