Cyanine extinction coefficient

Phthalocyanine-based dyes are especially useful for CD-R, as the chromophore absorption band falls in the desirable spectral range, and they are noted for excellent photostability. Unlike cyanine dyes, phthalocyanines tend to have very poor solubility, particularly in solvents such as alcohols and aliphatic hydrocarbons (which do not attack polycarbonate and are therefore used for spin coating). Therefore, the main barrier to the wider use of these dyes is the relatively high cost of synthesizing soluble derivatives. Suitable modifications to the Pc core which have been developed, notably by Mitsui Toatsu, are shown in Scheme 7. The bulky R groups reduce undesirable molecular association (which in turn lower the extinction coefficient and hence reflectivity), whereas partial bromination allows fine-tuning of the film absorbance and reflectivity. The metal atom influences the position of the absorption band, the photostability, and the efficiency of the radiationless transition from the excited state.199 This material is marketed by Ciba as Supergreen.204... 

Figure 9.44 The common nitrogenous ring structures of cyanine-type dyes. Indolium-based dye derivatives are the most frequently used due to the high extinction coefficient of the indol groups.

Perhaps the most widely studied chemical class of near-IR absorbers are the cyanines. The chemistry and synthetic routes to cyanines are discussed in other parts of this book (Chapter 2, section 2.3.1.4 and Chapter 3, section 3.5.1.7). The factors influencing the position of their absorption maxima and molar absorption (extinction) coefficients areC ... 

The spectral features in the UV and visible re ons of phosphamethin-cyanines resemble those of the correspondingly substituted methin- and azamethin-cyanines. The position and extinction coefficient of the maxima as well as the general shape are quite similar (Fig. 1). 

By treating benzimidazole-phosphamethin-cyanines 8a with methanolic silver tetrafluoro-borate solutions, Greif isolated colorless, crystalline silver complexes. Their absorption bands lie at shorter wavelengths. The extinction coefficients are httle changed. Here, too, a clear dependence of the position of the absorption maxima on the nature of the N-alkyl substituents can be observed (Table 3). 

Squarylium dyes such as (83) [75] have probably received less attention than cyanine dyes due to the fact that the majority of syntheses furnish symmetrical species which are difficult to monofunctionalize in reactions such as the formation of peptide conjugates. The unsymmetrical types have been reported but seem to suffer from about 50% decrease in extinction coefficient. Squaiyliums are also more difficult to handle due to their low solubility. Very few water-soluble systems have been reported. These compounds are also used exclusively as fluorophores, but quantum yields are highly dependent on substituents and environment. 

Dyes such as erythrosin B [172], eosin [173-177], rose bengal [178,179], rhodamines [180-185], cresyl violet [186-191], thionine [192], chlorophyll a and b [193-198], chlorophyllin [197,199], anthracene-9-carboxylate [200,201], perylene [202,203] 8-hydroxyquinoline [204], porphyrins [205], phthalocyanines [206,207], transition metal cyanides [208,209], Ru(bpy)32+ and its analogs [83,170,210-218], cyanines [169,219-226], squaraines [55,227-230], and phe-nylfluorone [231] which have high extinction coefficients in the visible, are often employed to extend the photoresponse of the semiconductor in photoelectro-chemical systems. Visible light sensitization of platinized Ti02 photocatalyst by surface-coated polymers derivatized with ruthenium tris(bipyridyl) complex has also been attempted [232,233]. Because the singlet excited state of these dyes is short lived it becomes essential to adsorb them on the semiconductor surface with... 

Figure 45. Absorption spectra of a vinylogous series of symmetrical cyanine dyes. The absorption maximum increases with increasing chain length. The extinction coefficient maximizes for seven methine carbons in the chain. Figure adapted from [152].

The extinction coefficients and quantum yields of many fluorophores depend on the microenvironment. For example, pH can affect either Cexc or (f). Fluorescein is fluorescent at pH 8 but is almost nonfluorescent at pH 6. Also there are fluorophores that are sensitive to solvent polarity. Dansyl and 7-nitrobenz-2-oxa-l,3-diazole (NBD) are much more fluorescent in hydrocarbon environments than in water. Other fluorophores are sensitive to the microviscosity. The cyanine label Cy3 is significantly more fluorescent in viscous solvents and when bound to proteins and DNA compared to when it is in water. Cyanines and rhodamines, on the other hand, are not sensitive to polarity or pH changes between 4 and 11. 

Stock solutions of the sulfocyanine succinimidyl active esters may be made in dry DMF (0.3-1.0 mg active ester/100 ml) and are stable for days when stored at 4° in a desiccator. The active esters are also stable in distilled water for several hours provided the pH of the solution is not basic. Aqueous solutions of the dyes can be used for labeling antibodies if use of DMF is not suitable for certain antibodies. The concentration of cyanine fluorophore in the stock solution is determined by measuring the absorbance of an aliquot of the appropriately diluted stock solution in phosphate-buffered siline (PBS) and using the extinction coefficient of the dye (Table I). 

DNA can be used to destroy mismatched duplexes and provide room temperature discrimination of mismatches [79]. Two separate reports of using DiSC CS) andPNA for genetic screening have appeared [79,80]. While the sensitivity of these methods is limited by the extinction coefficient of the dye aggregate and the affinity of the dye for the duplexes, the cyanine dye colorimetric indicator remains a useful laboratory reagent for assessing PNA hybridization. 

Borate salts are especially useAil in combination with cyanine dyes. Depending on the cyanine used, there are different absorption maxima in the visible region with usually high molar extinction coefficients (e 10 L moP cm ). Radical formation by borate is illustrated in reaction (42). 

Likewise, quantum mechanical calculation succeeds in giving a theoretical explanation of some facts that the resonance theory could not explain, for example, why bis(pyridine-2)monomethine cyanine and bis(pyridine-4)monomethine cyanine possess the same lowest energy transition contrary to the 2,2 - and 2,4 -quinoline monomethine dyes, together with a molecular coefficient extinction lower than that of the 4,4 -quinoline dye (11). Calculation shows also that there is no theoretical reason for observing a relationship between and pK in a large series of dyes with different nuclei as it has been postulated, even if limited observations and calculations in short homogeneous series could lead to this conclusion (105). 

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