Spectrum conjugated dyes

Azo-coupled products are widely used as dyes for textiles because their extended conjugated tt electron system causes them to absorb in the visible region of the electromagnetic spectrum (Section 14.9). / -(Dimethylamino)azobenzene, for instance, is a bright yellow compound that was at one time used as a coloring agent in margarine. 

The loss in colour is due to a loss in conjugation of the aromatic molecule. Dyes absorb light in the visible region of the electromagnetic spectrum by virtue of transitions between electronic energy levels. 

Fig. 23 Normalized absorption spectra of the free BSA protein (1), BSA-dye 50 conjugate (2) and steady state fluorescence emission spectrum of the BSA-dye conjugate (2 )...

Daub, Grimme, and coworkers have reported chiroptical switches based on binaphthyl boron dipyrromethane (BDP) conjugates. It is known that BDP dyes with appropriate functionalization can be reversibly oxidized and reduced.58 The CD-spectroelectrochemical studies of R-56 show a decrease in the intensity of the Cotton effect at 501 nm by applying a reduction potential to the solution. The initial CD spectrum is restored completely after reoxidation thus, the CD signal intensity at 501 nm for R-56 can be switched on and off electrochemically.59... 

Excitation of the Eu3+ or Tb3+ ions has traditionally been indirect, by broad-band UV excitation of a conjugated organic ligand which is followed by intramolecular energy transfer to the lanthanide ion / system, followed in turn by /- / emission.614 However, more recently, following the advent of tunable dye lasers, direct excitation of an excited / level is in many cases preferable. By scanning this frequency, an excitation spectrum can be obtained whose energy values are independent of the resolution of a monochromator and not subject to spectral interferences. 

Lucifer Yellow probes are water-soluble to at least 1.5%. The absorbance maximum of the derivatives occurs at about 426—428 nm with an emission peak at about 530—535 nm, in the yellow region of the spectrum. The quantum yield of Lucifer dyes is about 0.25. The good intensity of luminosity from these dyes makes possible detection of small quantities of labeled molecules intracellularly. The fluorescent conjugates are readily visible in living cells at concentrations that are nontoxic to cell viability. The low molecular weight and water solubility of these dyes allow passage of labeled compounds from one cell to another, potentially revealing molecular relationships... 

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]. 

The E,Z-isomerization of the styiyl dyes 2c containing aza-15-crown-5 ether moiety is characterized by great hypsochromic shifts, equal to 170 nm, of the spectrum of [(Z)-2c]Ca2+ with respect to the spectrum of [(E)-2c] Ca2+ (see Figure 1). Apparently, it can be explained by the fact that in anion- capped complex the molecule of dye acquires a twisted conformation with marked disruption of the conjugation in the chromophoric system. When ( )-2a is converted into the Z-form, the stability of complex increases approximately 2.5 fold. On going from the cationic dye 2a to the betaine 2c, stability of the complexes formed by Z-isomer increases by more than three orders of magnitude [16]. 

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