Stokes shift analysis

It has been calculated that small solute dipoles are even more effectively solvated by solvent quadrupoles than by solvent dipoles. In these terms it is understandable that quadrupolar contributions are more important in the jt than in the E.f(30) scale. Similarly, triethylphosphine oxide, the probe solute of the acceptor number scale, is much smaller than betaine(30) and thus might be more sensitive to quadrupolar solvation. Thus, at long last, the shape of Figure 13.1.2 and similar ones seems rationalized. Note by the way that the quadrupole and CT mechanisms reflect, respectively, inertial and inertialess solvation pathways, and hence could be distinguished by a comparative analysis of absorption and fluorescence shifts (Stokes shift analysis). Flowever, for 4-nilroanisole fluorescence data are not available. 

The difference in temporal dispersion in fibers, associated with the Stokes shift and broad spectral content of fluorescence as compared with the excitation, still has to be fully investigated with respect to the effect on convolution analysis. 

Little is known about the fluorescence of the chla spectral forms. It was recently suggested, on the basis of gaussian curve analysis combined with band calculations, that each of the spectral forms of PSII antenna has a separate emission, with Stokes shifts between 2nm and 3nm [133]. These values are much smaller than those for chla in non-polar solvents (6-8 nm). This is due to the narrow band widths of the spectral forms, as the shift is determined by the absorption band width for thermally relaxed excited states [157]. The fluorescence rate constants are expected to be rather similar for the different forms as their gaussian band widths are similar [71], It is thought that the fluorescence yields are also probably rather similar as the emission of the sj tral forms is closely approximated by a Boltzmann distribution at room temperature for both LHCII and total PSII antenna [71, 133]. 

Steadily in the order 359, 385, 395, and 402 nm. The emission spectra exhibit a clearer vibrational fine structure than the absorption spectra. For spiro-sexiphe-nyl, 35b, a detailed analysis shows that the vibrational splitting of 0.20 eV corresponds to a phenyl breathing mode in the Raman spectrum [108]. If for spiro-sexiphenyl the outer biphenyl moieties are fixed parallel as in 4-Spiro (43), the absorption maximum is shifted from 346 to 353 nm (amorphous films) and the fluorescence maximum from 420 to 429 nm, maintaining the Stokes shift. The corresponding spectra are shown in Figure 3.17. The absorption signal at 310 nm in the spectrum of 43 can be attributed to the terminal fluorene moieties. The quantum yields for the fluorescence in the amorphous film are 38% for 35b and as high as 70 10% for 43 [89]. 

Analysis of the ultrafast dynamic Stokes shift of the fluorescence of ferulic acid analogue in comparison with that of the denatured PYP. 

In the case of the denatured PYP, the chromophore is surrounded by completely disordered environment of the water. The relaxations due to the interactions between the excited chromophore with a large dipole moment and surrounding disordered water environment produce a large extent dynamic Stokes shift of the fluorescence. Nevertheless, it is much slower compared with that taking place in the disordered PNS of the ferulic acid analogue as demonstrated in the analysis of the previous section (3.3). 

Indeed, an INM analysis of the optical Kerr signal of acetonitrile by Ladanyi and Klein [43] coupled with a similar analysis of solvation dynamics [12] shows that both processes are dominated by rotational motions and further that p(u) is essentially identical in both cases, providing theoretical backing for earlier guess of Cho et al. that both optical Kerr and Stokes shift responses could be described by a common p(u) in this solvent [44]. Calculations based on computer simulations for water [45] and acetonitrile... 

In the case of electron transfers in solution there appears to be a greater cohesiveness of views, and the need for vibrational assistance is well established for reactions accompanied by vibrational changes (e.g., changes in bond lengths). A detailed analysis of the experiments could be made because of the existence of independent data, which include X-ray crystallography, EXAFS, resonance Raman spectra, time-dependent fluorescence Stokes shifts, among others. 

Phycoerythrin Phycoerythrin is a fluorochrome derived from red sea algae. It is particularly useful in flow cytometric applications requiring dual-color analysis because, like fluorescein, it absorbs 488 nm light from an argon laser. However, it has a longer Stokes shift than fluorescein, and therefore the fluorescences of the two fluorochromes can be distinguished. 

Several fluorescent labeling dyes are commercially available (Alexa series, Oregon green, Rhodamine and Cyanine dyes, etc.). They are all characterized by the presence of double bonds on every other carbon atom of a cyclic structure, containing the electron that once on excitation emitted fluorescent light. The cyanine dyes are the most widely used at the moment. They are bright, easily added to the nucleotides, stable to photo-bleaching and with a Stokes shift value of about 20 nm. The cyanine dyes used in microarray analysis are Cy3 (absorption at 550 nm and emission at 570 nm) and Cy5 (absorption at 649 nm and emission at 670 nm) that are already available as phosphoramidite derivatives. 

This problem may be tackled by a more systematic analysis of the Stokes shift. Pines and coworkers assumed that the first absorption transition of 1-naphthol and the two absorption transitions of 2-naphthol may be described by Pekarian functions. These functions were analyzed by the Kamlet-Taft analysis (Figures 25 and 26). 

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