Between chromophores

Appreciable interaction between chromophores does not occur unless they are linked directly to each other, or forced into close proximity as a result of molecular stereochemical configuration. Interposition of a single methylene group, or meta orientation about an aromatic ring, is sufficient to insulate chromophores almost completely from each other. Certain combinations of functional groups afford chromophoric systems which give rise to characteristic absorption bands. 

Miscellaneous Disazo Dyes. Another group of disazo dyes is prepared by condensation of two identical or different aminoazo compounds commonly with phosgene, cyanuric chloride, or fumaryl dichloride, the fragments of which act as blocking groups between chromophores. 

The slope divided by the intercept gives the rate ratio kjket. Table 6.7 gives the results for compounds (7), n = 2-4 in benzene solution. The detailed mechanism of energy transfer must be able to account for the 25-fold decrease in ket in going from n = 2 to n = 4. While inspection of molecular models shows that the average distance between chromophores... 

In complex (81), the electron-donating phenothiazine moiety is separated from the Ru(bpy)2 " unit by a triazole bridge that carries a formal negative charge. An investigation of this system shows that such anionic bridges can mediate electron transfer between chromophore and quencher. ... 

It should also be kept in mind that the Beer-Lambert law often is not vahd at higher concentrations, since there occur interactions between chromophores and other molecules . This effect is observed especially at reading of proteins in the UV. The solvent may influence the absorbance too, because, for example, some of the aromatic amino acid residues are buried within hydrophobic core of the molecule and become exposed during unfolding of the protein when the composition of the solvent is changed or the protein is denaturated by dilution. 

Our experiments and numerical simulations have proven that interference between chromophore and solvent responses greatly obscures the experimental observables in IR spectroscopy on water at waiting times >0.5 ps. However, the water dynamics can still be obtained if the thermal effects are carefully characterized and self-consistently included in the model. This results in the longest time scale for the frequency correlation function of 700 fs. 

The approaches based on explicit representations of the environment molecules include full quantum mechanical (QM) and hybrid QM/MM methods. In the former, the supramolecular system that is the object of the calculations cannot be very large for instance, it can be composed of the chromophore and a few solvent molecules ( cluster or microsolvation approach). A full QM calculation can be combined with PCM to take into account the bulk of the medium [5,13], which is also a way to test the accuracy of the PCM and of its parameterization, by comparing PCM only and PCM+microsolvation results. The full QM microsolvation approach is recommended when dealing with chromophore-environment interactions that are not easily modelled in the standard ways, such as those involving Rydberg states. An example is the simulation of the absorption spectrum of liquid water, by calculations on water clusters (all QM), clusters + PCM, and a single molecule + PCM only the cluster approach (with or without PCM) yielded results in agreement with experiment [13] (but we note that this example does not conform to the above requirement for a clear distinction between chromophore and environment). 

The third chapter ends with two contributions on the effects of the environment on the excitation energy transfers (EET) between chromophores. 

Areas of particular interest to the vision area were in defining the rules which determined the absorption effectiveness of a chromophore, the elucidation of the "liquid crystalline" state of matter, the electronic characteristics of useful chromophore and the mechanisms of interfacing between chromophores and their associated "signal" receivers. 

Limitations of space prompt us to reduce the display of numerical applications. Our selection of examples is focused on two cases (1) the absorption/emission of solvated chromophores and (2) the energy transfer between chromophores in homogeneous and heterogeneous environment. In both cases, the emphasis will be on the analysis of the effects of the environment on each process with clear connections to theoretical and modelistic aspects discussed in the previous section. The details of the calculations will be omitted as they can be found in the quoted literature. 

Fig. 2.3 Solvent screening of electronic couplings between chromophores in the four photo-syntletic proteins PE545 (pink triangles), PC645 (blue inverted triangles), PSII/LHCII (green circles). The protein medium is modeled as a dielectric continuum medium with a relative static constant of estat = 15 and optical dielectric constant of n2 = 2. Calculated values for the solvent screening factor s for the various chromophores pairs. The Forster value I jnl and the Onsager value 3(2n1 + 1) are indicated by the horizontal line...

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