Chromophores calculating distances between

Energy transfer has been used to calculate distances between chromophores in biomolecules (51), not only polynucleotides but also In proteines. Conrad and Brand (52) studied blchromophorlc systems [12] in order to explore the potential of energy transfer measurement as a means of calculating distances between fluorescent residues on polypeptides and proteins in solution. 

The distance between the chromophores Is approximately 21 8 as measured on molecular models and no ground state Interaction could be observed. In dioxane, the singlet energy transfer occurs by a Forster-type mechanism. On the basis of this mechanism, the distance can be calculated from the transfer efficiency. For [16a] a value of 21.211.6 X was found, while for [I6b] one obtained a value of 16.7 1.4 X. This latter discrepancy was explained on the basis of preferential orientation of the chromophores. That this phenomenon Indeed plays an Important role, was proved by Leermakers (59,60) In a series of indole alkaloids. The same author (59) also Illustrated the absence of triplet-triplet transfer at low temperature in compound [16b]. 

Fluorescence resonance energy transfer (FRET) experiments commonly use the fluorescent spectrum and relaxation times of the Forster donor and acceptor chromophores to find the distances between fluorescent dyes at labeled sites in protein, DNA, RNA, etc. FRET is a type of spectroscopic ruler . The computation uses either experimental quantum yields or relaxation lifetimes to calculate the efficiency of resonance energy transfer Ej. 

Metal phthalocyanines functionalized with four helicenes (62) have also been reported to form chiral columnar aggregates.76 In chloroform solutions of these metal phthalocyanines aggregation into columns occurred upon addition of ethanol, as was observed by UV-Vis spectroscopy. CD spectroscopy revealed that the chromophores within the columnar aggregates are in a chiral environment, implying that the chirality of the peripheral helicenes has been transferred to the supramolecular aggregates. These phthalocyanines stack with a typical intermolecular distance of 3.4 A, and calculations have indicated that to allow this distance the two phthalocyanine moieties have to be rotated because of the bulkiness of the helicenes. It can easily be imagined that a phthalocyanine provided with both R and S helicenes cannot stack in such a defined manner because of the steric interactions between the nonconform helicenes. 

Ab initio calculations at the B3LYP/6-31+G level show the existence of only one conformation for the adduct. The blue shifted band assigned to the adduct indicates a-OH--7i interaction between water and the chromophore [110-112]. The calculations made by these authors show two alternative structures. The more stable is the one with the alcohol as HB donor, and one of the water hydrogens placed at a distance of 1.98 A with respect to the mass center of the aromatic ring in the alcohol molecule (Fig. 3.10). This -OH--7I interaction is responsible for the two blue shifted chromophore bands. The less stable structure has the alcohol as HB acceptor, and no -OH-"71 interaction. 

---