Excitation energies indole molecule

To understand the fundamental photochemical processes in biologically relevant molecular systems, prototype molecules like phenol or indole - the chromophores of the amino acids tyrosine respective trypthophan - embedded in clusters of ammonia or water molecules are an important object of research. Numerous studies have been performed concerning the dynamics of photoinduced processes in phenol-ammonia or phenol-water clusters (see e. g. [1,2]). As a main result a hydrogen transfer reaction has been clearly indicated in phenol(NH3)n clusters [2], whereas for phenol(H20)n complexes no signature for such a reaction has been found. According to a general theoretical model [3] a similar behavior is expected for the indole molecule surrounded by ammonia or water clusters. As the primary step an internal conversion from the initially excited nn state to a dark 7ta state is predicted which may be followed by the H-transfer process on the 7ia potential energy surface. 

The Forster mechanism for non-tiivial transfer of excitation energy is well estabhshed 123), Transfer may occur over distances as large as 100 A or more, provided there is sufficient overlap between the emission band of the donor and absorption band of the acceptor. Weber showed by means of fluorescence polarization studies that transfer between phenol molecules and between indole molecules as well as phenol- indole transfer occurs over distances of A 124.125), ePR studies of frozen solutions indicated that energy transfer occurs between tyrosine and tT3q)tophan over distances of this order or larger .186),... 

FIGURE 14.2 Indole is a typical molecule or side group (of the peptide tryptophan) for excitation energy transfer in proteins. 

A fluorescence spectrum is characteristic of a given compound. It is observed as a result of radiative emission of the energy absorbed by the molecule. The observed spectrum does not depend on the wavelength of the exciting light, except that the spectrum will be more intense if irradiation occurs at the absorption maximum. The spectral intensity is called the quantum efficiency and is usually abbreviated as . The quantum yield or quantum efficiency, d>, which is solvent dependent, is the ratio Approximate values of quantum efficiencies are as follows naphthalene, 0.1 anthracene, 0.3 indole, 0.5 and fluorescein, 0.9. 

The indole group of tryptophan (Trp) has a higher molar extinction coefficient than the phenolic and phenyl side chains of tyrosine (Tyr) and phenylalanine (Phe), respectively (see Table 1, Chapter 12). Thus although its quantum yield is similar to that of lyr, its fluorescence emission is much mote intense. Furthermore, its excitation spectrum overlaps the emission spectrum of Tyr and therefore fluorescence resonance energy transfer (FRET, see Chapters 2 and 3) from lyr to Trp occurs readily when both residues are in close proximity (i.e. located in the same protein molecule) and favourably orientated. The intrinsic fluorescence of a protein is therefore dominated by the contribution from Trp... 

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