I think self quenching depends on molecular contacts in the order of Angstrom.

Hi Aditya

There are two different types of quenching or energy transfer based on what you observe: In one type, the quantum yield of the 'donor' is decreased while the lifetime of the donor remains unchanged.  In the other, both the quantum yield and the lifetime of the donor is decreased.  The mechanisms that are used to explain these are respectively a Dexter electron (or energy) transfer and the Forster energy transfer.  In the Dexter mechanism there is overlap of the electronic orbitals such that there is an exchange of electrons between the donor and the acceptor.  You can view this as the electron in the excited state of the donor moving to the excited state of the acceptor while the electron in the ground state of the acceptor moves to the ground state of the donor.  In the Forster mechanism, there is an exchange of energy, through a dipole-dipole interaction, that allows a relaxation of the electron from the excited state to the ground state of the donor while there is an excitation of an electron from the ground state to the excited state of the acceptor.  These mechanisms explain the observations as follows - in the Dexter mechanism, the quenching is 100% efficient for those molecules in close enough contact to be affected, hence the decrease in quantum yield reflects the fraction of molecules that are in contact, but those that are not in contact behave normally and since they are the ones that are observed, the lifetime does not change.  In contrast, in the Forster mechanism, the interactions occur over a distance, so the quantum yield change is related to the probability of energy transfer.  This is like a parallel pathway for relaxation of the excited state of the donor, and hence both the lifetime and the quantum yield is affected.

Note that there is no specific evidence that there is an electron transfer since we cannot track the electrons, so the Dexter mechanism may be a limiting form of the Forster mechanism where the energy transfer is 100% efficient.  The key point is that there are two sets of observations which need explanation, tied to whether the lifetime is affected by the quenching process.

Whether the quenching occurs by like or different molecules is, in principle, irrelevant.  So in your case, you could perhaps link the self-quenching terminology to those cases where there is no change in lifetime and the homo-FRET to those cases where there is a change in lifetime, but I am not sure whether that is a generally agreed upon distinction.

I hope this helps, and congratulations on finishing your degree.

Thanks a ton Nils!

If you are referring to the self quenching due to stacking of fluorophores, then you are advised to read about exciplex and J-aggregates. I think you can also find very useful information in the fluorescence bible " Principles of fluorescence spectroscopy" by Joseph R. Lakowicz.  If you have got the third edition then see page 147 onwards to find a suitable answer for your question. Regards.