Is it possible to differentiate intra and intermolecular pi-pi stacking by CD spectroscopy?
That would be a good question for the applications people at your CD manufacturer. I used to work for Jasco in the US and they had such an expert on staff.
Assuming you mean CD through excitonic coupling, I think that would be very hard. If the relative positions and orientations are the same, the answer would be no. Electronic CD can be rather sensitive to the precise orientation, so in a lucky case where those things would be different for intra- and intermolecular stacking, maybe.
However, as far as I know there are no papers on excitonic CD in tryptophan pairs, at least not in the 270-290 nm region. There are a few on possible influences in the UV range (around 220nm), but as far as I know there are only suggestions of such an influence and no definite conclusions reached about structural parameters. I have not really kept up with the literature, but a quick glance (on Web of Science) there is not much new.
A long time ago I did some calculations for tryp-tryp interaction in tetramerized melittin, where two pairs of tryptophans are rather close. It is not too hard to calculate it, given a structural model. Measuring, however, is another matter.
What system are you thinking of and what kind of equipment do you have to your disposal?
It might be worth recording spectra at different concentrations. An intra-molecular interaction should resist dilution, but an inter-molecular interaction might dissociate at lower concentrations. Another excellent approach would be to study these peptides by NMR. The side chain 1H signals of the Trps will be different and their chemical shifts will provide insight into the relative orientations of the rings. If you observe NOE signals between the Trps, that would allow you to determine their orientation in a more rigorous manner.
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