Some dusty neurons in the back of my head recall a discussion as to if there was really anything particularly favorable about perpendicular aromatic stacking, or if it is just the most statistically likely arrangement. Might be worth looking up for your case.
Phoebe
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From: CCP4 bulletin board [[log in to unmask]] on behalf of William G. Scott [[log in to unmask]]
Sent: Tuesday, September 13, 2016 6:05 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Tryptophan-Adenine interaction: T-shaped stacking?
> On Sep 6, 2016, at 8:07 PM, WENHE ZHONG <[log in to unmask]> wrote:
>
> I am not very familiar with the chemistry in terms of ð-stacking. So I am wondering whether it is a T-shaped stacking interaction between the aromatic rings? Any thought?
Dear Wenhe:
Please take a look at these references:
Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization
S. K. Burley and G. A. Petsko
Science Vol. 229, No. 4708 (Jul. 5, 1985), pp. 23-28
Stable URL: http://www.jstor.org/stable/1695415
also, the basis in pi orbital stabilization interactions comes from this, I believe:
Symmetry, Topology and Aromaticity, M. J. Goldstein and Roald Hoffmann. Journal of the American Chemical Society / 93:23 / November 17,1971
https://www.dropbox.com/s/y7blru2u37dsfiu/67s_0.pdf
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu
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