Talk:Stacking (chemistry)

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merge notice: this article definition indentical to that of Stacking (chemistry) V8rik 21:44, 4 June 2006 (UTC)[reply]

This article is badly written, filled with factual and grammatical errors, I will hopefully return in a few days to tidy it up

Stacking and pi-pi

I don't have free full-text access to this article at home : Angew Chem Int Ed Engl. 2008;47(18):3430-4. , but it seems to suggest that the pi-pi interaction description here is inaccurate. The arguments make sense to me (that Coulombic attraction between CH and pi are more responsible). Word is that the author quotes wikipedia as a source of the disinformation. It would be nice if people who saw litter were more inclined to pick it up than complain about it, but that's probably asking too much, especially if the author can use it to make their paper more noteworthy. I'll see if I have the free-text to this via work, and if so consider fixing it after reading it. As I've got the memory of a goldfish, I will probably forget, hence this note. 81.187.202.205 (talk) 22:52, 23 July 2009 (UTC)[reply]

Okay, I've had a look at the citation above, it looks good and the consequence is essentially that this whole article is screwed. I'll sort it out during my vacation, at least to the extent that it's not explicitly rubbish. According to the article, well supported by modelling in my judgement, much of stacking effect comes from Van De Waals interactions as is evidenced, for example, by similar energies from stacking cyclohexane and benzene. pi-pi interactions it seems can contribute to stacking, but only in certain (non-typical) circumstances. For example, it's umlikely to be a major contributor to the stacking effect in nucleobase (biological) circumstances. This is not yet reflected in most of the secondary literature. Obviously, there shouldn't be excessive weight to this one piece, but we need to explicitly unconfuse stacking from pi-pi and mention the two approaches ("orthodoxy" vs "recent research suggests"). This would have been a whole lot easier with Open Access, grumble grumble, Wiley, grumble grumble. 131.111.21.21 (talk) 13:30, 24 July 2009 (UTC)[reply]

Started rewrite by adding initial section. Haven't got to rewriting rest of article yet, just put in an attention of experts box. 81.187.202.205 (talk) 02:38, 25 July 2009 (UTC)[reply]

This pi-pi disinformation has been repeated in umpteen biochemistry textbooks over the yearsbut constant repetition does not make it true. The electrostatic basis of stacking is discussed at length in the text "Principles of Nucleic Acids" by Wolfram Saenger, Springer 1984 ISBN0387907629;ISBN0387907610 (pbk.) I no longer have my copy so I can't quote pages.96.54.53.165 (talk) 00:51, 22 December 2009 (UTC)[reply]

Has this article been abandoned? I just stumbled upon this page, and it drew my attention that the authors were going to re-write the article (a year ago?). For whoever continues to work on this article, please be careful in adapting the article to a single source (or only a few sources). For example, based on Stefan Grimme's 2008 article, the article says "Electrostatic forces actually considerably weaken this effect in aromatics" and "Therefore DNA nucleobases (having one or two rings) probably do not significantly stabilise DNA's stacked structure as a result of their aromaticity" The article you cited, though, is limited to non-charged aromatic arenes (where charges are small), and it also used "classical electrostatics" in the energy decomposition, which I believe means it treated each atom in the molecule as a point charge (so quadrupoles were omitted). Figure 2 shows a ~3-4 kcal/mol improvement in interaction energy with only 3 rings (just like nucleic acid base pairs). The article by Grimme is a good article in a very reputable journal, but the conclusion is that the "pi-stacking effect" is caused by "nonlocal electron correlations between the pi electrons." Anyway, I wanted to pitch in a word of encouragement that the article isn't "screwed." It just needs a few more references to round out the perspective. Hopefully someone will have time to pick this back up soon. 11:53, 11 June 2010 (jf) —Preceding unsigned comment added by Phaethonfire (talk • contribs)

There are definitely some problems with this article. I recently looked at the latest literature on this, and it is certain there is something special about stacking pi systems together. Here are some slides on what I figured out. Eugene Kwan (talk) 03:49, 22 November 2010 (UTC)[reply]

UV absorbance

UV absorbance by the aromatic rings in DNA is suppressed due to stacking. (Compare UV absorbance of denatured DNA versus dimerised DNA.) Would Van der Waals forces suppress this? Or pi-pi interactions? 76.120.195.172 (talk) 06:44, 7 December 2010 (UTC)[reply]