Talk:Stacking (chemistry)

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

message: 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)
replies: text: 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)
thread_title:  Stacking and pi-pi 

message: 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)
thread_title:  UV absorbance 

message: Impressions: The article is reasonably organized, but is lacking in a significant number of details and diagrams.
Suggestions:
- How about some plots of preferred orientations and distances in the PDB?  Calculations?  Figures for high-level geometries of stacked dimers?
- A figure would go a long way towards explaining the Houk/Wheeler, Hunter/Sanders, Sherill, etc. models.  Schemes for the torsion balances and other examples you mention would also be useful.
- I like Grimme's work.  That should also get a scheme.  Maybe you could comment on which computational methods are appropriate for studying these interactions.
- What are the implications of the pi-stacking phenomenon, both for chemistry and biology?  I think that at least in catalysis, it's much more complicated than one would like.  Rather than having one stacking interaction that is clearly discernible and responsible for selectivity, it is but one of many factors.  Are there specific reactions in which pi stacking is implicated?  How important is it for protein folding?  Ligand-receptor interactions?
- Some comments regarding the energetics of the interaction would be useful.  Is having more "pi-surface" cooperative in any way?  If it is a purely dispersive interaction, is it likely to increase in the transition state?  At least for cation-pi interactions, that seems likely.  Here, it's not so clear.
Eugene Kwan (talk) 22:05, 24 October 2011 (UTC)
replies: text: Isn't kcal more common in computational chemistry? --Ben (talk) 20:26, 10 May 2012 (UTC)
thread_title:  More Comments 

message: thumb|100px|generic metallocene
Would the linked-title to this talk-section I added above constitute this kind of pi-stacking: i.e. transition metal chelate eta-six co-ordination? (cf. so-named, systematic S. Singh # 21bd) 66.96.79.217 (talk) 01:50, 21 April 2016 (UTC)
replies: text: As far as I can tell from that article and your question (which could be clearer) the benzene and cyclopentadienyl in this cocaine analog are practically on opposite sides of the molecule (I'll admit I'm slightly unclear on what they mean about the solid cone angles).  So far as I can tell, your question is almost the same as asking whether a generic metallocene is a case of pi stacking... but I could be wrong.  Now you can have stacked metallocenes, but I think what they usually have in mind is something like this with the two aromatic rings together.  When they're on opposite sides of a metal, they may be interacting somehow via the multilobed orbitals on the metal, but I don't think that counts as stacking.  I'm not that well informed in these things, so if you want a better answer, go to WP:Reference desk/Science - but if you're asking whether you should add that cocaine analog as an illustration of stacking for this article, I'm just barely confident enough to vote no. Wnt (talk) 12:44, 21 April 2016 (UTC)
thread_title:  [[List of phenyltropanes#η6-3β-(transition metal complexed phenyl)tropanes|''η''<sup>6</sup>-coordinated moiety upon benzene (cyclopentane on benzene?)]] 

message: I'm going to leave this citation here. There is a lot of misinformation online and I would hope that Wikipedia might be a means to get through that, even in scientific circles. Fix this page please!
:Nonetheless, the term pi-stacking has been widely adopted in scientific literature and remains in use. I see no reason to strictly depart from these sources. TheBartgry (talk) 10:07, 21 September 2020 (UTC)
replies: text:  The term “pi-stacking” is widely missued as Martinez and Iverson make clear. Calculations show that the face-to-face orientation is electrostatically unfavorable.  Furthermore, the avaiable experimental data (e.g., crystal structures) support that the staggered orientation is far more common than face-to-face orientation. The "evidence for" section of this article is actually "evidence against".  I have revised the lead and the "evidence" section heading to make that clear.  Boghog (talk) 10:20, 21 May 2022 (UTC)
thread_title:  Rethinking the term “pi-stacking”