Date: Fri, 8 Oct 2021 16:22:15 +0000
Hi Dan,
The alpha/beta convention is based on the relative position of the anomeric carbon and the highest-numbered stereocenter of the sugar in a Fischer projection. Looking at the cyclic conformations works for most hexopyranosides, but in many other cases (such as the example you gave) it is not applicable..
So by definition alpha indicates that the OH at the anomeric center is, in a Fischer projection, on the same side as the OH at the farthest chiral center; beta = opposite sides (https://iupac.qmul.ac.uk/2carb/06n07.html).
For D-xylopyranose:
[cid:3a0bf57c-c9db-4c63-8f79-8215560c04c4]
Hope I could help ..!
Best,
Rafael
--- Rafael Nunes, MSc BioISI - Biosystems & Integrative Sciences Institute/ CQE - Centro de Química Estrutural Faculdade de Ciências da Universidade de Lisboa Campo Grande, Ed. C8, office 8.5.50d/ lab 8.5.41 1749-016 Lisboa, Portugal rsnunes.fc.ul.pt +351 217 500 000 (ext 28567) ________________________________ From: Daniel Roe <daniel.r.roe.gmail.com> Sent: Friday, October 8, 2021 12:09:28 AM To: AMBER Mailing List Subject: [SPAM] [AMBER] Help with carbohydrate nomenclature Hi All, I'm hoping someone can shed some light on an issue that's been bugging me for a while about determining alpha/beta forms of carbohydrates in cyclic form. So I get that there is the anomeric carbon (carbon bearing hemiacetal/acetal, typically C1/C2), the anomeric reference carbon (which I think is the highest stereocenter in the ring) and the configurational carbon (highest numbered stereocenter). The configuration around the configurational carbon determines D/L, and as I understand it _the relative orientation of the oxygen on the anomeric carbon to the oxygen on the anomeric reference carbon_ determines alpha/beta (see e.g. https://www.masterorganicchemistry.com/2018/02/19/the-big-damn-post-of-sugar-nomenclature/#anomericcarbon). Specifically, if they are on the same side that's beta, and opposite is alpha. This seems to hold for most sugars. Take for example alpha-D-glucopyranuronic acid (https://www.rcsb.org/ligand/GCU). Here the orientation of the O at the anomeric carbon (C1) and the anomeric reference carbon (C5) are clearly opposite, hence alpha. However, take as another example alpha-D-xylopyranose (https://www.rcsb.org/ligand/XYS). Now, assuming I'm correct in that the anomeric carbon is C1 and the anomeric reference is C4 (which appears to be the highest numbered stereocenter), the oxygens bound are clearly pointing in the same direction. And for the beta (https://www.rcsb.org/ligand/XYP) they are on opposite sides. Now I'm sure I'm just not understanding the nomenclature correctly (or making some other obvious mistake), but I just can't seem to wrap my head around why XYS is alpha and XYP viceversa, when for almost every other sugar I've looked at it's been the other way (opposite=alpha, same=beta). Can anyone explain this? Thanks, and sorry for the long post! -Dan _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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