Thanks for the info!
-Dan
On Fri, Oct 8, 2021 at 12:23 PM Rafael Nunes <rsnunes.fc.ul.pt> wrote:
>
>
> 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
>
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Received on Fri Oct 08 2021 - 13:00:02 PDT
