Hi, and thanks for the reply!
On Thu, Oct 7, 2021 at 10:34 PM Hector A. Baldoni <hbaldoni.unsl.edu.ar> wrote:
>
> Dear Professor Roe,
>
> Your explanation seemed complicated to me, even more so you first take
> as a reference carbon (C5) for one example (GCU) and then carbon (C4)
> for the others (XYS and XYP).
I'm taking the definitions from sources like "Nomenclature of
Carbohydrates", Journal of Carbohydrate Chemistry (1997), 16:8,
1191-1280 (
https://doi.org/10.1080/07328309708005748), although it is
highly likely I'm either misreading or misinterpreting some of the
nomenclature.
> A more direct and simple way to determine the type of anomer is the
> following: Orient or draw the carbohydrates in the C4/1 form (ie C4 up
> and C1 down), then the alpha anomers will have the anomeric oxygen
> axial, and the beta anomers will have the equatorial anomeric oxygen
> equatorial.
I'll give this a try, thanks! Ultimately I'm hoping that I can also
figure out what's going wrong with my interpretation of the
definitions of the various atoms found in that Journal of Carbohydrate
chemistry article.
-Dan
> I hope this mnemonic rule would be useful to you.
>
> Cheers,
> Hector.
>
>
>
> El 2021-10-07 20:09, Daniel Roe escribió:
> > 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
>
> --
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
> First things first. But not necessarily in such order.
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Received on Fri Oct 08 2021 - 03:30:02 PDT
