Uncomplete stereo-chemistry display

Marvin 3.2 / Marvin 4.05





Hi,





The chirality R/S just can't be set on one of the two chiral centers of the following molecule which is absolute chiral. Wheras Marvin 3.2 displays chirality S on one chiral center and no R/S chirality on the second one, Marvin 4.05 does not display any R/S chirality at all.





What can I do to have the proper display with Marvin 4.05





Thank you for your help.





Pierre-Olivier

Hi Pierre-Olivier,





One of the chiral centers is not defined correctly. (Atom numbered 8.)


This has one up and one down ligand opposite of each other, but this has ambiguous meaning. (Imagine that if both the up(wedge) and the down(hash) bonds are in 45 degrees to the screen's plane, they actually form a line in 3D with atom 8!)





I recommend to change one of the bonds to non-stereo single bond or move the H across one of the single bonds.





To switch on R/S display, check menu items under View/Misc/"R/S Labels".





I just tried 4.05, and it works for me.





Best regards,


Szabolcs

Hi Szabolcs,





I am not sure you can suppose thet bonds are in 45 degrees ....





However I think the problem is elsewhere : when I check View/Misc/"R/S Labels with Marvin 4.05 it says indeed with no ambiguity that the chirality is S, but it does not display (S) : is this the new behavior of Marvin ? Marvin 3.2 used to display (S) and (R).





Regarding the molecule I sent Marvin 3.2 fails to display (S) and indicates that the chirality is OFF. Marvin 4.05 says it is indeed (S) but does not display it, but this is not bug if you confirm the new behavior.





Pierre-Olivier

Hi Pierre-Olivier,

pojouret wrote:

I am not sure you can suppose thet bonds are in 45 degrees ....

Of course, in a proper 3D molecular model it cannot happen.





I was only trying to point out that if you try to interpret the 2D diagram in 3D, you can get extreme and ambiguous cases. Please see the diagram attached. In theory, you could choose alpha and beta between 0 and 90 degrees to correspond to the 2D diagram. If alpha > beta, you get (S) configuration, if alpha < beta, you get R, and if alpha = beta (for example, 45 degrees): none, because the two stereo bonds are in a line.

pojouret wrote:

However I think the problem is elsewhere : when I check View/Misc/"R/S Labels with Marvin 4.05 it says indeed with no ambiguity that the chirality is S, but it does not display (S) : is this the new behavior of Marvin ? Marvin 3.2 used to display (S) and (R). Regarding the molecule I sent Marvin 3.2 fails to display (S) and indicates that the chirality is OFF. Marvin 4.05 says it is indeed (S) but does not display it, but this is not bug if you confirm the new behavior.

Yes, this is a feature introduced since Marvin 3.2 that R/S display can be switched on/off. However, Marvin applications (viewer/sketcher) save your preference, and next time it will start with your last setting. There is also an applet parameter called "chiralitySupport" for this. See the relevant documentation here:


http://www.chemaxon.com/marvin/doc/dev/sketchman.html#parameters


http://www.chemaxon.com/marvin/doc/dev/viewman.html#parameters





Best regards,


Szabolcs