certain meso structures

The following two structures are called identical by JChem 3.0.10, even though they're not:

Code:

Marvin  05020513552D   8  7  0  0  0  0            999 V2000   -10.6875    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -7.8296    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -9.9730    3.7563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -9.9730    4.5813    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0    -9.2586    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -9.2586    2.5188    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0    -8.5441    3.7563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -8.5441    4.5813    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0   1  3  1  0  0  0  0   3  5  1  0  0  0  0   5  7  1  0  0  0  0   7  2  1  0  0  0  0   3  4  1  1  0  0  0   5  6  1  1  0  0  0   7  8  1  1  0  0  0 M  END   Marvin  05020513572D   8  7  0  0  0  0            999 V2000   -10.6875    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -7.8296    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -9.9730    3.7563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -9.9730    4.5813    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0    -9.2586    3.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -9.2586    2.5188    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0    -8.5441    3.7563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -8.5441    4.5813    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0   1  3  1  0  0  0  0   3  5  1  0  0  0  0   5  7  1  0  0  0  0   7  2  1  0  0  0  0   3  4  1  1  0  0  0   5  6  1  6  0  0  0   7  8  1  1  0  0  0 M  END

Note how no parity is shown for C(5), even though it is a stereocenter. Can you help?

Hi,





The mentioned atom cannot be a stereo center, because it doesn't have 4 different ligands, just three (including the implicit hydrogen).





This is because the two connected carbon atoms cannot be distinguished by topology (in other words they have the same graph-invariant value).





Best regards,





Szilard

Szilard wrote:

Hi, The mentioned atom cannot be a stereo center, because it doesn't have 4 different ligands, just three (including the implicit hydrogen). Szilard

But it is a stereocenter. C(2) and C(4) are different from one another: one is R, the other is S. So the central C is attached to four different ligands. In one compound the stereochemistry is denoted as r, and in the other as s. (Note the lower case, because both stereoisomers are achiral.)

Hi,





It seems I was wrong about this issue, sorry.





One of my colleagues will answer this question soon.





Best regards,





Szilard

Well, it still seems that Szilard got close to the root of the problem anyway.





The main problem is that the graphinvariant calculation currently does not include chirality information to avoid a combinatorial explosion. For this reason the middle atom seems to have no parity information as Szilard mentioned. This is what affects both R/S display and searching amongst other things.





We will try to think out a good solution without slowing everything down.





Best regards,





Szabolcs

Bob,





Both the searching and chirality display of these molecules will be fixed in the next major releases. (Marvin 4.0 and JChem 3.1.) You can sign up for the release notification mailing lists by watching these topics:





http://www.chemaxon.hu/forum/ftopic290.html





http://www.chemaxon.hu/forum/ftopic287.html





Best regards,


Szabolcs

Good news. Thanks. I hope you were able to find a good solution that doesn't slow everything else down.

bobgr wrote:

Good news. Thanks. I hope you were able to find a good solution that doesn't slow everything else down.

Yes, we were, but we are still working on it.





Regards,


Szabolcs

Hi,





I know this bug was fixed in JChem 3.1. JChem 3.0.15 was released after JChem 3.1 was released. Is the bug fixed in JChem 3.0.15, too?





-- Bob

No, this fix is only available in the 3.1.* releases.





Best regards





Szabolcs