Axial chirality / helicity and P / M nomenclature - problem

Hi Marvin developers, to say it first:

Having the P / M nomenclature for molecules with axial chirality / helicity such as front/end substituted allenes is a real highlight of the Marvin software.

We are using the anitbiotic mycomycin in our tutorials, because it has many properties to show stereochemical nomenclature. But in our last course we had the problem, the P / M nomenclature is only shown at the molecule, but not in the IUPAC naming line, please see the attached molecule and the attached screen shot.

What's wrong ?

And in the next post I will show one problem more.

Best regards, Hans-Ulrich

Hi, and now the problem with 3D structures:

In our courses we produced many 3D-structures for Mycomycin, using "Clean 3D with Hydrogenize" and it worked perfectly. All students got the correct 3D structure having 8M chirality. But now there were problems: The naming tool sometimes produced the correct 8M-naming, but sometimes there was "M" in the 3D display and "8P" in the IUPAC name.

Attached there are two examples for 3D mol files of the same molecule:

Mycomycin-M-1.mol has the "8M" structure but it produces an incorrect IUPAC naming "8P".

Mycomycin-M-2.mol is correct both in the 3D display and in the IUPAC naming.

What's wrong ?

Best regards, Hans-Ulrich

Dear Hans-Ulrich,

Thank you very much for your report. The core problem is that axial chirality is sometimes lost or switched when converting from explicit to implicit hydrogens. You can see this by using the Structure/Remove/Remove Explicit Hydrogens menu entry. The errors in the name are a side-effect of that.

Interestingly, if you manually delete the H atom, the chirality stays correct, and therefore the name too.

We will report when the problem is fixed.

Best regards,

Daniel Bonniot

This issue has been fixed in Marvin 5.7. Sorry for not signaling that here earlier.