Automatic redrawing of aromatic rings

 I've noticed that with newer versions of MarvinSketch, it automatically redraws/isomerises the double bonds in some aromatic rings.

Firstly, m-xylene which is not changed:

CC1=CC(C)=CC=C1

If one CH₃ is converted to Br to give 1-bromo-3-methylbenzene, then the double bonds are automatically isomerised:

CC1=CC(Br)=CC=C1

With older versions of MarvinSketch, this isomerisation did not occur, and the SMILES generated was different:

CC1=CC=CC(Br)=C1

 

Can you please explain why this occurs? And is it possible to "switch off" this feature?

 

Thanks in advance!

Hi,

I've tried to reproduce the issue that you've reported, but by typing "Br" over the specified carbon no change happened to the double bonds. Can you specify what you mean by "converting" to Br? And also at which point of the workflow does the isomerisation happen? It also could be helpful if you would provide information about the usage which is corrupted by this new behaviour.

Regards,
Domi

dkiss wrote:

Hi, I've tried to reproduce the issue that you've reported, but by typing "Br" over the specified carbon no change happened to the double bonds. Can you specify what you mean by "converting" to Br? And also at which point of the workflow does the isomerisation happen? It also could be helpful if you would provide information about the usage which is corrupted by this new behaviour. Regards, Domi

Hi Domi,

I have redrawn the molecules below. The first one is m-xylene - note the position of the double bonds. If I copy that molecule and then change the 'CH₃' to 'Br' (i.e.  1-bromo-3-methylbenzene), MarvinSketch automatically moves/isomerises the double bonds in the ring.

By contrast, with older versions of MarvinSketch, this did not occur and the molecule looked like the third image.

It appears as though the newer MarvinSketch is now producing a different SMILES for the same compound compared to older versions i.e. for older versions, MarvinSketch gave CC1=CC=CC(Br)=C1 as the SMILES string by default, whereas for newer versions, it generates CC1=CC(Br)=CC=C1.

 

Hi,

I've moved the topic to 'visualization' they will reply you soon. (As far as I've tested it the versions 14.7.14., 14.8.18. and 14.9.22 don't move the bonds on atom number change).

Regards,
Domi

Hi There,

Could you send us a picture of the About dialog of Marvin Sketch, where this issue is present ? 

Thanks,

Tamas Fazekas-Vigh

tfazekas wrote:

Hi There, Could you send us a picture of the About dialog of Marvin Sketch, where this issue is present ? Thanks, Tamas Fazekas-Vigh

Apologies, I should have been clearer - this is the MarvinSketch Java applet, version 6.2.1.

 

 

Hi there, 

This behavior was fixed in 6.3, or at least I could not reproduce it in later versions, but was able to do so in earlier versions. Sadly there is no "off" switch, you will have to update Marvin Sketch to a newer version in order to fix it.

Regards,

Tamas Fazekas-Vigh

tfazekas wrote:

Hi there, This behavior was fixed in 6.3, or at least I could not reproduce it in later versions, but was able to do so in earlier versions. Sadly there is no "off" switch, you will have to update Marvin Sketch to a newer version in order to fix it. Regards, Tamas Fazekas-Vigh

Updating seems to have resolved this - many thanks!