crystal structure representation

Hallo MarvinSketchers,

 

I wonder, wether there are options for displaying infinite structures implemented in MarvinSketch?

I need to make a drawing, similar to those gained, when looking for crystal structures in the cambridge crystallographic database (CSD) and inspecting their diagrams.

A bond, which leaves the asymmetric unit and enters it "on the other side" again, is usually drawn in a zig-zag-chain way or some sort of dashed line (which would be "any bond", misused already for coordination bond issues to be solid style)...

Is there anything like this in MarvinSketch? Or some other way/idea to create some kind of "broken-off" bonds?

Thanks a lot!

Hi,

 

Can you please send us an example structure? I downloaded Mercury to see how the structures are visualized, but could not understand the point...

 

Best regards,

 

Akos

Hi!

 

Found a descent example on the open-access site of Acta Crystallographica E:

http://journals.iucr.org/e/issues/2010/11/00/fk2024/index.html

This structure should be possible to draw in MarvinSketch, but with the problems arising, discussed here (https://www.chemaxon.com/forum/viewpost31825.html).

The other point is illustrated in the attachment, screen-shooted from within ConQuest. Zig-Zag-Bonds represent bonds to the next asymmetric unit.

Thanks a lot,

Guntram
PS: Could you please change my account name to Guntram? It's not possible in my account options. Thanks!

Hi Guntram,

I think it is possible to draw the first example with Marvin using generic brackets and any bonds (see my try attached). What do you think is missing for that?

Regarding the example on the snapshot you sent: I think now I understand the point you mentioned, but is this zig-zag bond a standard representation among inorganic chemists? Is it a IUPAC recommentdation?

Best regards,

Akos

Hello again!

 

The zigzag-thing is maybe not the too much used representation. So maybe we skip this.

But concerning the other drawing --> this is good! Thank you! Now it still got the problem, that I can't put hydrogrens on the ćoordinating groups.

When I connect them via single bonds, I get the automated valence (the "wrong" ones) and when I use some any-bond, there won't be any hydrogen at all. But I really want to have coordinated amines, e.g. .

The only way to do so, will be to create a corresponding group?

 

Thanks again,

Guntram

Hi Guntram,

Yes, I understand that the proper solution would be to be able to display the coordinate bond with single bond. And yes, a possible workaround is to use contracted superatom Sgroups (named e.g. "NH3", where th number is automatically displayed in subscript) with single bonds, but in this case the calculations are still wrong (e.g. the formula will show 1 hydrogen less at each nitrogen), and the name of the SGroup does not have leftname function (so if it is on the left side of the bond, the H3 is still displayed on the right).

Best regards,

Akos

Hello Akos!

Any progress with the coordination bonds?

I'm still not able to draw a useful aqua ligand :-(.

Thanks for updating me,

Guntram

Hi Guntram,

Unfortunately, this feature is not ready yet due to other more important feature requests. Probably it will be released in a 5.5.x version.

Best regards,

Akos