Drawing, exporting & interpreting ionic and coordinate b

Drawing ionic and coordinate bonds

I see there is a tool in Marvin sketch to explicitly draw a coordinate/dative bond, is there a way of explictly drawing an ionic bond (in any of the ChemAxon tools) so that it is designated as such (i.e. not just by using the "any bond" tool)?

Exporting ionic and coordinate bonds

We need  to be able to export a file type that can understand ionic and dative bonds. SDFs for instance cannot contain coordinate/dative or ionic bonds as there are no suitable bond types. PubChem have created a work around for this which is a 'PubChem non-standard bond'. After the bond table in the SDF there is a section displaying non-standard bonds (first two columns are the atom numbers, final column is the bond type 5 = dative, 7 = ionic) e.g.

 

> <PUBCHEM_NONSTANDARDBOND

1  10  5

2   9   7

http://pubchem.ncbi.nlm.nih.gov/deposit/deposit_help.html#Gateway_Substances

Do any of the ChemAxon tools export SDFs with PubChem non-standard bonds? Are there any other file types that can contain this information that ChemAxon tools do export?

 

Opening files containing ionic/coordinate bonds

Can SDF files with PubChem non-standard bonds been opened in any of the ChemAxon tools to display the chemcial structure containing ionic and coordinate/dative bonds? Are there other file types that can?

 

Are there any plans to incorporate any of this functionality? Apologies if it is already availiable and I have missed it.

Thanks.

Hi,

Dative/coordinate bonds are saved in MOL/SDF format as data SGroup, and
imported back properly in MarvinSketch.

Presently there is no ionic bond in MarvinSketch. PubChem non standard bonds are not supported either, so they are not exported to or imported from any file format. At the moment we do not plan to implement these features.

Best regards,

Akos