Lone Pairs as Special Nodes

I remember in earlier versions of MarvinSketch, that it was possible to add lone pairs as special nodes to ensure that the molecular geometry is correctly modelled by the calculations. Whatever happened to that - is it still possible for version 14.x.x.x , only now requiring a different technique?

Hi,

if you mean the special atoms marked with an LP label, then I have to say that we removed it completely from our system since Marvin 6.1.0.

You are still able to add lone pairs to the atoms, their placement is automatic, and as we believe accurate regarding the geometry of the structure. However to add lone pairs, you have to customize your MarvinSketch UI to have the functionality on the toolbars or in the menu.

You can find help for the customization here.

We are happy to hear your feedback about the decision, and ready to learn more about your workflows where it is considered useful, or necessary to use them, we felt it is neither straightforward nor used by our users since we introduced the new lone pair representation.

Regards,
Istvan 

Thank you. I've added the toolbar command, however I can't enable its functionality, even after disabling Automatic Lone Pair Calculation as per instruction via the customization details.

Besides turning off the automatic lone pair calculation, please set "Lone Pairs" visibility option in View menu>Advanced as well. It should work this way.

We will improve our documentation based on your feedback.  Sorry for the inconveniences.

Best regards,

Efi

Thank you, it is now functional. However, this method of manually determining the number of lone pairs is not sufficient for my requirements. It is merely an ascetic modification, and does not replace the aforementioned widget. Gradient optimisation is somewhat useful to cover the simplest of cases. For instance, to create a square pyramidal complex, one can start with an octahedral one, and remove one ligand, before gradient optimizing it. However, this does not work for all cases. Take sulfur tetrafluoride, removing two fluorine ligands from the octahedral equivalent, and then running the gradient optimisation, simply produces a tetrahedral geometry.

Sincerely,

 

Bernard Kriel