extra H added

I opened the attached structure in MarvinSpace 5.0.3. When I told it to show the H atoms, it added one to the N at the ring junction. This N is neutral, so it should not have an H atom added.





The MarvinSpace viewer in MarvinSketch 5.0.3 doesn't add the extraneous H. Go figure. However, when I command-click (Mac user) in the window to bring up the menu, then choose Draw Type -> Hydrogens, it takes a further click in the window to get the H atoms to appear.

Hi Bob,





instead, a lone electron pair should be displayed, is that correct?








Thanks


Miklos

I didn't know MarvinSpace displayed lone pairs. Yes, that N atom has a lone pair. So if lone pair display is turned on, it should display a lone pair; otherwise, it should display nothing.

MSpace can display lone pairs, Display->Draw Type->Ligand->Lone Pairs.





For some reasons that has not yet been analysed the valence of the N atom in the fused rings is not properly calculated in MSpace. MSpace takes a geometry based approach unlike MarvinSketch that considers topology only. This results in the difference you experienced when compared MSketch to MSpace.





We'll fix this valence problem.





Regards,


Miklos