Hi, I am still looking for a tool to produce reasonable coordinates for planar molecules. The molecules should be in the xy-plane and the bond lengths should have reasonable values. Our quantum chemical programs analyse the topology of the molecules by searching for neighbors in a range of normal experimental bond lengths. The molecules MarvinSketch produces have normally those tolerable bond lengths, but the C-H bond lenghts have 1.54 A. This is much too long.
In the attached image there is shown, the tool Add Explicit Hydrogens produces all C-H bond lengths as 1.54 A (the same length is produced for O-H and N-H bonds, being also too long).
Using Clean 3D with Hydrogenize produces reasonable bond lengths. But now the molecule is not in the xy-plane. So using now Clean 2D brings it back to this plane, but it changes once more the bond lengths and the C-H bonds have 1.09 A. This value is a good reasonable C-H bond length. But now the problems checker says "6 bonds found with wrong length".
Saving this structure as xyz-file gives a structure having CC 1.54 and CH 1.09 values for the bond lengths. And these structures are usable.
But using Clean 2D once more a second time now changes the C-H bond lengths to 1.54 A.
So there are at least two problems to be solved:
1) The failure in the problem checker showing reasonable bond lengths as wrong.
2) The much too long C-H and N-H and O-H bond lengths Clean 2D is producing.
Best regards, Hans-Ulrich
PS: This is not the first time I am discussing the C-H bond length problem in this forum. And one of our programs has been adapted to C-H bond lengths having 1.54 A. But we cannot do this for all programs.
PS2: Please remember: We would like to use Marvin for teaching.