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I am wondering if anyone can suggest an easy way to draw ligands with dative bonds to metals in the editor in WebMO. Specifically, if I want to attach an ammonia ligand to a metal I usually follow these steps:
- draw an N attached to the metal;
- give the N a +1 charge;
- add the hydrogens;
- give the N a neutral charge.
This can be an issue and sometimes causes problems with the geometry optimization. Any suggestions would be greatly appreciated.
What I usually do, especially if the ligand attached to the metal is going to be in the same conformation as the ligand itself, is draw the ligand and optimize it. Then choose "restart from this geometry" from the completed job and add my metal and any other ligands and submit. If I'm doing the same ligand a lot I will also add it to the available "fragments" (I'm happy to tell you how to do this if you need). This should work fine for ammonia. There is no real need to indicate the charges on the atoms in the molecule (the charges won't be exactly what you might calculate based on lewis structure anyway). Just make sure the overall molecule charge is correct on the submission page (or the input file if you edit it). It's a little more complicated if the ligand attached to the metal is NOT in the lowest energy conformation. For example, butadiene. In that case, you will need to optimize the geometry with a frozen dihedral corresponding to the rotation about whatever bond gives you the "correct" vs "wrong" conformation for metal binding. Then you follow the steps above!