[Jmol-users] Coordination Compound Questions

[Otis R. <osr...@ch...>]

All-

I'm looking for some advice from inorganic chemists (or others) on the 
subject of appropriate molfiles for coordination compounds. To put the 
question in perspective, we are assembling a database of organic 
compounds found in  standard organic text. This list will, of course, 
include some coordination compounds. The database will include, _A_ 
SMILES that Jmol creates for the model, _THE_ unique SMILES  that NIH 
Resolver creates, a common name, the IUPAC name, and a hook to the molfile.

It is the SMILES & molfile that present a problem for coordination 
compounds. What is the standard (if any exists) for creating coordinate 
bonds in a molfile? It appears that a common approach is to not show 
bonds at all (PubChem and Emolecules seem to do this for example), with 
the resulting SMILES being a multi-structure SMILES. For our purpose, a 
single bound geometry retaining entity is preferred. We can create the 
unconnected model in Spartan, and then append/edit the molfile 
connection table to show coordinate bonds. Is there a preference or some 
standard for the molfiles of these compounds? Single, partial, 
unidentified are among the molefile options.

Bob is the master of Jmol SMILES, so I'll direct the second question to him.

The SMILES on these compounds present another problem in Jmol. By way of 
example,  if we construct an unconnected ferrocene in SPARTAN and then 
edit the molfile connection table so that the cyclopentadienyl anion 
carbons are assigned "aromatic" and the coordinate bonds to iron are 
assigned as type 8 ("any", evidently interpreted by Jmol as partial ), 
then we get the following SMILES from Jmol:

[C@H]12[Fe]3456789%10[C@H]%11[C@@H]%10[C@@H]9[C@@H]8[C@H]%117.[C@H]16[C@@H]5[C@@H]4[C@H]23

The NIH Resolver reads this and returns evidence that it understands the 
bond connections - correctly connected 2D molfile and correctly 
connected GIF image. This appears to be a correct SMILES for the 
ferrocene that we constructed. It appears that the SMILES is very 
confused about the geometry of the cylopentadienyl anion hydrogens, but 
the connections are correct.

Unfortunately, Jmol does not seem to recognize what it created. With the 
same model in the Jmol window, the following :

var x = 
"[C@H]12[Fe]3456789%10[C@H]%11[C@@H]%10[C@@H]9[C@@H]8[C@H]%117.[C@H]16[C@@H]5[C@@H]4[C@H]23"; 
var y = {*}.find("SMILES",x);echo @y

does not produce a match. Resolver will also produce a unique SMILES 
from Jmol's SMILES:

[C@H]12[C@@H]3[C@@H]4[C@@H]5[C@H]1[Fe]23456789[C@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10

The following SMILES Find (Resolver in Jmol) is a perfect match:

var x = 
"[C@H]12[C@@H]3[C@@H]4[C@@H]5[C@H]1[Fe]23456789[C@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10"; 
var y = {*}.find("SMILES",x);echo @y

Help!

Otis

-- 
Otis Rothenberger
chemagic.com