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:
[...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@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 =
"[...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@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:
[...@h]12[c@@H]3[C@@H]4[C@@h]...@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 =
"[...@h]12[c@@H]3[C@@H]4[C@@h]...@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
------------------------------------------------------------------------------
Centralized Desktop Delivery: Dell and VMware Reference Architecture
Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
client virtualization framework. Read more!
http://p.sf.net/sfu/dell-eql-dev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
