Micrococcin P1 Part 2 and the Advantages of Online Publishing
Posted by: Antony Williams in UncategorizedCopyright©2009 Antony Williams
A couple of days ago I asked whether readers could see any issues with the structure of Micrococcin P1 published in the C&E News article this week. A few people took a stab on blog and off blog but only Stuart Cantrill from the Nature Publishing Group got it right. One double bond in the wrong place. Subtle, but rather important. General structure drawing tools will help with things like this. For example, a human might not see the issue in the structure of Taxol to the left very easily. Software tools designed to flag valency issues will show the issue easily.
In the expanded image the pentavalent carbon is marked. 
The same type of tools would have shown a positive charge on the sulphur in the ring for the incorrect structure of Micrococcin.In the same way, software tools can recognize charge imbalances and incomplete stereochemistry.
I sent an email to the editor of C&E News when I noticed the structure issue but didn’t get a response. Nevertheless it is an advantage of online publications that images can be swapped out easily. This has been done for the online article here at this point and the change, while subtle, is there (shown below). 
The structure is now on the ChemSpider database here.
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May 23rd, 2009 at 7:30 am
Hi Tony
About the utility of structure drawing programs to detect hypervalent connections: Fine and well for common main group elements.
What about the d-block? I am not familiar with other programs; ChemSketch doesn’t do too well in this regard. Probably because of the way inorganic chemists like to depict structures, as opposed to the organic chemists.
May 25th, 2009 at 8:24 am
Tony, valence definition by software is fine if you’re drawing what I guess I would be inclined to call “normal” structures. However when you start drawing the structures of organometallics (as in for the long-range 1H-15N 2D review that I’m working on) the valence definition gets to be a large pain in the tail. It would be good if software developers would provide the capability to turn that feature off if the user wants to.
May 25th, 2009 at 11:31 pm
Rifleman – ChemSketch has multiple possible valences assigned to elements so you might be seeing a side effect of that. However, I would agree that inorganic and organometallic chemists like to represent structures their way and commonly this does break valency rules and causes problems. However, all highlighting to show errors can be negated in the the display too.
May 25th, 2009 at 11:33 pm
Gary – it’s a good thought that there should be an option to NOT highlight valency errors if the user chooses to override this option. Why Not? In ChemSketch this could be dealt with by defining a drawing style as a template and loading that before drawing.