Friday, June 22, 2012

Depiction of chemical graphs

I read just now about the new ChEBI release and particular this nice drug with gold in it:

This is a wonderful structure!

Notice the InChI given for this structure below, which shows actually a charge-separated structure. And this InChI has a "/q;;+1". That suggests to me that only the gold is charged, and thus that the full structure is charged. That does not match the drawing.

Is that inconsistent? Yes. Welcome to cheminformatics :)


  1. Not sure if this answers your question but the standard InChI doesn't handle bonds to a metal - it just splits off the Au and says it's a disconnected structure. If you use /RecMet you get a non-standard InChI that does.

    1. Yes, makes sense. People should put more attention to the "other" output of the algorithms, the warnings, etc.

      But what do you make of the charge? Even if disconnected, I would still expect the overall charge to be zero, as in the drawing. But the InChI made if overall +1 ...

    2. The p-1 is the correction to the charge in certain circumstances.

  2. This is a bit silly indeed and can be explained by the limitations of the neutralization rules in InChI. After disconnecting Au and the R-S group InChI puts a negative charge on S and a positive charge on Au. Next, InChI tries to neutralize the disconnected components one by one. It puts a hydrogen on S, to make it neutral, but it leaves Au+ as it is.