Peter wrote up an item on Nick’s\nCrystalEye’s RSS feed, and I have been enthusiastic about\nchemistry-enriched RSS feeds for some time. CMLRSS has the chemical data inline in the RSS; see\nDOI:10.1021/ci034244p, the use of CMLRSS in Chemical blogspace\ndescribed here and\nhere ,\nand the CMLRSS support in Bioclipse .
\n\nNick’s RSS feed does not put the chemistry inline, but does link to the raw CML file:
\n\n<entry>\n <title>No title supplied</title>\n <link rel=\"enclosure\" href=\"http://wwmm.ch.cam.ac.uk/crystaleye/summary//acs/inocaj/2008/3/data/ic702497x/ic702497xsup1_THP4-SINC-publ/ic702497xsup1_THP4-SINC-publ.complete.cml.xml\" hreflang=\"en\" />\n <!-- much more, that I skipped for brevity -->\n</entry>\nThe example shown by Peter was nicely chosen: something is wrong with that example. It uncovers a\nbug in the pipeline, that could have been uncovered by a simple agent monitoring the RSS feed.\nThat is why this technology is important! It allows pipelining of information between services.
\n\nAnyway, before you read on, check the structure in the example\nyourself (Bis(pyrimidine-2-carboxylato-K2N,O)copper(II)).
\n\nDone? Checked it? You saw the problem, right? Good.
\n\nI have scanned the CIF source, but that does not seem to contain the problem. It nicely shows a\ngeneral limitation of commonly used chemoinformatics tools: the lack of proper atom typing (a\nproblem I have been looking into for the Chemistry Development Kit;\nsee Atom Typing in the CDK and\nEvidence of Aromaticity .).
\n\nYou will have noted that the 2D diagram in Peter’s blog is charged. I checked the\ncomplete CML source code\nfor the CrystelEye entry, and that contains the charges on the two oxygens bound to the cupper\ntoo. However, the copper is not charged. That leads to a rather unlike situation; that is,\nthat crystal structures will about attract the whole laboratory to itself in a blink of an\neye: there is nothing to balance the double-negative charge! It is conveniently summarized in this bit of the CML:
\n\n<formula formalCharge=\"-2\" concise=\"C 10 H 6 Cu 1 N 4 O 4 -2\">\n <atomArray elementType=\"C H Cu N O\" count=\"10.0 6.0 1.0 4.0 4.0\"/>\n</formula>\nNow, I also checked the raw CML;\nthat seems to be unaffected too. So, the bug must be somewhere in the software that converts\nthe raw CML into complete CML. And, before the InChI calculation, because that one is wrong\ntoo. A agent scanning the RSS feed, would have detected this. Someone interested in writing\nup a grant proposal on this?
\n\nBTW, the system is not awfully wrong: the negative charge on the acidic carboxyl groups is\nto be expected. But if the bond between the oxygen and the carbon would have been coordinating,\nnot covalent, and the copper would have been +2, then it was fine. Because many chemoinformatics\ntools do not have really support for dative bonds, a covalent bond could be drawn, but then\nthe oxygens should be uncharged… right, not? :)
\n\nOh, and surely, one can do much, much more with those feeds. I blogged about that earlier in\nAutomatic Classification of thousands of Crystal Structures .
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