Chemicalizing a blog.

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I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in identifying chemical content. So this is by way of an experiment. I list below some of the substances about which I have blogged, to see how the chemicalizer works.

  1. Mauveine
  2. Copper phthalocyanine
  3. Lapis Lazuli (this is a difficult one, since the active ingredient is actually trisulfide radical anion or S3-.; lets see if any of that is picked up!)
  4. Cyanohydrin (a generic term, but more specifically HCN + Formaldehyde)
  5. diberyllium
  6. Calixarene (another generic term)
  7. 1,3-dimethylcyclobutadiene and carbon dioxide
  8. Z-DNA and Z-d(CGCG)2
  9. Cyclohexane, cyclohexene, cyclohexadiene and benzene (the third of these is ambiguous as I have written it)
  10. CH3NO (a formula, with many isomers of course)
  11. Dicarbon or C2 and a cyonium cation or  CN+

That should suffice to see how such a list can be chemicalized.

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7 Responses to “
Chemicalizing a blog.

  1. Steven Bachrach says:

    Some of the molecules are underlined but the links do not work (at least for me!). I thought structures would also automatically appear.

  2. Same here. I’m also now seeing two photographs of Henry, whom may be chemicalized too?

  3. I see the same thing, some underlining but no working links. It certainly looks like an interesting service one the technical issues are solved.

  4. Andrew White says:

    I seem to be having a bit more success then the earlier responders. I get underlinings for copper phthalocyanine, trisulfide, diberyllium, 1,3-dimethylcyclobutadiene, cyclohexane, cyclohexene, cyclohexadiene, benzene and “dicarbon on”, and I get pop-up ChemDraw style views of copper phthalocyanine, 1,3-dimethylcyclobutadiene, cyclohexane, cyclohexene and benzene. The others give a pop-up window with a question mark. Clicking on the ChemDraw style drawing for those that work does indeed link to a page on the chemicalize.org website about that structure. (No mention of any crystal structure, though.)

  5. Henry Rzepa says:

    The reason why the chemicalization of my blog did not produce the desired effect has now been diagnosed (thanks Andras!). I had earlier activated ChemDoodle, and both chemicalize and ChemDoodle make use of a function called jQuery, but reasons unclear to me, they do not co-exist. The developers of chemicalize and ChemDoodle are now pondering how to achieve this. I hope it can be fixed fairly soon, but at least the mystery is now resolved.

  6. Henry Rzepa says:

    One solution to the issue of running both Chemicalize and ChemDoodle was achieved by mangling the header of the WordPress theme used for the blog, by inserting the code

    <?php wp_enqueue_script(“jquery”); ?>

    <?php wp_head(); ?>

  7. Henry Rzepa says:

    Thanks to ChemAxon, I have upgraded to V 1.07 of the Chemicalize plugin, and its all working now. Thanks Andras.

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