Totally Synthetic Useful Org Prep Daily

I am delighted at the increase in activity of blogs about synthetic organic chemistry. This is about how to make carbon compounds, many of which occur as natural products (produced by plants, bacteria, etc.) which often have valuable medicinal properties. They aren’t easy to make in the lab, and require complicated multistep processes.
The results of this work are reported in the peer-reviewed literature and you normally to have to subscribe to the journals (or secondary abstracting services) to know what is going on. But there is now a chemical blogosphere in which practising (young?) chemists report on key papers and processes when they appear. The standard of reporting and the (voluminous) commentary is very high indeed – there are virtually no irrelevant trivia – and some of the comments are perceptive in that they praise or deprecate some or all of the primary work.
I’m quite sure that this blogosphere will develop to become a key part of informatics (publishing, retrieval, etc.) in this area. Obviously the blogs are openly accessible, and several (like mine) use Creative Commons or Science Commons licenses. They have immense potential to change the model of chemical information. Jean-Claude Bradley of Useful Chemistry reported in Org Prep Daily says:

As you mention the desire to control format and quick indexing by Google are precisely why this bottom up approach to disseminating scientific information will become increasingly important over time. With Google as the UberDatabase, the usefulness of publication gatekeepers becomes more and more questionable. It is then up to the author to make it easy for their work to be found. For example, in organic chemistry, adding InChI strings of the molecules used and produced at the end of posts makes it that much easier to locate molecules on Google.

Indeed Google becomes the UberDatabase. Currently it deals primarily with text strings although I am sure we can expect more magic soon for things like images, music, etc. Chemistry can be done with a clever trick – the InChI. This takes a complete chemical structure and turns it into a magic string – try our WWMM Web Services GoogleInChI server to get a feel for this. If the chemistry in the blogosphere is published as InChIs then Google acts as an UberChemicalDatabse.
The main challenge is to get InChI – which is only a year old – adopted as the main way of indexing molecules. That is where the blogosphere comes in. So we are starting to talk with the main chembloggers to see what tools are required and what type of social computing will work in this area.
Among the synthetic chemistry blogs are:

  • TotallySynthetic a very detailed account of selected key papers from the recent literature. These syntheses may consist of many steps A->B->…Z
  • Org Prep Daily which highlights a typical and important step (C->D) of general applicability
  • Useful Chemistry where J-C B reports the chemistry as he does it!

I also have to mourn the passing of Tenderbutton’s blog – he has laid down his “pen” to finish his thesis. Like The Chem Blog and In The Pipeline this was a more discursive blog (although it had frequent comments on organic synthesis).
As Org Prep says:

The Org Prep Daily access rate has been pretty high this week – clearly with the help of the plugs from Dylan, Kyle, Tot Synth and also Jean-Claude in their blogs. I guess there are few hundreds regular readers now, just few weeks after this site started. I am particularly pleased that Google search terms like “ninhydrin solution TLC”, “azide from mesylate”, “IBX Dess-Martin” and “TFFH” are getting through and directing people here. I plan on writing Org Prep Daily in the near future, at least until the end of this year, to see if this kind of interest would continue.
There has been a similar project, Synthetic Pages going on for several years now. They have a seriously useful synthetic procedure collection there and I definitely recommend Synthetic Pages to everyone’s attention. I wish them best luck with their effort. The reason why I did not send my procedures in there was that I wanted to start my own page with a more personal touch. A site that would have some day-to-day activity, where one could have a comment sections after each procedure. I think the blogg format may work for this purpose. The main inspiration came from Dylan’s Tenderbutton but the decisive factor was the WordPress software and free hosting at WordPress has made this a fairly effortless undertaking, even for a computer-naive person like me.
Two things about the near future of Org Prep Daily: 1) I have not taken any vacation since I started at Scripps Florida and I am taking some time off, one week from now (my dad is visiting) so there will be a brief hiatus on updates – for about one week- beginning from next Saturday.
2) Call for authors: It is clear that it wouldn’t be possible for me to keep up with two-procedures-a-day updates if every procedures here was to be based on my experimental output (and I woudn’t want to go on by posting rubbish). When I started Org Prep Daily, I already had a collection of procedures from current and past projects. Since I am not in industry anymore, posting the building-block-and-reagent procedures was non-problematic for me; and I have made lots of these over the years. But my store of good procedures will eventually run out – maybe in one month time. So I am going to invite other people to write for this page.

This is a vision for social computing in the chemblogosphere. There is tangible synergy between multiple efforts – they diversify and mutate and give each other support. I can see a future where enough chemists are excited by this that most things of note end up in the blogosphere. That’s where we need tools like InChI and others to help us – we are developing some exciting tools and there will be more posts on this subject quite soon.

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One Response to Totally Synthetic Useful Org Prep Daily

  1. Pingback: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Presentation to Open Scholarship 2006

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