My first talk at ACS09 fall meeting on Crowdsourcing Solubility and ONS

Yesterday (August 16, 2009) I gave my first talk at the ACS meeting in Washington. It was part of an outstanding session on Chemical Text Mining and Public Molecular Databases, organized by Antony Williams and Alex Tropsha.

9:00 AM 1 U.S. EPA computational toxicology programs: Central role of chemical-annotation efforts and molecular databases
Ann M. Richard, Maritja A. Wolf, ClarLynda R. Williams-Devane, Richard Judson
9:25 AM 2 Linking public and commercial chemical data: ChemSpider and SureChem
Nicko Goncharoff
9:50 AM 3 Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources
A J Williams
10:30 AM 4 Turning mining inside out
Colin R Batchelor
10:55 AM 5 Chemreader: A tool for extracting chemical structure information from digital raster images
Jungkap Park, Kazu Saitou, Kerby Shedden, Gus R. Rosania
11:20 AM 6 Exploiting a hidden treasure: Automated chemical entity recognition in Chemisches Zentralblatt
Valentina Eigner-Pitto, Heinz Saller, Peter Loew
1:30 PM 12 Online chemical modeling environment: database
Sergii Novotarskyi, Iurii Sushko, Robert Körner, Anil Kumar Pandey, Igor V. Tetko
1:55 PM 13 Public molecular databases: How can their value be increased by generation of additional data in silico?
Vladimir V. Poroikov, Dmitry Filimonov, Marc C. Nicklaus
2:20 PM 14 Chemical space management of large libraries for new active small molecules selection for prostate cancer treatment
Andrew V. Scorenko, Andrei A. Gakh, Andrey V. Sosnov, Mikhail Yu. Krasavin
2:45 PM 15 Crowdsourcing nonaqueous solubility and synthesis using Open Notebook Science
Jean-Claude Bradley, Khalid Mirza, Rajarshi Guha, Andrew Lang, A. Williams
3:25 PM 16 ChemXSeer: A cyberinfrastructure for environmental chemical kinetics
Karl T. Mueller, William J. Brouwer, C. Lee Giles, Prasenjit Mitra, Carl Lagoze
4:15 PM 18 Reliable reactions and stable structures
Jonathan M Goodman

Many of the presentations highlighted the use of ChemSpider or full collaborations (such as the integration with SureChem patent data). The acquisition of ChemSpider by RSC was repeatedly discussed and this seems to have accelerated such collaborative projects. Colin Batchelor from the RSC provided a great talk on their approach of using ontologies to better leverage the power of chemistry publications. [The presentations were judged and Colin won first prize - I won second, which was pretty cool :) and won me a ticket to the CINF lunch on Tuesday]

I also got to meet Gus Rosania in person for the first time. We had met via the blogsphere a while back over our interests in malaria and Open Notebook Science. Gus was there to share his results from ChemReader, a software package he developed to automatically read chemical structures from images.

I started my presentation by detailing the recent events surrounding the report of the oxidation of secondary alcohols using NaH. The timing of this was perfect because it really showed how useful it can be to immediately share the full data of experiments. This is the type of thing that would have been extremely helpful during the initial reports of Cold Fusion but the tools for sharing in such a detailed way were just not available. Carmen Drahl just wrote an article about this for the August 17, 2009 issue of Chemical & Engineering News (subscriber access).

Crowdsourcing Solubility using Open Notebook Science

View more presentations from Jean-Claude Bradley.

Our attempt to reproduce an oxidation by NaH

Yesterday I was discussing with my students the controversy over the claim that NaH can act as an oxidant for secondary alcohols (Wang, JACS09). There has been a lot of discussion and an attempt to reproduce one of the experiments has appeared on Totally Synthetic.

Khalid Mirza and Marshall Moritz thought it would be worthwhile to see if we can shed any light on the situation. I was also curious to see what the reaction did over time, before quenching.

We had 1-phenylethanol on hand, for which the Wang paper claims a 75% conversion (by GC) to acetophenone. All the details can be found on the notebook page UC243.

The reaction was monitored by taking aliquots of the solution then adding benzene-d6 to lock during NMR acquisition without quenching the reaction. After 19 hours at room temperature there was no change in the spectra, except for loss of the alcoholic proton. Acetophenone would have been easily detected at 7.9 and 2.6 ppm (ChemSpider spectrum)


In a comment on Carbon-Based Curiosities, European Chemist points to a 1965 paper where oxidants on the surface of NaH are likely responsible for oxidative behavior (Lewis JOC). This would certainly explain why some researchers are reporting some oxidation products but with widely divergent yields. For example, Totally Synthetic reported a 15% NMR yield for the conversion of the 4-chloro derivative to the corresponding ketone while Wang isolated the product in 86% yield.

As many have pointed out, this is a very good example of the way Web2.0 tools and community can complement traditional publishing to move science forward.