Thursday, August 20, 2009

My talk at ACS FA09 on Social Networking Tools and Teaching Chemistry

Yesterday (August 19, 2009) I gave my last talk at the American Chemical Society meeting in Washington. I presented on Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more for the Symposium on Using Social Networking Tools to Teach Chemistry, organized by Laura and Henry Pence:
12:05 PM Wikis in chemical education: The best of two worlds
Laura E. Pence
12:25 PM ChemPaths: Learning to meander — an online portal to ChemEd DL resources for intrinsically linked learning
Justin M. Shorb, John W. Moore
12:45 PM ChemEd DL WikiHyperGlossary
Robert E. Belford, J. W. Moore, Daniel Berleant, Michael Bauer, Jon L Holmes, Kyle E. Yancey
1:05 PM Social media: Immersion and its discontents
Elizabeth M. Dorland
1:35 PM Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more
Jean-Claude Bradley, Andrew Lang
1:55 PM SNS, IM, and textng vs. traditional e-mail and voice messaging as a means of facilitating instructor-student contact: Trends and habits of student usage, and techniques to avoid electronic overload (or withdrawal)
Robert B. Gregory
2:15 PM Faculty development, collaborative inquiry, and Web 2.0
Joanne L. Stewart
2:35 PM Are netbooks the next big thing in the chemistry classroom?
Harry E. Pence
2:55 PM Managing laboratory research data using cloud computing as an organizational tool
Harry E. Pence, Jacqueline Bennett
It was a really entertaining symposium. Laura Pence talked about using Wikispaces (the same platform I use) for student projects and emphasized how helpful it is to compare wiki page versions to evaluate each student's contributions. Justin Shorb presented on his work to wikify a chemistry textbook. Despite a broken arm, Bob Belford did a great job in presenting his Wikihyperglossary project. It marks up chemistry terms on web pages, similar to the approach taken by ChemMantis.

Liz Dorland provided a wonderful overview of how Second Life can be used from an educational standpoint, very much complimentary to the content I had on my slides. There is just so much content and so many projects now on that virtual world that it is difficult to appreciate without actually going in and taking a tour but sometimes a good talk can motivate people to give it a closer look.

Robert Gregory's talk was very funny and somewhat shocking: he gave out his cell phone and asked his students to contact him 24/7 - including 2:00 AM when he was sleeping. Joanne Stewart gave an overview of how inorganic teachers kept in contact using various social networking tools and valuable it was for both collaboration and support.

Harry Pence
gave two very humorous talks at the end. The most interesting point for me was his collaboration with Jacqueline Bennett, who used Google Spreadsheets to collect experimental results from her students. An example of that work recently appeared in Green Chemistry, 2009, 11, 166 - 168. This is especially relevant for our research - because we also use Google Spreadsheets to aggregate results - but her reaction involves finding the right solvent for mixing an aldehyde and amine and obtaining a pure imine as a precipitate, exactly the same approach for our preparation of Ugi products. Perhaps there is a future collaboration there.

All of the presentations were recorded and I will post a link when available.

Here is the summary of my talk and the recording:

Jean-Claude Bradley describes the use of social networking tools to teach undergraduate organic chemistry. Public free wikis can be used effectively to manage class information as well as serve as a versatile platforms to process student assignments and provide rapid feedback. Examples of using Second Life to deliver quizzes, play games and offer students an environment to create projects involving 3D molecules, spectra and posters are detailed. The continuously evolving role of blogs, podcasting, screencasting and newer faster interactive platforms such as FriendFeed will be outlined. New technologies create the need for new skills to be taught to students - some relating to networking and some involving knowlege of the language to navigate the chemical webspace (such as SMILES and InChI).

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Tuesday, August 18, 2009

Spectral Game talk at ACS Fall 09

Yesterday (August 17, 2009) I gave my talk on the Spectral Game at the Using Technology to Enhance Learning in Organic Chemistry symposium at the American Chemical Society meeting. I was not able to attend the entire symposium but luckily I did catch David Soulby's talk on using Google groups to distribute NMRs for labs that require many students to submit samples. I am a fan of using free and hosted services to simplify workflows of all types.

Also in attendance at the symposium were Liz Dorland and Bob Hanson. It was good to catch up with them. Bob shared a story of how he has been assigning his students tasks in his organic chemistry class which lead to updating Wikipedia. There is so much potential for using the educational infrastructure to create better scientific content for everyone.

My talk on the Spectral Game highlighted the role of openness in teaching and research to create new educational tools, especially for learning NMR. Tony Williams said a few words at the end about ChemSpider, RSC and some upcoming opportunities to publish synthesis articles on ChemSpider.

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Monday, August 17, 2009

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).

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Friday, August 14, 2009

Making the Web Work for Science July 28th 2009

A panel discussion on bringing digital tools to the world of science with panelists Stephen Friend, Jimmy Wales and John Wilbanks moderated by Tim O'Reilly. This is a pretty general overview of issues revolving around new ways of communicating science.

Making the Web Work for Science - Full from Jordan Mendelson on Vimeo.


Friday, August 07, 2009

NaH and the hydrino controversy

There has been so much discussion this past week about the use of NaH as an oxidant that I was surprised to see the very same material involved in another chemical controversy. (from Meryn Stol's FriendFeed post).

In this case, BlackLight Power claims to be able to generate energy by dropping the electronic energy of a hydrogen atom to below its ground state, creating hydrinos. One method relies on heating NaH in contact with Raney nickel. In this report, Mills and co-authors appear to provide enough experimental conditions and spectroscopic characterization data to allow others reproduce what they have done.

If you are not a chemist it is difficult to appreciate just how outlandish these claims are. They fly in the face of some extremely well tested theories that form the foundation of what we call chemistry today.

There is an abundance of wacky ideas out there. What makes this case particularly interesting is that that BlackLight Power has $60M in venture capital, intellectual property protection and licensing deals. The company and the standard chemistry model are on a collision course that will play out very soon. Either the company does not deliver or there will be some explaining to do by mainstream academics.

Reading the discussion forum on the technology, it seems like the current situation is in a kind of stalemate. Both detractors and supporters are waiting for others to repeat the experiments. Apparently Mills is remaining secretive until they build their power plant. It does not look like they are sharing the hydrino products they claim to have created.

I think that this is actually a perfect opportunity for Open Science - especially Open Notebook Science. The experiments are more difficult than those that claimed NaH to be an oxidant (which we and Totally Synthetic have investigated). I'm not sure that our lab has the required equipment to maintain the temperatures and conditions but certainly most materials science departments should have it.

And once the putative hydrino products are created they should be stable for sharing with others to analyze. The Mills report cited above even has NMR data for both dihydrino gas and the hydride form (-4.5 ppm). I don't know enough about the NMR of hydrides to know how meaningful that is but certainly it could be investigated further. It sounds like a project that could be tackled for a senior design assignment provided that students had access to the necessary equipment.

The main focus from a commercial angle is the energy generation. But the difficulty there is that failure or success of such experiments can be downplayed by both sides because it is so difficult to reproduce exactly the same conditions. But if only one person makes this new form of matter and is willing to share it, any chemist with access to standard instruments like NMR, IR, etc. will be able to confirm that it exists without ambiguity.

Doing these experiments openly and discussing them can only lead to a resolution. Even if it turns out that the characterization data can be interpreted with our standard model of chemistry that would be satisfying.

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Wednesday, August 05, 2009

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.

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Monday, August 03, 2009

Daniel Rein is Aug09 Submeta ONS Award Winner

Daniel Rein, working under the supervision of Jean-Claude Bradley at Drexel University, is the August 2009 Submeta Open Notebook Science Challenge Award winner. He wins a cash prize from Submeta.

Daniel used both NMR and the sequential precipitation technique to obtain solubility data. See his experiments here:

Two more Submeta ONS Awards will be made during 2009. Submissions from students in the US and the UK are still welcome.
For more information see:

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