Ugi Reaction as Mettler-Toledo Application Note

Our JoVE paper Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling (Jean-Claude Bradley, Khalid Baig Mirza, Tom Osborne, Antony Williams, Kevin Owens) was adapted as an Application Note for Mettler-Toledo. Lots of interesting things can be done easily when you publish in a journal with an Open Access option.


I just noticed that our number of views is almost at 8000 on JoVE. After a little over a year the views are still coming in at a fairly steady pace. Article-level metrics are one of the best things in the scientific publication process to have come along for authors.

From ONS to Peer Review: our JoVE Article is Published

Our article "Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling" is now published on the Journal of Visualized Experiments (JoVE). I am very pleased with this because it showcases some interesting approaches to communicate science that were not possible not so long ago.

First, and foremost, this demonstrates that lab notebook pages and blog posts can be used to support claims made in a peer reviewed article. In a way this isn't drastically new since it has been possible for a while now to cite web pages in the peer reviewed literature. The key question is whether the reference is appropriate, regardless of its format. When providing a reference for a melting point or spectrum, nothing is more relevant that the lab notebook page where the specific batch of product was obtained and characterized.

Second, we have demonstrated that it is possible carry out research under Open Notebook Science conditions, write an article openly on a wiki, post it on a pre-print server (like Nature Precedings) and finally publish it in an peer reviewed journal. No, this won't work with every publisher. But if communicating science openly (beyond the confines of the regular Open Access model) is important to you, there are options out there that don't take anything away from the traditional system of academic validation.

Third, this is a good example of the use of video to enhance the communication of a protocol for a chemical reaction. But this is not a shortcut by any means. The process of writing a script and preparing for the shoot was very time-consuming because we were describing a whole workflow. When using video as raw data to record details of a specific experiment, it can actually save time that would otherwise be required to describe using text.

Finally, JoVE is an example of an Open Access journal with some Web2.0 capabilities, like the ability to leave comments and label them as agreeing or disagreeing with the authors. The final article can now also serve as a location for continuing the scientific conversation.

JoVE shoot at Drexel

On Saturday July 12, 2008, in my lab at Drexel, we recorded our JoVE shoot for the use of Mettler-Toledo's MiniBlock and automated liquid handler for optimizing a Ugi reaction.

It took about 6 hours and I was very impressed with the professionalism of Ian, the camera man JoVE sent us. The preparation time was much more than that and I appreciate JoVE's flexibility in compressing their regular operating timeline because of our limited time with the equipment.

One of the main challenges was finding an appropriate level of detail and selecting illustrative video sequences to describe the protocol. After working with Tom, Khalid and Aaron from JoVE I think the resulting script should be helpful for people wishing to repeat the experiment. Khalid and I recorded the intro and conclusion and the rest of the script will be recorded by JoVE.

The good news is that the shoot went well I think. Multiple takes were recorded for most sequences so it should be possible to piece together a decent video. However, we discovered flaws in the way we have been programming the MiniMapper, which would explain the strange and inconsistent results we obtained at first.

Thanks to Tom Osborne digging through the log files of our runs to identify the problems, I think we have a liquid handling protocol that is correct now. The first experiment using it (EXP199) is showing reasonable results so far, with the higher concentrations 0.2M and 0.4M and methanol or methanol/ethanol methanol/acetonitrile mixtures showing the higher yields. We'll see if we can get good reproducibility in next few runs. Once that is done we can wrap up the JoVE paper.