Sunday, June 15, 2008

Ugi Reaction on MiniMapper - Trial 1 Preliminary Results

After receiving the MiniMapper two weeks ago we now have some numbers to look at from Trial 1.

The idea here was to repeat a Ugi reaction known to work in methanol at 0.5M concentration (EXP099) and explore the experimental space varying solvent, concentration and an excess of some of the reagents.

All 48 reactions gave precipitate (EXP189). We still have to optimize the lighting and camera angle to see this clearly for all tubes:

In reviewing the results I noticed an inconsistency between the experimental design and the information in the GoogleDoc used to plan the details of the experiment. But because the MiniMapper stores the log of its actions in an XML log file, Khalid was able to make corrections to the worksheet.

Based on the weight of product and the limiting reagent, a yield for each reaction was calculated (column AC).

The best 4 yields (48-61%) were found for 4:1 acetonitrile/methanol solutions at the lowest concentration (0.1 M). It is counterintuitive that a multi-component reaction should work better at lower concentration but this is an effect that I noted previously.

Ironically, the absolute lowest yield (1.4%) was found for the 0.5M methanol reaction that was supposed to be the positive control!

This may be due to a malfunction in the delivery of one of the reagents. However, the other reactions carried out at this concentration in methanol were all low yielding (10-15%), compared to when it was run manually in EXP099 (37%).

I must stress that these results are very preliminary since we have not yet shown that the isolated materials are all pure Ugi products. As the NMRs come in I'll update the status.

But I think that this was a good first trial to demonstrate what kind of questions can be asked with the power of automation and the importance of reporting automated logs in Open Notebook Science.

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At 12:18 AM, Blogger Rajarshi said...

Is the test tube layout standardized? If the camera angle can get fixed, this would be pretty amenable to automated image analysis

At 5:00 AM, Blogger Jean-Claude Bradley said...

Rajarshi - the test tube layout is standard and it is clear that it will require more than on camera angle but yes I think we could get it to the point of automated analysis. The camera people from JoVE will be here soon and they were suggesting using a macro lens for each tube - more on this shortly.
I hope you'll contribute to our trial #3 - due in about a week where I'll solicit suggestions from the community for experiments to do. These could be either to test a hypothesis on yield or which combinations lead to Ugi precipitates. More on this shortly too.
Thanks for the feedback!

At 8:26 AM, Blogger Noel O'Boyle said...

Are you aware of the design of experiments field? I'm can't say I know much about it, but it might allow you to maximise the amount of information you get with the minimum number of experiments (rather than trying every combination of solvent, concentration, etc.

At 6:09 AM, Blogger Jean-Claude Bradley said...

Kevin Owens is assisting us with experimental design. But there are many different approaches, depending on what questions we really want to answer. I certainly would welcome suggestions for experiments in our Trial 3 - open to the public. If someone with a particular expertise in experimental design were to contribute that would be a nice example of crowdsourcing.


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