NMR prediction on ChemSpider chemistry

As Tony recently mentioned, there is a new button on ChemSpider to predict H NMR spectra based on the nmrdb.org web service:


To give it a spin I am posting the experimental spectrum of Ugi product UC-150D underneath the predicted one.


This is going to be extremely helpful and yet another reason for using ChemSpider in active chemistry research. However, this tool does not replace the need for understanding how to interpret NMR spectra.

First, two of the predicted peaks - the phenanthrene H at 8.5 ppm and the benzylic H at 5.7 ppm - are off by almost half a ppm. Second, the algorithm does not take into account the diastereotopic nature of the methylene group centered at 4.8 ppm. This is predicted to be a singlet but appears, as expected, as a pair of doublets.

With this new tool there is a danger that students might think that they don't need to learn the finer details of NMR analysis since the predicted spectrum just pops up so conveniently. I hope people will report on what they find to be most and least reliable as they work on real problems.

The beauty of ChemSpider is that both the theoretical and experimental spectra can be stored in the same record. Yet another reason to continue to routinely upload our spectra.

MiniMapper in Lab chemistry

As I mentioned previously, Mettler-Toledo is giving us a trial with their MiniMapper/MiniBlock system. Tom Osborne was in my lab yesterday to set it up. We got as far as setting up the software to recognize the positions of bottles and racks and pumping through some methanol.


Once we're set up it looks like we'll be able to come pretty close to just copying columns from the Google spreadsheet of planned experiments to the MiniMapper software. This will make it very convenient for crowdsourcing Ugi experiments.

Actually the worksheet for trial #3 is already set up to accept suggested experiments from anyone - no login required. Just note your name in the contributor column and put in a little explanation for your reasoning. For example, after looking at the master table of Ugi reactions, you may have a hypothesis that aromatic aldehydes lead to Ugi product precipitates at 0.5 M concentration in methanol. Just set up a dozen experiments probing that question. See the MettlerTrial wiki page for more info. I'll explain more about this later but if anyone wants to discuss collaboration contact me.

We have the capacity of doing 96 experiments in parallel but Khalid will probably start with a dry run with pure methanol or a small section from Trial #1.

Tom made a good point about how organic chemists need to think differently when designing experiments in parallel with automation. We have done parallel runs in vials but it gets tricky for people to keep track of everything. Machines are much better at this type of thing. You have to ask different questions when faced with 96 reaction tubes vs. a round-bottomed flask.

And it looks like the MiniMapper software keeps a log in XML format - obviously more on that after our first trial...

Gates Submission on ONS, crowdsourcing and malaria chemistry

On Friday I submitted a proposal to the Gates Foundation's Grand Challenges Explorations:

Creative, unorthodox thinking is essential to overcoming the most persistent challenges in global health. The first vaccines were developed over 200 years ago because revolutionary thinkers dared to try an entirely new approach to preventing disease.

The power of innovation is at work in countless other fields, from space travel to the Internet: now is the time to harness that power to save lives and improve the health of millions of people in the developing world.

Grand Challenges Explorations will foster innovation in global health research and expand the pipeline of ideas that merit further exploration. The initiative will use an agile, accelerated grant-making process with short two-page applications and no preliminary data required. Initial grants will be awarded multiple times per year at approximately $100,000 each. Additional funding of $1 million or more will be available for projects that show promise.

There is a 2 page limit so the proposal was painted in very broad strokes. Since Nature Precedings doesn't take proposals anymore, I just uploaded it to Noam Harel's SCIEnCE wiki. The core concept is leveraging crowdsourcing and Open Notebook Science to develop new anti-malarial agents. It is similar to the last NSF proposal I submitted, except that the purpose is squarely on drug development, which is not allowed for NSF funding.

I also broke it down into short sections and contributed it to the Thoughtmesh project just to see how that works.