Analytical / General Interest / Organic

Online Resources for Doing Organic Chemistry

Organic chemistry can make sweet t-shirts too. Link at end of post.

Yes!!! 100% conversion to product, zero impurities, and a workup so easy I finished it while writing this sentence!Well, that’s what writing it down on an o-chem problem set might make it seem like at least. Turns out doing organic chemistry in practice isn’t so straightforward, but fortunately the work of generations of chemists have been compiled into online resources for us.

Before we discuss these resources, let’s look at two general types of challenges one might face while doing organic chemistry:

1. Okay – I remember the general reaction for how to make something from classes, but what reaction conditions do I use? How should the workup go?

2.Cool – I isolated a product mixture…but the NMR spectrum has peaks I can’t identify…

Solving the first challenge could take many paths – maybe you ask a fellow chemist, look up papers with similar reactions, or use SciFinder’s database. Another method could be ‘thumbing’ through the journal Organic Syntheses, accessible online. Searchable by compound names, structure, and keywords, one might wonder if it is any different than SciFinder. It is! Unlike articles found on SciFinder, reactions published in Organic Syntheses are checked by at least one other chemist who verifies that it works. Ever futilely attempt a synthesis from a paper over and over again? Well, the folks running Organic Syntheses already had the preps and workups checked for you – plus their preps are reported in much more detail than most preps in other papers. Even if you are not reproducing a specific procedure, you can at least get an idea of the general reaction conditions for a specific reaction type. An additional resource for doing chemistry is Not Voodoo – it is a compilation of techniques and hints – everything from how to properly clean glassware, isolate your product, and even how to stay motivated.

Alright! You’ve done your reaction. Time for challenge two – identifying everything you can via spectroscopy. Two resources which may aid you are the Spectral Database for Organic Compounds and a compilation of common NMR impurities. The main page of the Spectral Database (once you agree to the disclaimer) lets you search by either compound identity or by peak position (where ‘peak’ could be an NMR peak, IR stretch, mass-spec m/z value…). An example – say you think your material is contaminated with something, and you look up the 1H spectrum of this suspect compound in the database. Ah ha! It matches the mystery peaks in the 1H spectrum of your product! Complementing this is the compilation of common NMR impurities – a very nice paper which lists in table format the peak positions nearly every solvent you could think of in nearly every NMR solvent you can think of. This is rather useful because the peak position of an impurity solvent in your product can depend quite a bit on what deuterated solvent you took the NMR with.

Finally, feel free to post comments with your favorite online organic chemistry resources!

URL of the fun t-shirt art above.

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