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I just read this In the Pipeline post and I was slightly confused by a statement on the use of tin. Lowe reports on this paper, which describes a synthetic route to spiro heterocycles using tin compounds, and caveats the finding with the comment that

No one's crazy about using tin, but the transformation is too useful to pass up.

Why is the use of tin undesirable in synthetic chemistry?

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Organotin compounds are rather toxic. They are also persistent in the environment and have a long biological half-life.

The problem is that trialkyltin byproducts from your reaction are difficult to separate from the product. In the lab, this is painful and (usually) involves multiple columns, but when you want to get a drug past the FDA into the clinic you have to meet purity standards for heavy metal contamination. To a medicinal chemist, a transformation that won't make it into pilot plant and production is useless.

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    $\begingroup$ While I fully agree with the answer you provided, Tin really is hard and important to get rid of in some cases, I would like to add that the Stille Coupling is widely used in industry. This uses organo-Tin reagents in a Palladium coupling. General link on Stille Coupling $\endgroup$ – Eljee Dec 11 '14 at 8:55
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    $\begingroup$ There are a few points in the answer and in comment that I feel could use some clarity. I've never met a process chemist willing to scale a Stille reaction up for production, but med chemists use it all the time on relatively small scales. Organotin waste is a huge problem at scale, but if you're just aiming for milligrams of something to test, a Stille coupling may be perfectly reasonable. You can try to switch to a less distasteful route if the molecule survives the initial testing. $\endgroup$ – Zhe Mar 26 at 20:27

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