Because stable isotopes are not radioactive, they are much safer to handle and are not regulated like radioactive materials. Stable isotopes may be used, for example, to track processing effects on a molecule, determine the physical distribution of the molecule in the product during or after processing, or even metabolic effects

The first step in custom synthesis of molecules incorporating stable isotopes is to choose an atom (or atoms) to tag. Common stable isotopes used are ²H, ¹³C, ¹⁵N, and ¹⁸O. The synthesis process involves constructing the chosen molecule with one or more of the stable isotopes replacing the common atom in the molecule. For example, a hydrogen atom could be replaced with ²H at one end of a molecule and a carbon atom could be replaced with a ¹³C on the other end of the same molecule. Using two or more isotopes would allow one to determine of processing steps broke the molecule, where it split, and where the parts ended up in the product.

The second step involved is to use the tagged molecule in place of its analog molecule in standard processing. Because the stable isotope only differs in mass and not charge, the interaction during processing is unchanged from the normal molecule.

The third step is to collect samples of the processed product and perform mass spectroscopy or NMR on the samples. This analysis provides determination of the physical distribution and structure of the molecule. Isotopic ratios can also provide information about concentration, or dilution, of tagged molecules due to processing.

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