Organic Synthesis

Organic chemistry means the chemistry associated with any molecule that contains at least one carbon atom.  The term “organic synthesis” can be considered synonymous with the term organic chemistry, but more commonly means the chemistry that is specifically performed to synthesize a product molecule from starting smaller starting reagent molecules.  As organic chemistry involves molecules that contain carbon, organic synthesis is most generally concerned with the construction of molecules by making carbon-carbon bonds, and by adjusting the redox state of individual carbon atoms, for example, by making carbon-hydrogen bonds (reduction), or carbon-oxygen bonds (oxidation).  There are hundreds if not thousands of methods for performing these general reactions, each method having utility in specific cases. The synthesis of molecules that occur in nature, called natural products, or modifications of these molecules, is probably the largest sub-discipline of organic synthesis.  This includes molecules that have biological activity, and become the products of the pharmaceutical industry.  The synthesis of polymers is also a sub-discipline of organic synthesis, although is generally called polymer chemistry.  The use of biological systems to produce a naturally occurring molecule, which is then modified  to give a non-naturally occurring molecule, is also a sub-discipline of organic synthesis.

A chemist practicing organic synthesis will have a degree in Organic Chemistry, Synthetic Organic Chemistry, or possibly Organic Synthesis, depending on the granting institution.  Most basically, a chemist practicing organic synthesis will be able to put together individual chemical reactions in a series, the synthetic route, to construct a target molecule from given starting materials, or conversely, consider a given molecule and propose a route to construct it beginning with starting materials that are the least expensive, or the route that has the smallest number of steps, or a route that avoids or uses a particular intermediate compound.   A chemist practicing organic synthesis will have considerable knowledge of the individual methods for forming carbon-carbon bonds and adjusting the redox state of carbon atoms, and the analytical methods that are needed to understand if the chemical reaction that the chemist has performed has given the desired result.  These analytical methods will cover simple physical methods used at the bench with simple equipment, such as TLC (thin layer chromatography) to methods requiring more elaborate equipment, such as HPLC (high performance or high pressure liquid chromatography), GC (gas chromatography), MS (mass spectrometry), or IR (infra-red spectroscopy) and most importantly, NMR (nuclear magnetic resonance spectroscopy).    A chemist practicing organic synthesis should have considerable knowledge and experience in each of these, the ability to understand and interpret the output of each, and how to prepare samples for each.

An organic chemist practicing organic synthesis is different from a chemical engineer.  While the chemical engineer will understand the thermodynamics of chemical systems, and the steps needed to run a chemical reactions at large scale and arrange equipment for heating or cooling and other physical actions, it is the organic chemist that will design the multiple step from the starting materials to the final product, apply the appropriate analytical methods required along the way, and be able to evaluate alternatives synthetic routes – for example,  a route that could be used to avoid a patented route, or improve patent protection.  Technical diligence on a synthetic route would be a role filled by a chemist practicing organic synthesis, or expert witness opinions when disputing if a synthetic route is equivalent, or different, from another synthetic route. The literature of organic synthesis is vast, and various databases are available that can be searched when researching a reaction or designing a synthetic route.  Knowledge of the literature of organic synthesis is a requirement of the organic chemist.

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