What does a Synthetic Organic Chemist do?

By Michael Edmonds 08/10/2012 5


It has always amazed me how many different “types” of scientist there are, though in retrospect I guess I shouldn’t be amazed.

Our world is so vast and human beings are so curious that the opportunities to poke, peer, deconstruct and create are seemingly endless. Indeed, science is so vast I doubt I that I have more than a surface understanding of what many of my Sciblogs colleagues actually do. Perhaps they are in the same position regarding my area of expertise – synthetic organic chemistry. If so, then let me provide some more detail.

Traditionally, undergraduate synthetic organic experiments typically involve mixing two or more chemicals together for a certain period of time, under certain conditions to produce a new compound. This is done by following the “recipe” provided in the laboratory manual. Indeed, to the uninitiated, synthetic organic chemistry can seem like cooking. In reality it is very far from it (and that is not just because you aren’t allowed to lick the spoon).

Once a student moves into postgraduate level synthetic chemistry, it becomes about using what we know about organic reactions to produce a specific chemical compound or molecule. Sometimes it will be a molecule which may have never existed before, but which has been predicted to have potentially useful properties. Other times it will be an existing molecule that we need a more efficient way to produce (for example, potential drug molecules found it rare plants).

The synthetic organic chemist examines the molecule they want to make to see how it might be constructed. Using his/her knowledge of organic chemistry, bonds which should be easy to form are identified and the molecule is deconstructed until one has identified how the molecule may be assembled beginning with molecules that can be readily bought from chemical companies (or occasionally from natural sources). Where molecules can be put together in different ways the chemist assesses which is the more efficient/more likely to work. My supervisor refers to this as molecular chess – personally, I always found chess to be much easier.

Once a potential route to the target molecule has been identified the chemist gathers the starting materials and begins to alter and combine them. I used to describe this as being like putting LEGO pieces together, but it is often far more complicated. Sometimes, a chemical reaction will not only alter part of a molecule that you want to change, it will also alter another part. This often means the introduction of a chemical protecting group to protect the part of your molecule that you don’t want to change.

The route to the target molecule involves a sequence of reactions. Sometimes it might only require a sequence of 4 or 5 reactions. Other pathways may require 50+ reactions. And in most chemistry* the product of each reaction must be purified and confirmed as the desired intermediate compound before moving on to the next step. Purification may involve distillation, crystallisation or use of the often time consuming but effective chromatography. Confirmation of the chemical structure of the intermediate utilizes a range of analytical techniques including nuclear magnetic resonance (NMR), mass spectrometry (MS) and optical rotation, to name but a few.

When chemists put together a route to a target compound they rely on the chemical literature to determine whether each reaction will work. However, even subtle differences in the structure of ones own compounds compared to literature compounds can mean success is elusive. A chemist must always be ready with an alternative reaction, even backtracking the synthetic approach back several reactions in order to take an alternative route.

The first time a reaction is carried out seldom yields the best result. So each reaction may be carried out many times to obtain the best results. Reaction times will be altered and different temperatures used. Catalysts many be varied and the  ratios of the starting materials varied. The reaction may be carried out under high pressure or under an inert gas.  This can be one of the most tedious parts of the process (though optimising a reaction is not as frustrating as not being able to get a reaction to work at all.

The life of a synthetic organic chemist is a frustrating one. Reactions which should work, sometimes will not. Early mornings and late nights may be necessary to “babysit” the occasional slow reacting and sensitive reaction. However, is also immensely satisfying to hold in your hand a vial containing a few pure drops of a new compound that has never knowingly been created before. To know that all the blood, sweat and tears put into its creation has paid off, and maybe, just maybe, this compound will, either directly or indirectly, lead to  a better future for humankind.

*Note – while much chemistry involves purification of each new compound, recent developments have seen the use of “one pot” syntheses (where two or more reactions occur in the same reaction vessel without purification of intermediates) and continuous flow multi-step syntheses (where reaction products move from one vessel to another with purification occurring in situ), an approach likely to revolutionise synthetic chemistry over the next decade.


5 Responses to “What does a Synthetic Organic Chemist do?”

  • in paragraph 4, what does the author mean when he says “other natural resources?” Could he/she explain with examples please?

    • “other natural resources” refers to compounds which can be extracted from plant materials or even microbes.
      For example, one of previous colleagues extracted shikimic acid from star anise to use this as a starting material in a synthesis, while some modern anticancer drugs e.g. Taxol, use compounds extracted from vats of micro-organisms as starting materials.

      I hope that helps

  • I just got offered a synthetic organic chemistry research opportunity at my university, but wasn’t exactly sure what I’d be getting myself into, so I came looking for answers and you had them! Super helpful! Thanks!

  • fantastic article…could u suggest the best university in U.S.A for synthetic organic chemistry? a list showing the order of colleges would be indeed of much help

    • You can look up US News and World Report for best graduate chemistry programs, but it would be best to look up individual chemists, since you can find excellent chemists at institutions that aren’t ranked super highly overall. If you are already part of an institution, the best course of action would be to find someone in a chemistry department (probably an organic chemistry professor), tell them you’re interested in synthesis, and ask them who’s work you should read. That will give you an idea of the biggest names in the field.