Structure of synthetic experiments

The aim of synthetic chemistry experiments to change the chemical structure of one compound into another. Practically, this is achieved over a number of stages and most experiments will have the following structure.

Step 1 Chemical Transformation

The first stage of any synthetic chemistry experiment is to perform the chemical transformation. 

Usually, the starting materials are mixed together with a solvent. There may also be reagents or catalysts that help to form the product. 

Reactions can be at room temperature, heated or cooled, depending on the conditions that are needed. Sometimes reactions need to be free of air and moisture if the starting materials, intermediates or reagents are sensitive to water.

The 'chemical and physical properties' section gives more information on how to select an appropriate solvent, whilst the 'setting up reactions' section explains how to know if you need to heat or cool reactions.

Step 2 Monitoring Reactions

If an experiment has been repeated many times reliably, it is possible that you don't need to monitor the reaction because you know when it will be complete. This is why many experiments in undergraduate courses tell you the time to stir a reaction for rather than ask you to monitor it. 

However, when a reaction is new or unreliable it is important to monitor how it is progressing. Is the reaction forming the desired product? Do the conditions need adapting to make it work (e.g. heat to a higher temperature)?

Thin layer chromatography (TLC) and liquid chromatography mass spectrometry (LC-MS) are by far the most common techniques that can be used to provide this information. These techniques that are covered in the 'monitoring reactions' section.

Step 3 Purification

After the reaction is finished, the product needs to be isolated from the other chemicals. Even if the reaction has converted all the starting materials into products cleanly, reagents and solvents will still need to be removed to isolate the product.

In many cases, reactions are incomplete or form by-products, so there are further complications to how to purify the reactions.

For most experiments in synthetic chemistry, there is more than one stage of a purification process and the purification of an experiment can take longer than the reaction itself. The 'purification techniques' section gives guidance to the various techniques for purifying chemical reactions.

Step 4 Analysis

At the end of the experiment there two main questions that need answering:

1. Have I made what I wanted to make, or if not, what happened in my experiment instead?

2. If I've made the correct product, how pure is it?

There are various techniques that can provide this information, however there is no single technique that gives complete structural information so usually you would perform more than one analytical technique to build the evidence of what happened in your experiment. The 'analytical techniques' section will give an overview of the main techniques used for structure and purity determination.

Example - Borohydride reduction of benzophenone

The reduction of benzophenone is a good example of a reaction in synthetic chemistry that follows the standard structure.

The first step is the chemical transformation. Sodium borohydride is needed as a reaction, and ethanol acts as both the solvent and the proton source for the alcohol. The reaction works at room temperature so it stirred without heating or cooling.

The reaction can be monitored by thin layer chromatography and shows the reaction is complete when there is a clear change in the spots showing the starting ketone has fully reacted and formed the alcohol.

The next step is purification, where the reaction mixture is poured onto aqueous acid. The acid quenches and reacts with the remaining sodium borohydride. Ethanol also dissolves in the water, whilst the product precipitates out because it's poorly soluble in water. This means the product can be isolated by filtration.

There is a second purification step by recrystallisation in 40 - 60 oC petroleum ether. This gives the product as a pure white solid.

Finally, the product can be analysed using infrared spectroscopy to show the O-H bond is present in the molecule, and melting point analysis to show how pure it is by comparing the measure melting point range to it's known value.