3-D molecular modelling

Background

This is one of the mandatory laboratory components listed under the Applications and skills section of Topic 10.1 Fundamentals of organic chemistry. You can, if you wish, set time aside to do this as a separate practical exercise. Personally I think it is good practice for students to always have access to a modelling kit while they are learning about organic chemistry so it should form part of their normal lessons. There are some good programmes or Apps that enable them to do this virtually but impress upon them that however realistic the virtual 3-D imagery is - and there are some very good ones - it is still in fact two dimensional as it is shown on a two dimensional flat screen. Whilst it is good to use these at times I think it is wise to also use hands-on three dimensional modelling kits such as molymod®. One of the problem areas that students find difficulty with is using VSEPR theory to predict the shape of a molecule and they need to experience the real three-dimensional shapes of tetrahedrons, trigonal bipyramids and octahedrons etc. to really appreciate them. For students who wish to learn more about why 3-D representations are important and the different ways in which they can be drawn see How to draw organic molecules in 3-D.

If you can, it is a good idea to have models of larger structures such as sodium chloride, diamond, graphite and buckminsterfullerene displayed permanently in your laboratory or classroom.

Some suggested exercises

Some particular exercises worth doing are:

1. Build models of methane, ethane and propane to see that there is completely free rotation about the C―C single bond.

2. Build models of butane and 2-methylpropane to introduce the idea of structural isomers.

3. Build models of ethanol and ethoxyethane to show the importance of functional groups. This can then be extended to C₄H₁₀O to see if they can find the four possible alcohol structures and the three possible ethers.

4. Give different students one black ball and the same four different colours together with the connectors and get them to make a tetrahedron with the colours around the central black ball. Ask them to see whether they all produce the same molecule or whether some are mirror images of the others.

5. Build models to illustrate cis-trans and E/Z structures around a C=C double bond.

6. Make models of butan-1-ol and 2-methylpropan-1-ol to show that both are primary alcohols then also make models of butan-2-ol and 2-methylpropan-2-ol to show a secondary and tertiary alcohol and then also ask them to use the models to put the four isomers in order of increasing boiling point. They should also be able to see that butan-2-ol is the only one of the four isomers with a chiral carbon atom.

7. Ask them to come up with as many different ways they can think of that are commonly used by chemists to model a simple molecule such as propan-2-ol (see below for some possibilities).

8. Finally, a nice exercise suggested by Adrian Thompson, a chemistry teacher at Ecole Active Bilingue Jeannine MIB Docs (2) Teamel in Paris. Place about six pre-assembled structures into numbered black bin liners. In small groups students in turn feel the structures (without looking) in order to come up with the condensed and full structural formulas. This helps students to mentally visualize molecules better.

Some other suggestions

It is probably best to search yourself to find apps that are compatible with the device(s) you use or are familiar with. The lists below contain suggestions but it is worth checking out these apps carefully as they can easily change or become outdated and some only work for phones or tablets and are not always both IOS and Android compatible.