Bringing molecules into the third dimension

Teaching many key concepts in chemistry, such as chirality, requires the visualisation of molecular structures in 3D, something that students often struggle with. Although molecular modelling kits help, playing around with plastic sticks and joints often isn’t enough to help students ‘see’ molecules in their true form. It doesn’t help that chemical structures are normally drawn in 2D, for simplification reasons, when most molecules are in fact 3D. In the classroom, drawings using wedged and dotted bonds - that have been coined 2.5D - are often the best that can be achieved. Looking at molecular structures on a computer, however, offers students the chance to not only visualise, but also rotate, invert and perceive the symmetry of molecules.

The Cambridge Structural Database (CSD) – compiled by the Cambridge Crystallographic Data Centre (CCDC) – is the global repository for small-molecule organic and metal-organic crystal structures and holds over 700,000 real 3D crystal structures. Over 700 of these structures are freely available in the WebCSD teaching subset. 

In collaboration with Greg Ferrence from Illinois State University, US, the CCDC has developed several undergraduate teaching exercises for use with this teaching subset. Subjects covered include aromaticity, ring strain and conformation, valence shell electron pair repulsion, and hapticity. In 2011, Newcastle University and the CCDC began a new collaborative effort to develop teaching activities initially for school outreach use.