Creating good molecular diagrams

Humans tend to make a snap judgement on something or someone based on his/her/its appearance. This is true even in science! The main aim of creating a good paper or poster is to encourage people to read about your research.

So what is a 'good' molecular diagram? First you have to decide what it is you want to show, and how you want to show it. When making pictures from crystal structure data you usually wish to display a molecular plot (showing connectivity and molecular geometry), or a packing plot showing inter-molecular interactions and features of the global crystal structure.

There are a few different drawing styles used: ball-and-stick plots, displacement ellipsoid plots, stick/line diagrams and spacefill plots.

Ball-and-stick diagrams

These are the most common way to display molecular structure whether data are gleaned from crystallographic studies or by molecular modelling. Spheres of arbitrary radii are used to represent the atoms whilst the stick lengths generally correspond to the bond length. They are 3D pictures meaning molecules with unusual geometry can usually be shown quite easily. The atomic colour scheme has become pretty standard (grey for carbon, blue for nitrogen, red for oxygen etc...).


Displacement ellipsoid plots

Displacement ellipsoid plots

These are similar to ball-and-stick plots except that here the shape and size of each atom is represented by an ellipsoid of a given probability of location of electron density. Ellipsoid plots are far more revealing than ball-and-stick plots since they can highlight crystallographic problems. In this example the ellipsoids of the butyl carbon atoms are very large, indicating possible disorder.  This is not evident in the above ball-and-stick diagram.  Publishing in crystallographic journals requires an ellipsoid plot, and you should use them in regular chemical journals (where the rules are not so strict on crystallography) too. A good ellipsoid plot shows you have completed the structure correctly, so why not show it off a bit?!


Stick diagrams

Stick diagram

Stick diagrams are most commonly used in packing diagrams to show features of the global crystal structure, rather than of the individual molecules.  The diagram to the right is a full packing diagram, but partial packing diagrams showing intermolecular interactions (hydrogen-bonding, aromatic stacking...) are just as effective in stick representation.  The program Mercury is very good at drawing such pictures.


Spacefill plots

Spacefill plot Space filling diagrams represent each atom by its van der Waals radius. Such diagrams are useful for demonstrating the presence or absence of channels within a crystal structure (important if you're trying to design porous framework materials, for example). They can also be used to show voids created by removal of disordered solvent by the SQUEEZE routine of PLATON. In this case, the small distance between the molecules shows that there are no voids, and the crystal packing is very efficient.


Most journals require a labelled ellipsoid plot. The requirements as to the labelling style vary. Some require brackets, some without, and you need to check. The label position is another important point since they can obscure atoms. NEVER allow labels to touch atoms or bonds, don't put labels inside rings if you can help it (it looks messy) and only label essential atoms. Labelling a phenyl ring is probably not worth the effort. Also don't label hydrogen atoms unless you are specifically discussing them.