Hi Paul! I am actually performing simulations in physical chemistry/biophysics. I have studied crystallography quite a lot. In classical MD simulations we use ball and stick representation to define a certain residue where atoms are bonded, since force fields there are rather straight forward. In crystallography, you define a unit cell and some species exist in their ionic forms what probably makes ball and stick as not the best representation. I have used VESTA, Mercury and Platon. I can tell you that in my opinion the usage of some hybrid representation is more suitable. For example, there is a clear idea about atoms which have to be bonded in certain molecules and separating them might make a confusion when one wnats to find a structure solution. H-bonds are more questionable in cases when the software shows you several possible positions of hydrogen atoms. A non-experience simulation person might get confused opening such a file with a lot of hydrogens (I am saying this, because I've seen such people). Double bonds are also good to show for similar kinds of people. Many people who perform simulations based on solutions from crystallography have no background in chemistry and therefore can produce some science-fiction instead of science.

As a first approximation to chemical structure it is a usefull picture. That alone is certainly old fashioned.

However there may be not enough info in this alone:

What is the nature of the bonds, what kind of bonds do you have, are they saturated or dangling, what is their strength, what possibilities does you compound have to further bond, etc.

The program Gaussian may help to see how ingredients may bond, with quantum calculation.

In crystals say you may have say, metals or ionic compounds or silicon with diamond structure, all totally different. It determines the very nature of your solid.

Hey Paul,

I'll add my point of view as crystallographer with a chemist education and now surrounded by physicists.

- I don't want to go in historical details of the material models used traditionally and their possible influence on how sticks are perceived in crystal structures, also because I should look deeper into this historical matters before saying something. -

Personally, I believe that sticks have a powerful influence on how we perceive the structure while looking at it and I think that any scientist regardless of her/his background is very unlikely to have a purely topological perception of the meaning of sticks. On the contrary, I think they always, to some extent, associate it to some force, either lattice forces or molecular bonds or supramolecular interactions and so on. In this regard I really like Crystal Explorer's feature to calculate and display lattice forces as set of lines or sticks in their "energy frameworks" analysis.

Among chemists solid lines and dashed lines are commonly used to represent respectively chemical bond and supramolecular interactions, thus losing often the distinction between strenghts of different interactions. On the other hand, in the case of chemical bonds we make use of the approximate bond order to show different number of sticks between atoms, but in this case there is a much more precise physical meaning associated to the "bond order" concept other than simply energy value, so representing a single chemical bond both in case of an aliphatic CH and an alcoholic OH (having very different bond energies) is still legitimate.

I personally think it is reasonable (and less confusing) to use sticks to represent any stabilising interaction one is willing to highlight. However, I also think that to avoid troubles there should not be any ambiguity regarding their hierarchical order in terms of energy: first: pure covalent bonds, then: weaker ones like NH or metal-coordination bonds, and so on until you go to hydrogen bond interactions, electrostatic interactions and various lattice forces. What I mean by no "ambiguity regarding their hierarchical order" is, for instance, that showing the structure of water by subtly outlining the OH chemical bonds and drawing sticks to show supramolecular OH interactions (or using similar sticks in both cases) can be very dangerous for the energetic meaning of the resulting picture and its effect on the scientific thinking of the viewer.

Then, if the aim is not at all to provide a physically meaning description of the structure but just to simplify the understanding of its geometry, I totally support the use of sticks for pure topological purposes. However, it should be super stressed that this is for topological display only and that has no energetic meaning because I think that any scientist, in general, when looking at a stick in a structure sees something strong and physically meaningful much before seeing a simple geometrical object like mathematicians would see at first glance, I guess.

Anyway, you raised a very important issue, with an all but irrelevant impact on scientific communication and teaching! I'm very curious to follow its development... also to find out whether my impressions are correct.

Best,

Stefano