What is simple? Polyethylene, molecular modeling, and molecular machines

A simple molecular chain

A 2D simplification of
its typical complex,
disordered, 3D structure

A scientist recently remarked to me that molecular modeling techniques cannot accurately predict the mechanical properties of typical polymers, even one as simple as polyethylene, a hydrocarbon consisting of long chains of –(CH₂)– units. He was, I think, suggesting that molecular modeling may tell us little about molecular technologies based on structures that would be far more complex.

It’s important to understand why this plausible line of reasoning is mistaken.

Where can molecular mechanics models give accurate predictions? One area includes precisely structured solids with stable, covalent bonding and no conformational degrees of freedom. Ideally structured, hydrogen-terminated silicon crystals provide examples, as does a large class of existing and potential polycyclic structures with modest strain and saturated bonds. The elements H, C, N, O, F, Si, P, S, and Cl provide a broad palette, and the higher adamantanes are hydrocarbons in this class.

[ Note: When operation of a device involves only low stresses and strains, the elastic responses of structures of this sort typically are nearly linear, which greatly simplifies (for example) calculations of entropic contributions to free energy.]

Where do molecular mechanics models encounter difficulties? One area includes disordered solids with extensive non-covalent interactions and conformational degrees of freedom, and polyethylene is a good example. Its deceptive simplicity stems from the simplicity of its molecules; its challenging complexity stems from the organization and interaction of those molecules.

At room temperature, polyethylene forms a disordered structure consisting of of small crystallites threaded by multiple, partly-folded chains. Under increasing tension, chains unfold and slide, distributing tension unevenly and breaking in more-or-less random patterns. The mechanical properties of the material (for example, stress-strain curves and maximum elongation to failure) depend on polymer chain lengths and processing history: both milk jugs and plastic bags are commonly made of polyethylene, but so is Dyneema, a polyethylene material in which the same repeating units — but in longer, highly oriented chains — form fibers that rival high-strength steel.

In short, polyethylene forms complex, disordered materials that are quite unlike well-ordered proteins or other components suitable for use in atomically precise systems. Noncrystalline solids that form spontaneously from simple molecules will often be more difficult to model than even quite complex molecular machinery, in part because they have no specific structure.

This example illustrates aspects of the contrasting perspectives of scientific inquiry and engineering design. I’ve recently written about the methodology of exploratory engineering as a basis for applying the predictive power of scientific knowledge to achieve a limited — yet powerful —set of insights into future technologies, and in an earlier post I described why the intricate molecular systems that can be made today are challenging to model, and why the intricate molecular systems that are easiest to model cannot (yet) be made.

I see many steps between where we are and what we can see ahead, several turns further along a winding road. I expect bionanotechnology to play a central role, and for design, biomolecular modeling is already surprisingly capable.