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Molecular Shapes

March 26, 2018

Iron atoms are chemically indistinct, but iron as we see it can be different materials. That's because these atoms can array themselves into different crystal structures with different properties. It's possible to see iron change into three allotropes just by heating at atmospheric pressure (1 bar, see figure). By convention, allotropes are designated by Greek letters, with α- (alpha-) being the form at lowest temperature, proceeding up the alphabet (β-, γ-, δ-, etc,). This has embarrassed a few scientists when an even lower temperature form of an element was discovered.

Phase diagram of pure iron

Phase diagram of pure iron.

(Modified Wikimedia Commons image by Daniele Pugliesi. Click for larger image.)

The iron phase most familiar, since it's the one we can hold in our hands, is α-iron, also called ferrite, that has the body-centered cubic crystal structure. Ferrite exists from the lowest temperatures up to 912 °C, and it's magnetic up to its Curie temperature of 771 °C. For a time, the non-magnetic (actually, paramagnetic) form of α-iron, existing in α-iron above 771 °C, was called β-iron, but metallurgists are more concerned with structure than magnetism, so the term, "β-iron," is now obsolete.

Marching up the Greek alphabet to γ gets us to γ-iron, also called Austenite, named after British metallurgist, William Chandler Roberts-Austen (1843-1902), that exists from 910-1394 °C. γ-iron has the face-centered cubic crystal structure. Above 1394 °C, there's δ-iron with the body-centered cubic crystal structure. At normal pressure, the δ-iron melts at 1538 °C.

If we're willing to subject iron to very high pressure, on the order of 100,000 bar, it's possible to form ε-iron, also called hexaferrum. ε-iron has the hexagonal close-pack crystal structure, consistent with the concept of pressing the iron into a dense state (see table).

Crystal Structure Packing Fraction
Hexagonal close-packed 0.74
Face-centered cubic 0.74
Body-centered cubic 0.68
Simple cubic 0.52
Diamond cubic 0.34

While ε-iron is not technologically useful, it might be an important phase in geology. The pressure at Earth's core is estimated to be about 1,500,000-3,000,000 bar, well above the pressure at which ε-iron exists at rroom temperature. ε-iron might even exist at the much higher temperature of Earth's core, about 3000 °C, at those pressures. Proving this experimentally, however, might be as difficult as a journey to Earth's core. The triple point between the α-, γ- and ε- phases of iron has been calculated to be at a temperature of 770 K (497 °C) and a pressure of 11 GPa.

Crystalline materials are not the only materials used to construct our modern culture. Polymers, formed from organic molecules are ubiquitous materials; and, while some of these can be up to 80% crystalline, non-crystalline polymers, such as the synthetic fiber, nylon, have desirable mechanical properties. Polymers are formed from smaller organic molecules called monomers that link together into long, linear chains through carbon-carbon bonding.

The atoms of organic molecules, such as the monomers from which polymers are made, can arrange themselves differently in space, just like the iron atoms in crystalline iron. There can be several forms of molecular configuration, called enantiomers, that are mirror images of each other and are characterized by how they rotate the plane of polarization of transmitted light. Rotation clockwise in the propagation direction marks the molecule as dextro-rotary (d-), and levo-rotary (l-) if it's counter-clockwise.

The d- and l- nomenclature comes from the Latin words for right, dexter, and left, laevus. Such molecules might have in addition to the d- and l- forms a configuration in which there is no optical activity, called meso-rotary. Quite importantly, just one enantiomorph of some pharmaceuticals is useful, the other being non-active, and sometimes toxic.

Three stereochemical configurations of tartaric acid

Three stereochemical configuration of tartaric acid. (Drawn using Inkscape.)

Organic molecules don't exist just as linear chains of carbon atoms with other elements attached, but also as rings. We have the examples of benzene, C6H6, and its close cousin, Pyridine, C5H5N. Such an unexpected ring structure for molecules was first published in 1865 by German chemist, Friedrich August Kekulé (1829-1896), as the structure for benzene.

Benzene structure with Ouroboros

The structure of benzene, C6H6.

By Kekulé's own account, this idea came to him in a daydream of the ouroboros, the image of a snake biting its own tail.

(Ouroboros image and the benzene structural diagram, via Wikimedia Commons)

A team of physicists from the University of Vienna (Vienna, Austria) and the Johannes Gutenberg University Mainz (Mainz, Germany) have researched a method to separate chemically identical linear macromolecules from ring macromolecules.[1-2] They used computer dynamics simulations that incorporate hydrodynamic effects to design microfluidic channels to do this separation of polymers in dilute solutions.[1-2] At this time, the technique still requires experimental verification.

Since some of their properties are so different, separation of chemically identical linear macromolecules from ring macromolecules could be important in some applications. Circular molecules lack ends, so they are more resistant to degradation, and also less likely to become entangled. Such properties of ring molecules are important in Nature since they enhance the resilience of DNA and RNA against degradation.[2]

The approach to separation taken by the research team is based on the idea that linear and ring molecules, and mixtures thereof, can flow differently under the proper conditions.[2] There is essentially no difference in flow rate when these molecules flow in channels with smooth and repulsive walls.[1] If the channel walls are studded with attractive spots arranged on lines parallel to the flow, ring polymers have an order of magnitude higher velocity than linear chains.[1] This effect is more pronounced when the polymer molecules are more rigid.[1] The linear chains are immobilized on these spots, but the ring molecules can roll along them (see figure).[2] The project was funded by the European Union's Horizon 2020 research and innovation program.[2]

Polymer linear chain and ring flowing in a microchannel

Polymer linear chain (top) and ring (bottom) flowing in a microchannel studded with attractive points (green dots). Also shown is the flow profile and the rolling motion of a polymer ring. (Top image and bottom image, copyright Lisa Weiss, University of Vienna.)


  1. Lisa B. Weiss, Arash Nikoubashman, and Christos N. Likos, "Topology-Sensitive Microfluidic Filter for Polymers of Varying Stiffness," ACS Macro Lett., vol. 6 (December 5, 2017), pp 1426-1431, DOI: 10.1021/acsmacrolett.7b00768.
  2. Nanomaterials: How to separate linear and ring-shaped molecules, University of Vienna Press Release, December 6, 2017.

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