Line them up: Self-assembly of molecules for making graphite or carbon fibres

How do the molecules align in carbon materials and form these coloured regions under polarised light?
Image Credit: link

tl:dr The self-assembly of disc-shaped molecules into aligned regions is important for making synthetic graphite for batteries and understanding how soot pollution forms. We showed in this paper how curving the molecules disrupts this molecular alignment a process that had been long hypothesised. Check out the preprint or the paper recently published in the journal Carbon.  

Self-assembly and liquid crystal displays

Getting molecules to line up is more important than you might think. Liquid crystal displays (LCD) work by aligning and misaligning rod-shaped molecules using an electric field to let through or block polarised light. 

Image Credit:link

Image Credit: link

The molecules in liquid crystal displays are rod-like (Calamitic) and they form ordered configurations. These are not truly crystalline with solid and liquid phases but are disordered phases and are therefore called mesophases. 

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These aligned regions can be nicely visualised through cross-polarisers and provide for some stunning images. 

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The most important liquid crystal structure for carbon materials science was discovered in India in 1977. Chandrasekhar, a world leader in liquid crystal structure based at the Raman Research Institute discovered that disc-like molecules can form liquid crystals. These discotic structures form similar configurations to the rod-shaped molecules used in LCD displays but have some unique electronic properties. But this type of alignment is critical for making carbon fibres, synthetic graphite for electrodes in electric motors and it is also important in making graphite for batteries. But to understand this a little bit of a historical digression is helpful. 

Discovery of the mesophase

Two Australian scientists Geoffrey Taylor and J.D. Brooks were exploring the geology of the Wongawilli coal seam in New South Wales in Australia in the 1960s (see below the picture of some of this coal coming out of the ground at the beach in Sydney). 

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In parts of this rock formation, ancient magma had pushed its way between the coal seam and led to some heat-treated regions of the coal (these are often called cokes). This provided a nice thermal gradient in the coal from the molten magma at thousands of degrees to low temperature as you went further away from the magma. This provided a fossilised record of the impact of heat on coals structure.

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Looking under the microscope with a polarising lens Taylor and Brooks observed spheres where the molecules were all aligned. 

Image Credit: Harry Marsh

These were called mesophase spheres and are regions where all of the graphitic molecules are aligned in stacks. This happens when the heat from the magma melts the molecules and they can start to align in a mesophase.

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In their 1965 Nature paper, Brooks and Taylor showed that by heating up specific disc-shaped (discotic) molecules extracted from coal (pitch) they could reproduce this effect in the lab. They also observed that the spheres would fuse together and form a continuously ordered phase that was only explained fully by Chandrasekhar in 1977. 

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One of my favourite pictures of this is an electron microscope image showing one half where the spheres have merged and the other where they are still separated.

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Since the 1960s, this technique has allowed for synthetic graphite to be made in large quantities for electrodes, batteries and carbon fibres. However, only very special pitches from fossil fuels will form a mesophase (so-called mesophase pitches). They are hard to make meaning synthetic graphites are still expensive. 

In particular, it is not clear why almost all carbon-rich materials, such as cellulose in wood, do not form mesophases and instead form disordered forms of carbon. So recently a new push has been made to understand this molecular alignment. In what follows some very recent work other groups have recently published on the molecules present in pitch and then some of our work using computer simulations to look at mesophase development.

Observing the molecules

So what do these mesophase pitch molecules look like? Only very recently have researchers been able to image the molecules using a technique called non-contact atomic force microscopy. This technique attaches a carbon monoxide atom to the end of a sharp needle. This is wobbled electronically using a tuning fork and the interaction of the carbon monoxide tip and the molecule allows for a picture of the bonding network in aromatic molecules to be imaged.

Image credit: IBM Research Zurich

The pitch molecules can be seen in the figure below. The molecules all have a basic aromatic domain where the carbon atoms are arranged in a hexagonal "chicken wire". There are also small chains or hydrocarbons on the edge of these molecules. The raw pictures and the drawings derived from these images are shown below.

Image Credit: Used with permission from Elsevier. Scale bar in the AFM images is 

We can use a molecular viewing software (Avogadro) to see what a molecule would look like. So for example P-15 you can see it forms a disc-like shape with some small chains attached at the edges.

Image Credit: Jacob Martin CC-ND

In order to look at how these molecules align in the mesophase, we made use of computer simulations.

Aligning mixtures of disc-like molecules

To answer the question of how these molecules align we made use to computer simulations. Previous work had approximated the molecules as small squashed spheres (ellipsoids) and only a small amount of work was done on mixtures of different sized PAH. Instead we made use of the atomic forcefield developed in our group previously by Totton and Misquitta. 

Kimberly Bowal and I made use of molecular dynamics simulations that allow for the study of these molecules as they align. However, the timescales possible to simulate with molecular dynamics simulations are usually restricted to picoseconds to nanoseconds (a billionth of a second) whereas the mesophsae alignment occurs over seconds. Therefore we can use stochastic approaches (replica exchange molecular dynamics) to speed up the dyanamics. We (Kimberly Bowal, Peter Grancic and myself) also developed a new Monte Carlo method to reproduce the result. We found columnar arrangements of the molecules were the most stable. This showed the development of a mesophase in a nanodroplet with an atomic description for the first time. More details on this can be found in a previous blog post. 

Image Credit: Kimberly Bowal

The question for this current paper was what will disrupt this ordering of these molecules in the mesophase. 

Impact of curvature on the mesophase

Curvature is found in the carbon materials formed from materials that do not form a mesophase and has long been suggested to disrupt the formation of a mesophase (I have a previous blog post on how curvature is integrated into aromatic molecules through pentagonal rings). I have also recently shown that in order to simulate these curved species correctly the flexoelectric dipole must be correctly described which Kimberly Bowal and I developed in a series of papers. 

We made use of the replica exchange molecular dynamics approach described before and were able to find the most stable configurations of clusters of mixed sized curved PAH (see below).

Comparing the flat and curved molecules it is clear that the curved species do not have a specific orientational order. This is due to the ability of curved molecules to form snaking columns of molecules that do not all align in one direction. Therefore we showed for the first time that curvature is able to disrupt the mesophase ordering. 

This might help to explain the impact of oxygen on disrupting the mesophase. Prof. Randy vander Wal and Dr Joseph Abrahamson recently demonstrated that two oxygenated precursors can either form a graphitising or non-graphitising carbon depending on whether the loss of oxygen (through carbon monoxide loss) led to the formation of a hexagonal flat PAH or a pentagonal ring that would form curved PAH. 

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There may be some hope for transforming more materials into graphite as curved PAH are known to orient themselves in electric fields as they are polar.  Adding aliphatic chains on the edge of cPAH has also allowed for aligned columnar stacking of curved PAH.

In summary, molecular simulations can demonstrate how the mesophase forms and how it can be disrupted. Further interesting directions include understanding how other structures like crosslinks could disrupt the mesophase. Alternatively, strain or external electric fields could be used to align the molecules to reduce the cost of synthetic graphite. 

Further reading

Classic text book "Liquid Crystals" by Chandrasekhar, S. from 1977 the revised version is free to read online at the archive. 

Liquid Crystals and Carbon Materials Physics Today 53, 3, 39 (2000); https://doi.org/10.1063/1.883020

Chen, Pengcheng, et al. "Petroleum pitch: Exploring a 50-year structure puzzle with real-space molecular imaging." Carbon 161 (2020): 456-465.