On Christmas morning, millions around the world looked in their stockings & hoped not to see coal. – yet they’d probably love to see the same element, carbon in a different arrangement – because diamonds and coal are the made up of the same thing! And we know a lot about coal in part thanks to Rosalind Franklin – yes, *that* Rosalind Franklin – the scientist who, along with her student Raymond Gosling, is responsible for that blurry X “picture” of DNA called “Photo 51” which proved key to figuring the double-helical structure of DNA! Turns out that DNA stuff was only a brief stint in an incredibly productive, though tragically short, career. Before it, she performed research on coal and carbon that made possible carbon fiber technologies (and after it, she made key insights into the structure of viruses). So, today, hop aboard the carbon allotrope Express to learn about different forms of carbon and Franklin’s contributions to carbon research.

refreshed & video added 12/26/21

TLDR: The same pure element can hook together into different 3D solid forms, called allotropes – coal, graphite, and diamond, for example are all made up of “all” carbon, so they’re called carbon allotropes. Graphite & diamond are both crystalline forms of coal but they have different arrangements of their carbon atoms – in graphite, carbon is organized into sheets, and in diamond it’s really locked in through connections to other carbons in all directions. In coal, however, the carbons don’t have a strict orderly structure (it’s “amorphous”) – at least at the overarching structural level. But that doesn’t mean that it can’t have “microstructures” and Franklin found that different types of coal have different microstructures that influence how those coals react, what they can absorb, etc. 

We’ve talked a lot about hydrocarbons – carbon hooked up to hydrogens – and how they make great skeletons for “organic” biochemical molecules like proteins & DNA, which are based on hydrocarbons with some other elements, like oxygen and nitrogen, sprinkled in as parts of “functional groups” in place of hydrogen. But turns out carbon can be pretty cool all by itself. 

The basic unit of all these elements is an atom. And in a solid, atoms are stuck in place & only have enough energy to vibrate. In a crystalline solid, the place they’re stuck in follows a repeating floor plan (think of a brick wall or a tiled floor in 3D). The same element can have multiple such floor plans leading to crystals w/different properties –  we call these different arrangements allotropes & carbon (C) has multiple. 3 of the main carbon crystal allotropes are diamond, graphite, & fullerenes

Note that I did *not* say coal. Coal *is* a solid form of carbon, but it is not crystalline. Instead it’s an amorphous solid (no defined shape) – instead of following a floor plan, the C atoms in coal stick together more “willy-nilly.” 

side note: protein crystallographers know all too well the difference between a crystal and an amorphous clump of protein gunk! The technique of x-ray crystallography for determining protein structure relies on protein molecules organizing in a perfectly-repeating pattern, so that, when we beam x-rays at them, those rays get deflected by the atoms of each copy the same way & their signals add up – so we can capture the reflected rays on a detector as a “diffraction pattern” and work backwards to figure out the protein structure. much more here: http://bit.ly/xraycrystallography2 

If the protein molecules aren’t orderly arranged, their signals will scramble each other, and make the data uninterpretable. Therefore, we spend a lot of time trying to find the right conditions for crystallization – testing out a bunch of different “cocktails” of different salts, etc. – and looking at well after well under a microscope to look for the crisp edges of crystals but mostly seeing gunky stuff…

But anyways, back to coal…Its “random” carbon packing makes it easy to incorporate impurities because the carbons don’t have to fit into a carefully “calculated” repeating structure. So coal is usually not *pure* carbon – instead it often also contains hydrogen, oxygen, nitrogen, & sulfur (Sulfur has a rotten-egg smell so maybe if someone’s been really naughty Santa leaves them high-sulfur coal…)

Those other elements have lots of opportunities to sneak in because coal is formed over long periods of time when dead things (which contain those other elements in addition to carbon) decay & new things pile on top of them & start squeezing out moisture. But as the decaying material (peat) gets subjected to higher and higher pressure & temperatures it’s not just moisture getting squeezed out – some impurities do too, so more pressure, less moisture & fewer impurities. And coal can be classified accordingly.

  • anthracite (hard coal) is the “five star” coal variety. It’s formed under very high pressure & is 86%-98% C (by weight)
  • bituminous coal (soft coal), the most common form, is formed under lower pressures, so it’s only 69%-86% C
  • sub-bituminous coal & lignite have even less C, though definition-wise, a rock must be combustible & have at least 50% C to be called coal

As we talked about with candles, http://bit.ly/candlechemistry , combustion involves breaking things down by reacting them with oxygen. When you break down carbon this way, you don’t just create heat and light – you also produce carbon dioxide. This carbon dioxide is a big problem because it traps heat, contributing to global warming. And there are other additional problems to burning coal – when you burn it you release those impurities, which contribute can react with oxygen to form pollutants like sulfur oxide (which can cause acid rain) & nitrogen oxides which contribute to smog & react with other pollutants to make worse pollutants like ozone. And some of the not-totally-combusted coal escapes as soot.

Enough with the naughty “presents” for now (don’t worry we’ll come back to them to discuss Franklin’s contributions) – let’s talk carbon’s crystalline forms!

Going back to the atoms – atoms are made up of a central nucleus containing positive protons & neutral neutrons surrounded by a “cloud” of negative electrons (e⁻) & atoms interact with one another through their outer (valence) e⁻ which they can share to form strong covalent bonds. You need 2 electrons to make a single bond (usually one shared by each binding partner), and 4 for a double. C has 4 valence e⁻, so it can covalently bond to up to 4 other C’s

Diamond: In diamond, each C is covalently bonded to this max (4 other C) to form a tetrahedron & the tetrahedrons join together to form a 3D network

  • diamond’s very strong, unlike my delicate protein crystals. My protein crystals are fragile because their protein molecule “building blocks” only connect to one another through weak intERmolecular forces that involve partial charge based attractions, as opposed to actual electron sharing. But diamond is strong because the repeating units of a diamond (single C atom atoms) connect to one another through strong covalent bonds (remember these are the kind of bonds that involve electron sharing, like those that hold the atoms of each individual protein together). Therefore, diamond’s like 1 huge molecule but it’s not a true molecule because it doesn’t have a set # of atoms.
  • In order for a material to conduct electricity, e- must be able to move freely through it. In diamond, all the e- are tightly held, so diamond does NOT conduct electricity

Both diamonds and coal are made from carbon, but they’re *not* made from each other – diamonds formed much deeper in the mantle part of Earth’s crust where pressures & temps are way higher. They formed hundreds of millions to billions of years ago and only made it to mineable depths thanks to really deep volcanic eruptions. Those eruptions were super powerful- they blasted the pre-made diamonds through Earth’s crust so fast that they didn’t have time to incorporate impurities along the way and, even though there are more potential impurities in this higher up stuff, the diamonds are so tightly made that they’re not gonna let anything else in between their carbons. As a result you end up with pristine diamonds sitting there for millions to billions of years.

Graphite: Graphite is made up of stacks of GRAPHENE -> 1-layer sheets of covalently-bonded C

  • unlike in diamond, in graphene, each C is only covalently bonded to 3 other C, in a flat honeycomb crystal lattice layout. Since it’s only using 3 valence e- for this “next-door-neighbor” bonding, the 4th gets “delocalized” (no longer owned by it’s original owner). Instead, it goes into a “shared” pool where it can move freely among the sheet, so electricity can move through the planes of layers (but NOT between layers)
  • atoms within a graphene sheet are actually held together tighter than atoms in a diamond, BUT diamond’s bonds extend in 3D whereas graphene’s strong bonds are only 2D – they’re restricted to 1 sheet. So why don’t the layers just fall apart? The same reason geckos can walk on walls –  van der Waals forces! Basically, even “owned” e- are constantly moving around randomly (though their turf’s restricted) – sometimes they’ll randomly clump more to one side, leading to partial charges that can lead to temporary charge-charge interactions w/other atoms in other sheets. And you have lots of surface area to have these interactions, so it’s kinda like how if you alternate the pages of 2 phone books, the friction between the pages can make for a super super strong joining. Those chance attractions make it so that the layers don’t just fall apart but, since the individual interactions are weak, if you apply some force,  the layers can glide over each other –  & off onto your paper from your pencil! 

Fullerenes: Fullerenes are a family of carbon-only structures with the shape of hollow spheres, ellipsoids, or tubes whose walls are made up of 5, 6, or 7-C rings. They have a wide range of sizes that depends upon the # of C atoms

  • Buckminsterfullerine (C60)(buckyballs) & relatives are closed, highly symmetrical spheres that look like soccer balls 
  • CarboN NanoTubes (CNTS) (aka buckytubes) are like graphene rolled up into a tube and capped w/half a buckyball. Their diameter is ~50,000X smaller than human hair, but can be “really long” – long as in cm range (this may seem short but considering the dimeter…). They’re strong & efficient heat conductors, making them “all the buzz” in nano materials
  • carbon nanobuds are buckyball-like “buds” covalently attached to outer side walls of carbon nanotube (like a warty tube)

So how does Rosalind Franklin play into all this? More on Rosalind here: http://bit.ly/rosalindfranklincoal and Photo 51 here: http://bit.ly/fiberdiffractiondna but today I’m just going to highlight her coal work, which was largely carried out in the 1940s when she served as an assistant research officer or the British Coal Utilization Research Association (CURA). She worked there until 1947, studying the physical structure of coal – and publishing numerous papers on the topic that are still widely-cited. Among other things, she found out that different forms of carbon can form different “meshes” at the molecular level that can filter out and trap various other molecules. By determining that different types of coal have different microstructures – and that their porosity is temperature-dependent – she was able to classify different types of coal and predict their usefulness for different tasks. Her work also helped make possible carbon fiber technology and earned her a PhD in physical chemistry from Cambridge in 1945.

Analogously to how inorganic rocks are said to contain “minerals,” coals are said to contain “macerals” which are the carbon-containing parts. These macerals can be further grouped and then ranked by by degree of “coalification” – the more carbon, the higher the “rank” and the more heat it can provide – from the low-carbon lignite (aka brown coal) to subbituminnous coal, bituminous coal, and then the “five-star coal” called anthracite. 

People were (and still are) interested in being able to take lower-quality carbon products and make them “better” – through things like “carbonification” where they heat coal up to make it purer. But what was different at the atomic level? To get at this, Franklin started with some simple yet beautiful experiments…

When we looked at concentrations the other day, that was measuring how much of one thing there is compared to all the things, or all the space. So, for example, a frequent way to report concentration is molarity (M), which tells you the number of copies of something (such as sugar molecules) there is in 1 L. Since the things we’re looking at are really small, there are usually huge numbers of them in a liter, so instead of dealing with 20+ digit numbers, molarity counts in terms of moles – like a dozen except that instead of 12, a mole means 6.02×10^10²³ – of anything. So a 1M glucose solution would mean 6.02×10^10²³ glucose molecules per liter of whatever it’s dissolved in (usually water). 6.02×10^10²³ is called Avogadro’s number, and it’s often a bit too big for what we need, so we can talk of millimolar (mM) (thousandth of 1M), micromolar (μM) for millionth, etc. http://bit.ly/dimensionalanalysising 

But another way to talk about how stuffed something is is density. Unlike concentration, which just looked at amount of things, density takes into account how heavy those things are. At the definition level, density is mass/volume. We often use the terms “mass” and “weight” interchangeably, but weight takes into account gravity – gravity kinda pushes down on things, making them seem heavier the stronger the gravitational force – so when you’re on the moon, where gravity’s way weaker you’ll weigh less (~16.5% what you weigh on Earth) – but you’ll have the same mass because mass doesn’t depend on gravity – instead it just depends on how “massive” the things in it are.

And by “massive” I mean how much physical stuff there is in it – and the physical stuff of matter is atoms – some atoms are heavier than other atoms – it has to do with how many protons & neutrons they have. The more of these subatomic particles they have, the more massive the atom, but not necessarily the more space they take up. This is because how much space something takes up, while at some level is limited by how much stuff is in each molecule, is also limited by how that stuff is spread out – both within individual molecules and between groups of molecules. 

As a result, if you take the same number of copies of the same atom, you can arrange them so that they take up more or less space (occupy different volumes) and thus have different densities. The closer together you pack them, the higher the density, and vice versa. So, even if she couldn’t (yet) “see” how the carbon molecules were arranged in coal, Franklin could learn a lot about their packing just by measuring their densities.

You can easily measure weight on a scale, but if we want to calculate density we also need to know the volume. Say you have a rectangular brick of coal. To find the volume of a brick it’s just length times width times depth, right? Well, if you do that you get the volume of the thing as if it were completely full –  it ignores any holes inside. So for example, that brick could be hollow or full and this “lump volume” would still be the same. 

There’s no easy tape measure way to get the volume of something that’s lumpy, so instead, something called the Archimedes’ liquid displacement method is used – drop something in a liquid and see how much the liquid level rises. So, for example, if you had 50mL of water in a beaker and you plopped in a rock and the water level rose to 55mL, you can say the volume of the rock is 5mL. 

This works if the liquid molecules don’t interact with the object. But things get complicated if the molecule you’re displacing (e.g. water) is actually messing with and/or getting into the thing you’re trying to measure. 

The “apparent density” you measure can get skewed from the “lump density” in a couple of ways – I say “skewed” but it’s actually giving you the “true density” that takes into account gaps inside the object.

  1. the thing can chemically interact with the material, potentially even breaking it down (ok, this one does actually mess things up, but number 2’s good!)
  2. the thing can sneak into pores in the material 

Franklin used this second “problem” as an asset – because the thing can only sneak in if the holes are big enough, she could use different size liquid molecules as “probes” to see how big the holes were in different coals.

Even a fine mesh can’t keep out really really small stuff – so she used Helium (He), the second smallest atom (hydrogen’s smaller, but it’s also more reactive) to get at the “true” density which which to compare to when she repeated the measurement with increasingly larger probes: methanol, water, hexane, & benzene. If the probing liquid molecules were small enough, they’d sneak in and the true volume and density as determined using helium would be the same as the apparent densities they measured. But if the probes couldn’t get in, the volume would appear higher and thus the apparent density would appear lower. And this would imply that the pores (or at least their openings) were too small to allow them in. And since the size of those probing molecules were known, she could estimate the size of the pores

So, what happened? When she used methanol, she found that the apparent densities were higher than the true density – she had run into that issue #1 – the methanol was reacting chemically with the coal, making it seem more dense. not cool… But the other molecules didn’t react with the coal so they were usable. But could they get in? Sometimes…

She found that the “low-quality” coal – which had low amounts of carbon (lots of other elements in there) – had big pores that had no problem taking in the big probes like hexane & benzene. But the top-of-the-line coal (which had lots of carbon) didn’t just have lots of carbon atoms, it had those carbon atoms arranged into a finer mesh that kept out even small stuff. https://profiles.nlm.nih.gov/101584586X78

This ability to selectively let in certain molecules but not others is often called “molecular sieving” – it’s frequently used in carbon-based filters that do things like separate nitrogen from oxygen in the air. And it’s one of the reasons Britain’s government was interested in coal research – such sieving could be used in gas masks to protect soldiers in the war (they knew carbon could do it, but they didn’t know *why*/how – and Franklin provided the answers)

That was with “untreated coal” – but what about heat-treated coal? When she heated the coals, it became more porous, but some of the pores became closed off so that even helium couldn’t get in. And this led to the lower reactivity of such “carbonized” coals that people were wondering about.

She also found that certain types of carbon which she named “graphitizing carbon” would change its structure so that the carbons arranged themselves into orderly sheets. While graphitization can be good if you want synthetic graphite, it can also be bad if you don’t want it.  Graphitization can be a problem for certain metal alloys (mixtures of elements) that contain carbon – like steel, which has iron and carbon. If you heat it and the carbons come out of that nice amorphous (shapeless) mixture into crystalline sheets that don’t let iron in, the steel can crack. So it was important to figure out what was happening and how you could know what types of coal make good starting material for different tasks

To characterize what was going on, she turned to X-ray diffraction. Photo 51 is often mislabeled as a crystal diffraction image, but it’s actually a fiber diffraction image – X-rays were beamed at DNA fibers instead of DNA crystals. Franklin used a 3rd type of x-ray diffraction here, powder diffraction – it uses tiny crystals that have all different orientations, so the resultant pattern is a series of rings, with distances between the rings providing information about the spacing between planes in the crystals. And if you rotate the sample you can get diffraction from different angles – so it’s commonly reported by a plot of intensity of x-rays scattered at different angles

When she upped the temperature, the interplanar spaces fell, which she interpreted as a change from planes randomly rotated (disordered layers) to planes adopting a more orderly layering. I think of it kinda like how in “simulated annealing” in computer modeling you allow for more freedom to explore options so you don’t get trapped in local minima – if molecules don’t have enough energy to explore, the can get stuck without finding the best (lowest-energy-requiring) orientation – but if you let them explore more they can reach that happy place.

And graphite is the most thermodynamically stable form of solid carbon (its happy place) – so you’d think all carbon would want to get there – and would get there if you gave them enough exploration energy (high temp heat treatment). Franklin found if you did this with cokes (products of coal processing), that’s indeed what happened. But with chars (which typically come from things like wood I think), you only got a porous, isotropic material with little graphite-like regions, but not that overall layering throughout – this was the first time this key distinction between cokes & chars was shown.

Franklin thought this difference was because, in all coals there were little graphite-like minisheets – and in graphitizing carbons, these minisheets were already nearly parallel, but in non-graphitizing carbons, there were already different interatomic interactions that were harder to break up and get to reorganize. It’s still not clear exactly what’s going on, but it might involve big ball-like things called fullerenes. https://profiles.nlm.nih.gov/101584586X81

You can learn more about Franklin’s cool coal work in this article: http://www.personal.rdg.ac.uk/~scsharip/REF_paper.pdf

and here are her key papers:

Franklin, Rosalind. “A Study of the Fine Structure of Carbonaceous Solids by Measurements of True and Apparent Densities: Part I. Coals.” Transactions of the Faraday Society 45, (1949): 274-286 https://profiles.nlm.nih.gov/101584586X78 

Franklin, Rosalind. “A Study of the Fine Structure of Carbonaceous Solids by Measurements of True and Apparent Densities: Part II. — Carbonized Coals.” Transactions of the Faraday Society 45, (1949): 668-682. https://profiles.nlm.nih.gov/101584586X79 

Franklin, Rosalind. “Crystallite Growth in Graphitizing and Non-Graphitizing Carbons.” Proceedings of the Royal Society of London 209, (1951): 196-218 https://profiles.nlm.nih.gov/101584586X81 

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0

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