Welcome to The Plague Pit.

For this issue – number 20 – I’m very grateful to Adrian Tsui. Adrian is a sixth former at Winchester College, studying Physics, Chemistry and Biology. He has a place at Downing College, Cambridge to read Natural Sciences, starting in 2020. He’s also a dedicated musician.

Adrian has written a pair of articles on chemistry in the pandemic. Here’s the first:

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In a world changed by COVID-19, we find ourselves constantly searching for ways to defend ourselves from our common invisible enemy. You might be washing your hands more often, or cleaning and disinfecting the house more than usual.

These actions have one thing in common. They require the use of antiseptics or disinfectants – products that we have often overlooked in the past.  But how these products work? And how are they made? In this article – and one that follows it – I’ll try explain a little bit of what’s going on here.

I’ve assumed a basic level of scientific knowledge. However, you may come across some scientific topics that you may not be familiar with. If so – DON’T PANIC. This is not a textbook. You can find definitions to the scientific terms in the Glossary at the end of this post

Please do not try or attempt any of this at home or without supervision. If done incorrectly, it can be very dangerous and even fatal in certain instances.

100 words on history

One of the main reasons why we are unlikely to see another Black Death is the substantial improvement in hygiene (and general cleanliness). The massive breakthrough was with Sir Joseph Lister (Fig. 1, below) who pioneered aseptic surgery using carbolic acid (phenol), one of the first antiseptics. (An antiseptic is a type of disinfectant which can be applied to the body.) Officials were experimenting with carbolic acid to reduce the smell of sewage, so Lister tried applying dressings soaked in carbolic acid to his patients’ wounds.

Out of a total of 11 patients treated with this method, only one had died because of unrelated complications. Carbolic acid is no longer used as an antiseptic because it is harmful to cells, but still finds its use in cleaning surfaces and equipment.

Soap: The most underrated weapon of all?

Many people would rather hoard toilet paper than bars of soap. On the contrary, soap is possibly the most underrated of weapons in our chemical warfare arsenal; when used properly, it has been shown to be even more effective than alcohol-based disinfectants.

(i)          C₃H₅(C₁₇H₃₅COO)₃ + 3 NaOH → C₃H₅(OH)₃ + 3 C₁₇H₃₅COO^– Na⁺

              glyceryl tristearate + sodium hydroxide → glycerol + sodium stearate

A fat molecule (Fig. 2b) can be thought of as three fatty acids stuck to a glycerol ‘backbone’.

You can make your own soap easily by heating fats, such as tallow or vegetable oils, with a small amount of lye (sodium hydroxide to the chemists). This reaction (i), known as base hydrolysis, yields glycerol, a good skin conditioner, and the soap (the metal salt of the fatty acid; sodium stearate in this case).

The practice of soap-making has essentially remained unchanged across all cultures throughout history, and with it the root of the word ‘soap’ in Indo-European languages. The Celts, whose saipo was made from animal fats and vegetable ashes, claim to have introduced soap to the Romans, which they call sapo.

This name allegedly comes from Mount Sapo, a site of animal sacrifice; rainwater washed the animal fats with wood ash into the Tiber, where the soapy water was found to be useful in washing clothes. In reality, we now believe that soap-making dates back to the Babylonians in 2800 BC, who boiled fats with processed ashes to make a soap for cleaning wool and cotton.

The role of the processed ashes is exactly that of the lye mentioned earlier. Wood ash is the unburnt residue after the combustion of wood, which mainly consists of basic salts like potash, a mixture of potassium salts.

Unlike the other residue components (like chalk, CaCO₃), potash is soluble in water. To separate out potash, the wood ash is first mixed with water, so the soluble potash dissolves. This solution is then decanted out^†, and the insoluble residue discarded. Further processing yields potash lye^†† (potassium hydroxide, KOH), whose function is exactly that of the sodium hydroxide in (i).

The reason why soap washes grease away easily is because they are amphipathic: the soap molecule has a hydrophilic (water-loving) head and a hydrophobic (water-hating) tail. The tails surround the similarly hydrophobic grease, while the heads point outwards into the water (Fig. 3b, below). The grease breaks down into smaller units, and is washed away, surrounded by soap molecules.

Viruses are basically self-assembled nanoparticles wrapped in a fatty membrane. Soap dissolves this packaging, exposing the viral proteins and genetic material. The amphipathic nature of soap also disrupts the interactions holding the viral proteins together, effectively destroying the virus.

Ethanol and isopropyl alcohol: The most convenient weapons

Only a small amount of soap is needed to cover the entire hand, which makes it one of the most efficient destroyers against viruses. Then what is the craze behind all the gels, wipes and foams which have been cleared off the shelves in a panicked frenzy?

These two commonly used alcohols, ethanol and propan-2-ol – also called isopropyl alcohol or rubbing alcohol – find themselves in a great proportion of disinfectant products (Fig. 4, above). I will be mainly writing about ethanol, since it has played a much larger part in the development of human civilisations since antiquity (and I am not only referring to the recreational aspect). The properties of isopropyl alcohol are similar to those of ethanol, so repeating myself is not absolutely necessary here.

Ethanol was historically produced by fermentation – the essential process in making alcoholic beverages and bread to this day. According to the ‘drunken monkey’ hypothesis, proposed by physiologist Robert Dudley, one of our primate ancestors developed a taste for overripe fruits which had fermented. Ethanol contains nearly twice as much energy as carbohydrates of the same mass, so overripe fruit would have provided our primate ancestors with valuable additional nutrients.

A mutation then occurred in our ancestors on the ADH4 gene (which codes for an alcohol-metabolising enzyme) which allowed us to metabolise ethanol up to 40 times faster. This presented a huge advantage, as our ancestors with this gene could now ingest more alcohol without experiencing the ill effects. There is also strong evidence that our love for alcohol drove the Agricultural Revolution (‘history’s biggest fraud, according to Yuval Noah Harari’s Sapiens), by encouraging hunter-gatherers to settle down and congregate around religious sites.

Excavations at Göbekli Tepe, one of the world’s oldest known temples, reveal six barrel-shaped stone vessels, and in them a residue containing oxalate, a chemical left behind when water and grain mix. All around the site are animal bones, which indicate a site of extravagant feasting; the crude broth brewed there may have been intended as a reward, similar to how we buy people who help us a pizza and a few beers.

In a sealed bottle containing apples and yeast, the yeast converts the sugars in the apples to ethanol and carbon dioxide. It obtains energy from this process (ii), while we get our cider.

(ii)         C₆H₁₂O₆ → 2 C₂H₅OH + 2 CO₂

              glucose → ethanol + carbon dioxide

Fermentation is an example of anaerobic respiration, the process by which some organisms generate energy without oxygen. (In animals, anaerobic respiration produces lactic acid instead of ethanol.) It is important that we keep our bottle airtight, as the presence of oxygen would allow the yeast to oxidise the sugars completely to carbon dioxide, in the familiar process of aerobic respiration. (iii) is the extremely simplified overall equation; aerobic respiration is really a rather complex chain of events. However, do notice the presence of oxygen, which (ii) does not require.

(iii)       C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O

              glucose + oxygen → carbon dioxide + water

Ethanol and isopropyl alcohol are now industrially produced by the hydration of ethene (iv) and propene (v).Ethene and propene are produced from the cracking of long-chain hydrocarbons, for example from crude oil. Crude oil is a mixture of long-chain hydrocarbons; (vi) gives an example with decane, a 10-carbon hydrocarbon.

(iv)        C₂H₄ + H₂O → C₂H₅OH

              ethene + steam → ethanol

(v)         C₃H₆ + H₂O → CH₃CH(OH)CH₃*

              propene + steam → propan-2-ol (isopropyl alcohol)

(vi)        C₁₀H₂₂ → C₂H₄ + C₈H₁₈

              decane → ethene + octane

In our sealed bottle, however, the production of ethanol must eventually come to an end. Ethanol is toxic at high concentrations, so the yeast is killed by the steady accumulation of its own metabolic product. Ethanol is still much tamer than its alcohol cousin, methanol (CH₃OH), which attacks the optic nerve and causes blindness.

Methanol is also metabolised to the toxic methanoic acid (also called formic acid; found in some ant stings), whereas ethanol to the much friendlier ethanoic acid (also called acetic acid; main component in vinegar). The toxicity of methanol finds its use in making denatured alcohol, where chemicals are mixed with ethanol to make it undrinkable. This is helpful if the alcohol is not intended for human consumption, as drinkable alcohol is taxed very heavily. To further discourage people from drinking it, foul chemicals like pyridine (smells disgustingly fishy) are sometimes added.

Ethanol and isopropyl alcohol are amphipathic (remember soap?). This allows them to weaken the fatty membranes of bacteria and viruses, and interfere with the delicate interactions which give proteins their structure. This causes proteins to coagulate (clump together), rendering them useless.

However, the observant people among you may have noticed that your alcohol handrubs never contain more than 80% alcohol. If the alcohol solution is too concentrated, coagulation happens too quickly, forming a shell of coagulated protein around the rest of the microbe. This stops the alcohol from penetrating fully, and so the microbe is merely inactivated and not dead.

Bacteria are pretty tough organisms, and will revive themselves in more favourable conditions. (Viruses are not considered to be living organisms, but similar things can be said.) This is why WHO recommends formulations of 75% isopropyl alcohol or 80% ethanol for handrubs, which are concentrated enough to destroy microbes, but not protect them from further harm.

In my second article for The Plague Pit – coming in the next week or two – I’ll be writing about bleach, the heavy artillery of disinfectants….

Adrian Tsui

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^† Etymologists believe that the ultimate root of the word ‘soap’ in all Indo-European languages is the Proto-Indo-European *seib- ‘to pour out, drip, trickle’. (The asterisk indicates a reconstruction.)

†† The word for potassium, the extremely reactive metal, comes from potash; potassium metal was first produced from the electrolysis of potash lye by Sir Humphry Davy in 1807.

*For the aspiring chemists: the hydration of propene yields both propan-1-ol and propan-2-ol. Look up Markovnikov’s rule on the Internet to find out why much more propan-2-ol is produced (i.e. the major product).

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Glossary

A-D

Acid: a proton donor. Solutions of acids typically have pH <7. A weak acid does not dissociate completely, but a strong acid does. Also see base, dissociation, proton and hydrolysis.

Amphipathic: describes a molecule which has both hydrophilic and hydrophobic regions.

Base: a proton acceptor. Solutions of bases, called alkalis, typically have pH >7. Also see acid, proton, and hydrolysis.

Carbohydrate: a molecule containing carbon, hydrogen and oxygen, general formula C_mH_nO_2n. Examples include glucose, C₆H₁₂O₆; sucrose, C₁₂H₂₂O₁₁; starch and glycogen, both polymers of glucose.

Cracking: the breakdown of longer hydrocarbons into shorter ones. Requires high temperatures. This is how kerosene, petroleum etc are made.

Dissociation: when compounds split into smaller units such as ions. For example, acids undergo dissociation to form protons, and salts undergo dissociation to form cations (positive) and anions (negative). Also see acid and proton.

Dynamic equilibrium: a state in which reactants and products transition between each other at equal rates, so there is no net change in concentration. Obeys Le Chatelier’s Principle. Also see Le Chatelier’s Principle.

E-H

Electrode (in electrolysis): a solid electric conductor used to make contact with the electrolyte. Also see electrolysis.

Electrolysis: the process of passing a direct current through an electrolyte to drive the non-spontaneous chemical breakdown of a compound.

Gene: the basic functional unit of heredity; a sequence of genetic material which codes for a protein.

Hydration: a reaction involving the addition of water.

Hydrolysis: chemical breakdown of a compound due to reaction with water. Can be catalysed by the presence of acid or base (hence acid/base hydrolysis). Also see acid and base.

Hydrocarbon: a molecule made up of hydrogen and carbon only.

L-S

Le Chatelier’s Principle: The position of a dynamic equilibrium shifts to counteract any change in the environment. Also see dynamic equilibrium.

Metabolism: describes all chemical reactions involved in sustaining life in cells and the organism.

Neutralisation: the reaction between an acid and a base. Typically produces a salt and water. Also see acid, base, and salt.

Proton: a hydrogen ion, H⁺. Acids donate protons, while bases accept protons. See acid and base.

Salt (chemistry): an electrically neutral ionic compound. Forms crystals. Not to be confused with table salt.

Table salt: sodium chloride, NaCl. Not to be confused with salt.