Frothing at the Brain

I promised we’d talk about how dissolving something can be considered reaction, so here we go.

Remember what we were saying about metal ions in solution? How they aren’t stable on their own so they form complexes with anything that can donate electrons to them? Well, the same is true of almost everything. A molecule doesn’t just exist in a vacuum, unless it’s actually in a vacuum. If there are other things around, the total energy of the system is lower – that is, everything is happier and more stable – if they interact.

What happens is something called solvation. It’s easiest to visualise with water and something simple like salt, but the principle applies to all molecules in solution. Solvation is the term for the coordination of solvent molecules to something dissolved in them. No solvation, no solution – the molecule might be suspended in some water, but it isn’t dissolved in it without solvation.

Imagine a sodium ion. It’s a little round thing with a +1 charge, floating around in some water. It’s surrounded by water molecules, which are slightly negative at the oxygen end and slightly positive on the hydrogens. The water molecules are all moving around, but there’s a shell around the sodium ion where all the oxygen ends are pointing inwards. Those waters keep swapping places with the rest, they’re not static, but whichever waters find themselves around the ion will point towards it.

Likewise, imagine a chlorine ion in solution. It’s a big round thing with a -1 charge, so all the nearby water molecules have their hydrogens pointing towards it. The ions are solvated. When you drop a crystal of sodium chloride into water, the water molecules coordinate to the outermost ions in the crystal and pull them off into solution. No formal bonds are created and nothing officially changes, but there’s interaction between the electrons and that’s a reaction.Dece

Today, we’re going to make pretty crystals.

Take about a cupful of water and put it in a saucepan. Bring the water to the boil. When it’s boiling, start adding table salt. Keep putting more salt in until it stops dissolving.
Take your hot salty water and pour it into a clean glass or jam jar (carefully – boiling water and cold glass don’t always play nicely together, so you might want to warm the glass under the hot tap first). Dangle a thread from a cocktail stick into the liquid, and put the whole thing somewhere it won’t be disturbed.
Over the course of the next few hours, the salt will fall out of solution and precipitate onto any rough surfaces available to it – namely, the thread – forming crystals. Jostling the setup interrupts the crystal formation and results in smaller, more flawed crystals, so make sure it’s kept still and resist the urge to play with it.

Of course, dissolving and then precipitating something isn’t really a reaction. Except it is. Well, sort of. We’ll talk about it tomorrow.

Enzymes are magnificent things. An enzyme is a protein – a long string of amino acids folded up in a complex and specific way – that causes a reaction to happen. Most of them are catalysts, so they aren’t changed by the reaction. The reactants attach to the enzyme, which changes them enough to make them react, and the products fall off, leaving the enzyme as it was in the first place.
The really interesting thing about enzymes is how efficient they are. They are really, really good catalysts. Several thousand times faster than the reaction would otherwise be in some cases. Nature and evolution have given us some amazing things. Haemoglobin (which isn’t technically an enzyme, it’s a transport protein) is very delicately tuned to have the correct binding strength with oxygen. People have been trying for years to duplicate the “active site” where the oxygen is transported and we can’t do it. Without the whole surrounding protein structure, the iron doesn’t bind oxygen at all, or it binds it irreversibly, or it dimerises around the oxygen – there are several common failure modes, but every time we solve one we encounter another. We can’t make a simple thing that does the same job as the immensely complex natural protein that our cells synthesise every day.
Enzymes are as bad. Duplicating their effects is very difficult. There’s a whole field of chemistry all about mimicking natural proteins and enzymes. It’s called biomimicry and it exists because simple chemistry, the kind you can do in test tubes (and kitchens) is messy, inefficient and unreliable compared to what nature can do. To turn sugar into alcohol by chemical methods would be a real challenge. Doing it with yeast is just a matter of adding a bit of water and not heating it above about fifty degrees, it’s easy, it’s reliable. The enzymes in the yeast will do what they always do and you will end up with the desired products, every time, and with hardly any energy required.

So far, we’ve extracted indicator from red cabbage, used vinegar to clean copper, and burned things to produce heat and light. All these are useful things, and all these are reactions. The more you study chemistry, the more you realise that it is not some abstract theory apart from daily life. It’s everywhere. It’s in everything.

One of the most important reactions in our culture is the one that turns sugar into carbon dioxide and ethanol. We’ve used it since ancient times for two purposes: to make alcohol to drink, and to make bread rise. It’s an interesting example because it depends absolutely on another organism: yeast. We don’t do the reaction with chemicals. We put living yeast into a mixture, and we wait for it to feed on the sugars and produce alcohol and gas. Then we filter the yeast out and drink the alcohol, or we put the bread in the oven and let the heat kill the yeast.

Breadmaking is fun and tasty. Try it out, it’s cool.

I apologise for the belated nature of this post; I’ve been fighting off a migraine all day.

Today’s reaction shows up another of the fundamental rules of chemistry: it is exactly like cooking, only with chemistry you mustn’t lick the spoon.

Interesting compounds are everywhere. The one we’re using today is part of a very useful class known as indicators. “Indicators” on its own is obviously not a very informative name, since it gives no clues to what is being indicated, but it’s become the shorthand for any compound that visibly changes colour when the pH of its environment changes.
The pH is a measure of the concentration of H+. Any molecule that contains hydrogen has a point where it will start losing H+ ions to the environment, depending on the concentration of positive and negative ions that are around. Some coloured molecules have a different colour depending on whether the hydrogen is bonded, or has been lost as H+. So by putting those molecules into a given environment and watching what colour they turn, you can figure out the pH.
Litmus is the classic indicator, giving its name to the “litmus test”, which has made its way into popular culture. But it’s by no means the only indicator out there, or even the best. It’s certainly not the easiest to get hold of.
The easiest indicator to get hold of is found in red cabbage, which is actually a purple colour. If you cut up and boil some red cabbage, and then strain out the juice, or even better blend it first and then strain it, you end up with a solution of a dye molecule which reacts to pH. It will go red or blue depending on what you add to it. Add things like vinegar, baking powder and salt to small portions of your red cabbage juice, and see what colour it goes. Use that information to test other things around your house and deduce whether they’re acidic or alkaline. It’s fun.

When a metal dissolves in a solution of negative ions, like say the ethanoate (CH3COO-) in vinegar, it forms a salt. Metal salts are not molecules. In their pure form, they are ionic crystals, huge lattices of ions stacked together like marbles and held by magnetic attractions. In solution, they form complexes. A complex is a positive ion, usually a metal ion, surrounded by negative ions or neutral molecules. The ions, or the electron-rich parts of the molecules, push electrons towards the positive ion in the middle. The extra electrons make that positive ion more stable, which is why complexes form in the first place.

Something with a lot of excess charge – with too much electron density, or too little – and nowhere to store it is unstable. Almost any kind of interaction is better than nothing. A metal ion is a single nucleus without enough electrons. Unlike something big, like a dye molecule, there is nowhere else for those electrons to be supplied by. The metal is stuck with the positive charge.

So when that metal is floating around in a solution that has negative ions, or pairs of electrons that aren’t being used in bonding – even double bonds, in a pinch – the things that have spare electrons coordinate with the positive metal ion. The exact method by which this happens is too complicated to cover here, but the important point is that these electrons, the ones that are donated to the positive ion, are not forming covalent bonds. The electrons are shared between the negative thing and the ion, but the link between the two things is weak. It’s easily broken. It doesn’t take a full bond’s worth of energy to break the connection.

The connection is weak enough that the ligands (the negative things coordinated to the positive ion) can swap places with their counterparts in solution. You can use isotopically labelled ligands to track how fast this happens, and you can watch the colour change when you add a better ligand to the solution. It’s called reversible bonding, and while it may seem like an obscure branch of chemistry, that’s only because of how chemistry is taught. Reversible bonding – the formation of complexes around metal ions – is kind of important. It’s how haemoglobin transports oxygen.

Still got that vinegar we used for our first reaction? It’s going to come in useful again.

Take some vinegar and put it in a jam-jar if you’ve got one, or a glass if you haven’t. Drop a copper coin, preferably an old dull one, into the vinegar and leave it for a few hours.
To stop the vinegar escaping, you’ll need to cover the reaction mixture. That’s where the jam-jar comes in useful, because you can put the lid on. If you’re using a glass, I suggest cling film may be your friend. If the mixture isn’t covered, then the vinegar is going to evaporate, which will first of all make the place smell of vinegar, and second of all stop the reaction from happening. The ethanoic acid in the vinegar is what does the interesting bit, and it will evaporate off long before the water does. You can’t tell by looking whether there’s enough left in solution to make things happen, so best to cover your bases and your mixture.

After a few hours, take the coin out of the vinegar. If everything has worked properly, you should have a nice clean shiny coin. The oxidised salts that dull the surface of the copper will dissolve in acid, exposing new metal.
If you use distilled vinegar, which is clear and colourless, then you may find it has turned a pale blue colour from the copper salts dissolved in it. Pretty, isn’t it?

Yesterday we defined an exothermic reaction as one where energy is released, because the total energy stored in the bonds decreases.
This leads us to two new concepts: activation energy and stability.

On of the noticeable things about most reactions is that they only go one way. You can turn methane and oxygen into carbon dioxide and water very easily, but turning them back is very difficult. In fact, if you leave methane and oxygen in contact, without setting light to the mixture, they will still slowly degrade into carbon dioxide and water. The products are more stable than the reactants.
They are more stable because they store less energy. That’s what “more stable” means. Atoms are lazy creatures who do not want to be more energetic than they have to be. They’d rather be cool than hot, they’d rather be water than hydrogen and oxygen. The universe moves down the energy gradient.

Imagine you are an atom. You want to be as close to sea level as possible. You’re sitting happily in your little valley, until something pushes you up the slope. There yu are, balanced on the ridge. On one side is the valley you started from; on the other is a much deeper valley, one where the floor is closer to sea level. So that’s the way you roll down, into the lower valley. If you started from the lower valley, you’d still want to roll back into it, because you have lower energy on that side. That’s more or less why it’s hard to turn products back into reactants: even if you heat them up enough to start breaking bonds, the ones that reform will correspond to the products.

The ridge between the two valleys is the energy required to start breaking bonds so that new ones can form, and it’s called the activation energy. No matter how much energy is stored in the bonds and how much more stable the products would be, the reaction can’t start until something supplies the activation energy to get it going. TNT is much safer than nitroglycerin, because the activation energy for TNT is much higher. You have to deliberately detonate TNT, whereas a sharp knock can set off nitroglycerin. The stability of the products is almost identical, but the activation energy is different.

Today’s experiment serves to illustrate the second most useful thing about chemistry.

The first thing, obviously, is that it serves to turn stuff into other stuff. The second thing is that is serves to store and release energy. Chemical bonds take energy to make and break. If you break some high-energy bonds, and make some lower-energy bonds, then the leftover energy has to go somewhere. It becomes heat, making all the nearby molecules vibrate faster, and if there’s enough of it it becomes light, giving off photons.

Such reactions are called exothermic, literally outward-heating, and they’re very useful for several reasons. They are self-sustaining once you get them started; you have to put in energy to break the initial bonds and get the reaction going, but once it starts it generates enough energy to break the next set of bonds for itself. They provide an easy way to be sure that something is happening and you’re not just going to be stirring some unreactive water for hours. And they give off heat and light, which are themselves very useful things.

Allow me to introduce you to rapid exothermic oxidation. For millenia, it has been the heat source of choice for the human race, at night and in cold places. It’s dangerous if not handled carefully, because many things in the world, including people, can undergo the same basic reaction. Anything based on hydrogen and carbon, which is most of the living world, but especially things like dry plant cellulose, can react swiftly and highly exothermically with the oxygen in the atmosphere to produce carbon dioxide, water vapour, and other more complex products depending on the exact makeup of the reactive matter.

Are you there yet? This is the Internet, telling you to set things on fire. Matches, candles, nothing valuable, dangerous, or belonging to other people. Be careful and be safe, and enjoy the raw, unscientific, gloriously practical reaction that is combustion.

Yesterday we touched on the idea that molecules can have positive and negative parts, and that this is important for reaction. Actually, I understated the case. Almost every reactive molecule has some parts that are more positive than others, and almost every reaction relies upon this fact. The exceptions are the free radicals and the reactions they undergo, and they are a small and comparatively poorly understood part of the chemical world.

The concept you need is a “dipole”. Two poles. One positive, one negative. A dipole is a group of atoms bonded together which have a positively charged part and a negatively charged part. We aren’t usually talking about full, formal charges here, the kind you can write as a plus or minus and call an ion. Instead, we’re talking about differences in electron density. The electrons involved in the bonds between the atoms spend more time on atom A than atom B, so atom A is comparatively negative and atom B is comparatively positive. Chemists write this as δ+ and δ-.

If you were reading along last year, then you’ll remember the idea that some collections of atoms make up “functional groups”. Most functional groups are dipolar, and a student of chemistry very quickly learns to read them. You acquire electron-density-vision. For instance, C=O, the carboxyl group, is a dipole. The oxygen is δ-, the carbon is δ+, and therefore when a carboxyl reacts, it almost always involves something electron-rich giving electrons to the carbon and the resulting negative charge being temporarily stored on the oxygen. Understanding dipoles lets you move from what a reaction produces to knowing how it gets there, and that makes predicting the outcome much easier.