The smallest piece of an element that is still that element β and why almost all of it is empty.
~11 min read
An atom is the smallest piece of an element that is still that element. Take a lump of carbon and halve it, halve the half, and keep going. Eventually you reach a single atom, and the next cut changes what you have β still particles, but no longer carbon.
Start with size. A carbon atom is about 0.34 nanometres across β a third of a billionth of a metre. Close to a million and a half of them would span a printed full stop. Take that up to something you handle: one drop of Lemon holds on the order of a hundred billion billion limonene molecules, and since each is twenty-six atoms joined together, the drop holds near three thousand billion billion atoms.
Matter made the point that an atom is almost entirely empty. Here is the figure: the nucleus is about one sixty-thousandth of the atomβs width, and carries more than 99.9 per cent of its mass. Scale the atom up until the nucleus is a pea and the outer edge sits at the far side of a sports stadium, with nothing in between but a few electrons.
Every atom of every element is built from the same three particles. What differs between one element and another is how many of each it has.
| Particle | Charge | Relative mass | Where it sits |
|---|---|---|---|
| Proton | Positive (+1) | 1 | In the nucleus |
| Neutron | None (0) | 1 | In the nucleus |
| Electron | Negative (β1) | About 1/1836 | In the space around the nucleus |
An electron weighs about one eighteen-hundredth of a proton, so in a carbon atom the electrons together are about three hundredths of one per cent of the mass. The nucleus is where the weight is. The electrons are where the room is.
Diagram to come
A single carbon atom, making two points at once. Centre: a small dense nucleus holding six protons and six neutrons, colour-coded and distinguishable, deliberately drawn far too large to be to scale, with a printed note saying so. Around it, two concentric shells β the first carrying 2 electrons, the second carrying 4, with the second shell visibly having room left. A leader line marks the outer shell as the valence shell. A small inset in one corner shows the true scale relationship: the nucleus as a dot with a ring at sixty thousand times its radius, so the reader can see exactly what the main drawing exaggerates.
The proton count is the atomβs identity, and the only thing that is. Six protons is carbon β in a diamond, in the sugar of an apple, in the backbone of a limonene molecule. Eight is oxygen, one hydrogen, seven nitrogen, sixteen sulfur. That count is the atomic number, and it is what the periodic table is sorted by.
This is where the last lessonβs definition makes sense. An element cannot be broken down by chemical means because chemistry never reaches the nucleus. Burning, dissolving, distilling, digesting β each is electrons being rearranged, and not one adds or removes a proton.
In an atom on its own the electrons match the protons, so the charges cancel and the atom is neutral. Bonding is what happens when two atoms adjust that balance.
There is a problem with the picture just described. Protons are all positively charged, and like charges repel. Six packed into a space a few femtometres across should fly apart with enormous force. Something is holding them.
That something is the strong nuclear force β by far the strongest in nature, acting between protons and neutrons alike, but only over about one femtometre, roughly the width of a proton. Inside that range it overwhelms the electrical repulsion completely; just outside it, it is effectively absent. That short reach is why nuclei are small and dense.
Neutrons are what make larger nuclei possible. Each adds strong-force attraction without adding any repulsion, so it works as nuclear cement. Light elements manage with roughly equal counts β carbon runs six and six β while heavier ones need proportionally more. For a given element, some combinations sit comfortably and some do not, and the ones that do not come apart over time.
Everything a chemist cares about is the electrons. The nucleus sets identity and mass, then takes no further part. Bonding, reactivity, aroma, why one constituent behaves differently from another β all electrons, and specifically the ones furthest out.
Electrons occupy distinct energy levels, usually drawn as shells, and each level holds a limited number. The first holds two, the second eight, and for the light elements that build essential oils the third behaves as though it holds eight as well. Electrons fill from the inside out.
The outermost occupied shell is the valence shell, and the electrons in it are valence electrons. Inner-shell electrons are held tightly and shielded by the ones outside them, and take no part in chemistry. Valence electrons are exposed, loosely enough held to be shared or moved, and they are the only electrons that ever meet another atom.
| Element | Electrons | Shell arrangement | Valence electrons |
|---|---|---|---|
| Hydrogen (H) | 1 | 1 | 1 |
| Carbon (C) | 6 | 2, 4 | 4 |
| Nitrogen (N) | 7 | 2, 5 | 5 |
| Oxygen (O) | 8 | 2, 6 | 6 |
| Sulfur (S) | 16 | 2, 8, 6 | 6 |
| Neon (Ne) | 10 | 2, 8 | 8 β full |
Those five reactive elements are, between them, nearly the entire contents of your shelf. Read the last column and you have predicted most of their behaviour.
The whole of bonding, in one line
Count the valence electrons. That single number tells you how many bonds an atom forms, which atoms it will join, and therefore what molecules are possible. Bonding, functional groups and eventually the chemistry wheel introduce no new principle. They are this number, applied.
The diagram of neat rings around a nucleus comes from a model published in 1913, and it is wrong in a specific and interesting way. It pictures the electron as a small object travelling a defined path, the way a planet circles a sun. Nothing about an electron works like that.
By the mid-1920s the mathematics had moved on, and what it describes is not a path but a probability. An electron has no location between one measurement and the next. It has a distribution β a map of where it is more and less likely to be found. That map is an orbital, and the surface usually drawn is the boundary inside which it is found about ninety per cent of the time. A cloud of likelihood, not a track.
The shapes are not all round, either. The lowest, s orbitals, are spherical; the next, p orbitals, look like two lobes either side of the nucleus and come in sets of three at right angles. What is drawn as one second shell of eight electrons is really one s orbital and three p orbitals holding two each. Those shapes are why molecules have geometry β why carbonβs four bonds point to the corners of a tetrahedron rather than lying flat.
So why do chemists still draw shells? Because a model is judged by what it predicts, not by whether it is literally true. For counting valence electrons and reading a structure off a page, the shell picture gives the right answer with almost none of the mathematics. Keep both, and use whichever the question needs.
Here is the pattern the whole of chemistry runs on, and it needs stating carefully. Atoms with a completely filled outer shell are unusually stable. Atoms with a partly filled one are not, and they reach a lower-energy arrangement by sharing or transferring electrons until the outer shells involved are effectively full.
Note what that does not say. Atoms do not want anything. They have no goal and no preference. A filled-shell arrangement simply sits at lower energy than an unfilled one, and physical systems settle into lower-energy arrangements the way water finds the bottom of a valley. Water is not seeking the sea; no other outcome is stable. Chemists say an atom "wants" eight electrons as shorthand β useful, but taken literally it has you expecting intent.
The noble gases sit out
Helium has two electrons and a first shell that holds two. Neon has eight in its outer shell, argon the same. They begin full, so there is nothing to gain by reacting, and they very nearly never do.
Oxygen takes two
Six valence electrons, two short of eight, so oxygen forms two bonds. That is the whole reason water is HβO. It is also why oxygen creates functional groups: joined to a hydrocarbon it brings unshared pairs of electrons, pulling charge to one side of the molecule.
Nitrogen takes three
Five valence electrons, three short, so three bonds. Nitrogen appears only in small amounts in essential oils but is everywhere in the body, since every protein is built on it.
Hydrogen takes one
One electron and a first shell that holds two, so hydrogen forms exactly one bond. It is the cap on the end of things, finishing a carbon chain wherever nothing else is attached.
Carbon takes four
Four valence electrons and four gaps, exactly halfway. Carbon has no bias towards giving electrons away or taking them, so it shares β in four directions, with almost anything, including other carbon atoms.
Four is the most versatile number available to an atom, and carbon is the only common element that has it. Because carbon bonds strongly to itself, one carbon can hold another indefinitely β chains, branches, rings, rings fused to rings. Each skeleton is a different molecule, which is why the terpenes exist in such variety.
Diagram to come
Five atoms in a row, each drawn as a nucleus with its outer shell only. Electrons are dots on the ring; empty positions are open circles, so the gaps are visible at a glance. Order: hydrogen, carbon, nitrogen, oxygen, neon. Beneath each atom, the bonds it forms are drawn as that many short stubs projecting outward β four for carbon, three for nitrogen, two for oxygen, one for hydrogen, none for neon. Neon has a closed ring and no stubs and is visually set apart from the other four. Without reading a word, the reader must be able to see that the number of empty positions equals the number of stubs.
The proton count fixes which element an atom is. The neutron count does not, and it is free to vary. Atoms of the same element with different numbers of neutrons are called isotopes, and every element has several.
Carbon is the one to know. Carbon-12, six protons and six neutrons, is about 98.9 per cent of all carbon; carbon-13, with seven neutrons, is almost all the rest. Isotopes of an element have the same protons, so the same electrons and the same shell arrangement: they bond identically and make the same molecules. What differs is mass, and mass is measurable.
That is where it reaches the shelf. Isotope ratio analysis is one of the tests used to judge whether an oil is what the label says, and it works because a molecule records where its carbon came from.
Two molecules can therefore be chemically identical β same formula, same structure, indistinguishable on a chromatogram β and still be told apart by the isotopes they are built from. That is one of several checks behind what a purity standard tests.
It is one check, not a proof. An adulterant built from plant-derived feedstock can carry a plausible isotope signature, because its carbon really did come from a plant. That is why isotope analysis sits alongside chromatography, mass spectrometry and chirality testing rather than replacing them, and why reading a constituent profile means reading the whole panel.
The instrument is an isotope ratio mass spectrometer. The sample is burned, turning all its carbon into carbon dioxide. That gas is ionised, accelerated and bent through a magnetic field, which deflects lighter ions more sharply. Detectors count how many arrive at each mass. The output is not an amount of carbon but a ratio.
The differences are tiny, so the result is reported as a deviation from an agreed international reference material, in parts per thousand. A negative value means the sample is poorer in carbon-13 than the reference β the normal state of anything a plant built. Different photosynthetic pathways leave different values, which is why the same technique tells cane sugar from beet sugar.
Hydrogen can be read the same way, using the ratio of deuterium β hydrogen with a neutron β to ordinary hydrogen. A plantβs hydrogen comes from the water it drank, so that ratio carries information about where it grew. The measurement is made on the molecule, by an instrument that does not care what the label says.
Take all of that and build something real. Limonene dominates every citrus oil on your shelf, and its formula is CββHββ. That is the whole composition: ten carbon atoms, sixteen hydrogen atoms, nothing else.
Count what that means. Twenty-six atoms in total, ninety-six protons, seventy-six electrons. No oxygen anywhere in it β limonene is a pure hydrocarbon, which is why it carries no functional group and why its behaviour is simpler than that of the oxygen-carrying constituents you meet later. Its molecular mass is about 136, against 18 for water.
The formula does tell you one thing beyond the count. Ten carbons each forming four bonds, every spare position filled by hydrogen, would carry twenty-two hydrogens. Limonene carries sixteen. Each missing pair means a ring closed or a double bond formed, so six missing hydrogens means three β one ring and two double bonds, worked out from the formula alone.
What the formula does not tell you is where anything is. It gives composition, not arrangement, and arrangement is where the character lives. Ξ±-Pinene is CββHββ, and so are myrcene, camphene and Ξ³-terpinene β same atoms, same mass, one ring and two double bonds each β and they smell nothing alike. Pinene reads as pine resin. Limonene reads as orange peel.
It goes finer still. Limonene comes in two forms that are mirror images β same atoms, same connections, differing only in handedness. One reads as sweet citrus, the other closer to turpentine, because your olfactory receptors are themselves handed and fit one and not the other. Handedness is measured on a purity panel rather than assumed.
Diagram to come
Three panels reading left to right. Panel one: the formula CββHββ set large, with brackets beneath showing ten carbon atoms and sixteen hydrogen atoms as counted circles β the formula as pure inventory. Panels two and three: skeletal structures of limonene and of Ξ±-pinene drawn side by side at the same size, each with its ring and double bonds clearly visible, each labelled with the same formula underneath. Under each structure, a one-word aroma note. A bracket spanning panels two and three states that the formula is the same and the structure is not. The reader must be able to see at a glance that one identical formula produced two visibly different skeletons.
Now put real figures on it. Lemon is 60β75 per cent limonene, Wild Orange 80β97 per cent, Grapefruit 90β97 per cent β which is why the three share a family resemblance in the diffuser despite coming from different fruit. Lavender is a different proposition: 25β45 per cent linalyl acetate, 20β47 per cent linalool, and more than 150 compounds in a single drop.
Which products you can buy differs from country to country across the markets this app serves, so not every name above will be on your shelf. The chemistry does not change with the catalogue.
Keep oils away from eyes and inner ears, and out of reach of children. If you are pregnant, nursing, under medical care or taking medication, speak to your healthcare practitioner before use. Nothing here is intended to diagnose, treat, cure or prevent any disease.
The next lesson is the periodic table, and it will look like a different subject until you notice it is a picture of this one. It is sorted left to right by proton count, so the atomic number climbs as you read across. The rows are shells: a new row begins when the previous outer shell has filled. The columns are valence electrons, which is why elements in a column behave alike. It is not a list to be memorised β once you have this lesson you can read it rather than consult it.
After that comes bonding, which is what atoms do with their valence electrons, and then terpenes, which is what carbon does when allowed to bond to itself ten or fifteen times.
Where to go next
Lesson 3 of 18 Β· Science