Welcome to chapter two, foundations of chemistry. Chemistry turns up in almost every conversation this book prepares you for, usually without announcing itself. A nurse says a cleaning solution is a thousand parts per million. A pharmacist says a drug is the S enantiomer. A lab scientist says a sample was run on the mass spectrometer. If you last did chemistry at school, the ideas are probably still there, but rusty and disconnected from anything you build. This chapter rebuilds them from the ground up, with the engineering arithmetic attached, and then shows how chemistry is actually practised, and with which tools.
Three practical reasons this matters to someone with a full workshop and an electronics bench. First, everything you make is a chemical system. A machined stainless part, a moulded polypropylene housing, a lithium battery, a sewn polyester strap, a glass vessel: each reacts with what it meets, whether disinfectant, sweat, saline, oxygen or heat, and changes over time. Second, measurement in medicine is overwhelmingly chemical. Most laboratory tests and many bedside sensors measure a concentration. Third, the workshop itself is a chemical environment, with real hazards in its solvents, adhesives, fluxes and resins. Chapter three then takes these ideas into the molecules of life and the materials you build with.
We start with what everything is made of.
An atom is a tiny, dense, positive nucleus of protons and neutrons, surrounded by a cloud of electrons. Almost all the mass is in the nucleus; almost all the volume is electrons. If the nucleus were a pea in the middle of a football pitch, the electrons would be out around the stands. The number of protons, the atomic number, defines the element: six protons is carbon, always. And here is the key idea. Chemistry is the behaviour of the outer electrons. Atoms are most stable with a full outer shell, so sodium gives one electron away, chlorine takes one, and carbon shares four, which is why carbon can build the long chains of organic chemistry.
Two variations on an atom matter. An ion has gained or lost electrons, so it carries a charge but is still the same element. The body's electrolytes are ions: sodium, potassium, calcium, chloride, bicarbonate. Their gradients across membranes run nerves and muscle. An isotope has a different number of neutrons: same chemistry, different mass, and sometimes an unstable nucleus. Fluorine-18 emits positrons with a half-life of about a hundred and ten minutes, and attached to glucose it becomes the main PET tracer. Because isotopes are chemically almost identical, the body handles a radioactive atom exactly as it handles the stable one. That is the entire trick of nuclear medicine.
The periodic table is not a list. It is a map of electron arrangement. Each row adds a new electron shell, so atoms get bigger going down. Each column shares the same number of outer electrons, so its members behave alike. Lithium, sodium and potassium in group one all form plus-one ions and react vigorously with water. Fluorine, chlorine and iodine in group seventeen form minus-one ions and are strong oxidisers. The noble gases on the right barely react at all. Metals sit on the left and in the middle, non-metals on the right. Once you read it this way, you can predict which ion an element will form without memorising anything.
Four elements, oxygen, carbon, hydrogen and nitrogen, make up about ninety-six percent of body mass. Calcium and phosphorus build bone and run energy and genetic chemistry, and a long tail of trace elements, iron in haemoglobin, zinc and copper in enzymes, iodine in thyroid hormone, is essential in tiny amounts. A second set turns up in what you build. Stainless steel is iron, chromium, nickel and molybdenum, and nickel is a common skin sensitiser. Titanium is biocompatible thanks to its oxide film. Silver is antimicrobial. Iodine and barium are X-ray contrast agents because of their high atomic number, and lithium powers batteries.
Gases are where chemistry meets breathing. The ideal gas law, P V equals n R T, ties pressure, volume, amount and absolute temperature together, and Boyle's law is why expanding your chest draws air in. Dalton's law says each gas in a mixture contributes pressure in proportion to its share. Oxygen is about twenty-one percent of dry air at sea level, giving a partial pressure of about a hundred and fifty-nine millimetres of mercury. By the time air reaches the trachea it is warmed and saturated with water vapour, which takes forty-seven of those millimetres, so oxygen drops to about a hundred and forty-nine. Henry's law says dissolved gas follows partial pressure, which is why oxygen dissolves poorly in plasma and why haemoglobin exists.
Atoms are far too small to count, so chemists count them in batches called moles. One mole is about six times ten to the twenty-three particles, Avogadro's number. Its usefulness is that the mass of one mole in grams equals the molecular mass. Water is about eighteen grams per mole, sodium chloride about fifty-eight, glucose about a hundred and eighty. Moles are what reactions care about. One molecule of glucose reacts with six of oxygen, not one gram with six grams. And moles are the bridge to the concentration units that fill every lab report.
Medicine uses a bewildering set of concentration units. Millimoles per litre for electrolytes and, in most of the world, glucose. Milligrams per decilitre for glucose in the United States. Percent weight per volume for intravenous fluids, so point nine percent saline is nine grams per litre. Percent volume per volume for alcohol disinfectants. Parts per million for chlorine strength, which in dilute water is about a milligram per litre. Osmolality for tonicity. And units of biological activity for insulin and heparin, which are not defined by mass at all. Knowing which one you are looking at is the first defence against a tenfold error.
Two conversions show why this matters. A blood glucose of five millimoles per litre, times a hundred and eighty grams per mole, is nine hundred milligrams per litre, or ninety milligrams per decilitre. The factor of about eighteen between the units is a real source of clinical error. Normal saline is nine grams per litre, divided by fifty-eight point four, which is a hundred and fifty-four millimoles per litre. Each salt unit splits into two particles, giving about three hundred and eight milliosmoles, close to plasma, which is the whole reason that strength was chosen. And for dilution, the amount of solute is conserved: concentration times volume before equals concentration times volume after.
A chemical equation is a mass balance, and it also has an energy balance. Breaking bonds costs energy and forming them releases it. Exothermic reactions give out heat: combustion, the curing of epoxy and polyurethane, and respiration. Endothermic reactions absorb it, like an instant cold pack. Even an exothermic reaction usually needs a push to start, and that push is the activation energy, the barrier the reactants must climb. A catalyst offers a route with a lower barrier, so the reaction runs faster without the catalyst being consumed. It changes how fast equilibrium is reached, not where it lies. Enzymes are the body's catalysts.
Reaction rate rises with concentration, surface area, catalysts and temperature. The temperature effect is captured by the Arrhenius equation, and for many reactions near room temperature it boils down to a rule of thumb: the rate roughly doubles for every ten degree rise. That one rule explains why medicines are refrigerated, why a polymer stable for years at room temperature can fail in months in a hot car, and why accelerated ageing tests work at all. Many processes are first order: a constant fraction disappears in each interval. Radioactive decay, drug elimination and the killing of microbes by heat all behave this way. In sterilisation that is the D value, the time to reduce a population tenfold.
Many reactions run both ways, and when the forward and reverse rates match, the system is at equilibrium. It is dynamic, but its composition is steady. Le Chatelier's principle says that if you disturb an equilibrium, it shifts to partly counteract the disturbance. The body's most important example is carbon dioxide, water, carbonic acid and bicarbonate. Breathe out more carbon dioxide and the equilibrium shifts to consume hydrogen ions, so pH rises. Retain it and pH falls. That is how the lungs adjust blood pH within minutes. A more practical chemistry lesson from the same section: never mix cleaning products. Bleach and an acid release chlorine gas; bleach and ammonia release chloramines.
Oxidation is the loss of electrons and reduction is the gain, and they always happen together. Redox is everywhere: respiration oxidises food, bleach and peroxide disinfect by oxidising microbial proteins, which is also why they corrode metals and degrade plastics, and metals corrode by being oxidised. Separate the two halves and connect them with a wire, and the electron transfer becomes a current. That is a galvanic cell. The anode is oxidised and dissolves; the cathode is where reduction happens. Zinc against copper gives about one point one volts. The same physics drives a dissimilar-metal joint to corrode.
Electrochemistry sits unusually close to medical devices. A glucose meter uses an enzyme to oxidise glucose, and the electrode measures the resulting current. A blood gas analyser uses a glass electrode for pH and reduces oxygen at a platinum cathode. ECG electrodes are silver and silver chloride because that gives a stable, low-noise interface with skin. Breath alcohol testers use a small fuel cell. Hearing aid batteries are zinc–air cells activated by pulling the tab. And the unwanted version is corrosion of implants and instruments where dissimilar metals touch or a crevice traps electrolyte.
A battery's voltage comes from its chemistry, its capacity from how much active material it holds, and its energy is roughly voltage times capacity. A three point seven volt, two thousand milliamp-hour lithium-ion cell stores about seven watt-hours, enough to start a fire if released in seconds. That is thermal runaway: damage, overcharging or heat starts exothermic decomposition, the heat speeds the reactions further, and the cell can vent flammable gas and ignite. It is exactly the positive-feedback loop chapter one warned about. Use cells with protection circuits, proper chargers, and enclosures that cannot crush or puncture them.
Organic chemistry is the chemistry of carbon, which bonds four ways and builds chains and rings of any length. The carbon skeleton gives a molecule its shape, and small functional groups give it its chemistry. Learn to recognise hydroxyl, carboxyl, amine, ester and amide groups, and most of biochemistry and polymer science becomes readable. Isocyanates, used in polyurethanes, deserve special mention as potent respiratory sensitisers. Some molecules come in two mirror-image forms, like left and right hands. They are identical in a bottle, but the body's receptors are themselves handed, so they often treat the two forms differently. Thalidomide is the cautionary example.
Chemical hazards are communicated by the globally harmonised system of pictograms and the sixteen-section safety data sheet, and controlled by a hierarchy that runs from elimination through substitution, engineering controls and procedures, to protective equipment last. In your own workshop: solvents are highly flammable and their vapour travels. Epoxy hardeners, isocyanates and solder flux fume are sensitisers. The hazard most often underestimated by experienced makers is sensitisation. An irritant hurts and then stops. A sensitiser changes your immune system so every later exposure, however small, provokes a reaction, often for life. Treat "I've used it for years without gloves" as a warning.
A two-litre oxygen cylinder at two hundred bar holds roughly four hundred litres of gas at atmospheric pressure, about three hours at two litres a minute. Accelerated ageing uses the ten degree rule: at fifty-five degrees against twenty-five, the rate is two cubed, eight times faster, so a year is simulated in about forty-six days, provided the higher temperature does not cross a transition the material would never meet. Faraday's law tells you how much metal an electrochemical current moves. A corrosion current of just one microamp flowing for a year dissolves about nine milligrams of iron, and concentrated at a crevice that is enough to perforate a thin wall.
Now how chemistry is actually practised. When someone says "send it to the chemistry lab", you should know which lab, what it will do, and what it needs from you.
Chemistry is not one job. Analytical chemists answer what is it and how much, using chromatography, mass spectrometry and spectroscopy. Clinical chemists run thousands of patient samples a day on automated analysers. Pharmaceutical chemists design drug molecules, turn them into medicines, and test every batch. Materials and polymer chemists qualify device materials, study leachables and analyse failures. Electrochemists work on sensors, batteries and corrosion. Water chemists keep dialysis and sterile-services water pure. And radiopharmacists make PET and nuclear medicine tracers against the clock of their half-lives. Toxicology, food chemistry and sterilisation chemistry complete the list.
Whatever the branch, an analysis follows the same chain. Start with the question, and how well it must be answered. Collect and label the sample, prepare it by weighing, dissolving and diluting, separate the components, detect and quantify them against calibration standards and quality controls, and report a result with its units and uncertainty. Errors can enter at every link. A superb mass spectrometer cannot rescue a mislabelled or badly diluted sample. The quality of a result is a property of the whole chain, which is exactly chapter fifteen's point about trustworthy measurement.
A quick tour of the instruments. A spectrophotometer measures how much light a solution absorbs, and the Beer–Lambert law turns that into concentration; pulse oximeters use the same principle. FTIR reads bond vibrations and identifies an unknown plastic or residue in about a minute. HPLC and gas chromatography separate mixtures for purity and residue checks. Mass spectrometry sorts molecules by mass and finds trace drugs and leachables. ICP-MS finds elements at trace levels, such as nickel leaching from an implant. A handheld XRF gun tells you which grade of stainless a part really is. And thermal analysis shows glass transitions, melting and moisture.
Behind the instruments sits infrastructure. Analytical balances weigh to a tenth of a milligram. Volumetric glassware and calibrated micropipettes deliver volumes precisely, and pipetting technique is a classic source of error. A fume hood protects the user from vapours; it is not a biological safety cabinet. Laboratory information systems and electronic notebooks track every sample and keep the audit trail. For software, PubChem and the NIST WebBook are free references, RDKit is the standard Python cheminformatics toolkit, and a units library such as Pint carries units through every calculation and refuses mismatches.
Pharmaceutical chemistry runs a long pipeline. A target protein or pathway, discovery and optimisation of lead molecules, preclinical work on safety and dose, then three phases of human trials, from tens of people to thousands, then regulatory approval, and then manufacture with every batch tested and the product watched after launch. Ten to fifteen years is typical, and most candidates fail. Chemistry runs through every stage, from making the molecule to choosing its crystal form and formulating it as a tablet, injection or inhaler. Devices that deliver drugs inherit all of that chemistry.
Where can you contribute? Teaching instruments are a natural fit: an LED colorimeter, a simple spectrophotometer, conductivity and pH logging rigs, built with electronics, optics and a machined or moulded housing. Open-source potentiostats for teaching. Laboratory fixtures and racks, in materials chosen for the solvents and disinfectants they will meet. Scientific glassblowing is a skilled trade in its own right. And lab automation, including scripts that move data from instruments into information systems, though in a regulated lab that must be validated. The best first build is an LED colorimeter calibrated with a dilution series of food dye.
A ward manager asks for help making up chlorine disinfectant from tablets, currently done with a bucket and a jug. In this invented case each tablet releases one and a half grams of available chlorine, and policy asks for a thousand parts per million, which is one gram per litre, so each tablet needs one and a half litres. The chemistry turns the request around. The useful product is an unambiguous fill mark, because "about two-thirds of a jug" is twenty percent out. The solution decays, so it needs a made-up time. Chlorine corrodes aluminium, so polypropylene or HDPE. And perhaps best of all is a pre-made product. Whatever is built, test strips should confirm it works.
Do the exercises. Make a serial dilution of food colouring and build a calibration curve with a phone camera or, better, a simple colorimeter, then measure an unknown. Do the clinical arithmetic with units at every step. Make a zinc and copper cell in salt water, and leave a stainless screw on an aluminium plate in salt water for a week. Sort plastic offcuts by whether they float. And audit five substances from your own workshop using their safety data sheets, then change one thing.
The limits. This chapter makes you literate in chemistry's language and arithmetic; synthesis, method development and interpreting analytical results are professional skills. A home-built colorimeter with a straight calibration line is a teaching instrument, not a validated method. Reading a safety data sheet is necessary, but it is not a risk assessment for someone else's workplace. Accelerated ageing supports a claim; it does not replace real-time data. And nothing here licenses you to handle hydrofluoric acid, concentrated oxidisers or radioactive material. Next, chemistry and molecular biology for the maker.