Modelling Chemical Change
In 2013, CSIRO researchers used 3D molecular models to design a drug that blocks 4 cancer proteins simultaneously — all before a single gram of compound was ever synthesised in a lab.
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● Know
- Scientists use models (drawings, equations, particle diagrams) to explain reactions.
- Word equations and symbol equations are two common types.
- Reactants go on the LEFT of the arrow, products on the RIGHT.
● Understand
- A model is a useful simplification — it captures the important bits but isn't reality itself.
- Atoms must balance: the same atoms (and same number) on both sides.
- Different models suit different purposes — particle diagrams for visualising, equations for tracking atoms.
● Can do
- Write a word equation for a familiar reaction.
- Draw a particle-level diagram of a state change or simple reaction.
- Spot a missing or unbalanced atom in an equation.
Hold 2 coloured marshmallows and a toothpick: push the toothpick between them and you have just built a model of the water molecule H₂O — 2 hydrogen atoms bonded to 1 oxygen. It is clearly not a real molecule (a real water molecule is 0.000 000 000 28 m across), but it shows exactly the right shape and the right number of atoms. A scientific model is a simplified picture of how something works. It can be a physical object like a ball-and-stick molecule, a drawing like a particle diagram, or an equation that describes a relationship. Every model leaves things out on purpose — that is what makes it useful.
The trick is to choose the right model for the job. A particle diagram of water shows how particles are arranged, but it does not show colour or temperature. A computer simulation can show movement and energy changes, but it relies on approximations. No single model does everything, so scientists use many models together to build a fuller picture.
A ball-and-stick model of methane (CH₄) clearly shows the four C-H bonds and the tetrahedral shape. However, it does not show that the atoms are constantly vibrating, or that the bonds are regions of electron density rather than solid rods.
CSIRO uses supercomputer simulations to model protein folding and drug interactions. These digital models allow researchers to test thousands of compounds virtually before running expensive lab trials, saving time and resources.
Students often think a model is a perfect copy of reality. In fact, every model is a deliberate simplification. Knowing what a model shows and what it hides is just as important as knowing how to use it.
Chemical reactions rearrange atoms into new substances. A word equation names the reactants and products: iron + oxygen → iron oxide. The arrow means “reacts to make.” Reactants always go on the left, products on the right.
A symbol equation uses chemical formulas and must be balanced. Balancing means placing big numbers in front of formulas so that the same number of each type of atom appears on both sides. This obeys the law of conservation of mass: atoms are never created or destroyed, only rearranged.
The word equation for rusting is iron + oxygen → iron oxide. The balanced symbol equation is 4Fe + 3O₂ → 2Fe₂O₃. There are four iron atoms and six oxygen atoms on each side, so mass is conserved.
At BlueScope Steel, chemists use balanced equations to calculate exactly how much iron ore and carbon are needed to produce a batch of steel. Without accurate stoichiometry, the furnace would waste raw materials and produce impure metal.
Some students think the big numbers in a balanced equation change the subscripts inside the formula. They do not. The formula H₂O is fixed; the big number 2 in 2H₂O simply means two water molecules.
Scientists use many kinds of models, each with strengths and weaknesses. Ball-and-stick models show bond angles clearly but do not represent atom size realistically. Space-filling models show relative sizes but can hide bond angles. Computer simulations can model dynamic processes like bond breaking over time, but they depend on the accuracy of the underlying code.
The key skill is matching the model to the question. If you want to know shape, use ball-and-stick. If you want to know how a reaction proceeds over time, use a simulation. Using the wrong model can lead to false conclusions.
A space-filling model of DNA shows how tightly the base pairs fit inside the double helix, but it obscures the hydrogen bonds that hold the strands together. A computer animation of the same molecule reveals those bonds breaking during replication.
The Australian Synchrotron produces high-resolution molecular models by bouncing intense light off crystals. These models reveal atomic positions with extraordinary precision, helping researchers design new medicines and materials.
Students sometimes believe that because a model is digital or looks realistic, it must be more accurate than a simple drawing. Accuracy depends on the data and assumptions behind the model, not on how pretty the picture is.
Common mistakes with equations and models can derail an entire explanation. One error is writing an unbalanced equation, which violates conservation of mass. Another is treating a model as if it were reality — for example, believing that bonds are literally sticks. A third is using the wrong model for the question, such as using a static diagram to explain a dynamic process.
Always check your symbol equation by counting atoms on both sides. Always ask what your model leaves out. And always be ready to switch models when the question changes. Scientific literacy means knowing the limits of your tools as well as their strengths.
A student writes H₂ + O₂ → H₂O and claims it is balanced because the words describe the same reaction. In fact, there are two oxygen atoms on the left and only one on the right. The correct balanced equation is 2H₂ + O₂ → 2H₂O.
ANSTO nuclear engineers use multiple models — mathematical, computational, and physical — to predict reactor behaviour. Each model covers different aspects, and cross-checking between them is essential for safety.
Many students think a word equation is enough to prove conservation of mass. Word equations name the substances, but only a balanced symbol equation proves that atom counts are equal on both sides.
Here's a student's working. One line has an error — click it.
- A student writes: 'Hydrogen + Oxygen → Water'.
- They claim the equation is balanced because the words on each side describe the same reaction.
- The balanced formula equation is 2H₂ + O₂ → 2H₂O.
Models and equations are the languages of chemistry. A good scientist moves fluently between them: using a particle diagram to visualise a reaction, a word equation to name the substances, and a balanced symbol equation to count atoms and predict masses.
When you evaluate a model, ask two questions: What does it show well? What does it hide? When you evaluate an equation, ask: Are the formulas correct? Is it balanced? Answering these questions transforms a memorised fact into a deep understanding that you can apply to new situations. This flexibility is what separates a student who recalls facts from a scientist who solves problems.
To explain combustion, you might draw a particle diagram showing oxygen and fuel molecules colliding, write the word equation methane + oxygen → carbon dioxide + water, and then balance the symbol equation CH₄ + 2O₂ → CO₂ + 2H₂O. Each model captures a different layer of the story.
Indigenous Australian fire-management practices are a traditional model of controlled chemical change. By timing burns to seasons and fuel loads, Aboriginal rangers have maintained ecosystem health for millennia — a model now integrated with modern CSIRO fire science.
Some students think that once an equation is balanced, the reaction will definitely happen. Balancing only checks atom conservation; it says nothing about whether the conditions are right for the reaction to occur.
At the start of this lesson, you thought about how chemists use ball-and-stick molecular models to design drugs before ever stepping into a real lab — saving years of expensive trial and error.
Now that you've built and used models to represent chemical changes, does the idea of atoms rearranging (rather than disappearing) make more sense to you? How did your understanding of what happens to atoms during a reaction shift?
1. What is the main purpose of a scientific model?
2. In a balanced chemical equation, what must be true?
3. Which of the following is a limitation of a ball-and-stick molecular model?
4. What does a word equation show?
5. Why can atoms not be created or destroyed in a chemical reaction?