Most biochemical reactions are catalysed by enzymes, and understanding how enzymes ‘work’ at the molecular level is a fundamental problem that can help in the development of enzyme inhibition or enzyme engineering strategies. Computer simulations (especially QM/MM methods) can provide information that is often inaccessible experimentally, like details of unstable species (e.g. transition states or short-lived intermediates) or energetic analysis that reveals the role of individual enzyme–substrate interactions. In this chapter, an overview is presented of theoretical methods used in computational enzymology to calculate potential energy profiles and barrier heights, potentials of mean force, two-dimensional free energy surfaces, minimum free energy paths or rate constants with inclusion of quantum nuclear effects. Some recent applications of these methods are also illustrated with examples.