Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products. Peaks on the energy diagram represent stable structures with measurable lifetimes, while other points along the graph represent unstable structures that cannot be isolated.

This high-energy unstable structure is called the transition state or activated complex. In this high-energy process, bonds are in the process of being broken and/or formed simultaneously. The structure is so strained that it transitions into new, less strained structures.

George Hammond formulated a principle that relates the nature of a transition state to its location on the reaction diagram. The Hammond Postulate states that a transition state will be structurally and energetically similar to the species nearest to it on the reaction diagram. In the case of an exothermic reaction, the transition state resembles the reactant species, whereas, in the case of an endothermic reaction, the transition state resembles the products. In a multi-step reaction, each step has a transition state and corresponding activation energy. The transition states of such reactions are punctuated with reactive intermediates, which are represented as local minima on the energy diagrams.

Reactive intermediates are products of bonds breaking and cannot be isolated for prolonged periods of time. Some of the most common reactive intermediates in organic chemistry are carbon ions or radicals. Carbocations are electrophiles, and carbanions are nucleophiles. Carbon radicals have only seven valence electrons and may be considered electron deficient; however, they do not, in general, bond to nucleophilic electron pairs, so their chemistry exhibits unique differences from that of conventional electrophiles. Radical intermediates are often called free radicals.