The most basic tool of the chemist in predicting the course of chemical reactions is thermodynamics. Chemical reactions proceed according to our understanding of basic physical laws; there is a tendency for the entropy of a chemical system to increase (this equates to an decrease in the order of the system) and the free energy (the energy available to do work or potential energy) to decrease. In predicting the likely course of chemical reactions, the basic factors considered are chemical bond types, level of free energy, temperature, etc. However, not all chemical reactions proceed spontaneously. The reason for this is the existence of what is termed an 'energy barrier.' Molecules have complex dynamics and structures that may constitute a hindrance to the progress of a reaction. For example, for a reaction to proceed, two molecules might be required to come together at a high energy and be aligned very specifically with respect to one another, such that particular chemical bonds are close to one another. Catalysts effectively overcome the structural hindrance to the progress of chemical reactions. They are said to reduce the 'energy of activation' (i.e. the amount of energy required for the reaction to proceed) during the transition phase of the reaction.

The basic stages of a catalysed reaction are as follows:

1. The enzyme binds to the reagent(s) (substrate) to form the enzyme-substrate complex.
2. The reaction proceeds to the transition phase of the reaction.
3. The products are formed and are released from the enzyme.

The diagram below shows the reduced activation energy compared to the activation energy for an un-catalysed reaction. Also, the overall free energy change for the catalysed and un-catalysed reaction are the same. This illustrates that catalysts do not alter the thermodynamics of a chemical reaction. The reduction in the energy of activation only alters the kinetics (i.e the rate) of the reaction.

Catalysts participate in chemical reactions but emerge from reactions unchanged. Catalysts accelerate the rate of a reaction towards equilibrium, but they do not change the final state (thermodynamic equilibrium) of a given chemical system.

When we observe a chemical reaction we are observing the interplay between different physical principles. The physical laws that govern how molecules move in a liquid solution, how they collide, and how the kinetic energy is distributed amongst them, are quite independent of the laws of thermodynamics as they apply to an analysis of the chemistry.

In a very simplified way the rate of a chemical reaction can be understood as being consequent on two basic components:

1. Thermodynamics - an analysis of which can indicate how far a system is away from thermodynamic equilibrium, and thus inform a chemist how the reaction will proceed.
2. Factors that constitute a hindrance to this process, a major one being structure. Molecules have shapes that are purely contingent factors, as far as thermodynamics of the chemistry is concerned, but which nevertheless influence the rate of the reaction because molecules may have to come together at particular energies and orientations for the reaction to proceed.

This is essentially a story about energy and structure. Conventionally, we think of the process of catalysis as a process involving the lowering of an energy barrier. It may be more useful to think of catalysis as a process that bridges the discontinuity between thermodynamics and structure. To get a more intuitive feel for this idea, imagine the situation of a large, land-locked lake high in the mountains. On the one hand, we know that the situation is far from equilibrium, that eventually the water will find its way to the sea. On the other hand, we understand that the structure of the land prevents this from happening spontaneously. In fact, we see the interplay between thermodynamics and structure all around us. Potential energy is 'land locked' in the contingencies of its structured environments and rarely dissipates via the most direct means. Catalysts somehow remove the obstacles that bar the way to thermodynamic equilibrium.

Catalysis has been studied for many years, nevertheless, it is still a poorly understood process. In the last twenty years or so, ideas involving quantum mechanics and soliton waves have introduced alternative perspectives to traditional 'over the barrier' theories. These theories involve dynamic interactions between the reagents and the enzyme and also involve a phenomenon termed 'quantum tunneling'. We shall examine one of these theories in greater depth.