The simulation of chemical reactions should be ideally carried out by the tools provided by Quantum Mechanics. In practice, very small systems can be solved only by means of quantum theory. The potential energy that gives title to this section is the potential that molecular nuclei feel under the kinetic and potential energy influence of electrons. This electrons/nuclei separation comes from the Born-Oppenheimer approximation (section 1.2.1.2) which is a mathematical strategy and a conceptual milestone that gives meaning to the molecular entities and escapes from the no intuitive quantum conception of matter.
Big molecules such as enzymes and other condensed phase systems are too big to be computationally affordable with quantum methods, even to compute only their potential energy. To overcome these limitations these last years the so-called Quantum Mechanics / Molecular Mechanics (QM/MM) methods have been one of the most successful applications.
In order to explain the QM/MM methods used in this thesis, it is important to review the currently available
methods in Quantum Mechanics and Molecular Mechanics, its advantages and its failures. In this way,
we can justify the appearance and the success of hybrid methods in general and of the QM/MM strategies in particular.