This chapter outlines the theory underlying the calculations on which the remainder of this thesis is based.
Ab initio techniques, such as the method described herein, attempt to solve the quantum mechanical equations governing the behaviour of the system studied. In practice, the exact solution of these equations is an intractable problem, hence a number of approximations must be made. In contrast to semi-empirical approaches, the approximations used in ab initio methods do not rely on the specific nature of the system studied, but instead are based on general physical principles. Thus, ab initio methods may be transfered between widely differing applications with confidence (See for example ,  and ).
There are many complexities underlying the application of these techniques to different classes of system. In this chapter we will only discuss in detail those which are pertinent to the study of biological and in particular, molecular systems. A full account may be found in the article by Payne et al. .