Small organic molecules, field-electron

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

This chapter is an introduction to the field of intermolecular interaction and to the modem ab initio electronic structure methods - primarily those based on perturbation theory - that have been developed to study them. We will be mainly concerned with applications to small organic molecules for which accuracies of the order of a kj mol" or less are sufficient. High-accuracy calculations on small dimers can be orders of magnitude more accurate, but these are the subject of a specialist review (see Szalewicz et al. 2005 for a review and references). Nor are we concerned with empirical methods. Our focus will be on first principles methods for the interactions of closed-shell systems in the non-relativistic limit. In the last decade, ab initio methods have been used to successfully model the structure of liquid water. (Bukowski et al. 2007) studied the interactions between DNA base tetramers (Fiethen et al. 2008) and predicted the crystal structure of an organic molecule (Misquitta et al. 2008b). The goal of this chapter is to describe the main theoretical developments that have been responsible for these applications. 

This restriction rules out all discrete models exclusively based on semiempirical force fields, leaving among the discrete models the MC/QM and the MD/QM procedures, in which the second part of the acronyms indicates that the solute is described at the quantum mechanical (QM) level, as well as the full ab initio MD description, and some mixed procedures that derive the position of some solvent molecules from semiclassical simulations, replace the semiclassical description with the QM one, and repeat the calculation on these small supermolecular clusters. The final stage is to perform an average on the results obtained with these clusters. These methods can be used also to describe electronic excitation processes, but at present, their use is limited to simple cases, such as vertical excitations of organic molecules of small or moderate size. This limitation is due to the cost of computations, and there is a progressive trend toward calculations for larger systems. 

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