Before embarking on the study of complex biological systems which are the subject of later chapters in this thesis, it is important to ensure that the methodology outlined previously may be applied with confidence to biological systems. For this reason, it is prudent to perform a validation study of a molecule which is well understood. The acetylcholine molecule, shown in Figure , has been widely studied due to its central rôle in neural transmission and thus is an ideal candidate for this purpose. A number of semi-empirical computational studies have been performed on this molecule with the aim of ascertaining its most stable conformation [63, 64, 65, 66]. Comparison of the results obtained from the calculations described in this chapter with those obtained from conventional experiments and semi-empirical calculations will allow conclusions to be drawn regarding the use of ab initio techniques in place of semi-empirical methods.
Figure: The acetylcholine molecule showing the definitions of dihedral angles D1 through D4. Oxygen atoms are shown as red, nitrogen as light blue, carbon as grey and hydrogen as white.
The conformation of acetylcholine may be described by the dihedral angles D1 through D4 as indicated in Figure . The definitions of these dihedral angles may be found in Appendix . The conformational energy map will be investigated as a function of the two central dihedral angles D2 and D3.
The calculations performed for this investigation are described in Section and the results are presented in Section . A summary of the conclusions which follow from these results is given in Section .