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 .