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Methods

 

Calculations were performed using the techniques described in Chapter gif. A cut off energy of 650eV was used for the plane wave basis set and the molecule was embedded in a cubic supercell with a side of length 8Å. As acetylcholine has a net charge of +1e, the post-hoc correction described in Section gif was applied to the total energy. Due to constraints on time and computing resources available, it was found that absolute convergence of the energy with respect to supercell size could not be obtained. However, convergence of energy differences between conformations was found to be practical to within tex2html_wrap_inline3055 kcal tex2html_wrap_inline3057 .

We have used the crystal structure of acetylcholine chloride [67] as the initial geometry of the acetylcholine molecule. This data does not define the positions of the three terminal hydrogen atoms of the acetyl group containing tex2html_wrap_inline3059 . Some previous studies have defined the positions of these atoms such that the dihedral angle tex2html_wrap_inline3061 , while others have defined tex2html_wrap_inline3063 . Total energy calculations were performed for these two possibilities and these showed that the arrangement with tex2html_wrap_inline3063 was energetically favourable. This arrangement was therefore used for the remaining calculations, with the hydrogen atoms arranged relative to tex2html_wrap_inline3059 in the usual tetrahedral geometry for a methyl group.

Three sets of calculations were performed:


next up previous contents
Next: Results and Discussion Up: Acetylcholine: A Validation Study Previous: Introduction

Matthew Segall
Wed Sep 24 12:24:18 BST 1997