We will use ethylene glycol as an example. C1 Choose another atom, place it along the Z-axis, and specify the distance between the two atoms. CC will be set to 1.5 angstroms. Choose a third atom near either of the previous two atoms and specify the angle formed by the three nuclei. Ethylene Glycol Choose a fourth atom related to either end of the previous chain and specify the dihedral angle formed by the four atoms.
Dihedral angel are easy to visualize using Newman projections.
The illustrations below show the Newman projection for ethylene glycol, looking down the C-C bond. Positive dihedral angles correspond to clockwise rotation in the Newman projection. To view the completed input for ethylene glycol and Dimethyl Sulfoxide click HERE . Then R, THET, and PHI are sperical coordinates. The solvent oxygen is pointing away from the solute, showing the hydrophobic interactions to be measured, rather than the more favorable sulfonyl-hydroxy hydrogen bond interaction.