Torsional angles proper

A set of rules determines how to set up a Z-matrix properly, Each line in the Z-matiix represents one atom of the molecule. In the first line, atom 1 is defined as Cl, which is a carbon atom and lies at the origin of the coordinate system. The second atom, C2, is at a distance of 1.5 A (second column) from atom 1 (third column) and should always be placed on one of the main axes (the x-axis in Figure 2-92). The third atom, the chlorine atom C13, has to lie in the xy-planc it is at a distanc e of 1.7 A from atom 1, and the angle a between the atoms 3-1-2 is 109 (fourth and fifth columns). The third type of internal coordinate, the torsion angle or dihedral r, is introduced in the fourth line of the Z-matiix in the sixth and seventh column. It is the angle between the planes which arc... 

Spanned by tbc atoms 4, 2, and 1, and 2, 1, and 3 (tlic ry-planc), Except of the first three atoms, each atom is described by a set of three internal coordinates a distance from a previously defined atom, the bond angle formed by the atom with two previous atoms, and the torsion angle of the atom with three previous atoms. A total of 3/V - 6 internal coordinates, where N is the number of atoms in the molecule, is required to represent a chemical structure properly in 3D space. The number (,3N - 6) of internal coordinates also corresponds to the number of degrees of freedom of the molecule. 

The other chain atom coordinates are obtained through repeated application of a screw operator. The side groups can be defined as for finite molecules with a proper combination of bond lengths, valence and torsion angles. Finally, the crystal structure description is completed by an overall rotation 4> and three overall translations x0 y0 z (or fewer, depending on the space group). 

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