Crystals Primer

Chapter 10: Molecular Geometry

10.1: Distances and angles

10.2: Best planes, lines and dihedral angles

10.3: Torsion angles

10.4: Thermal analysis

Details of the molecular geometry can be computed in CRYSTALS. Most calculations send a summary to the screen, and a detailed listing to the printer file. Some will also produce a .PCH file (fixed format ASCII) suitable for incorporation into publications in either tabular of 'cif' format.
 

The user has a lot of fine control over the distance-angle routine, which should help minimise unwanted output. For many cases the default settings are suitable. A text file suitable for editing into documents may also be produced

      !\DISTANCE
      !END

Planes, lines and the angles between them are computed with MOLAX (molecular axes). This routine also produces simple plots.

      !\MOLAX
      !ATOM FIRST UNTIL LAST
      !PLANE
      !EXEC
      !ATOM C(1) UNTIL C(6) P(1)
      !PLANE
      !EXEC
      !ATOM P(1) FE(1) P(2)
      !LINE
      !ATOM P(3) FE(1) C(17)
      !LINE
      !ANGLE 3 AND 4
      !END

This task computes the best plane through the whole structure, through a P-phenyl group, and lines through two groups of atoms. The corresponding vector (plane normal or line axis) is stored for each PLANE or LINE calculation. The ANGLE directive requests the angle between the 3rd and 4th vectors, i.e. the two lines. EXEC, as in EDIT, forces immediate execution of the preceeding directive.
 

Torsion angles are computed with

      !\TORSION
      !ATOM C(1) C(2) C(3) C(4)
      !ATOM C(6) C(7) C(8) C(9) UNTIL C(11)
      !END

This computes one torsion atom in the first command, and 3 in the second. The output can be sent to a text file.
 

During the course of refinement, CRYSTALS keep a watch on the thermal parameters and issues warnings if they go too small or too aspherical. However, it is often instructive for the user to examine both the principal axes and the TLS molecular motion tensors, in association with a Cameron thermal ellipsoid plot.

      !\ANISO
      !ATOM FIRST UNTIL LAST
      !AXES
      !EXEC
      !ATOM C(1) UNTIL C(6) P(1)
      !TLS
      !END

These commands compute the principal axes of all the atoms, and then do a TLS analysis on the P-phenyl group. EXEC forces immediate execution of the preceeding commands.