Dialog Box: Urey-Bradley Ligand-Ligand Bond Specifications [Urey-Bradley Data dialog, Forces menu]
Specifications for Urey-Bradley ligand-ligand "bonds" are similar to those for valence bonds (Bonds dialog) except for the secondary force constant f'. This value is used only if the second model (Use given f') in the main Urey-Bradley Data dialog is selected.
The specifications given in this dialog apply throughout the structure, and not to any specific U-B polyhedron type. For example, in the silicate garnet crystal structure in which there are three different cations, with coordination numbers of 4, 6 and 8, but only one anion, oxygen, a single U-B bond oxygen-oxygen specification could conceivably be applied to all three polyhedra. However, the O-O distances differ greatly and it is probably advisable to assign different force constants to different ligand-ligand distances.
Once specifications have been entered, the force-constant values and least-squares flags may be changed in the overall Forces List, accessible from the Control Window.
Distance dependence. Using this option can avoid having to specify different force constants for different ligand-ligand bond lengths, and may cut down drastically on the number of force constants required when bond lengths are variable. According to this rule, the repulsion force constants involving two specific types of atoms tend to be related according to
F' = F (d0/d) ^ n
where d is the actual bond distance, d0 is a reference distance, typically the average distance for this type of bond, and n is the exponent, usually about 9. In VIBRATZ, the force constant F is specified in this dialog and may be subject to least-square refinement, and F' is applied to a particular bond. The reference distance d0 may be the average for this particular bond specification (determined at run time), or it may be a fixed value which you enter. Neither the exponent nor the fixed reference distance are subject to least-squares refinement. The correction factor (F'/F) applied for each ligand-ligand "bond" is given in the output in the column under "d-factor".
This relationship is applied to the main UB ligand-ligand "bond" force, that is F = f. If the secondary UB force f' is dependent on the main force f, as specified in the main Urey-Bradley Data dialog, it is derived from the adjusted value of f. If the secondary UB force f' is independent, it is not subject to adjustment.
This distance dependence was incorrectly referred to in initial releases of VIBRATZ V2.0 as "Badger's rule" - see Bonds and Manual Bonds for Badger's rule as applied to valence bonds.