Dialog Box: Urey Bradley Data [Forces menu]
This dialog gives some overall specifications for the Urey-Bradley model and provides access to the data for individual polyhedron type and ligand-ligand pseudo-bond specifications.
Currently all Urey-Bradley information is automatic, not manual, that is specifications are in terms of atom types and bond distance limits, rather than in terms of individual generated atoms.
Use of Urey-Bradley forces requires entering data in four separate places.
1) All central-ligand (C-X) bonds must be defined in the Bonds dialog.
2) The ligand-central-ligand (X-C-X) angles corresponding to each ligand-ligand "contact" in each U-B polyhedron must be defined in the Angles dialog. This is true even if there are considered to be no valence angle forces apart from those which are derived from the U-B ligand-ligand bonds, since there are always derived U-B angle forces and these must be added to any valence angle forces. Thus the list of angles should be complete, including the atom types involved in all X-C-X angles which correspond to X-X contact, and excluding angles which do not correspond to X-X contact. In an octahedron, for example, the 90 degree angles should be included, but the 180 degree angles should not.
3) The U-B polyhedra themselves must be defined in the Urey-Bradley Polyhedron Specification dialog, accessible from this dialog (upper list).
4) The U-B ligand-ligand (X-X) "bonds" must be defined in the Urey-Bradley Ligand-Ligand Bond Specification dialog, accessible from this dialog (lower list). These are defined throughout the structure (all U-B polyhedra), not just for individual polyhedra.
Once you have specified the U-B polyhedra as in 3) above, you may select the Derive from Angles button - this will derive all the U-B ligand-ligand (X-X) "bonds" as in 4) from the list of valence angles as in 2) above. The list of X-X "bonds" will need to be edited, if only to insert the proper force values - distance limits may also need to be revised. The upper distance limit is just calculated from the upper limits in the angle specification.
The three radio buttons at the top of the dialog specify the way the "internal tension" kappa and the linear force constants F' and H' are handled.
(a) If the F' derived from kappa option is selected, H' force constants are set to zero and the values of the F' force constants are calculated from the formula for kappa. (b) If the Use given F' option is selected, the values for F' are entered along with values for F in the Urey-Bradley Ligand-Ligand Bonds dialog. In this case, or if (c) the F' = -0.1 F option is selected, the H' values are derived from kappa and F' using the formula for kappa. See Urey-Bradley Forces - Theory for more explanation of these options.
Print out derived valence forces. Those forces in the Urey-Bradley/Shimanouchi model which are not of the conventional quadratic nature (namely F' and H') must be converted to quadratic pseudo-valence forces. This results in additions to the C-X bond forces, X-C-X angle forces and C-X bond-bond, bond-angle and angle/angle interactions. These are added to any forces of these types which may be defined independently of the Urey-Bradley forces (Urey-Bradley forces are those arising from the interactions of the ligands with each other). If this box is checked, there will be a printout in the Output file (and the output window if selected) of the relevant forces. If these forces are then added to any true valence forces, and explicit Urey-Bradley forces are removed, the results should be exactly the same.