Dialog Box: Bond Force List [Forces menu]
This is for "automatic" bond location - VIBRATZ searches the structure for bonds using the specified atom types (usually atomic numbers) and distance limits. For "manual" bond location, using sequence numbers of specific generated atoms, or by point-and-click, see Manual Bonds.
The upper list gives a list of the valence bond forces. The data for each one is in a single line in the scrolling list or spreadsheet. To add a new entry, press the down arrow key while the focus is on the last row, or click the Add button. The lower list gives the specifications for each force constant in terms of atom types - an unlimited number of specifications is allowed (there must be at least one).
This is for entering the specifications for standard valence bonds (not Urey-Bradley ligand-ligand contacts - see the Urey-Bradley Data dialog).
No. (number). Since bonds are always first in the overall force constant list, this number is the same as the fcon number used in specifying interactions.
Force. The force constant, in md/A.
The Polarizability determines the contribution of the specified bond to the Raman intensity (see Theory and Implementation). Generally a value of 1.0 should be given to the most polarizable bonds.
Nspc. Number of atom type specifications for this bond (lower list).
LstSq. If this box is checked, this force constant will be refined by least squares.
Show. If this box is checked, the bond will be shown in the Atoms Window.
DMin/Dmax. Bond-length minimum and maximum. If the maximum is zero, it will be reset to the default value. This default value is fixed in the Basic Parameters dialog.
The Atom types in the specifications in the lower list or spreadsheet should key to entries in the Input Atoms list - normally the atomic number is used. However, bonds may be differentiated by assigning different atom types (Atom Types dialog, Input menu) to structurally or chemically distinct atoms of the same element, as well as by using bond lengths.
Once specifications have been entered, the force-constant values and least-squares flags for bonds may be changed in the overall Forces List, accessible from the Control Window.
Badger's rule. Using this relationship can avoid having to specify different force constants for different bond lengths, and may cut down drastically on the number of force constants required when bond lengths are variable. The general form used is
F = 1.86 / (d-d0)^3
Badger used this equation to relate distances and force constants in different diatomic molecules, and d0 was a constant characteristic of certain combinations of rows in the periodic table, but it is used in VIBRATZ to relate the force constants for individual bonds of a given type to the different individual distances. Thus in VIBRATZ d0 is derived by solving the above equation when F is the overall force constant (the FCON entered in this dialog) and d is the average bond distance for this bond type. Then for individual bonds in this group, F is derived from the individual d. The entry "Badger" in the output gives the ratio of the force constant for the individual bond to the overall force constant.
Note: The first releases of VIBRATZ V2.0 used an incorrect equation as "Badger's rule" for valence bonds
F'' = F (d0/d) ^ n
This is actually the equation for variation of Urey-Bradley repulsion forces. If you selected "Badger's rule" variation previously, the corrected form will now be used, and the exponent and base distance value (if used) entered previously will be ignored.