Manual Bonds
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Dialog Box: Manual Bond Force List [Forces menu]

This is for locating sets of bonds using individual generated atoms rather than overall specifications based on type (atomic number) and length limits. For "automatic" bond specification of the latter type, see Bond Force List. This type of bond is not applicable to crystals or polymers.

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).

Each entry in the upper list is an "fcon" or force constant - this pertains to a set of actual bonds, specified by the list of pairs of atom numbers in the lower list. This set may or may not be equivalent by symmetry, and whether or not a set of bonds conforms with symmetry is up to you, when you specify the individual atom pairs (automatic bonds specified in the Bond Force List always conform with symmetry). All members of a symmetry-equivalent set should be included in one manual bond in this list, but one manual bond is not limited to a single symmetry-equivalent set - there may be several chemically similar bonds included.

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.

The Atom numbers in the specifications in the lower list or spreadsheet must be the numbers of actual generated atoms in the molecule. These are best obtained from the Atoms Window - in fact you can select bonds involving atoms which have been clicked in succession with the mouse. This process, after a query (), will bring up this dialog. Generated atom numbers with coordinates can also obtained from the Output Window. The numbers entered here are not necessarily the Input Atoms as entered in the Input menu, although the lists of input and generated atoms will be the same if there is no symmetry. If there is symmetry, there will be more generated atoms than input atoms.

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 ligand-ligand 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.