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3.2 Program Steps
Table 3.13: Standard Sybyl bond types.
Value
1
2
3
4
5
Type
single bond
double bond
triple bond
amide bond
aromatic bond
The Sybyl 5.2 force field was coded from an old Sybyl theory manual and directly from the original
reference [78], both from 1989. As with many other mechanics force fields, carbon, nitrogen and a few
other atoms that are in different bonding environments within a molecule are considered as being different
atom types as far as the Sybyl force field is concerned, and each atom type has its own specific parameters.
Force field parameters are defined only for the atom types listed (see Tables 3.12 and 3.13), although
van der Waals radii are defined for all atoms up to and including Xenon. There are defaults for most
parameters, so the force field can be used even for molecules for which it was not originally defined. In
these cases, “equilibrium” bond lengths and angles will be assumed to have values as calculated from the
original input geometry. Side effects of this assumption are: (1) slightly different starting structures for
the same system will optimize to different final geometries; and (2) if optimized structures are reoptimized,
they will again change.
The UFF Force Field
This is a general force field covering the entire periodic table. Unlike many other forcefields (e.g., the
Sybyl force field as discussed above), UFF parameters are estimated using general rules based on the
element only. It contains the following terms:
1. Bond Stretching
1
Es = Kij (RRij )2
2
where R is the current interatomic distance in angstroms, Rij is the sum of standard radii for atoms
i and j, plus a bond-order correction plus an electronegativity correction, and Kij is a stretching
force constant.
Rij = Ri + Rj Rbo Ren
where Rbo = 0.1332(Ri + Rj ) log(n) (n=bond order, C-N amide bond order is 1.41; bond order in
aromatic rings is 1.5) and
√
Ren = 2Ri Rj
80
Xi −
q
Xj
(Xi Ri + Xj Rj )
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