UFF force fields

In the past, when molecular mechanics methods were used for transition metals, it was by having a set of parameters for the metal that were parameterized specifically for one class of compounds. There have been a number of full periodic table force fields created, with the most successful being the UFF force field. All the full periodic molecular mechanics methods still give completely unreasonable results for certain classes of compounds. 

All calculations were performed using Gaussian98 [77], which required making some additions and corrections to the UFF force field because Gaussian98 does not have atom types for square planar rhodium or coordinated double bonds. Details about these changes can be found in the supporting information of our original paper [72],... 

The TRIPOS force fields in the SYBYL and Alchemy programs and the Chem-X, CHARMm, and COSMIC force fields all employ a simple harmonic potential (Eq. [1]) for bond stretching/compression. The CVFF, DREIDING, and UFF force fields support a Morse potential as well as a harmonic potential. The harmonic function is the default in DREIDING and UFF. 

The TRIPOS, Chem-X, CHARMm, COSMIC, and CVFF force fields all use only the harmonic approximation, whereas in the DREIDING force field, angle bending is described by a harmonic cosine function where 0 and 0o in Eq. [6] are replaced by cos 0 and cos 0q, respectively, to avoid a zero slope as 0 approaches 180°. In the UFF force field, angle bending is described with a small Fourier expansion in 0 (Eq. [7]). This functional form was selected to better describe large-amplitude motions. 

The UFF force field represents still another type of force field in that it is neither parameterized in the classical way nor based on ab initio quantum chemical calculations. Instead, the parameters in UFF are evaluated from general rules based on the elements, their hybridization and connectivity. The reason for this choice of parameterization scheme is that the goal of the UFF force field is to extend the calculations to the entire periodic table, making the large number of parameters required for such a task untenable by traditional prescriptions. 

The most commonly used cross terms are stretch-bend, stretch-stretch for two bonds to the same atom, stretch-torsion, bend-torsion, and bend-bend for two angles with a common central atom. MM2 and MMFF94 include only stretch-bend interactions. The TRIPOS, AMBER, CHARMm, DREIDING, and UFF force fields have no cross terms. MM3 and MM4 include stretch-bend, bend-bend, and stretch-torsion terms. 

In all PCM methods, the radii of the spheres used to create the cavity can be further defined in different ways, but in the course of this thesis only the two most common radii have been employed the UAO and UFF. These two radii use the united atom topological model applied on atomic radii of the UFF force field for heavy atoms and only differ in how the spheres for hydrogen atoms are described. More specifically, in the UAO radii the hydrogen atoms are enclosed in the sphere of the heavy atom to which they are bonded, while in the UFF radii they have individual spheres. 

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