Steric compassion

The points need not be on a lattice, such as is used in CoMFA. The CoMSIA method places the points inside the union surface of the superimposed molecules. The properties are not interaction energies, but rather the similarity of the molecular field of the ligand at a particular point with that of a probe atom. For this purpose steric, electrostatic, hydrophobic, and hydrogen bond acceptor and donor properties are considered. In the Compass method, probe atoms are placed along 162 equally spaced rays 2A from the union surface of the molecules in their initial superposition. The properties for analysis are the distance from the surface of the molecule to each of the probe atoms. 

Universal. The parameters in the Universal force field (UFF) [14-16] are calculated using general rules based only upon the element, its hybridization, and its connectivity. For this reason, the UFF has broad applicability but is inherently less accurate than extensively parameterized force fields such as COMPASS. Bond-stretching terms in the UFF are either harmonic or Morse functions. The anglebending and torsion terms are described by a small cosine Fourier expansion. For nonbonded terms, the LJ 6-12 potential and Coulombic terms are used for steric and electrostatic terms, respectively. 

Looking at the structure of HMR, it is clear that it occupies several sites on the surface. Some optimized adsorption structures on Pd(lll) surface modeled by molecular mechanics (MM) with the COMPASS (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies) force field are presented in Fig. 7.9. As the force fields cannot properly model chemisorption and, consequently, exact structures of the adsorbed molecules, the role of the metal surface in the MM calculations was mainly to act as a steric constraint. Depending on the adsorption structure, HMR covers 10-20 Pd surface atoms. 

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