Force Fields and Molecular Mechanics Calculations

Typical force fields such as the Tripos force field available in Sybyl or CVFF 24 available in Biosym contain torsional terms tliat have the form  

Equation (1) yields minima at dihedral values of 0° or 180° depending on whether the minus or plus sign is used and at other values in between depending on n. For saturated carbon compounds, the plus sign is taken when trans is defined as 180° and = 3 in most cases. 

For molecular dynamics (MD) simulations to accurately reflect chain motions and conformational changes at various temperatures, the rotational barriers must be correct whether they arise from an explicit dihedral term, vdW interactions, or both. Barriers that are too low will allow disorder to occur at simulated temperatures far below experimental temperatures at which transitions and disorders in PTFE are observed. The validity of the barrier heights, especially the one at trans, obtained from the MOPAC AMI calculations and derived force field parameters above was called into question upon comparison to high level ab initio calculations on perfluorobutane (PFB), perfluoropentane (PFP), and 

FC = force constant EQV =equilibrium value stretch constants in kcal/mol/A bend constants in kcaVmol/rad  

The failure of Set IV to yield reasonable unit cell parameters for conforma-tionally free helices is mostly due to the relatively small value of Fitting the parameters to the scaled AMI data tended to force s for C-C interactions to extremely low values. When this parameter was restrained to he at least 0.05 kcal/mol, the final value of for the F-F interactions was required to he larger (0.33 kcal/mol) as noted above, and the value to be correspondingly smaller. A dihedral term that properly describes the torsional behavior of perfluorocarbons may allow the vdW e parameters to have more typical values (0.01-0.1 kcal/mol). 

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