Molecular mechanics nonbonded interactions

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

You can choose to calculate all nonbonded interactions or to truncate (cut off) the nonbonded interaction calculations using a switched or shifted function. Computing time for molecular mechanics calculations is largely a function of the number of nonbonded interactions, so truncating nonbonded interactions reduces computing time. You must also truncate nonbonded interactions for periodic boundary conditions to prevent interaction problems between nearest neighbor images. 

It has been found that isotactic polypropylene produced by unbridged biscyclopen-tadienyl zirconium catalysts is formed through a mixed chain end control and enan-tiomorphic control.352 Molecular mechanics calculations led to the development of a model that takes into account nonbonded interactions to rationalize observed selectivities and predict properties of new catalyst systems.353... 

The success of the ligand-ligand repulsion model prompted its adoption as an element of a molecular mechanics program. In the resulting approach the valence angles around the metal ion are modeled solely by nonbonded interactions, using the usual van der Waals potential (for example, Eq. 2.9 kg = 0 in Eq. 2.7 Urey-Bradley approach)136. 6 Again, the fact that the electronic effects responsible for the directionality of bonds are not explicitly modeled here may seem questionable but extensive tests have shown the model to be reliable 371. An explanation for this apparent contra-... 

The s and f block elements present a particular challenge in the molecular mechanics field because the metal-ligand interactions in both cases are principally electrostatic. Thus, the most appropriate way to model the M-L bonds is with a combination of electrostatic and van der Waals nonbonded interactions. Indeed, most reported studies of modeling alkali metal, alkaline earth metal and rare earth complexes have used such an approach. 

When rotation occurs about a bond there are two sources of strain energy. The first arises from the nonbonded interactions between the atoms attached to the two atoms of the bond (1,4-interactions) and these interactions are automatically included in most molecular mechanics models. The second source arises from reorganization of the electron density about the bonded atoms, which alters the degree of orbital overlap. The values for the force constants can be determined if a frequency for rotation about a bond in a model compound can be determined. For instance, the bond rotation frequencies of ethane and ethylamine have been determined by microwave spectroscopy. From the temperature dependence of the frequencies, the barriers to rotation have been determined as 12.1 and 8.28 kJ mol-1, respectively1243. The contribution to this barrier that arises from the nonbonded 1,4-interactions is then calculated using the potential functions to be employed in the force field. 

For example, molecular mechanics calculations (MM2) showed that the methyl group geminal to the neopentyl group in 2,3,5,5-tetramethyl-2-hexene (51, Scheme 18) has the lowest rotational barrier and is the most reactive [79], Furthermore, the ethyl group in 2,3-dimethyl-2-pentene (52) has a much higher rotational barrier (5.76 kcal/mol) than the methyl groups and is totally inactive to 102. Similar trends hold with 2-methyl-2-butene (4). However, the barrier to rotation does not always predict the regioselectivity of the ene reaction of 102 with alkenes. As it was shown later [62], it is the nonbonded interactions in the isomeric... 

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