Chem 380.37 Lecture Notes 6

0301 00015 01010 00036 00000 00000 06726 01644 00121

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Unformatted text preview: 15 0.1010 0.0036 0.0000 0.0000 0.6726 0.1644 0.0121 0.0000 0.8158 0.1695 Eclipsed Ethane MM+ Amber 0.0301 0.0015 0.1010 0.0036 2.1330 2.6000 1.2013 0.3990 0.0121 0.0000 3.5775 3.0041 Notice first that the energies of staggered ethane calculated using MM+ and Amber differ by about 0.6 kcal/mol. Thus, the energies of molecules calculated using MM+ cannot be compared to those calculated using Amber. However, relative energies can be compared. For example, from MM+ the energy difference between eclipsed and staggered ethane is 2.76 kcal/mol, while the difference is 2.83 kcal/mol using Amber. These results are very similar, and these kinds of relative energies can be compared from force field to force field. It is sometimes dangerous to attribute too much weight to individual terms (bonds, angles, etc.) in the force fields when trying to qualitatively explain why one conformer is higher in energy than another. However, we see that the major difference in energy in both the MM+ and Amber force fields when going from staggered to eclipsed ethane is in the torsional energy. We might expect in this case that the steric repulsion introduced when the torsional angle is rotated from the staggered to the eclipsed form of ethane is manifest in the torsional energy of the molecule. Notice, however, that the non-bonded energy also changes when comparing the staggered and eclipsed forms of ethane. In the MM+ force field, the non-bonded energy of the eclipsed form is 0.53 kcal/mol higher than the staggered form, while for the Amber force field it is only 0.24 kcal/mol higher. Example 2 . n -butane Another example of the differences in force fields is provided by n-butane. Table 2 gives MM+ and Amber calculations for the anti and gauche conformers of n-butane. Table 2. Energy of n -butane c alculated u sing M M+ a nd A mber f orce f ields ( kcal/mol) Force Field Bonds Angles Torsions Non-bonded Other Total Anti conformer MM+ Amber 0.1569 0.0185 0.2954 0.0476 0.0071...
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