Minimum energy conformations molecular mechanics calculation

The minimum energy conformation of cyclohexane calculated with a molecular mechanics program is shown in Figures 3.31 and 3.32, and the summary of the different contributions to the steric energy are listed in Table 3.7. Note that the Cl—C2—C3—C4 dihedral angle is 56.33°, producing a torsional energy. Ex, of 0.343 kcal/mol. This value is quite close to the experimental value of 56.1°. ... 

The 16-mer, in its minimum-energy extended zigzag conformation, has a molecular length of approximately 100 A. The zigzag conformation is significantly lower in energy, by molecular mechanics calculations, than other non-extended forms. Once one end of the molecule binds to a gold probe, the other end could affix to the proximal probe with 2 eV stabilization on each end from the Au-S bonds. 

Fig. 6-4. Minimum energy conformations of L-PA and L-phenylalanine-A -methyl-anilide (L-PMA) based on molecular mechanics calculations and UV- and NMR-spectroscopic characterizations. (From Lepisto and Sellergren [25].)...

Figure 4.18 The structure of Tamiflu (oseltamivir phosphate), an antiviral agent active against type A influenza, and a molecular model of its minimum-energy conformation, as calculated by molecular mechanics.

Molecular mechanics (Chapter 4 Focus On) A computer-based method for calculating the minimum-energy conformation of a molecule. 

According to molecular mechanics (MM) calculations, the minimum energy conformation of the enolate is a twist-boat (because the chair leads to an axial orientation of the f-butyl group). The enolate is convex in shape with the second ring shielding the bottom face of the enolate, so alkylation occurs from the top. 

Quantum mechanical calculations are also useful in predicting minimum energy conformations of chromophores and for predicting properties such as dipole moments. Calculated dipole moments are shown for several chromophores in Table 4. Such calculations are particularly useful in understanding how chromophore molecular conformation changes with addition of substituents. 

The structure of movphme and a stereoview of its minimum-energy conformation, as calculated by molecular mechanics. 

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