Solutions For An Introduction to Medicinal Chemistry Chapter 17 Problem 1Q

The software allows accurate measurements of molecule’s dimensions in addition to its partial charges, molecular orbitals and electrostatic potentials. The molecular modeling software uses programs based on quantum mechanics and molecular mechanics.

A molecular mechanics program is used in the process of energy minimization, as it calculates the energy of a starting molecule and then varies its bond length followed further by bond angle and torsion angle for developing a new structure. The energy of this new structure is then calculated to see whether the structure is stable enough or not.

In case, the structure is found to be unstable, a slight change in bond length or bond angle creates a huge effect on the energy of the molecule. This will further result in a large energy difference. Since, the program has a tendency to recognize these effects; it carries out multiple alterations to create a nearest stable structure.

With such variations, in which only slight energy change (or minimum energy) occurs, the final structure is obtained. After obtaining a stable 3D (3-dimensional) structure, the program halts. The illustration of energy minimization is given in the figure 1.