Molecular Modeling Using Molecular Mechanics

 

Molecular Modeling Using Molecular Mechanics

Molecular models can be constructed in two main ways. Either researchers use an existing commercial force-field-based software package, or they build the molecule by assembling structural fragments stored in the molecular modeling program’s database.

Step-by-Step Procedure

Step 1: Selection of Structural Fragments
First, appropriate molecular fragments are selected from the software database (for example in INSIGHT II). The molecule containing the required functional groups or structural units is chosen. Typical fragments may include water, benzene, ammonia, methanal, methane, etc.

Step 2: Linking the Fragments
Next, the selected fragments are joined together. This is done by removing hydrogen atoms at the bonding positions and connecting the fragments at those points. During this process, the bonding state and geometry of each atom are checked and adjusted if necessary to ensure proper connectivity.

Step 3: Energy Minimization
Finally, the constructed molecular model is optimized using the force field. Energy minimization is performed to obtain the most stable (lowest energy) structure of the molecule.

Outcome

Following these steps produces a stick model of the target compound (for example, paracetamol) using molecular mechanics methods.