Question

The details of molecular modelling and give five examples of the models you developed.

Answer 1

Molecular modelling is a tool to visualize and understand the molecule in 3D. It is most widely used in drug design, material development. Computers are used for calculation and simulation. The molecular modelling are performed at either molecular level or atomic level. At molecular level, interaction of atom with other atom are considered i.e chemical bonds and Van der Waals. Molecular mechanics or molecular dynamics are two ways to understand molecule.

Molecular mechanics is classical method of molecular modelling where potential energy of system was calculated by using Force field theory. Molecular mechanics take assumption of each atom as particle having fixed Van der waal radius, polarisable fixed charge and fixed bond length.

In Molecular dynamics, computer simulation takes in to consideration of physical movement of atoms and molecules

In Quantum approach, molecular modelling was performed at electronic level thus are very accurate but time consuming.

Quantum method was generally used with molecular mechanics to give method accuracy and speed. Warshel, Levitt and Karplus had been awarded with Nobel prize for development of this method for study of complex molecular system.

Some examples of models

Quantum Molecular Model: CNDO, AM1, PM3, SAM1 etc.

Molecular Mechanics Model: Steepest descents method, Arbitrary Step Approach, Newton Raphson method etc.

Molecular Dyanamics Model: Finite difference method, time step method Etc.

Monte Carlo simulations