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Molecular mechanics methods are based on the following principles: 1) Nuclei and electrons are lumped into atom-like particles. 2) Atom-like particles are spherical and have a net charge. 3) Interactions are based on springs and classical potentials. 4) Interactions must be preassigned to specific sets of atoms.

Molecular modeling could be defined as a class of computerized work which applies the laws of physics supported with experimental data that can be used either for analyzing molecules including number and types of atoms, nature of the bonds, bond lengths, angles and dihedral angles, molecular energy, geometry ...

Basic Computational Chemistry Methods Computational methods include quantum mechanics methods and molecular mechanics methods, while molecular simulations include molecular dynamics simulations and statistical mechanics simulations.

Computational methods for molecular modeling can be separated into two categories: those that are based on quantum mechanics (QM) and those that are based on classical mechanics.

Molecular modeling software #1: ChemDoodle It can create chemical 3D structures with high-quality 3D graphics and quickly build and manage reaction schemes in real-time. ChemDoodle comes with some software tools, called “Widgets”.

Computational molecular modeling is an important tool for detailing the mechanisms of molecular recognition between proteins and inhibitors, which can be key to the understanding and development of new pharmaceuticals for the treatment of a number of diseases.

Molecular modeling is used to simulate the molecular behavior in chemical or biological systems (Leach, 1996). ingly, it is one of the leading techniques working with wide range of applications, such as drug design, biomaterials, emerging materials, and spectroscopy.

Molecular Mechanics is a computational method that computes the potential energy surface for a particular arrangement of atoms using potential functions that are derived using classical physics.