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1983; Jorgensen et al., 1984). In the united atom approximation, a molecule or a group of atoms is treated as a single unit, represented by a Van der Waals sphere with a charge point. Atomistic models represent every atom in a molecule. Each atom is usually modelled as a Van der Waals sphere with a point charge. According to Molecular mechanics, molecular model is the definition of how a molecule interacts with itself and other molecules. The total potential energy is composed in two parts intramolecular energy (how a molecule interacts with itself) and intermolecular energy (how a molecule interacts with other molecules. A molecule can possess different kinds of energy such as bond and thermal energy. Molecular mechanics calculates the internal energy of a molecule, the energy due to the geometry or conformation of a molecule. Energy is minimized in nature, and the conformation of a molecule that is favoured is the lowest energy conformation. Knowledge of the conformation of a molecule is important because the structure of a molecule often has a great effect on its reactivity. Molecular mechanics assumes the internal energy of a molecule to arise from a few, specific interactions within a molecule. These interactions include the stretching or compressing of bonds beyond their equilibrium lengths and angles, torsional effects of twisting about single bonds, the Van der Waals attractions or repulsions of atoms that come close together, and the electrostatic interactions between partial charges in a molecule due to polar bonds. To quantify the contribution of each, these interactions can be modelled by a potential function that gives the energy of the interaction as a function of distance, angle, or charge. The total internal energy of a molecule can be written as a sum of the energies of the interactions: Eintramolecular = Estr + Ebend + Estr-bend + Eoop + Etor + EVdW + Eqq (3.2) 29PDF Image | MOLECULAR SIMULATION STUDIES IN THE SUPERCRITICAL REGION
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