Computer Modeling and Simulation of Minimum Energy Paths of Flexible Molecules
Kleinebreil, Timothy P.
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This paper concentrates on flexible molecules which have the ability to change from one conformation to another. In general these conformations are known minima and we are interested in finding how the molecule transforms between two minima. In order to study the MEP it is necessary to know the potential energy related to the conformations. A molecule has high dimensionality because each atom in the molecule has its own three degrees of freedom . So if a molecule had N atoms, the total degrees of freedom would be 3N. With each atom having its own 3 degrees of freedom and therefore its own contribution to the potential energy, it is hard to visualize or even calculate a change in potential energy. Conveniently some molecules can be described with only two degrees of freedom, two angles 𝜙 and ѱ', which are called dihedral angels or torsion angles. This allows us to model the molecule much easier. Torsion angles, also known as dihedral angles, are very useful when describing molecular conformations.