Minimization of Energy
Energy minimization is essential to determining the proper atomic arrangement in space since the drawn chemical structures are not energetically favorable. The potential energy of an atomic structure contains different energy components like stretching, bending, and torsion. Hence, when an energy minimization program is run, it will immediately reach a minimum local energy value, and it might stop if the employed program is not exhaustive. In other words, an energy minimization might stop after it finds the first stable conformer that is structurally closest to the starting atomic arrangement. At this point, identified as the local energy minimum, structural variation yields a low change of energy. Hence, minimization can stop. However, this may not be the most stable conformer since the structural minimization stops before an energy barrier. This encumber of energy can be overcome by the use of suitable algorithms, which can increase the strain energy of the structure and finally lead to the most stable conformer, called global energy minimum. So, the identification of the energy minima is crucial to determining its behavior. Atomic modeling operation allows achieving the most stable conformational stage. Below figure shows different possible phases of an energy minimization operation.
Below videos show the energy minimization procedure of atomic structures by using various software.
References
[1] Roy, K., Kar, S., & Das, R. N. (2015). Computational Chemistry. Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment, 151–189. doi:10.1016/b978-0-12-801505-6.00005-3.