#GAUSSIAN SOFTWARE VS HYPERCHEM FREE#
Furthermore, changes in the degree of freedom of both partners during an interaction have a large impact on binding free energy. On the other hand, a molecular complex is not characterised by a single structure, as can be seen in crystal structures, but by an ensemble of structures. In fact, the multiple interactions present in a single two-molecule complex are a compromise between attractive and repulsive interactions. The same interaction may account for different amounts of free energy in different contexts and any change in molecular structure might have multiple effects, so it is only reliable to compare similar structures. At the same time, it is necessary to be aware of the fact that molecular interactions behave in a highly non-additive fashion. Therefore, it is important to know about interaction geometries and approximate affinity contributions of attractive interactions. This study seeks to identify such interactions between ligands and their host molecules, typically proteins, given their three-dimensional (3D) structures. Molecular recognition in biological systems relies on specific attractive and/or repulsive interactions between two partner molecules.
To better understand the basis of the activity of any molecule with biological activity, it is important to know how this molecule interacts with its site of action, more specifically its conformational properties in solution and orientation for the interaction.