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Updated: Jul 28, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
Application of the method for visualization of noncovalent interactions in conformational polymorphs of four organic
Pavel A Pirozhkov1, Andrei S Uhanov1, Anton V Savchenkov1
1Samara National Research University, 34, Moskovskoye shosse, Samara, Russian Federation.
Abstract:
A method for the visualization of noncovalent interactions using examples of the conformational polymorphs of four organic compounds: 2-(phenylamino)nicotinic, 2-(3-chloro-2-methylphenylamino)nicotinic, N-(3-chloro-2-methylphenyl)anthranilic and 2-(methylphenylamino)nicotinic acids is examined. The changes in noncovalent contacts are plotted against the angle between the planes of aromatic rings allowing a visual representation of conformational adjustment of molecules as well as packing features of crystal structures. According to the k-Φ criterion, the studied structures represent conformational polymorphs. Different types of hydrogen bonding are discussed within the framework of the method of visualization and molecular Voronoi-Dirichlet polyhedra. Good correlations are found between calculated and experimental data for several cases, such as the agreement between π stacking and polymorphic transition temperatures as well as between the area of a contact and the energy of conjugation. Also, an attempt has been made to assess the relative contributions of conformational and packing polymorphism in the formation of polymorphs.
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