2010 May 12 | Erin R. Johnson¹, Shahar Keinan¹, Paula Mori-Sánchez¹, Julia Contreras-García¹, Aron J. Cohen², and Weitao Yang¹
This study presents a method to detect non-covalent interactions in molecular systems using electron density and its derivatives. The approach identifies non-covalent interactions as low-density, low-gradient regions in real space, which are distinct from covalent bonds and electrostatic interactions. The method requires only atomic coordinates and is efficient for large systems such as proteins and DNA. It provides a rich representation of various non-covalent interactions, including van der Waals forces, hydrogen bonds, and steric repulsion. The method uses the sign of the second Hessian eigenvalue to distinguish between different types of non-covalent interactions, with the density on the interaction surface indicating the interaction strength. The approach is validated using a variety of molecular systems, including small molecules, complexes, and solids. The results show that non-covalent interactions can be visualized as continuous surfaces rather than simple atom-pair contacts, offering insights into the design of new and improved ligands. The method is also applicable to biological systems, such as proteins and DNA, where non-covalent interactions are crucial for function. The study demonstrates that the method is effective for visualizing non-covalent interactions in complex systems, providing a valuable tool for chemists and biologists.This study presents a method to detect non-covalent interactions in molecular systems using electron density and its derivatives. The approach identifies non-covalent interactions as low-density, low-gradient regions in real space, which are distinct from covalent bonds and electrostatic interactions. The method requires only atomic coordinates and is efficient for large systems such as proteins and DNA. It provides a rich representation of various non-covalent interactions, including van der Waals forces, hydrogen bonds, and steric repulsion. The method uses the sign of the second Hessian eigenvalue to distinguish between different types of non-covalent interactions, with the density on the interaction surface indicating the interaction strength. The approach is validated using a variety of molecular systems, including small molecules, complexes, and solids. The results show that non-covalent interactions can be visualized as continuous surfaces rather than simple atom-pair contacts, offering insights into the design of new and improved ligands. The method is also applicable to biological systems, such as proteins and DNA, where non-covalent interactions are crucial for function. The study demonstrates that the method is effective for visualizing non-covalent interactions in complex systems, providing a valuable tool for chemists and biologists.