Testing the ability of rhodanine and 2, 4-thiazolidinedione to interact with the human pancreatic alpha-amylase: electron-density descriptors complement molecular docking, QM, and QM/MM dynamics calculations.
In this paper we introduce AIM-UC, a free application that allows to create graphs related to Quantum Theory of Atoms in Molecules (QTAIM). The input data are files that contain 3D grid of electron density, in some known formats: CUBE from gaussian, grd from DMol and CHGCAR from VASP. Also it supports wave function files from AIMPAC. The application calculates 2D regular grids (electron densities and its laplacians) in a plane positioned by the user. By using bicubic interpolation and the Newton-Raphson method, the critical points at the plane can be calculated, and the gradient field and molecular graph can also be generated using the Cash-Karp Runge-Kutta method. It also permits plotting the electron density and its negative laplacian on the selected plane. Moreover, for both 2D grids, it is possible to calculate the contour maps using the “Marching Squares” algorithm. This application also permits finding the critical points in the 3D space. The output consist of plain text files and images in PNG, BMP and EPS (encapsulated post script) formats. AIM-UC was programmed in C++, using the GUI toolkit FLTK (fast light toolkit) and OpenGL (open graphic library).