Predicting Electron Distributions in Drug Molecules Using Density Functional Theory in Real Space
Published:
Author: Yeu-Guang Tung
Abstract: Electron distributions in drug molecules are crucial in drug design and can be predicted using density functional theory (DFT). We propose a comprehensive scheme to perform DFT calculations in real space instead of using the conventional orbital basis set. We detail the implementation of spherical space and basis, Pulay’s density mixing, Hamiltonian matrix construction, Kohn-Sham equation solution, and Bader’s charge analysis in discretized coordinate basis. We demonstrate that the demanding computation can be carried out in a highly parallel manner with simple codes by exploiting efficient algorithms in the PyTorch and NumPy packages. We perform calculations on the drug acyclovir and predict the electron distribution, partial charges, and energy levels in the molecule. The study may facilitate research in computational molecular science and structure-based drug design.