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The HF method uses single determinant to solve Schrödinger equation and obtain molecular orbitals. A variety of post-HF methods such as MP2 and CCSD are needed to treat molecular systems in ground states accurately, while the CIS and EOM-CCSD methods are developed to study excited states. All these methods can write out wavefunction files in single determinant so that the unique electron density distributions of the system at all these calculation levels are available. The quantum theory of atoms in a molecule (QT-AIM) performs density topological analyses and rigorously obtain properties such as net atomic charges and delocalization and localization indices for ground states at HF/CIS and post-HF levels and for excited states at CIS, EOM-CCSD levels. The density functional theory (DFT) develops a larger number of functionals to account for the electron–electron correlation via exchange-correlation potentials, and TD-DFT methods study properties of electronically excited states. The DFT and TD-DFT methods rely on electron density to solve Schrödinger equations and write out final wavefunctions in single determinant format. Therefore, density-based analyses can be also done for a variety of DFT and TD-DFT methods. Along with molecular orbitals, density-based analyses are applied to explain ambident reactivity, to identify bonding characteristics in organic transition metal compounds, and to evaluate the performance of current DFT and TD-DFT methods. © 2023 Elsevier Inc. All rights reserved.