In this study, Natural Bonding Orbitals (NBOs) were applied to isatin, 5-fluoroisatin, 5-chloroisatin, 5-methylisatin and 5-methoxyisatin using the Lee-Yang-Parr correlation functional B3LYP with 6-311++G(2d,2p) basis set. Natural bonding analysis was performed to consider the transfer interactions of intra-molecular charge, pre-hybridization and electron density within the isatin, 5-fluoroisatin, 5-chloroisatin, 5-methylisatin and 5-methoxyisatin. In natural bonding orbital analysis, the wave functions of the electrons were explicated in sets of occupied Lewis type terms, (bonds or lone pairs) and sets of unoccupied non-Lewis (anti-bond and Rydberg) localized natural bonding orbitals. The electron density between these orbitals was correlated to stabilize the interaction of donor-acceptor orbitals. Secondorder Perturbation Theory was employed to evaluate the stabilization energies of all possible interactions between donor and acceptor orbitals in natural bonding orbitals. The aim was to study the properties of these series and to produce a molecular geometry description, hyper-conjugative interactions, natural bond orbital (NBO) analysis and the HOMO-LUMO energy gap-dependent properties that are important for the stability of structures. From the results, it can be noted that for all forms, the HOMO-LUMO energy gap values decreased by substitution for the 5-fluoroisatin, 5-chloroisatin, 5-methylisatin and 5-methoxyisatin compounds and, with the exception of the deprotonated form in all the compounds, leading to less stable molecules. The anion form of the 5-methoxyisatin compound and the cation form of the 5-fluoroisatin, in which the HOMO-LUMO energy gap values increased, became more stable. It also appeared that the 5-CH 3-and 5-Cl groups caused an increase in the linear polarizability and anisotropic polarizability values in all forms; however, the 5-OCH 3 and 5-F groups caused different effects in different forms. Furthermore, we concluded that the intramolecular hyper-conjugative interactions between bonded atoms changed by groups. These changes caused changes in the electron density values in the atoms, which in turn led to a change in the stabilization energy values of the isatin, 5-fluoroisatin, 5-chloroisatin, 5-methylisatin and 5-methoxyisatin.