In the present work, using a systematic approach with DFT and TD-DFT techniques, we investigate the isomerization impact on Y18 and Y18-ID, two electron acceptors belonging to the Y family. Furthermore, the effect of the halogen atom was assessed by changing the original fluorine atoms with chlorine, bromine, and iodine. Two structural isomers were proposed for each acceptor, and a configurational (rotamer) for each structural isomer. A benchmarking was performed for relative energies, molecular planarity, light-harvesting features, frontier molecular orbitals alignment, electron-accepting indexes, reorganization energies, and average electrostatic potential. Mainly, structural isomerization yields the most significant modification to the studied properties and, to a lower extent, rotamerization. Nonetheless, the impact of rotamers might not be ignored, mainly in electron-accepting character and intermolecular electric field. Indeed, the modification that rotamers induce in some properties is comparable to that induced by the modification of halogen atoms.