Understanding fundamental behavior of luminescent nanomaterials upon photoexcitation is necessary to expand photocatalytic and biological imaging applications. Despite the significant amount of experimental work into the luminescence of Au-25(SR)(18)(-) clusters, the origin of photoluminescence in these clusters still remains unclear. In this study, the geometric and electronic structural changes of the Au-25(SR)(18)(-) (R = H, CH3, CH2CH3, CH2CH2CH3) nanoclusters upon photo excitation are discussed using time-dependent density functional theory (TD-DFT) methods. Geometric relaxations in the optimized excited states of up to 0.33 angstrom impart remarkable effects on the energy levels of the frontier orbitals of Au-25(SR)(18)(-) nanoclusters. This gives rise to a Stokes shift of 0.49 eV for Au-25(SH)(18)(-) in agreement with experiments. Even larger Stokes shifts are predicted for longer ligands. Vibrational frequencies in the 75-80 cm(-1) range are calculated for the nuclear motion involved in the excited-state nuclear relaxation; this value is in excellent agreement with vibrational beating observed in time-resolved spectroscopy experiments. Several excited states around 0.8, 1.15, and 1.25 eV are calculated for the Au-25(SH)(18)(-) nanocluster. Considering the typical underestimation of DFT excitation energies, these states are likely responsible for the emission observed experimentally in the 1.15-1.55 eV range. All excited states arise from core-based orbitals; charge-transfer states or other "semi-ring" or ligand-based states are not implicated.