This paper reports a novel procedure using nanosomes, made of bola-hydroxyl and mercapto-palmitic acids, for the production of gold clusters with robust luminescent emissions and very large Stokes shifts. It shows that these results cannot be explained by the currently accepted mechanism based on ligand-to-metal charge transfer absorptions involving electron-rich ligands attached to the cluster core. Exhaustive characterization of the cluster samples using Mass Spectrometry, HR-TEM/STEM, XPS, EXAFS, and steady-state and time-resolved luminescence allows to deduce that a mixture of two cluster sizes, having non-closed shell electronic configurations, are firstly generated inside the nanosome compartments due to the difference in bonding strength of the two types of terminal groups in the fatty acids. This initial bimodal cluster size distribution slowly evolves into very stable, closed-shell Au cluster complexes (Au-6-Au-16 and Au-5-Au-14) responsible for the observed luminescent properties. The very small (approximate to 1.2 nm) synthesized cluster complexes are water soluble and suitable to be used for the conjugation of biomolecules (through the terminal COO- groups) making these systems very attractive as biomarkers and offering, at the same time, a novel general strategy of fabricating stable atom-level quantum dots with large Stokes shifts of great importance in many sensor applications. (C) 2015 Elsevier Inc. All rights reserved.