The lipid dioctadecylamine (DODA) has been shown to self-organize in plate-like structures in aqueous solution. While in a previous model, we investigated by simulations its mesoscopic collective behaviour, here, we considered atomic partial charge distribution as determined by ab initio quantum chemical computations, and its relationship with different conformations of the DODA molecule. After comparison of the charges obtained at different levels of theory on the stretched form of DODA, we show that gas phase charges are sufficient to represent what appears to be an intrinsic property of the lipid, independently from the solvent. As the molecule becomes distorted, significant partial charge fluctuations appear along the aliphatic chains. (C) 2003 Elsevier B.V. All rights reserved.