Born–Oppenheimer molecular dynamics (BOMD) in combination with density functional theory, augmented with a damped empirical dispersion term, has been used to study the behavior of dilauroyl phosphatidylcholine (DLPC) isomers with temperature. In contrast to dimyristoyl phosphatidylcholine (DMPC), the BOMD results show the presence of various conformations at different temperatures. The molecular order–disorder process, quantified by the distance-fluctuation criterion as a function of temperature, is characterized by two transitions. This is in line with the known two-phase transitions of DLPC bilayers, involving trans to gauche conformational changes in the alkane chains. The different temperature dependence of the DLPC and DMPC molecules suggests that the experimentally observed unusual dynamics of DLPC bilayers compared to that of longer chain lipids is governed to a large extent by the intramolecular dynamics. A first-principles methodology applied at the molecular level can thus be an appropriate tool for microscopic analysis of the order–disorder transitions, which are related to the molecular structural transformations within large assemblies. © 2012 Wiley Periodicals, Inc.