Lateral force microscopy is used to measure the frictional forces generated in sliding a silicon nitride tip on perflurooctyl trichlorosilane (FOTS) and octadecyltrichlorosilane (ODTS) monolayers self-assembled (SAM) on silicon wafer. The work is motivated by a need to rationalize the high friction of FOTS in comparison to that found for ODTS, inspite of the former having a low surface energy compared to that of the latter. Having first established that the tribology here is a thermally activated process, we use the Eyring equation to estimate the energetic barrier height to sliding motion, system activation energy, shear coordination and pressure activation volumes. For a molecular species when the velocity and temperature are unchanged in a sliding experiment and the activation energy remains unchanged the change in shear coordination with increasing normal load controls the friction coefficient. In comparing the performance of the two test molecules the friction coefficient of the FOTS is found to be three times greater than that of the ODTS; the corresponding difference in barrier height is about 10%. Our results indicate that when the two molecules are well ordered, the shear coordination modulates the frictional differential but it is the difference in their system activation energy, principally determined by electrostatic repulsion between the neighbouring molecules which is a dominant influence on their friction differential. © 2008 Springer Science+Business Media, LLC.