The catalytic activity of the Zr-benzenedicarboxylate (Zr-BDC) UiO-66 increases by using synthesis modulators as trifluoroacetate (TFA) or hydrochloric acid (HCl), which can be removed post-synthetically. The catalytic activity of the Zr-benzenedicarboxylate (Zr-BDC) UiO-66 can be drastically increased if some BDC linkers are missing, as this removes the full coordination of the framework metal ions. As a result, metal centers become more accessible and thus more active for Lewis acid catalysed reactions. Addition of modulators (MDL) to the synthesis mixture can create more linker deficiencies (Vermoortele et al. , J. Am. Chem. Soc. , 2013, 135 , 11465) and leads to a significant increase in the catalytic activity due to the creation of a larger number of open sites. In this paper, we rationalize the function of the modulators under real synthesis conditions by the construction of free energy diagrams. The UiO-66 type materials form a very appropriate test case as the effect of addition of modulators hydrochloric acid (HCl) and trifluoroacetate (TFA) has been intensively investigated experimentally for the synthesis process and post-synthetic thermal activation. Under synthesis conditions, direct removal of BDC linkers requires a high free energy, but replacement of such linker by one or more TFA species might occur especially at high TFA : BDC ratios in the reaction mixture. Post-synthesis activation procedures at higher temperatures lead to substantial removal of the species coordinated to the Zr bricks, creating open metal sites. A mechanistic pathway is presented for the dehydroxylation process of the hexanuclear Zr cluster. For the citronellal cyclization, we show that the presence of some residual TFA in the structure may lead to faster reactions in complete agreement with the experiment. Hirshfeld-e partial charges for the Zr ions have been computed to investigate their sensitivity to substituent effects; a strong correlation with the experimental Hammett parameters and with the rates of the citronellal cyclization is found. The theoretical rationalization may serve as a basis for detailed active site engineering studies.