For three-dimensional (3D) metal organic frameworks (MOFs), the presence and nature of structural defects has been recognized as a key factor shaping the material's physical and chemical behavior. In this work, the formation of the "missing linker" defects has been addressed in the model biphenyl-4,4'-dicarboxylate (bpdc)-based Zr MOF, UiO-67. The defect showed strong dependence on the nature of the modulator acid used in the MOF synthesis; the defects, in turn, were found to correlate with the MOF physical and chemical properties. The dynamic nature of the Zr6 (node)monocarboxylate bond showed promise in defect functionalization and "healing", including the formation of X-ray-quality "defect-free" UiO-67 single crystals. Chemical transformations at defect sites have also been explored. The study was also extended to the isoreticular UiO-66 and UiO-68' systems.