Some metal organic frameworks (MOFs) incorporate nodes that are nanoscale metal oxides, and the hydroxy-containing functional groups on them provide opportunities for introducing catalytic sites with precisely defined structures. Investigations have been done to understand the structures of these groups on nodes and node vacancies, because, in prospect, atomic-scale modulation of the composition, areal density, and/or siting of the groups would open up possibilities for exquisite tuning of the siting and performance of subsequently anchored catalytic units (e.g., single metal ions, pairs of metal ions, or well-defined metal-ion-containing clusters). We have combined infrared (IR) spectroscopy and density functional theory (DFT) to demonstrate tuning of these sites, namely, hydrogen-bonded OH/OH2 groups on the Zr6 nodes of the MOFs UiO-66 and NU-1000 via the intermediacy of node methoxy (or ethoxy) groups formed from methanol (or ethanol). Methoxy (or ethoxy) groups on node vacancy sites are converted to a structure incorporating one vacant Zr site and one terminal OH group per face by reaction with water. Our results highlight how the combination of DFT and IR spectroscopy facilitates the determination of the identity and chemistry of the functional groups on MOF node vacancies and defect sites.