Crystalline 3-D materials bearing inter linked domains of differential porosity and functionality offer the potential for organizing and shuttling molecular and nanoscale matter to specific locations within 3-D space. Here, we present methods for creating prototype MOF materials that have such structural features. Specifically, the process of pore expansion via ligand exchange was studied for an isoreticular series of mesoporous MOFs based on bMOF-100. It was found that pore expansion occurs incrementally in small steps and that it proceeds gradually in an "outside-in" fashion within individual crystals. The ligand exchange reaction can be terminated prior to complete crystal conversion to yield intermediate product MOFs, denoted bMOF-100/102 and bMOF-102/106, which bear descending porosity gradients from the crystal periphery to the crystal core. As a proof of concept, size-sensitive incorporation of a gold thiolate nanocluster, Au-133(SR)(52), selectively in the bMOF-102/106 crystal periphery region was accomplished via cation exchange. These new methods open up the possibility of controlling molecular organization and transport within porous MOF materials.