3D Electron Diffraction Reveals Counterion Coordination in Co‐Existing Polymorphs of Ag 29 Nanocluster

We unravel the complete structural architecture of the polymorphic Na 3 [Ag 29 (BDT) 12 (TPP) 4 ] nanocluster (NC) using three‐dimensional electron diffraction (3D ED) of microscopic crystals. By drop‐casting nanocluster solution directly onto microscopy grids, we achieve in situ crystallization of nanometer‐sized polymorphs and independently resolve co‐existing cubic and trigonal phases crystal‐by‐crystal from a single grid square. Using difference electrostatic potential (DESP) maps derived from empirical 3D ED data, we pinpoint the specific lattice locations of the elusive Na + counterions and observe distinct coordination environments across the two polymorphs. In the densely packed, solvent‐free cubic phase, Na + binds exclusively to thermodynamically favored pockets formed by one core‐anchored and two staple sulfur atoms. Conversely, within the open, solvated trigonal lattice, Na + occupies both these core‐anchored sites and alternative positions coordinated entirely by three sulfur atoms of an outer Ag 3 S 3 staple motif. These findings establish 3D ED as a powerful tool for resolving nanoscale polymorphic mixtures and demonstrate how macroscopic crystal packing influences local ionic interactions, providing key structural insights for the design of cluster‐based assemblies.