3D Electron Diffraction Reveals Counterion Coordination in Co-Existing Polymorphs of Ag₂₉ Nanocluster

We unravel the complete structural architecture of the polymorphic Na₃[Ag₂₉(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 Ag₃S₃ 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.