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Abstract Chalcogenide aerogels (chalcogels) are amorphous structures widely known for their lack of localized structural control. This study, however, demonstrates a precise multiscale structural control through a thiostannate motif ([Sn2S6]4−)-transformation-induced self-assembly, yielding Na-Mn-Sn-S, Na-Mg-Sn-S, and Na-Sn(II)-Sn(IV)-S aerogels. The aerogels exhibited [Sn2S6]4−:Mn2+ stoichiometric-variation-induced-control of average specific surface areas (95–226 m2 g−1), thiostannate coordination networks (octahedral to tetrahedral), phase crystallinity (crystalline to amorphous), and hierarchical porous structures (micropore-intensive to mixed-pore state). In addition, these chalcogels successfully adopted the structural motifs and ion-exchange principles of two-dimensional layered metal sulfides (K2x Mn x Sn3-x S6, KMS-1), featuring a layer-by-layer stacking structure and effective radionuclide (Cs+, Sr2+)-control functionality. The thiostannate cluster-based gelation principle can be extended to afford Na-Mg-Sn-S and Na-Sn(II)-Sn(IV)-S chalcogels with the same structural features as the Na-Mn-Sn-S chalcogels (NMSCs). The study of NMSCs and their chalcogel family proves that the self-assembly principle of two-dimensional chalcogenide clusters can be used to design unique chalcogels with unprecedented structural hierarchy.