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Atomically precise nanoclusters (NCs) are of great interest due to their well-defined structures and molecule-like properties. Understanding their structure–property relationship is an important task because it can help tailor their structures to achieve specific desired properties. In this study, the temperature-dependent bonding properties of Ag44(SR)30 have been revealed by extended X-ray absorption fine structure (EXAFS) with a new structure analysis method, which includes two Ag–S and two Ag–Ag fitting shells. It has been proven that the EXAFS fitting quality can be improved significantly compared with the conventional method. New insights into Ag–S bondings were discovered based on the fitting results obtained from the new method. It allows us to observe two different bonding properties within the Ag–S motifs, which cannot be discovered by using the conventional method. Additionally, the metal core of Ag44(SR)30 exhibits uncommon thermal behavior, which could be connected to the absence of the center atom in the icosahedral core. Our results demonstrate that the new structure analysis method can provide a more reliable comparison of NCs structural changes than the conventional method, and it could be applicable to other NCs. The revealed temperature-dependent bonding properties can provide insights into the structure–property relationship of Ag44(SR)30, which can help design new NCs materials with tailored properties.