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As an electron-deficient element, boron possesses fascinating three-dimensional structures and unconventional chemical bonds. Nanoclusters of boron have also been found to exhibit intriguing structural properties, observed to have predominantly planar structures, in stark contrast to bulk boron allotropes, which are composed of the ubiquitous B₁₂icosahedral building blocks. Here, we report observation of the 2D-to-3D transition and bulk-like structural features in the size-selected boron clusters, as revealed by photoelectron spectroscopy, chemisorption experiments, and first-principles calculations. In the small to medium cluster size range, planar boron cluster anions are found to be unreactive and only B₄₆^–and B₅₆^–are observed to chemisorb C₂H₄and CO under ambient conditions, suggesting major structural transitions at these cluster sizes. Notably, B₅₆^–is also found to be able to chemisorb and activate CO₂. The global minimum of B₄₆^–is found to adopt a core-shell structure (B₂@B₄₄^–), consisting of a B₂core within a B₄₄shell, reminiscent of the interstitial B₂dumbbells in the high-pressureγ-B₂₈form of bulk boron. More remarkably, both the global minimum and the second most stable isomer of B₅₆^–exhibit nest-like configurations, featuring the iconic B₁₂icosahedral core surrounded by a B₄₄half-shell (B₁₂@h-B₄₄^–), signifying the onset of bulk-like structural characteristics in boron nanoclusters.