From AC-STEM Image to 3D Structure: A Systematic Analysis of Au55 nanocluster

TL;DR

This paper presents a systematic method to extract 3D atomic structures of nanoclusters from AC-STEM images, combining image analysis with atomic interaction modeling and DFT refinement, demonstrated on Au55.

Contribution

The novel approach integrates 2D AC-STEM image analysis with atomic interaction models and DFT to reconstruct and analyze 3D nanocluster structures.

Findings

Au55 cluster has mixed icosahedral and crystal-like structures.

Low energy barriers allow conformational changes at room temperature.

Multiple cluster configurations fit the experimental image nearly equally well.

Abstract

Aberration-corrected scanning electron microscopy (AC-STEM) can provide valuable information on the atomic structure of nanoclusters, an essential input for gaining an understanding of their physical and chemical properties. A systematic method is presented here for the extraction of atom coordinates from an AC-STEM image in a way that is general enough to be applicable to irregular structures. The two-dimensional information from the image is complemented with an approximate description of the atomic interactions so as to construct a three-dimensional structure and, at a final stage, the structure is refined using electron density functional theory (DFT) calculations. The method is applied to an AC-STEM image of Au55. Analysis of the local structure shows that the cluster is a combination of a part with icosahedral structure elements and a part with local atomic arrangement characteristic of crystal packing, including a segment of a flat surface facet. The energy landscape of the cluster is explored in calculations of minimum energy paths between the optimal fit structure and other candidates generated in the analysis. This reveals low energy barriers for conformational changes, showing that such transitions can occur on laboratory timescale even at room temperature and lead to large changes in the AC-STEM image. The paths furthermore reveal additional cluster configurations, some with lower DFT energy and providing nearly as good fit to the experimental image.