  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.
