Tag: STM

scanbot

Jules has put in the hard yards implementing nanonisTCP as a python module, and leveraged that to create scanbot, a tool for automating the tasks of preparing a good imaging & spectroscopy probe, as well as a suite of functions for performing nuanced, drift-corrected measurements over very long timescales.

See the below example of systematically grid scanning 100x100nm images to concatenate a comprehensive view of the surface. Right is the upper left red corner, where self-assembled molecular islands are visible.

Ceddia et al., (2024). Scanbot: An STM Automation Bot. Journal of Open Source Software, 9(99), 6028, https://doi.org/10.21105/joss.06028

MgPc ARPES

We had the opportunity to use the new toroidal analyzer at the Australian synchrotron to do ARPES of self-assembled monolayers of MgPc on Ag100.

Careful simultaneous fitting of different high-symmetry EDC measurements, in concert with the structural understanding gleaned from ncAFM & LEED characterization, allowed us to tease out a feature with bandwidth 20 meV, which was surprising to us given that we did the ARPES at room temperature.

Bruce Cowie & Anton Tadich made it possible to break into this kind of measurement with just a week of time; Anton has been instrumental in supporting the analysis that was required to get this one across the finish line.

Hellerstedt, J., et. al. (2022). Direct observation of narrow electronic energy band formation in 2D molecular self-assembly. Nanoscale Advances https://doi.org/10.1039/D2NA00385F

Counting Molecules

9-azidophenanthrene produces a rich manifold of products when deposited on Ag(111).

The images we took for this study inspired this work to develop a lightweight script to count the molecules we observed, and categorize them.

Our personal journey of computer vision rediscovery led us to Zernike moments, a rotationally invariant basis set that solves the problem of identifying the same molecules with relative rotations, in an image.

We put some effort into making this module user-friendly, the example scripts offer a reasonable template to apply to any old SXM file you might want to histogram.

Hellerstedt, J., et. al. (2022). Counting Molecules: Python based scheme for automated enumeration and categorization of molecules in scanning tunneling microscopy images. Software Impacts https://doi.org/10.1016/j.simpa.2022.100301

github repo

MgPc-MgPc Hybridization

ncAFM atomic registration of MgPc molecule on Ag100
nc-AFM atomic registration of single MgPc molecule on Ag100 (surface atoms top and bottom stripes)

Marina Castelli studied the phthalocyanine containing magnesium (MgPc) via 5K scanned probe microscopies extensively during her PhD.

‘Routine’ STM characterisation showed that the molecules were interacting with one another on the Ag100 surface.

ncAFM showed identical contrast for all molecules, pointing to an electronic origin to the observed changes in appearance.

Our key observation was to track the shape of the occupied LUMO for different pairwise distances, an electronic feature that otherwise remained isoenergetic.

With multipass dI/dV mapping we were able to quantitatively track from four- to two-fold rotational symmetry, over distances out to ~3 nm. We found the spatial extent of this attractive hybridization quite surprising.

“Long-Range Surface-Assisted Molecule-Molecule Hybridization”, Small (2021). 10.1002/smll.202005974

FLEET PR
ArXiv link

STM image of MgPc molecules on Ag100 surface
STM image showing the neighbor-induced symmetry reduction