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 Impactshttps://doi.org/10.1016/j.simpa.2022.100301
Ben Lowe contributed a talk to the scanning probe microscopy focus session, with an update on how we’re closing in on understanding the mechanism of formation for some unusual metal-organic products identified with ncAFM measurements.
The key difference we observed on Ag111 was the Kondo effect, an STS peak at Fermi we tracked up to 150 K!
The consistent spatial distribution of this feature across the MOF was another key observation.
Bernard put in the hard yards with DFT/ +U calculations in conjunction with mean-field Hubbard modelling to rationalise our experimental observations as strong Coulomb interactions between electrons within the kagome MOF.
We’re excited by the possibilities for solid-state architectures to offer further access & control of these intriguing quantum states.
Kumar, D., et. al. (2021). Manifestation of Strongly Correlated Electrons in a 2D Kagome Metal–Organic Framework. Advanced Functional Materials, 2106474. https://doi.org/10.1002/adfm.202106474
We stumbled on a very curious observation in the summer of 2018 with DABQDI molecules provided by Olivier Siri‘s team.
While evaluating its experimental suitability for 1d coordination with metals, which has already proven to be fruitful, we noticed the molecules forming chain-like structures even before we introduced metal adatoms.
The low temperature SPM results are sublime: unusual mechanical stability, distinctive intermolecular bonding, and near-Fermi electronic states lighting up at the ends of the chains.
It took an extraordinary cast of theorists hailing from Pavel’s core group, FZU, Charles, Reykjavik, & Madrid Universities to unravel this puzzle and explain these observations as concerted proton tunneling causing a delocalization of electrons.
“Significance of Nuclear Quantum Effects in Hydrogen Bonded Molecular Chains”, ACS Nano, 2021. 10.1021/acsnano.1c02572
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.