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,

Mott transition in kagome MOF

Ben & Bernard’s work on the two-dimensional kagome metal-organic framework is out this week (26 April 2024) in Nature Comms.

It was fantastic to see interesting electronic properties emerge at relatively big energy scales for this sort of work, when we were finally able to get the 2d kagome MOF composed of Cu adatoms & DCA molecules, to self-assemble on insulating hexagonal boron nitride (hBN) supported by a Cu111 metallic substrate.

We teamed up with Ben Powell’s group at UQ for the many-body expertise required to understand the tunnel junction and substrate work function dependent modulations of the electronic gap in the language of Mott physics.

Lowe, B., Field, B., Hellerstedt, J. et al. Local gate control of Mott metal-insulator transition in a 2D metal-organic framework. Nat Commun 15, 3559 (2024).

Striped Phase

While pursuing metal-organic frameworks, we stumbled on something unexpected but experimentally robust back in June of 2019. DCA molecules and Au adatoms on Ag111 form DCA-Au-DCA units, and the cyano groups aren’t involved as you’d intuitively expect.

It took some heroic effort and creative thinking from Adam & the team in Prague to “just run this one through the computer real quick”, but nonetheless we’re pleased to have this explanation of the selective C-H scisson necessary to justify the observed end products.

Lowe, B., et. al. (2022). Selective Activation of Aromatic C–H Bonds Catalyzed by Single Gold Atoms at Room Temperature. J. Am. Chem. Soc.


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

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

github repo

2021 AIP summer meeting

The AIP summer meeting was a hybrid event this year 6-9 Dec. ’21 with the border restrictions still in place preventing us from travelling to Brisbane.

Iolanda kindly invited me to talk about Marina’s MgPc hybridization work as well as new results of orbital tomography performed at the Australian Synchrotron (in preparation).

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.

Thanks also to Peggy Schönherr, Peggy Zhang, Peter Jacobson, and Iolanda DiBernardo for contributing talks to the SPM focus session.

Bernard Field talked about how he’s pushing forward how we can rationalise our observations of self-assembled MOF structures, stemming from our recently published experimental results that Agustin talked about in the MOF focus session.

Kagome metal-organic framework

Dhaneesh Kumar has extensively studied the on-surface properties of the DCA molecule for his PhD. After getting a good handle on just the DCA on Ag111, we started sprinkling some Cu atoms into the mix.

We observed the same honeycomb kagome structure that forms on Cu111– as seen in an ncAFM force volume shown in the right image. It has also been synthesized on graphene.

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.

ncAFM force volume of DCA (structure superimposed upper right) self-assembly on Cu111 surface. dZ denotes lift of sensor away from surface for each frame.

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.

STS maps
dI/dV STS mapping at biases indicated upper left
DCA Cu Kagome schematic
Schematic of Kondo screened spin moments within the MOF. Blender by Dhaneesh

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.

ArXiv link
FLEET blog

Concerted Proton Transfer

We stumbled on a very curious observation in the summer of 2018 with DABQDI molecules provided by Olivier Siri‘s team.

ncAFM image of 26 molecule chain. Unfiltered data.
STM chain manipulation
Repeated manipulations with STM tip are capable of dragging a DABQDI chain around the Au111 surface.

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

ArXiv link

March Meeting 2021

I’m presenting Marina’s work on MgPc hybridization in Focus Session B56 on Monday 15/3 at 1318 (CDT).

Link to my presentation slides.

Other talks from our group:
Dhaneesh Kumar, “Kondo Effect in a 2D Kagome Metal-organic Framework on a Metal” (15/3 1218 CDT)

Bernard Field, “Electronic and Magnetic Structure of Metal-Organic Lattices on Substrates” (15/3 1242 CDT)

Ben Lowe, “Atomic-Scale Evidence of Surface-Catalyzed Gold-Carbon Covalent Bonding” (18/3 1206 CDT)

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

ArXiv link

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