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

Thin-film Dirac semimetal review article

Iolanda DiBernardo reviewed the development of Na3Bi as a topological electronic material.

The physics of Dirac semimetals (“3d graphene”) is introduced, and the results from the last half decade are tied together in one narrative, in particular our work at Monash demonstrating that Na3Bi grows directly on insulators, and that indeed an electric field will open a topological gap, two key ingredients to achieving a working “topological transistor”.

“Progress in Epitaxial Thin‐Film Na3Bi as a Topological Electronic Material”, Advanced Materials, 2021. 10.1002/adma.202005897