welcome to somewhereville (.com)

Above: Experimental Conditions for Hydrogen Abstraction. a) Schematic showing the setup. Both probe and sample are Si(100). The probe is hydrogenated, while the sample is unpassivated to enable molecule adsorption. The sample has a sparse coverage of tall molecules (EAOGe-C2I). The x- and y-axes are used to laterally align a molecule with a target location on the build site, while the z-axis can adjust the separation between probe and sample, enabling the reaction to proceed. b-d) Zoom-in on the atomic configuration at the site of the reaction. Initially, the molecule is lined up with an atomic site on the probe apex (b); the molecule then approaches the targeted hydrogen atom until the reaction proceeds (c); finally, the molecule retracts, taking the hydrogen atom with it (d). Insets in (b) and (d) show inverted-mode STM images before and after H-abstraction. e) Potential energy of the system, calculated by density functional theory, as a function of the distance between the hydrogen atom and its host silicon atom, for two different separations of probe and sample (see Methods and Supplementary Section 2). For larger separation (triangles), the barrier to hydrogen transfer is about 1.2 eV . At a critical separation (squares), the reaction becomes barrierless. The black arrow represents the energetically downhill hydrogen transfer from the probe apex to the molecule and the green arrow indicates the retraction.

A Happy New Year for sure.

A new and innovative way to do scanning tunneling microscopy. And repeatable and controllable subtractive mechanosynthesis off a silicon surface under zero bias with a molecular tool based on a design approach developed a long number of years ago for the task. And the writing team threaded a narrow needle of depth and clarity perfectly.

https://arxiv.org/abs/2512.24431

Something wonderful. And the first big/very small step.

Authors: Eduardo Barrera, Bheeshmon Thanabalasingam, Rafik Addou, Damian Allis, Aly Asani, Jeremy Barton, Tomass Bernots, Brandon Blue, Adam Bottomley, Doreen Cheng, Byoung Choi, Megan Cowie, Chris Deimert, Michael Drew, Mathieu Durand, Tyler Enright, Robert A. Freitas Jr., Alan Godfrey, Ryan Groome, Si Yue Guo, Sheldon Haird, Aru Hill, Taleana Huff, Christian Imperiale, Alex Inayeh, Jerry Jeyachandra, Mark Jobes, Matthew Kennedy, Robert J. Kirby, Mykhaylo Krykunov, Sam Lilak, Hadiya Ma, Adam Maahs, Cameron J. Mackie, Oliver MacLean, Michael Marshall, Terry McCallum, Ralph C. Merkle, Mathieu Morin, Jonathan Myall, Alexei Ofitserov, Sheena Ou, Ryan Plumadore, Adam Powell, Max Prokopenko, Henry Rodriguez, Sam Rohe, Luis Sandoval, Marc Savoie, Khalil Sayed-Akhmad, Ben Scheffel, Tait Takatani, D. Alexander Therien, Finley Van Barr, Dusan Vobornik, Janice Wong, Reid Wotton, Ryan Yamachika, Cristina Yu, Marco Taucer

Abstract: Scanning Tunneling Microscopy (STM) enables fabrication of atomically precise structures with unique properties and growing technological potential. However, reproducible manipulation of covalently bonded atoms requires control over the atomic configuration of both sample and probe – a longstanding challenge in STM. Here, we introduce inverted-mode STM, an approach that enables mechanically controlled chemical reactions for atomically precise fabrication. Tailored molecules on a Si(100) surface image the probe apex, and the usual challenge of understanding the probe structure is effectively solved. The molecules can also react with the probe, with the two sides of the tunnel junction acting as reagents positioned with sub-angstrom precision. This allows abstraction or donation of atoms from or to the probe apex. We demonstrate this by using a novel alkynyl-terminated molecule to reproducibly abstract hydrogen atoms from the probe. The approach is expected to extend to other elements and moieties, opening a new avenue for scalable atomically precise fabrication.

Above: TIMe-Ge molecules on Si(100): 77 K STM scanning. (a) Experimental constant-current filled-states 77 K STM image of four TIMe-Ge molecules on Si(100)-(2×1) (I = 50 pA, V −2.0 V). Molecule deposition was performed onto a room temperature Si(100) substrate. (b) The four symmetry-equivalent on-dimer configurations of TIMe-Ge. An experimental STM tri-lobe is overlaid on the central triply-iodinated proxy. (c,d) Representative 77 K STM images of TIMe-Ge molecules deposited on Si(100) substrates held at <240 K and >400 K, respectively, prior to imaging. The dashed white ellipse in (c) marks a pair of dissociated, surface-bound iodine atoms. A minor low-pass inverse fast Fourier transform filter has been applied to highlight TIMe-Ge positions on the Si lattice. z = 0 for STM heights is referenced to the highest point of the Si dimer-row surface. Figure 2 in the article.

Those keeping track of diamondoid mechanosynthesis research of the mid-to-late 2000's and the very small number of us engaged in this very specific activity may note that the last of these papers was published in 2011 before effectively disappearing completely from academic (publication) activities. Those taking extra steps to keep track of those activities will note that the journal article submissions were replaced by patent applications. Lots of and lots of patent applications.

Saving the history of the 2010's and some of the early 2020's for a far future post, I am very pleased to report that the first academic and experimental foray into the applications of molecular tools for interesting future applications has been posted to arXiv recently (journal article acceptance to hopefully follow) thanks to the efforts of a very large and diverse group of researchers at CBN Nano Technologies (of which I am proud to call myself one).

Direct Link: https://arxiv.org/abs/2508.16798

Here, synthesized and activate-able molecules are deposited on Si100 and present, upon activation, nearly the smallest feedstock one could come up with for the carbon-based mechanosynthesis of anything – CH₂.

I point out as a particular highlight the consideration of design criteria for molecules we and others might want to use in the future for varied applications, which are listed below in a highly less-verbose form than the original draft included:

1. High molecular symmetry (makes many considerations easier)
2. Covalent bond formation (these are not weakly-bonding fragments)
3. “Loose legs, rigid body” (for surface sampling)
4. Lattice-matching (Legs "… should be at least long enough to reach from his body to the ground." – A. Lincoln)
5. Confidence in surface-bound orientations (nice to know they're there when you look)
6. An accessible, stable radical on the surface-bound molecule (the "business-end")

This work begins to bridge the gap between Molecular Toolsets (as proposed by Rob and Ralph) and demonstrations of molecules that contain functional groups that can be used for similar applications. As such, this work is partly "on the path" and, in light of all that was learned to get this specific work to the point of publication, partly identifying where one should start walking in the first place.

Still thinking small…

Authors: Taleana Huff, Brandon Blue, Terry McCallum, Mathieu Morin, Damian G. Allis, Rafik Addou, Jeremy Barton, Adam Bottomley, Doreen Cheng, Nina M. Ćulum, Michael Drew, Tyler Enright, Alan T.K. Godfrey, Ryan Groome, Aru J. Hill, Alex Inayeh, Matthew R. Kennedy, Robert J. Kirby, Mykhaylo Krykunov, Sam Lilak, Hadiya Ma, Cameron J. Mackie, Oliver MacLean, Jonathan Myall, Ryan Plumadore, Adam Powell, Henry Rodriguez, Luis Sandoval, Marc Savoie, Benjamin Scheffel, Marco Taucer, Denis A.B. Therien, Dušan Vobornik

Abstract: Scanning probe microscopy (SPM) investigations of on-surface chemistry on passivated silicon have only shown in-plane chemical reactions, and studies on bare silicon are limited in facilitating additional reactions post-molecular-attachment. Here, we enable subsequent reactions on Si(100) through selectively adsorbing 3D, silicon-specific "molecular tools". Following an activation step, the molecules present an out-of-plane radical that can function both to donate or accept molecular fragments, thereby enabling applications across multiple scales, e.g., macroscale customizable silicon-carbon coatings or nanoscale tip-mediated mechanosynthesis. Creation of many such molecular tools is enabled by broad molecular design criteria that facilitate reproducibility, surface specificity, and experimental verifiability. These criteria are demonstrated using a model molecular tool tetrakis(iodomethyl)germane (Ge(CH₂I)₄; TIMe-Ge), with experimental validation by SPM and X-ray photoelectron spectroscopy (XPS), and theoretical support by density functional theory (DFT) investigations. With this framework, a broad and diverse range of new molecular engineering capabilities are enabled on silicon.