Author: Damian Allis

Posted on

Investigations Of Intramolecular And Intermolecular Noncovalent Interactions On Alkaline Earth Metal Complexes of –OC(Ph)(CF3)2

Above: The most-stable gas-phase configuration (1a, two views shown) exhibits π···H THF interactions (shown in gold) and F···H interactions (shown in green). The next most stable configurations (1c, shown as representative) exhibit a significant π···π interaction (shown in purple) and F···H interactions. In the higher energy configurations most similar to the crystal structure (crystal), there is no π···π interaction, only several F···H interactions.

What the crystal giveth, the gas phase taketh away.

Available open access (h/t Le Moyne College, past home of the great Prof. John McMahon) at pubs.acs.org/doi/10.1021/acs.inorgchem.6c01110. A few key sentences from the paper that nicely summarize what the theoretical work predicts compared to the crystallographic characterization.

However, in light of our theoretical findings for 1-4 that show the predicted M···F interactions in the gas phase are weaker than F···H and π···H, the reasons for the observed solid-state structures may in fact be more complex than M···F stabilization alone. Indeed, reliance on solid-state interatomic distances to determine the importance of relatively weak interactions such as M···F, F···H and π···H, assuming that shorter-is-stronger, may lead to overemphasis of their importance. Not all interactions are favorable, and other more favorable interactions elsewhere in the solid state may force two atoms to be nearer than expected.

A number of my previous papers explore how molecular geometries in even seemingly rigid organic frameworks (such as dodecahedrane) change due to crystal packing interactions, an effect clearly observable from symmetry breaking, shifts, and splittings in vibrational spectra. Among the alkali and alkali earth series, where crystallographic characterization has long been a basis for assessing the strengths and weaknesses of observed interactions based on interatomic separations, this new study of Mg…F, Ca…F, and Sr…F interactions in both the solid-state (crystallography) and in the gas/solution-phase (theory) reveal that the complexes in the absence of crystal packing interactions take on different geometries and, as a consequence, interactions one might characterize as "stabilizing" due to their existing below reported cut-off values from other crystal studies go away in favor of other, more favorable intramolecular interactions being available. Obviously, this speaks to the balance between intramolecular and intermolecular stabilization in the solid-state, something being considered specifically for the Mg…F series in ongoing work.

Authors: Anna Y. O’Brien, Yuriko Takahashi, Miriam Gillett-Kunnath, Damian G. Allis, Ana Torvisco, and Karin Ruhlandt-Senge

ABSTRACT: Alkaline earth metals are relatively abundant, inexpensive and desirable as metal−organic complexes for applications in electronics and catalysis. Synthetic challenges arise from their high reactivity and the tendency of their compounds to form aggregates. Previous work demonstrated that certain fluorinated alkoxide ligands improved the volatility of alkaline earth metal and mixed-metal complexes, in part due to the presence of noncovalent secondary M···F interactions. This work further explores the impact of secondary interactions on their structure. The fluorinated alkoxide 2,2,2,2′,2′,2′-hexafluorocumyl alkoxide, −OC(Ph)(CF3)2 (“L”), introduces the possibility of both M···F and M···π stabilizing interactions. Synthetic methods including alkane elimination (Mg), direct metalation(Ca,Sr,Ba), and protonolysis (Ba) with complexation to L in the controlled presence and/or absence of neutral donors afforded MgL2(thf)2, (1) trans-CaL2(thf)4 (2), cis-SrL2(thf)4 (3), Sr2(μ2-L)3L(thf)3 (4), Sr3(μ2-L)4L2(OEt2)2 (5), [Ba(μ2-L)2]n·1/4 (OEt2) (6), and [Ba(μ2-L)2]n (7). Structural characterization shows the number of secondary interactions increase for the heavier metals and decreasing presence of the neutral donor, coinciding with increased nuclearity. Computational studies predict notable differences between preferred configurations that might exist in the gas-phase and those observed in the solid state.

Posted on

(Hetero)adamantane Synthesis: A Triple Alkylation Reaction

Above: Examples of subtractive and additive mechanosynthesis under IM-STM/UHV conditions. HAT between activated 19 (chemisorbed on a Si(100)-2×1 surface) and H:Si(100)-2×1 SPC apex (A) and possible reaction outcomes between activated 19 (chemisorbed on a Si(100)-2×1 surface) and Si(100)-2×1 SPC apex including additive (C2-transfer) and subtractive (Si-atom abstraction) mechanosynthesis (B). BDEs calculated using ωB97X-D/Def2-TZVPP of model compounds 1-ethynyl-1-germaadamantane (model of molecular tool) and ethynyl-tris(trimethylsilyl)silane (model of surface-bound acetylene). See the pre-print for more.

Available as a preprint: https://chemrxiv.org/doi/full/10.26434/chemrxiv.15002728/v2

I described it as "Prelude to Foundational" on an X post, as the entire process that resulted in "Atomically precise mechanosynthesis of carbon structures on hydrogenated Si(100) by inverted-mode STM" (APM-IM-STM) was long, involved, and exploratory — the ground-floor search for the most viable conditions for performing the reported work by our SPM experts, theoreticians, and synthetic chemists at CBN Nano Technologies (CBNNT). To that end, a considerable improvement in adamantane cage chemistry — including the generation of functionalized (hetero)adamantane cages containing carbon and germanium bridgehead atoms (with the option for more!) — was realized by the amazing CBNNT synthetic chemistry team in collaboration with Brilliant Matters.

My small contribution (to v2) provided additional context for the applications in our current hardware setup – the one that provided the data for both inverted-mode STM (IM-STM) and additive mechanosynthesis. Folks with a history tracking the technical studies in the MNT/AMM/APM community likely have seen papers exploring molecular tool designs for, specifically, carbon dimer transfers. This simple C₂ feedstock was the basis for proposing fabrication of diamond and related materials based on mechanosynthetic principles, from basic tool designs all the way through what became 1:40–2:40 of the famed Nanofactory Animation.

Whereas playing with the electronic structure of strained π-bonds to promote dimer transfer was key to the predicted behavior of DC10c (I now host a local copy of the PDF, since the journal version is no longer retrievable), most of the molecular transfer tool papers employed germanium bridgehead atoms for this task. The Ge–C bond is a fair bit weaker than the C–C bond, making dimer transfer highly favorable in configurations where the in-process build is ready to accept those dimers into an extended carbon lattice through basic radical coupling. While tin and lead would appear to be reasonable candidates based on their placement in the periodic table (C–Si–Ge–Sn–Pb), they were computationally demanding (and certainly were back in the early 2000s to get right), were prone to much more interesting chemistry owing to their large, polarizable electron shells (which risks the chemistry becoming more involved, including possible intramolecular reactions on delivery), and were certainly not the favorite elements to do organic chemistry with whenever the conversation came up with our chemists or with potential collaborators (which, as a chemical grandchild of John Verkade, I get). For many of the details on the use of germanium, see the bibliography and available papers at molecularassembler.com/Nanofactory/AnnBibDMS.htm. And, from this paper:

"Herein lies the significance of the functionalized germanium bridgehead as a first synthetic target for exploring additive mechanosynthesis through molecular transfer: bridgehead germaadamantanes provide a position for covalent bonding of species that can be activated for chemical transformations with far greater chemical tractability and stability than a comparable tin or lead analogue."

Fast-forward nearly 20 years, and the Ge bridgehead has survived a number of assessments of candidate tools to remain the delivery atom of choice, from Rob and Ralph's A Minimal Toolset for Positional Diamond Mechanosynthesis all the way to synthesis and first demonstrations. From all that work, this paper reports the significant improvements in yield and significant reduction in reaction steps for a convergent, triple-alkylation route to (hetero)adamantanes with interchangeable bridgeheads under mild conditions, turning two decades of Ge-bridgehead tool design into quantities sufficient for our mechanosynthetic exploration.

Things did get interesting on the long path to the first demonstrations. As is apparent from the APM-IM-STM paper, we are clearly jogging before running (from a purely diamondoid perspective, anyway) by working with a more tractable material in the form of Si(100) instead of diamond or any other carbon surface.

And here is the issue awaiting sufficient address. Bond-dissociation enthalpies for Ge–C and Si–C become uncomfortably close across an ethynyl (our C₂ dimer) fragment. As a result, every factor affecting bond strength at either position — dopant identity and placement on either side of the junction, current, defects, angle, and the residual theoretical uncertainty in the bonds themselves — becomes a variable driving the scission outcome. That, in turn, hints that additional levels of control are needed if the bridgehead, feedstock, and workpiece are to behave as they do in ongoing work and the desired outcomes (perhaps more philosophical than chemical — demonstrating a capability more than a specific product) are to be achieved.

Upcoming work (already discussed in presentations at conferences; I won't disclose details here prior to preprints being available, but am pleased to report such disclosures are imminent) explores just how uncomfortably close the bonds relevant to mechanosynthesis are in the current material/molecular-tool combination. Lessons learned from that process to follow.

Authors: Terry McCallum, Sam Rohe, Mathieu Morin, Hsin Yao Su, Samuel W. J. Shields, Kashif Tanveer, Marius Mamone, Nicolas Zindy, Damian G. Allis, Aru Joy Hill, and Michael Drew

ABSTRACT: (Hetero)adamantanes containing tetrel bridgeheads are important structures in surface and chemical sciences. Syntheses of diamondoid structures generally occur in a linear fashion, often using harsh conditions. These limitations make it difficult to access diverse (hetero)adamantane-based molecules with interchangeable functional groups for broad applications. The discovery of an expedient and convergent methodology for the synthesis of diamondoid scaffolds is described. The convenient synthetic route proceeding via a triple alkylation reaction represents a breakthrough in accessing the adamantane molecular class. Applications of this transformation to diamondoid tripods containing tetrel bridgeheads (C- and Ge-) were explored.

Posted on

Atomically Precise Mechanosynthesis Of Carbon Structures On Hydrogenated Si(100) By Inverted-Mode STM

Above: Mechanosynthetic C2 donation. (A) Schematic of the inverted-mode STM setup. EAOGe-C2I molecules are deposited on flat Si(100), and an H-passivated Si(100) silicon probe chip (SPC) with a flat, crystalline apex is positioned above the surface. The molecules function both as imaging probes, where an applied bias (VS) drives a tunneling current (IT) through the molecule, and as reagents capable of chemically reacting with the build site. (B-E) Mechanosynthetic sequence showing the evolution of the build site as it is imaged with and modified by a molecule (Tool 1). As the build sequence proceeds, both the tool termination (inset) and atomic composition in the target area (white rectangle) change. Starting from a bare build site (B), two Si dangling bonds (DBs) are patterned by bias pulsing in an inter-row (IR) configuration (C), followed by molecule de-iodination (D), and transfer of a C2 unit to the DB pattern (E). (F) Small-area scan of the build site following the C2 transfer, centered on the target area and imaged with a new, intact tool (Tool 2). (G, H) Simulated STM image and geometry of C2 in the IR configuration (IR-C2), reproducing the experimental image shown in (F). Figure 1 from arXiv.

I've been working on the theory side for over 22 years for such an announcement, and it is beyond gratifying to be able to finally report on experimental advances.

https://arxiv.org/abs/2605.27250

From 1986, when it was first proposed by K. Eric Drexler, to 2026, when its first instances as envisioned by many in the community (to a basic extent, anyway) have now been experimentally demonstrated – subtractive mechanosynthesis of surface hydrogen atoms and now additive mechanosynthesis of carbon dimers on passivated Si(100).

Atomically precise, positionally-controlled mechanosynthesis. High reliability. Including the demonstration of C-C bond formation in the form of short polyyne chains in surface configurations never before reported in the literature.

"Hypothetical" on the wikipedia page until this morning (fixed it). The controversy over its feasibility was never to be settled until it was done in a lab. I am pleased to report, thanks to the efforts of a great team at CBN Nano Technologies, Inc., that the "hypothoversy" has found its end.

At the very least, any nay-sayers outside of the original molecular manufacturing, (amm) atomically precise fabrication (apf), or atomically precise manufacturing (apm) communities can now say with conviction "that's not what I meant!"

Had this been in place prior to what the United States National Nanotechnology Initiative became, the field and the world might be significantly different today. And now awaiting publication of my chapter this summer in a new three-volume set from Springer Nature on Radical Longevity, where I'm fortunate to have been invited to provide my own highly biased perspectives on where this and upcoming work might go in the next decade or two.

Authors: Cowie M., Deimert C., Groome R., Inayeh A., Mackie C.J., Myall J., Rohe S., Sandoval L., Sayed-Akhmad K., Thanabalasingam B., Wotton R., Addou R., Asani A., Blue B., Bottomley A., Clarcia K.A., Enright T., Fan J.Z., Freitas Jr. R.A., Godfrey A.T.K., Hill A., Huff T., Jobes M., Kirby R.J., Ma H., Maahs A.C., MacLean O., Maley S.M., Marshall M., McCallum T., Merkle R.C., Morin M., Plumadore R., Rodriguez H., Savoie M., Scheffel B., Wong J.L., Allis D.G, Barton J., Drew M., Kennedy M.R., Taucer M., Takatani T., Vobornik D., Yamachika R., Durand M.

CBN Nano Technologies, Inc. (CBNNT); Ottawa, K1Y 4W5, Canada

May 26, 2026

The ability to build atomically precise structures on surfaces with complete control over both atomic placement and chemical bonding remains a central challenge in nanoscale fabrication. Here, we demonstrate simultaneous spatial and chemical control over the mechanosynthetic fabrication of carbon structures. Using inverted-mode STM, C2 units are donated from surface-deposited molecules to pre-patterned reactive sites on a hydrogen-passivated Si(100) surface. We demonstrate single-site C2 donation, spatially patterned multi-site C2 donation, and the stepwise assembly of polyyne structures through successive C-C bond formation. Together, these results establish controlled mechanosynthetic donation as a foundational capability for programmable atomically precise fabrication.