Towards Atom-by-Atom Fabrication: Mechanosynthetic donation and abstraction

Abstract: Enabled by inverted-mode scanning tunneling microscopy (IM-STM) and the use of functionalized molecular tools, we demonstrate positionally-controlled mechanosynthetic addition (donation) of carbon and subtraction (abstraction) of silicon atoms on a model build site: atomically clean and crystalline Si(100). The resulting structures represent the first demonstrations of an emerging ability to manipulate radical chemistry with positional control of specific atoms and moieties in 3D. Furthermore, by comparing the behavior of molecular tools designed for atomic donation versus abstraction, we highlight general principles governing molecular tool design for selective and reliable mechanosynthetic functionality.

• The paper presents a dual mechanosynthetic method enabling atom addition (donation) and precise removal (abstraction) on Si(100) using IM-STM.
• It employs tripodal adamantane derivatives to form Si–C bonds and create Si vacancies, achieving a 54±7% donation rate and 100% abstraction selectivity with optimized tool design.
• The study underscores that tailored molecular tool engineering and mechanosynthetic protocols can drive deterministic atom-by-atom fabrication for advanced nanodevice engineering.

Mechanosynthetic Donation and Abstraction for Atom-by-Atom Fabrication via IM-STM

Introduction

The work "Towards Atom-by-Atom Fabrication: Mechanosynthetic donation and abstraction" (2606.13876) establishes critical advancements in atomically precise fabrication (APF) by demonstrating both addition (donation) and subtraction (abstraction) of specific atoms on Si(100) with positional control, using functionalized adamantane-based molecular tools deployed by inverted-mode scanning tunneling microscopy (IM-STM). Prior research in SPM-enabled manipulation was restricted by reliance on metallic probes and electronic bias, which limited positional selectivity and feasible structures. This study extends the capabilities through a mechanosynthetic approach, achieving bottom-up covalently bonded architectures atom-by-atom and exploring the role of molecular tool design for specific atomic manipulations.

Mechanosynthesis with Molecular Tools: Architecture and Protocol

The molecular tools are tripodal adamantane derivatives, comprising customizable flexible legs for substrate binding, an adamantane core for spatial orientation, and a reactive feedstock at the bridgehead. The prototype tool, EAOGe-C2I, employs an ethyl-legged, oxygen-terminated, germanium-bridgehead design with an acetylenic-iodo functional group, providing a protected source of ethynyl radical upon deiodination.

Mechanosynthetic interactions occur under UHV and cryogenic conditions. Tools are vapor-deposited, oriented, and deprotected (deiodinated) ex situ from the build site. Subsequently, an IM-STM protocol positions the tool with sub-ångström precision relative to a Si(100) build site on custom-fabricated Si probe chips. The targeted atom addition or abstraction is induced solely by mechanical approach/retraction, without applied bias. The process is governed by competitive bond dissociation enthalpies (BDEs) between the tool's bridgehead and the surface, with outcomes confirmed through systematic IM-STM imaging.

Atomically Precise Addition (Donation) and Subtraction (Abstraction)

Positioned ethynyl radicals on the adamantane-derived tools enable the formation of Si–C bonds via donation events, resulting in diverse arrangements such as inter-row, on-dimer, and inter-dimer C2 insertions. The approach yields unique carbon and silicon surface features consistent with prior theoretical and STM studies of acetylene/ethylene dehydrogenation on Si(100), confirming covalent C2 incorporation. A minority of trajectories yield Si atom abstraction, generating silicon vacancies (SiV) with characteristic dynamic instabilities in IM-STM images. Subsequent abstraction events form higher-order defects such as dimer vacancies (DV) and induce spontaneous dimer reconstructions.

The outcomes of a mechanosynthetic event depend sensitively on STM trajectory, the competition between Si–C and Ge–C (or C–C) BDEs, and the dynamic rearrangement of pendant groups upon retraction. Statistical analysis shows donation rates of $54 \pm 7\%$ with EAOGe-C2I tools, revealing the limits of selectivity with z-only trajectories and highlighting the demand for tool optimization.

Structural and Chemical Characterization via Imaging Modality

IM-STM imaging enables distinction between initial and final tool states (e.g., pre-interaction -C2I, post-donation -Ge·, post-abstraction -C2Si·) based on imaging modality signatures such as RPI contrast, lattice site symmetries, and contrast inversion. The chemical nature of terminal functional groups on the molecular tool is shown to correlate with unique imaging characteristics, facilitating identification and assignment of the mechanosynthetic outcomes.

Optimizing Mechanosynthetic Selectivity

To enhance selectivity for silicon atom abstraction, a new tool (MAOC-C2I) was synthesized by substituting the germanium bridgehead with carbon and employing shorter methyl-alcohol legs for fewer configuration isomers. This single-atom modification led to perfect selectivity for abstraction ($100\%$ abstraction, $n=163$, across both 4 K and 77 K), with no observed donation events. Extended silicon vacancy structures, including dimer vacancy arrays and arbitrary patterns such as "L" shapes of up to 10 sequentially abstracted atoms, were realized even at elevated cryogenic temperatures.

This result constitutes strong evidence that molecular tool structure alone can deterministically bias mechanosynthetic trajectories in additive or subtractive atomic construction, ensuring precise outcome control for targeted device architectures.

Implications, Limitations, and Future Prospects

This research advances the field of bottom-up APF by providing protocols for both atom addition and subtraction, verified for both carbon and silicon at technologically relevant Si(100) interfaces. The robust mechanosynthetic control, achievable by rational tool design combined with IM-STM, suggests feasible pathways toward constructing more complex and defect-corrected 3D atomically precise nanostructures, moving beyond planar surface chemistry.

The demonstration of single-atom resolution subtraction with $100\%$ selectivity, device-quality patterning, and in situ error correction opens new practical paradigms in nanofabrication, quantum device prototyping, and ultimately scalable 3D atom-by-atom manufacturing. However, stochastic elements still limit the deterministic assembly of intricate multi-atom structures, particularly under simple z-only STM manipulation protocols and for tool variants with lower selectivity. Further understanding of substrate dynamics and bond energetics, as well as the design of new mechanosynthetic trajectories and tool chemistries, will be critical to extending these results to more complex functional building blocks and temperature regimes.

The demonstration here of subtractive and additive APF at the single-atom level on semiconductor surfaces also underpins theoretical models of mechanosynthesis, reinforcing the practicality of positional control in radical surface chemistry and providing a foundation for developing precise, programmable manufacturing techniques at the atomic scale.

Conclusion

The paper presents a significant step in atomically precise fabrication by establishing both additive and subtractive mechanosynthetic methods using rationally designed molecular tools and IM-STM on Si(100). The robust selectivity achieved through molecular tool engineering underlines the critical importance of tool chemistry for deterministic atom manipulation. These findings enable new technical routes for single-atom device engineering, error correction, and bottom-up nanofabrication, bringing atom-by-atom manufacturing closer to practical realization.