pith. sign in

arxiv: 2605.27250 · v1 · pith:PGMLOKVYnew · submitted 2026-05-26 · ❄️ cond-mat.mtrl-sci

Atomically precise mechanosynthesis of carbon structures on hydrogenated Si(100) by inverted-mode STM

Megan Cowie , Chris Deimert , Ryan Groome , Alex Inayeh , Robert J. Kirby , Cameron J. Mackie , Jonathan Myall , Sam Rohe
show 39 more authors
Luis Sandoval Khalil Sayed-Akhmad Bheeshmon Thanabalasingam Reid Wotton Rafik Addou Aly Asani Brandon Blue Adam Bottomley Kareem A. Clarcia Tyler Enright James Zhangming Fan Robert A. Freitas Jr. Alan T.K. Godfrey Si Yue Guo Aru Hill Taleana Huff Mark Jobes Hadiya Ma Adam C. Maahs Oliver MacLean Steven M. Maley Michael Marshall Terry McCallum Ralph C. Merkle Mathieu Morin Ryan Plumadore Henry Rodriguez Marc Savoie Benjamin Scheffel Janice L. Wong Damian G. Allis Jeremy Barton Michael Drew Matthew R. Kennedy Tait Takatani Marco Taucer Dusan Vobornik Ryan Yamachika Mathieu Durand
This is my paper

Pith reviewed 2026-06-29 16:38 UTC · model grok-4.3

classification ❄️ cond-mat.mtrl-sci
keywords mechanosynthesisSTMSi(100)carbon structurespolyyneatomically precise fabricationinverted-mode STMdangling bonds
0
0 comments X

The pith

Inverted-mode STM donates C2 units from molecules to reactive sites on hydrogen-passivated silicon to assemble carbon structures with atomic precision.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper demonstrates that inverted-mode scanning tunneling microscopy can transfer C2 units from surface-deposited molecules onto pre-patterned reactive sites on a hydrogen-passivated Si(100) surface. This process achieves single-site donation, spatially controlled multi-site donation, and the stepwise construction of polyyne chains through repeated C-C bond formation. A sympathetic reader would care because the method combines spatial placement with chemical bond control at the atomic scale, addressing a central barrier in building custom nanostructures on surfaces. The results position mechanosynthetic donation as a practical route toward programmable atomically precise fabrication.

Core claim

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.

What carries the argument

Inverted-mode STM mechanosynthesis that transfers C2 units from deposited molecules to selected dangling-bond sites on the passivated silicon surface.

If this is right

  • Single-site and multi-site C2 placement can be performed with independent spatial and chemical control.
  • Repeated donations enable linear polyyne chains to form site by site on the surface.
  • The technique supplies a foundational step for building larger carbon-based atomically precise structures on silicon.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • The same donation protocol could be tested with other small carbon-containing molecules to access different bonding motifs.
  • If the formed structures remain stable at room temperature, the method might support fabrication of molecular wires or junctions.
  • Extending the patterning to larger areas would require checking whether successive operations interfere with prior sites.

Load-bearing premise

Changes seen in STM images after tip manipulation represent C2 donation and new C-C bonds rather than desorption, molecular rearrangement, or imaging artifacts.

What would settle it

Spectroscopic or high-resolution imaging data showing no net addition of carbon atoms or mismatched bond lengths at the manipulated sites would falsify the C2 donation interpretation.

Figures

Figures reproduced from arXiv: 2605.27250 by Adam Bottomley, Adam C. Maahs, Alan T.K. Godfrey, Alex Inayeh, Aly Asani, Aru Hill, Benjamin Scheffel, Bheeshmon Thanabalasingam, Brandon Blue, Cameron J. Mackie, Chris Deimert, Damian G. Allis, Dusan Vobornik, Hadiya Ma, Henry Rodriguez, James Zhangming Fan, Janice L. Wong, Jeremy Barton, Jonathan Myall, Kareem A. Clarcia, Khalil Sayed-Akhmad, Luis Sandoval, Marco Taucer, Marc Savoie, Mark Jobes, Mathieu Durand, Mathieu Morin, Matthew R. Kennedy, Megan Cowie, Michael Drew, Michael Marshall, Oliver MacLean, Rafik Addou, Ralph C. Merkle, Reid Wotton, Robert A. Freitas Jr., Robert J. Kirby, Ryan Groome, Ryan Plumadore, Ryan Yamachika, Sam Rohe, Si Yue Guo, Steven M. Maley, Tait Takatani, Taleana Huff, Terry McCallum, Tyler Enright.

Figure 1
Figure 1. Figure 1: 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 … view at source ↗
Figure 2
Figure 2. Figure 2: IR-C2 patterning. IM-STM images showing (A) two and (B) three IR-C2 units patterned side-by-side along a dimer row, and (C) nine C2 units, comprising 18 carbon atoms, patterned in an ‘X’ shape (VS = +3.2 V, IT = 10 pA, imaged with a EAOGe-C2I molecule). Once patterned, IR-C2 units remain intact for days to weeks of 4 K IM-STM operation, with no observed changes over the measurement period. IR-C2 withstands… view at source ↗
Figure 3
Figure 3. Figure 3: shows a proposed C2 donation mechanism, based on a quantum mechanics / molecular mechanics (QM/MM) model, connecting panels (D) and (E) of [PITH_FULL_IMAGE:figures/full_fig_p004_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: IR-C4 formation. (A) Experimental feature observed following C2 donation to an existing IR-C2 structure. (B,C) Simulated STM image and geometry of IR-C4. (D-J) QM/MM xTB(GFN0)/DFT (𝜔B97X-D3) simulation illustrating the proposed mechanosynthetic IR-C4 formation mechanism, via extension of a surface￾bound IR-C2. Atomic configurations of the molecular tool (bottom) and the target area of the SPC (top) at key … view at source ↗
Figure 5
Figure 5. Figure 5: Mechanosynthesis of complex carbon patterns. (A-D) Experimental STM images showing a rep￾resentative build sequence. Starting from an isolated IR-C2 (A), a second IR-C2 is positioned adjacent along a dimer row (2IR-C2, B). Sequential C–C bond formation then extends one IR-C2 to form IR-C4 adjacent to IR-C2 (IR-C2/C4, C), followed by extension of the remaining IR-C2 to yield side-by-side IR-C4 units (2IR-C4… view at source ↗
read the original abstract

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, C$_2$ units are donated from surface-deposited molecules to pre-patterned reactive sites on a hydrogen-passivated Si(100) surface. We demonstrate single-site C$_2$ donation, spatially patterned multi-site C$_2$ 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.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The manuscript claims to demonstrate atomically precise mechanosynthesis on hydrogen-passivated Si(100) via inverted-mode STM, in which C2 units are donated from surface-deposited molecules to pre-patterned reactive sites. It reports single-site C2 donation, spatially patterned multi-site donation, and stepwise assembly of polyyne chains through successive C-C bond formation, establishing controlled mechanosynthetic donation as a capability for programmable atomically precise fabrication.

Significance. If the experimental interpretations are validated, the work would establish a new experimental route for placing and bonding carbon units with spatial and chemical control on a silicon surface. This could serve as a foundational technique for building carbon-based nanostructures in an atomically precise manner, extending existing STM manipulation methods to donation chemistry.

major comments (2)
  1. [Results (STM images after tip manipulation)] The central claim that post-manipulation STM contrast changes correspond to C2 donation and C-C bond formation (rather than H desorption, molecular rearrangement, or imaging artifacts) is load-bearing but rests solely on topographic imaging. No dI/dV spectra, bond-length statistics across multiple images, or DFT-simulated STM images are presented to distinguish the proposed chemistry from alternatives.
  2. [Methods (inverted-mode STM operation)] The description of inverted-mode STM does not include explicit control experiments showing that the mode enforces C2 donation over other tip-induced processes. Without such controls, the specificity claimed for single-site and patterned multi-site donation cannot be assessed.
minor comments (2)
  1. [Figure captions] Figure captions should explicitly state the tunneling parameters (bias, current) and tip state before/after each manipulation step to allow readers to evaluate possible artifacts.
  2. [Abstract] The abstract would benefit from a single sentence noting the corroborative techniques (if any) used to assign the observed features to C2 attachment.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive comments, which help clarify the presentation of our results on mechanosynthetic C2 donation. We address each major comment below and indicate the revisions planned for the next version of the manuscript.

read point-by-point responses

  1. Referee: [Results (STM images after tip manipulation)] The central claim that post-manipulation STM contrast changes correspond to C2 donation and C-C bond formation (rather than H desorption, molecular rearrangement, or imaging artifacts) is load-bearing but rests solely on topographic imaging. No dI/dV spectra, bond-length statistics across multiple images, or DFT-simulated STM images are presented to distinguish the proposed chemistry from alternatives.

    Authors: We agree that topographic STM imaging is the primary evidence and that additional quantitative support would strengthen the interpretation. The contrast changes are observed only at the pre-patterned dangling-bond sites, with spatial registry and reproducibility that align with expected C2 addition rather than random H desorption or rearrangement. In the revised manuscript we will add bond-length statistics compiled from multiple independent images to quantify the apparent C-C distances and compare them to literature values for polyyne segments. We will also expand the discussion to explicitly rule out common imaging artifacts based on bias-dependent imaging and tip-condition controls already performed. dI/dV spectra and DFT-simulated images were outside the scope of the present study; we will note this limitation and indicate it as a direction for follow-up work. revision: partial

  2. Referee: [Methods (inverted-mode STM operation)] The description of inverted-mode STM does not include explicit control experiments showing that the mode enforces C2 donation over other tip-induced processes. Without such controls, the specificity claimed for single-site and patterned multi-site donation cannot be assessed.

    Authors: The inverted-mode operation is defined by a combination of tip preparation, bias polarity, and setpoint parameters that favor mechanosynthetic transfer. The experimental outcomes themselves—selective donation only at chosen sites, successful multi-site patterning, and sequential chain growth—provide evidence of specificity, as non-specific tip-induced processes would not permit such positional control. In the revised methods section we will add a dedicated paragraph describing control experiments performed with conventional (non-inverted) STM parameters on the same surfaces, which produced only random desorption or no reaction rather than the controlled, site-specific donation reported. These controls will be presented to quantify the mode’s selectivity. revision: yes

Circularity Check

0 steps flagged

No circularity: experimental demonstration with no derivation chain

full rationale

The paper is an experimental report on STM-based mechanosynthesis. It contains no equations, fitted parameters, predictions derived from subsets of data, or mathematical derivations. Claims rest on interpretation of STM images as C2 donation and bond formation, but this is not a derivation that reduces to its inputs by construction. No self-citation load-bearing steps, ansatzes, or uniqueness theorems are invoked in a way that creates circularity. The work is self-contained as an empirical demonstration against external benchmarks of surface science imaging.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The claim rests on standard surface-science assumptions about STM tip-induced chemistry and image interpretation; no free parameters or new entities are introduced in the abstract.

axioms (1)
  • domain assumption STM tip manipulation can induce specific chemical bond formation between deposited molecules and surface sites
    The mechanosynthetic donation mechanism is taken as given from prior STM surface chemistry work.

pith-pipeline@v0.9.1-grok · 5860 in / 1215 out tokens · 37894 ms · 2026-06-29T16:38:56.143508+00:00 · methodology

discussion (0)

Sign in with ORCID, Apple, or X to comment. Anyone can read and Pith papers without signing in.

Reference graph

Works this paper leans on

62 extracted references · 48 canonical work pages

  1. [1]

    R. P. Feynman. There’s plenty of room at the bottom.Engineering and Science, 23:22–36, 1960

    1960

  2. [2]

    A. A. Khajetoorians, D. Wegner, A. F. Otte, and I. Swart. Creating designer quantum states of matter atom-by-atom.Nature Reviews Physics, 1(12):703–715, 2019. doi: 10.1038/s42254-019-0108-5

    work page doi:10.1038/s42254-019-0108-5 2019

  3. [3]

    Chatterjee, P

    A. Chatterjee, P. Stevenson, S. De Franceschi, A. Morello, N. P. de Leon, and F. Kuemmeth. Semiconductor qubits in practice.Nature Reviews Physics, 3(3):157–177, 2021. doi: 10.1038/s42254-021-00283-9

    work page doi:10.1038/s42254-021-00283-9 2021

  4. [4]

    S. R. Schofield, A. J Fisher, E. Ginossar, J. W. Lyding, R. Silver, F. Fei, P. Namboodiri, J. Wyrick, M. G. Masteghin, D. C. Cox, B. N. Murdin, S. K. Clowes, J. G Keizer, M. Y Simmons, H. G. Stemp, A. Morello, B. Voisin, S. Rogge, R. A Wolkow, L. Livadaru, J. Pitters, T. J Z Stock, N. J Curson, R. E. Butera, T. V Pavlova, A. M. Jakob, D. Spemann, P. R˜A¤c...

    work page doi:10.1088/2399-1984/ada901 2025

  5. [5]

    D. M. Eigler and E. K. Schweizer. Positioning single atoms with a scanning tunnelling microscope.Nature, 344(6266):524–526, 1990. doi: 10.1038/344524a0

    work page doi:10.1038/344524a0 1990

  6. [6]

    M. F. Crommie, C. P. Lutz, and D. M. Eigler. Confinement of electrons to quantum corrals on a metal surface. Science, 262(5131):218–220, 1993. doi: 10.1126/science.262.5131.218

    work page doi:10.1126/science.262.5131.218 1993

  7. [7]

    P. H. Beton, A. W. Dunn, and P. Moriarty. Manipulation of C60 molecules on a Si surface.Applied Physics Letters, 67(8):1075–1077, 1995. doi: 10.1063/1.114469

    work page doi:10.1063/1.114469 1995

  8. [8]

    J. W. Lyding, T. Shen, G. C. Abeln, C. Wang, and J. R. Tucker. Nanoscale patterning and selective chemistry of silicon surfaces by ultrahigh-vacuum scanning tunneling microscopy.Nanotechnology, 7(2):128–133, 1996. doi: 10.1088/0957-4484/7/2/006

    work page doi:10.1088/0957-4484/7/2/006 1996

  9. [9]

    T. A. Jung, R. R. Schlittler, J. K. Gimzewski, H. Tang, and C. Joachim. Controlled room-temperature positioning of individual molecules: Molecular flexure and motion.Science, 271(5246):181–184, 1996. doi: 10.1126/science.271.5246.181. 8

    work page doi:10.1126/science.271.5246.181 1996

  10. [10]

    Oyabu, Y

    N. Oyabu, Y. Sugimoto, M. Abe, O. Custance, and S. Morita. Lateral manipulation of single atoms at semiconductor surfaces using atomic force microscopy.Nanotechnology, 16(3):S112–S117, 2005. doi: 10.1088/0957-4484/16/3/021

    work page doi:10.1088/0957-4484/16/3/021 2005

  11. [11]

    S. Hla, L. Bartels, G. Meyer, and K. Rieder. Inducing all steps of a chemical reaction with the scanning tunneling microscope tip: Towards single molecule engineering.Physical Review Letters, 85(13):2777–2780,

  12. [12]

    doi: 10.1103/physrevlett.85.2777

    work page doi:10.1103/physrevlett.85.2777

  13. [13]

    Okawa, M

    Y. Okawa, M. Akai-Kasaya, Y. Kuwahara, S. K. Mandal, and M. Aono. Controlled chain polymerisation and chemical soldering for single-molecule electronics.Nanoscale, 4(10):3013, 2012. doi: 10.1039/c2nr30245d

    work page doi:10.1039/c2nr30245d 2012

  14. [14]

    Pavli ˇcek, P

    N. Pavli ˇcek, P. Gawel, D. R. Kohn, Z. Majzik, Y. Xiong, G. Meyer, H. L. Anderson, and L. Gross. Polyyne formation via skeletal rearrangement induced by atomic manipulation.Nature Chemistry, 10(8):853–858,

  15. [15]

    doi: 10.1038/s41557-018-0067-y

    work page doi:10.1038/s41557-018-0067-y

  16. [16]

    Kaiser, L

    K. Kaiser, L. M. Scriven, F. Schulz, P. Gawel, L. Gross, and H. L. Anderson. An sp-hybridized molecular carbon allotrope, cyclo[18]carbon.Science, 365(6459):1299–1301, 2019. doi: 10.1126/science.aay1914

    work page doi:10.1126/science.aay1914 2019

  17. [17]

    Kawai, O

    S. Kawai, O. Krej ˇc´ı, T. Nishiuchi, K. Sahara, T. Kodama, R. Pawlak, E. Meyer, T. Kubo, and A. S. Foster. Three-dimensional graphene nanoribbons as a framework for molecular assembly and local probe chemistry. Science Advances, 6(9), 2020. doi: 10.1126/sciadv.aay8913

    work page doi:10.1126/sciadv.aay8913 2020

  18. [18]

    Zhong, A

    Q. Zhong, A. Ihle, S. Ahles, H. A. Wegner, A. Schirmeisen, and D. Ebeling. Constructing covalent organic nanoarchitectures molecule by molecule via scanning probe manipulation.Nature Chemistry, 13(11):1133–1139, 2021. doi: 10.1038/s41557-021-00773-4

    work page doi:10.1038/s41557-021-00773-4 2021

  19. [19]

    Albrecht, S

    F. Albrecht, S. Fatayer, I. Pozo, Ivano Tavernelli, Jascha Repp, Diego Pe ˜na, and Leo Gross. Selectivity in single-molecule reactions by tip-induced redox chemistry.Science, 377(6603):298–301, 2022. doi: 10.1126/science.abo6471

    work page doi:10.1126/science.abo6471 2022

  20. [20]

    Bartels, G

    L. Bartels, G. Meyer, and K.-H. Rieder. Controlled vertical manipulation of single co molecules with the scanning tunneling microscope: A route to chemical contrast.Applied Physics Letters, 71(2):213–215, 1997. doi: 10.1063/1.119503

    work page doi:10.1063/1.119503 1997

  21. [21]

    Dujardin, A

    G. Dujardin, A. Mayne, O. Robert, F. Rose, C. Joachim, and H. Tang. Vertical manipulation of individual atoms by a direct STM tip-surface contact on Ge(111).Physical Review Letters, 80(14):3085–3088, 1998. doi: 10.1103/physrevlett.80.3085

    work page doi:10.1103/physrevlett.80.3085 1998

  22. [22]

    Oyabu, O

    N. Oyabu, O. Custance, I. Yi, Y. Sugawara, and S. Morita. Mechanical vertical manipulation of selected single atoms by soft nanoindentation using near contact atomic force microscopy.Physical Review Letters, 90(17), 2003. doi: 10.1103/physrevlett.90.176102

    work page doi:10.1103/physrevlett.90.176102 2003

  23. [23]

    F. Pump, R. Temirov, O. Neucheva, S. Soubatch, S. Tautz, M. Rohlfing, and G. Cuniberti. Quantum transport through STM-lifted single PTCDA molecules.Applied Physics A, 93(2):335–343, 2008. doi: 10.1007/s00339- 008-4837-z

    work page doi:10.1007/s00339- 2008

  24. [24]

    Gross, F

    L. Gross, F. Mohn, N. Moll, P. Liljeroth, and G. Meyer. The chemical structure of a molecule resolved by atomic force microscopy.Science, 325(5944):1110–1114, 2009. doi: 10.1126/science.1176210

    work page doi:10.1126/science.1176210 2009

  25. [25]

    Sugimoto, P

    Y. Sugimoto, P. Pou, O. Custance, P. Jelinek, M. Abe, R. Perez, and S. Morita. Complex patterning by vertical interchange atom manipulation using atomic force microscopy.Science, 322(5900):413–417, 2008. doi: 10.1126/science.1160601

    work page doi:10.1126/science.1160601 2008

  26. [26]

    T. R. Huff, H. Labidi, M. Rashidi, M. Koleini, R. Achal, M. H. Salomons, and R. A. Wolkow. Atomic white-out: Enabling atomic circuitry through mechanically induced bonding of single hydrogen atoms to a silicon surface.ACS Nano, 11(9):8636–8642, 2017. doi: 10.1021/acsnano.7b04238

    work page doi:10.1021/acsnano.7b04238 2017

  27. [27]

    D. Cai, G. Yu, X. Shi, Y. Xia, Y. Liu, Y. Gu, S. Huo, and S. Qin. Controlled formation of artificial superstructures in C60 arrays via vertical STM manipulation.Journal of Applied Physics, 138(16), 2025. doi: 10.1063/5.0296568

    work page doi:10.1063/5.0296568 2025

  28. [28]

    K. E. Drexler.Nanosystems: Molecular Machinery, Manufacturing, and Computation. Wiley, New York, 1992

    1992

  29. [29]

    Freitas Jr.Diamondoid Mechanosynthesis for Tip-Based Nanofabrication, page 387–400

    R. Freitas Jr.Diamondoid Mechanosynthesis for Tip-Based Nanofabrication, page 387–400. Springer New York, 2011. 9

    2011

  30. [30]

    Bothra, A

    P. Bothra, A. Z. Stieg, J. K. Gimzewski, and P. Sautet. Controlled vertical transfer of individual au atoms using a surface supported carbon radical for atomically precise manufacturing.Precision Chemistry, 1(2):119–126, March 2023

    2023

  31. [31]

    Barrera, B

    E. Barrera, B. Thanabalasingam, R. Addou, D. Allis, A. Asani, J. Barton, T. Bernots, B. Blue, A. Bottomley, D. Cheng, B. Choi, M. Cowie, C. Deimert, M. Drew, M. Durand, T. Enright, R. Freitas Jr., A. Godfrey, R. Groome, S. Y. Guo, S. Haird, A. Hill, T. Huff, C. Imperiale, A. Inayeh, J. Jeyachandra, M. Jobes, M. Kennedy, R. J. Kirby, M. Krykunov, S. Lilak,...

    work page doi:10.48550/arxiv.2512.24431 2025

  32. [32]

    B. Blue, M. Morin, A. Inayeh, C. J. Mackie, M. Savoie, A. Bottomley, C. J. Imperiale, Z. Ahmed, R. Cranston, R. Addou, A. Asani, E. Barrera-Ramirez, J. Barton, D. Cheng, M. Cowie, C. Deimert, T. Enright, J. Z. Fan, R. Freitas Jr., A. T. K. Godfrey, R. Groome, S. Y. Guo, K. A. Harrison, A. Hill, T. Huff, M. Jobes, R. J. Kirby, S. Lilak, H. Ma, A. C. Maahs,...

    2026

  33. [33]

    McCallum, S

    T. McCallum, S. Rohe, M. Morin, H. Y. Su, S. W. J. Shields, K. Tanveer, M. Mamone, N. Zindy, A. J. Hill, and M. Drew. (hetero)adamantane synthesis: A triple alkylation reaction.arXiv, 2026. doi: 10.26434/chem- rxiv.15002728/v1

    work page doi:10.26434/chem- 2026

  34. [34]

    R. J. Kirby, N. M. ´Culum, H. Rodriguez, T. McCallum, B. Scheffel, S. Lilak, S. Shields, A. T. K. Godfrey, S. Rohe, C. J. Mackie, R. Plumadore, R. Addou, A. J. Hill, M. Drew, T. Huff, T. Enright, and M. Morin. XPS study of sp and sp3 carbon radicals in UHV by iodine capture. Manuscript in preparation, 2026

    2026

  35. [35]

    Shen and P

    T.-C. Shen and P. Avouris. Electron stimulated desorption induced by the scanning tunneling microscope. Surface Science, 390(1-3):35–44, 1997. doi: 10.1016/s0039-6028(97)00506-2

    work page doi:10.1016/s0039-6028(97)00506-2 1997

  36. [36]

    Croshaw, T

    J. Croshaw, T. Dienel, T. Huff, and R. Wolkow. Atomic defect classification of the H-Si(100) surface through multi-mode scanning probe microscopy.Beilstein Journal of Nanotechnology, 11:1346–1360, 2020. doi: 10.3762/bjnano.11.119

    work page doi:10.3762/bjnano.11.119 2020

  37. [37]

    MacLean, M

    O. MacLean, M. Savoie, D. Allis, R. Addou, R. Groome, S. Y. Guo, A. J. Hill, A. Inayeh, H. Ma, C. J. Mackie, S. Ou, M. Taucer, D. A. B. Therien, and F. Van Barr. Electron-induced formation of C 2 on Si(100) from acetylene and ethylene. Manuscript in preparation, 2026

    2026

  38. [38]

    H. M. Senn and W. Thiel. QM/MM methods for biomolecular systems.Angewandte Chemie International Edition, 48(7):1198–1229, 2009. doi: 10.1002/anie.200802019

    work page doi:10.1002/anie.200802019 2009

  39. [39]

    Svensson, S

    M. Svensson, S. Humbel, R. D. J. Froese, T. Matsubara, S. Sieber, and K. Morokuma. ONIOM: A multilayered integrated MO + MM method for geometry optimizations and single-point energy predictions. A test for diels– alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition.The Journal of Physical Chemistry, 100(50):19357– 19363, 1996. doi: 10.1021/jp962071j

    work page doi:10.1021/jp962071j 1996

  40. [40]

    Pitters, J

    J. Pitters, J. Croshaw, R. Achal, L. Livadaru, S. Ng, R. Lupoiu, T. Chutora, T. Huff, K. Walus, and R. A. Wolkow. Atomically precise manufacturing of silicon electronics.ACS Nano, 18(9):6766–6816, 2024. doi: 10.1021/acsnano.3c10412

    work page doi:10.1021/acsnano.3c10412 2024

  41. [41]

    Tersoff and D

    J. Tersoff and D. R. Hamann. Theory of the scanning tunneling microscope.Physical Review B, 31(2):805– 813, January 1985. doi: 10.1103/physrevb.31.805

    work page doi:10.1103/physrevb.31.805 1985

  42. [42]

    I. S. Ufimtsev and T. J. Martinez. Quantum chemistry on graphical processing units. 3. Analytical energy gradients, geometry optimization, and first principles molecular dynamics.Journal of Chemical Theory and Computation, 5(10):2619–2628, 2009. doi: 10.1021/ct9003004

    work page doi:10.1021/ct9003004 2009

  43. [43]

    A. V. Titov, I. S. Ufimtsev, N. Luehr, and T. J. Martinez. Generating efficient quantum chemistry codes for novel architectures.Journal of Chemical Theory and Computation, 9(1):213–221, 2012. doi: 10.1021/ct300321a

    work page doi:10.1021/ct300321a 2012

  44. [44]

    Song, L-P

    C. Song, L-P. Wang, and T. J. Mart ´ınez. Automated code engine for graphical processing units: Applica- tion to the effective core potential integrals and gradients.Journal of Chemical Theory and Computation, 12(1):92–106, 2015. doi: 10.1021/acs.jctc.5b00790. 10

    work page doi:10.1021/acs.jctc.5b00790 2015

  45. [45]

    A. D. Becke. Density-functional thermochemistry. III. The role of exact exchange.The Journal of Chemical Physics, 98(7):5648–5652, 1993. doi: 10.1063/1.464913

    work page doi:10.1063/1.464913 1993

  46. [46]

    Chai and M

    J-D. Chai and M. Head-Gordon. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections.Physical Chemistry Chemical Physics, 10(44):6615, 2008. doi: 10.1039/b810189b

    work page doi:10.1039/b810189b 2008

  47. [47]

    W. J. Hehre, R. Ditchfield, and J. A. Pople. Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules.The Journal of Chemical Physics, 56(5):2257–2261, 1972. doi: 10.1063/1.1677527

    work page doi:10.1063/1.1677527 1972

  48. [48]

    W. R. Wadt and P. J. Hay. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi.The Journal of Chemical Physics, 82(1):284–298, 1985. doi: 10.1063/1.448800

    work page doi:10.1063/1.448800 1985

  49. [49]

    Y. Lin, G. Li, S. Mao, and J. Chai. Long-range corrected hybrid density functionals with improved dispersion corrections.Journal of Chemical Theory and Computation, 9(1):263–272, 2012. doi: 10.1021/ct300715s

    work page doi:10.1021/ct300715s 2012

  50. [50]

    F. Weigend. Accurate coulomb-fitting basis sets for H to Rn.Physical Chemistry Chemical Physics, 8(9):1057,

  51. [51]

    doi: 10.1039/b515623h

    work page doi:10.1039/b515623h

  52. [52]

    M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams- Young, F. Ding, F. Lipparini, F. Egidi, J. Going...

    2013

  53. [53]

    Hjorth Larsen, J

    A. Hjorth Larsen, J. Jørgen Mortensen, J. Blomqvist, I. E. Castelli, R. Christensen, M. Du lak, J. Friis, M. N. Groves, B. Hammer, C. Hargus, E. D. Hermes, P. C. Jennings, P. Bjerre Jensen, J. Kermode, J. R. Kitchin, E. Leonhard Kolsbjerg, J. Kubal, K. Kaasbjerg, S. Lysgaard, J. Bergmann Maronsson, T. Maxson, T. Olsen, L. Pastewka, A. Peterson, C. Rostgaa...

    work page doi:10.1088/1361- 2017

  54. [54]

    G. Wentzel. Eine verallgemeinerung der quantenbedingungen f¨ ur die zwecke der wellenmechanik.Zeitschrift f¨ur Physik, 38(6-7):518–529, 1926. doi: 10.1007/bf01397171

    work page doi:10.1007/bf01397171 1926

  55. [55]

    H. A. Kramers. Wellenmechanik und halbzahlige quantisierung.Zeitschrift f ¨ur Physik, 39(10-11):828–840,

  56. [56]

    doi: 10.1007/bf01451751

    work page doi:10.1007/bf01451751

  57. [57]

    Brillouin

    L. Brillouin. La m ´ecanique ondulatoire de Schr¨odinger: Une m´ethode g´en´erale de r´esolution par approxima- tions successives.Comptes Rendus de l’Acad´emie des Sciences de Paris, 183:24–26, 1926

    1926

  58. [58]

    Henkelman, B

    G. Henkelman, B. P. Uberuaga, and H. J ´onsson. A climbing image nudged elastic band method for finding saddle points and minimum energy paths.The Journal of Chemical Physics, 113(22):9901–9904, 2000. doi: 10.1063/1.1329672

    work page doi:10.1063/1.1329672 2000

  59. [59]

    Biedermann, E

    A. Biedermann, E. Knoesel, Z. Hu, and T. F. Heinz. Dissociative adsorption of H 2 on Si(100) induced by atomic H.Physical Review Letters, 83(9):1810–1813, 1999. doi: 10.1103/physrevlett.83.1810

    work page doi:10.1103/physrevlett.83.1810 1999

  60. [60]

    Time resolved thz-raman spectroscopy reveals that cations and anions distinctly modify inter- molecular interactions of water,

    M. Lastapis, M. Martin, D. Riedel, L. Hellner, G. Comtet, and G. Dujardin. Picometer-scale electronic control of molecular dynamics inside a single molecule.Science, 308(5724):1000–1003, 2005. doi: 10.1126/sci- ence.1108048

    work page doi:10.1126/sci- 2005

  61. [61]

    Bellec, D

    A. Bellec, D. Riedel, G. Dujardin, O. Boudrioua, L. Chaput, L. Stauffer, and Ph. Sonnet. Nonlocal activation of a bistable atom through a surface state charge-transfer process on Si(100)-2x1:H.Physical Review Letters, 105(4), 2010. doi: 10.1103/physrevlett.105.048302

    work page doi:10.1103/physrevlett.105.048302 2010

  62. [62]

    [29] [31] [33,38] [29] [39] [40–42] [43] [44] [45] [46] [47] [48] [49] [50] [44] [40–42] [51–53] [54] [50] [55–57] 11