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Supporting information: Thermodynamics of alkanethiol self-assembled monolayer assembly on Pd surfaces

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Authority of statements

Prose below summarizes this Supporting Information PDF and the short normalized extract (normalized/extracts/2017kumar-venue-paper_p1-2.txt). For full DFT setups, tables, and figures, use the SI PDF together with the peer-reviewed article on alkanethiol SAMs on Pd (2018kumar-langmuir-201-thermodynamics-alkanethiol).

Summary

This corpus entry registers the Supporting Information for Langmuir work on alkanethiol/alkanethiolate assembly on Pd(111), Pd(100), and Pd(110). The SI outlines high-coverage binding trends (Figure S1), plane-wave DFT slab protocols (Table S1) and coverage-resolved bonding vs nonbonding contributions to adsorption energies (Tables S2A–S2C), plus surface free-energy comparisons for short vs longer thiols (Figure S2). Section S4 documents ReaxFF extension for Pd–S environments, including a DFT training comparison on Figure S3. Section S5 gives DRIFTS auxiliary figures for CO on Pd catalysts (Figures S4–S5).

Methods

1 — MD application. N/A — production large-scale MD is not documented in this SI excerpt (no LAMMPS/GROMACS-style trajectory protocol is extracted here): the Supporting Information focuses on DFT slab protocols, energy decompositions, and ReaxFF vs DFT benchmarks. For this method:reaxff SI registration (MD slots must still be explicit N/A): N/A — periodic boundary conditions for any hypothetical MD are not stated here; N/A — ensemble (NVE/NVT/NPT) for MD; N/A — timestep (fs) for MD; N/A — MD trajectory duration (ps/ns); N/A — thermostat parameters for MD; N/A — barostat / pressure control for MD. Retrieve any SAM dynamics protocol from the main article PDF (2018kumar-langmuir-201-thermodynamics-alkanethiol).

2 — Force-field training / fitting (Pd–S ReaxFF extension). Section S4 describes extending ReaxFF to treat Pd–S chemistry using DFT reference data across bulk and surface sulfur environments on Pd(111), Pd(100), and Pd(110). Figure S3 compares DFT versus ReaxFF surface adsorption energies for sulfur on the three facets (including subsurface and coverage-based labels defined in the SI caption).

3 — Static QM / DFT (slab protocols and energy decomposition). Table S1 lists k-point meshes, slab layer counts, frozen layers, and in-plane supercell vectors for the Pd surface models (third lattice vector normal to the surface). Tables S2A–S2C decompose thiolate adsorption energies on each facet into bonding (\(E_b\)), nonbonding (\(E_{nb}\)), and total (\(E_\text{ads}\)) contributions across coverages. Figure S1 summarizes very high coverage binding trends versus alkyl chain length on the three facets (covalent / noncovalent / total panels).

4 — Review / non-simulation framing. N/A for the core DFT/ReaxFF blocks; Section S5 adds experimental-style DRIFTS context for CO on Pd catalysts (Figures S4–S5) as auxiliary characterization relative to the SAM thermodynamics story.

Findings

Outcomes and mechanisms (SI-level). The SI’s energy decomposition supports a picture where chain length, facet, and coverage jointly control whether covalent versus noncovalent contributions dominate thiolate binding at Pd surfaces—this underpins the main article’s interpretation of SAM thermodynamics and chemical potential trends.

Comparisons. Figure S3 is the direct DFT vs ReaxFF benchmark for S-on-Pd motifs; the SI text/caption flags where agreement is strong and where multi-coordination environments are harder to reproduce.

Sensitivity and design levers. Facet (111/100/110), coverage, and alkyl length (via Figure S1/S2 families) are the primary knobs exposed in the SI tables/figures for how binding partitions between bonding and nonbonding terms.

Limitations and outlook (as authored). As Supporting Information, this file is not a standalone substitute for the main text conclusions, pagination, or full discussion of SAM assembly kinetics.

Corpus / PDF honesty. Treat this slug as NON_PRIMARY SI per docs/corpus/NON_PRIMARY_ARTICLE_PAPER_SLUGS.md: it registers papers/Kumar_thiol_Pd_Langmuir_2018_SI.pdf. The version-of-record article narrative lives on [[2018kumar-langmuir-201-thermodynamics-alkanethiol]]; the local normalized/extracts/2017kumar-venue-paper_p1-2.txt file is SI front matter only—do not treat it as full coverage of Tables S1–S4.

Limitations

  • SI-only ingest: pagination, complete parameter lists, and main-text conclusions are not replaced by this page—use the article PDF for the full narrative.
  • The local extract covers SI front matter and section headings; deep table/figure values should be checked in the PDF.

Relevance to group

Co-authored PSU / Colorado study: van Duin group involvement in Pd–S ReaxFF development alongside DFT-driven SAM thermodynamics (2018kumar-langmuir-201-thermodynamics-alkanethiol).

Citations and evidence anchors

Reader notes (navigation)

  • This slug tracks papers/Kumar_thiol_Pd_Langmuir_2018_SI.pdf; the version-of-record article is 2018kumar-langmuir-201-thermodynamics-alkanethiol.