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A. + "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" + Crystal Growth & Design, 15(2), 642–652. (2015) + [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. + +We will recreate the Pt island structure shown in Figure 4b: + +![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/0-figure-from-manuscript.webp "Pt island formation on MoS2") + +## 1. Create MoS2 Substrate + +### 1.1. Load Base Material + +Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 2D material from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). + +### 1.2. Launch JupyterLite Session + +Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment. + +### 1.3. Open `create_adatom_defect.ipynb` Notebook + +Find and open the `create_adatom_defect.ipynb` notebook. Select MoS2 as input material. + +## 2. Configure and Create Structure + +### 2.1. Set Parameters + +Set up the slab and defect parameters in the notebook: + +```python +# Slab parameters +MILLER_INDICES = (0, 0, 1) # MoS2 basal plane +SLAB_THICKNESS = 1 # Single layer +VACUUM = 10.0 # in Angstrom +SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 1]] # 3x3 supercell + +# Defect configurations for all Pt atoms +DEFECT_CONFIGS = [ + { + "defect_type": "adatom", + "placement_method": "coordinate", + "chemical_element": "Pt", + "position_on_surface": [5/9, 4/9], # First Pt: atop central Mo + "distance_z": 1.2, # Distance from surface S atoms + "use_cartesian_coordinates": False + }, + { + "defect_type": "adatom", + "placement_method": "coordinate", + "chemical_element": "Pt", + "position_on_surface": [2/9, 4/9], # Second Pt: next clockwise atop Mo + "distance_z": 1.2, # Distance from surface S atoms + "use_cartesian_coordinates": False + }, + { + "defect_type": "adatom", + "placement_method": "coordinate", + "chemical_element": "Pt", + "position_on_surface": [5/9, 7/9], # Third Pt: next clockwise atop Mo + "distance_z": 1.2, # Distance from surface S atoms + "use_cartesian_coordinates": False + }, + { + "defect_type": "adatom", + "placement_method": "coordinate", + "chemical_element": "Pt", + "position_on_surface": [4/9, 5/9], # Fourth Pt: centered atop S + "distance_z": 1.6, # Distance between Pt atom layers, in Angstrom + "use_cartesian_coordinates": False + } +] +``` + +Key parameters explained: + +- Base layer Pt atoms (first three configs): + + * Positioned atop Mo atoms in a triangular arrangement + * Height 1.2 Å from surface S atoms to achieve separation from Mo atoms of 2.8 A -- from publication +- Top Pt atom (fourth config): + + * Centered above the triangle, atop S atom + * Height 1.6 Å from base Pt atoms (as they become the new surface layer) + +- `distance_z` sets the distance along the z-axis from the adatom to the topmost atom directly below it + +![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/1-jl-setup-nb.webp "Pt adatoms setup") + +### 2.2. Run the Notebook + +Execute the notebook to create the Pt island structure on MoS2 by selecting "Run" > "Run All Cells" from the JupyterLite menu. + +![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/2-jl-result-preview.webp "Pt island results preview") + +### 2.3. Pass the Result to Materials Designer + +The result can be passed to Materials Designer for visualization and viewed from the top: + +![Complete Island](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/4-wave-result-top.webp "Complete Pt island structure") + +And from the side: + +![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/5-wave-result-side.webp "Complete Pt island structure, side view") + +## 3. Analyze the Structure + +After adding all Pt atoms, verify the following: + +### 3.1. Base Layer Geometry + +- Three Pt atoms should form a triangular base +- Each base Pt should be positioned atop Mo atoms +- Distance from surface S atoms should be ~1.2 Å +- Relaxation is needed to achieve the exact geometry from the publication, can be performed elsewhere + +### 3.2. Top Atom Position + +- Fourth Pt should be centered above the triangle +- Position should be approximately above a surface S atom +- Height should be ~2.8 Å from surface (1.6 Å from base Pt atoms) + +## 4. Save the Structure + +The final structure will be automatically passed back to Materials Designer where user can: + +1. Save it on the platform +2. Export it in various formats +3. Use it for further transformations + +## Interactive JupyterLite Notebook + +The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells". + +{% with origin_url=config.extra.jupyterlite.origin_url %} +{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} +{% with notebook_name='specific_examples/defect_point_adatom_island_mos2_pt.ipynb' %} +{% include 'jupyterlite_embed.html' %} +{% endwith %} +{% endwith %} +{% endwith %} + +## Parameter Fine-tuning + +To adjust the island structure: + +1. Base Layer: + - Adjust `APPROXIMATE_POSITION_ON_SURFACE` to shift Pt positions + - Modify `DISTANCE_Z` to change height from surface + +2. Top Atom: + - Adjust position to change island shape + - Modify height to change Pt-Pt spacing + +## References + +1. Saidi, W. A. (2015). Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface. Crystal Growth & Design, 15(2), 642–652. [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. + +2. Jiao, M., Song, W., Qian, H.-J., Wang, Y., Wu, Z., Irle, S., & Morokuma, K. (2016). QM/MD studies on graphene growth from small islands on the Ni(111) surface. Nanoscale, 8(5), 3067–3074. doi:10.1039/c5nr07680c  [DOI: 10.1039/c5nr07680c](https://doi.org/10.1039/c5nr07680c){:target='_blank'}. + +3. Kristen A. Fichthorn and Matthias Scheffler, "Island Nucleation in Thin-Film Epitaxy: A First-Principles Investigation", Phys. Rev. Lett. 84, 5371 (2000). [DOI: 10.1103/PhysRevLett.84.5371](https://doi.org/10.1103/PhysRevLett.84.5371){:target='_blank'}. + +4. Jörg Neugebauer and Matthias Scheffler, "Mechanisms of island formation of alkali-metal adsorbates on Al(111)", Phys. Rev. Lett. 71, 577 (1993). [DOI: 10.1103/PhysRevLett.71.577](https://doi.org/10.1103/PhysRevLett.71.577){:target='_blank'}. + +5. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler, "Density-functional study of Mn monosilicide on the Si(111) surface: +Film formation versus island nucleation", Phys. Rev. B 76, 235426 (2007). [DOI: 10.1103/PhysRevB.76.235426](https://doi.org/10.1103/PhysRevB.76.235426){:target='_blank'}. + +## Tags + +`MoS2`, `platinum`, `adatoms`, `surface science`, `2D materials`, `nanoparticles`, `Mo`, `S`, `Pt` \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 4a31e3b0..ded60645 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -239,6 +239,7 @@ nav: - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md - Grain Boundary (2D) in h-BN: tutorials/materials/specific/grain-boundary-2d-boron-nitride.md - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md + - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md # COMMON UI COMPONENTS - Interface Components: