Pt Nanoparticles on MoS2(001) Surface via Adatoms.

Introduction.

This tutorial demonstrates how to create a platinum island on MoS2 by sequentially adding Pt adatoms, following the methodology described in the literature.

Manuscript

Saidi, W. 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. ¹²³⁴⁵

We will recreate the Pt island structure shown in Figure 4b:

1. Create MoS2 Substrate.

1.1. Load Base Material.

Navigate to Materials Designer and import the MoS2 2D material from Standata.

1.2. Launch JupyterLite Session.

Select the "Advanced > JupyterLite Transformation" 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:

# 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

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.

2.3. Pass the Result to Materials Designer.

The result can be passed to Materials Designer for visualization and viewed from the top:

And from the side:

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".

⛶ Full Screen

Parameter Fine-tuning.

To adjust the island structure:

1. Base Layer:
2. Adjust APPROXIMATE_POSITION_ON_SURFACE to shift Pt positions

3. Modify DISTANCE_Z to change height from surface

4. Top Atom:

5. Adjust position to change island shape
6. Modify height to change Pt-Pt spacing

References.

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1. W. A. Saidi. Density functional theory study of nucleation and growth of pt nanoparticles on mos2(001) surface. Crystal Growth & Design, 15(2):642–652, 2015. URL: https://doi.org/10.1021/cg5013395. ↩

2. M. Jiao, W. Song, H.-J. Qian, Y. Wang, Z. Wu, S. Irle, and K. Morokuma. Qm/md studies on graphene growth from small islands on the ni(111) surface. Nanoscale, 8(5):3067–3074, 2016. URL: https://doi.org/10.1039/c5nr07680c. ↩

3. Kristen A. Fichthorn and Matthias Scheffler. Island nucleation in thin-film epitaxy: a first-principles investigation. Phys. Rev. Lett., 84:5371, 2000. URL: https://link.aps.org/doi/10.1103/PhysRevLett.84.5371. ↩

4. Jörg Neugebauer and Matthias Scheffler. Mechanisms of island formation of alkali-metal adsorbates on al(111). Phys. Rev. Lett., 71:577, 1993. URL: https://link.aps.org/doi/10.1103/PhysRevLett.71.577. ↩

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. URL: https://link.aps.org/doi/10.1103/PhysRevB.76.235426. ↩