Create a Molecule on a Surface¶

This tutorial demonstrates how the Material Designer Interface can be used to create a geometry for modeling a surface chemical reaction, where a molecule interacts with a surface and undergoes, for example, a chemical adsorption process ¹.

The example system is a benzene molecule adsorbed on a gold (Au) (211) surface. The chemical structure of the benzene molecule is given in the expandable section below in the POSCAR input data format.

1. Reference structures¶

Benzene molecule, POSCAR ...

C H
00000000000000
0000000000000000 0.0000000000000000 0.0000000000000000
0000000000000000 20.0000000000000000 0.0000000000000000
0000000000000000 0.0000000000000000 20.0000000000000000
6
Direct
5000000000000000 0.4302298156365565 0.5000000000000000
5603808840462569 0.4651341647080757 0.5000000000000000
5603808840462569 0.5348658352919243 0.5000000000000000
5000000000000000 0.5697701843634434 0.5000000000000000
4396191159537430 0.5348658352919243 0.5000000000000000
4396191159537430 0.4651341647080757 0.5000000000000000
5000000000000000 0.3757603875449354 0.5000000000000000
6075652945069621 0.4379113406185772 0.5000000000000000
6075652945069621 0.5620886593814227 0.5000000000000000
5000000000000000 0.6242396124550644 0.5000000000000000
3924347054930378 0.5620886593814227 0.5000000000000000
3924347054930378 0.4379113406185772 0.5000000000000000

Alternatively, the benzene molecular structure can be retrieved from the Pubchem public repository ² and converted to POSCAR format using any online converter such as the OpenBabel Open Source Chemistry Toolbox ³.

2. Create the benzene molecule entry in the materials collection¶

The chemical structure for benzene can be imported from the Materials Bank into the account-owned collection, if not already present.

Alternatively, the above-mentioned POSCAR structure can be manually uploaded into the materials collection after saving its data contents to a new file on the local disk.

3. Open Materials Designer¶

Open an instance of the Materials Designer Interface.

4. Create the gold surface¶

In order to create a gold surface, first import a sample crystalline structure of pure gold into the current Materials Designer session from the account-owned collection.

Follow the instructions in this page to create a surface of gold with normal vector oriented along the [211] axis.

Order of structures is important

The gold surface must be created first so that it appears first in the left-hand sidebar, ensuring its cell is used when later combining the two materials together.

5. Import the benzene molecule into Materials Designer¶

The benzene molecule should be imported into the current Materials Designer session from the account-owned collection.

Once imported, the benzene molecule appears as a distinct entry in the left-hand sidebar, alongside the previously-generated gold surface.

Any other material structure entries listed in the sidebar — aside from benzene and the gold surface — should be removed.

6. Open the Multi-Materials 3D Editor¶

After both the benzene molecule and the gold surface are listed as separate structural items, open the Multi-Materials 3D Editor via the View Menu.

7. Combine the two materials¶

The Multi-Materials 3D Editor allows the two materials to be combined into a new unified entity.

The molecule should be positioned on top of the surface in as "symmetrical" a way as possible, for example by placing the center of the benzene ring over the central portion of the surface. Relocation of the benzene molecule position can be done following the instructions in this page, after selecting the benzene atom components under the Scene sidebar list.

Since in this example the plane of the 2D benzene molecule and the gold (211) surface are already parallel, a translation of the benzene atoms onto the surface is sufficient.

8. Exit the Multi-Materials 3D Editor¶

After correct positioning of the benzene molecule on top of the gold surface, exit the Multi-Materials 3D Editor.

A new material entry, called "New Material" by default, is created and listed in the left-hand sidebar. It contains the combined benzene-gold surface crystallographic structure as a single material entity.

Toggling of Orthographic Camera

Toggling the Orthographic camera via the 3D Editor helps verify the correct alignment and centrality of the benzene molecule over the surface.

This new entry should be renamed to a more memorable form and saved into the account-owned materials collection.

9. View the resulting material¶

An animation of the final combined benzene molecule-gold surface structure can be viewed below.

10. Run further analysis¶

The newly generated benzene-gold surface system can be used for further analysis, such as studying the adsorption energy.

The Nudged Elastic Band (NEB) method can be used for reaction energy profile calculations. Two alternative approaches for implementing NEB are available, based on VASP and Quantum ESPRESSO respectively.

11. Video walkthrough¶

The animation below demonstrates the creation of a combined benzene molecule/gold surface crystallographic system using the Materials Designer Interface.

In this example, a 3×3×3 slab supercell of the primitive unit cell of gold is used as a surface approximation (larger supercell dimensions should be used for a more realistic surface representation). The benzene molecule is placed over the gold surface at a molecule-surface distance of approximately 3.6 Å, as measured by the difference in z coordinates of the benzene and gold surface atoms.