

Create Molecule on a Surface¶

In this tutorial, the user will learn about how the Material Designer Interface of our platform can be used to create a geometry for modeling a surface chemical reaction, whereby a molecule interacts with a surface, and undergoes for example a chemical adsorption process ¹.

We consider the example of a benzene molecule adsorbed on a gold (Au) (211) surface throughout the present tutorial. The chemical structure of the benzene molecule is given in the expandable section below for reference purposes, in the POSCAR input data format.

Structures¶

Benzene molecule, POSCAR ...

C H
1.00000000000000
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 20.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 20.0000000000000000
6 6
Direct
0.5000000000000000 0.4302298156365565 0.5000000000000000
0.5603808840462569 0.4651341647080757 0.5000000000000000
0.5603808840462569 0.5348658352919243 0.5000000000000000
0.5000000000000000 0.5697701843634434 0.5000000000000000
0.4396191159537430 0.5348658352919243 0.5000000000000000
0.4396191159537430 0.4651341647080757 0.5000000000000000
0.5000000000000000 0.3757603875449354 0.5000000000000000
0.6075652945069621 0.4379113406185772 0.5000000000000000
0.6075652945069621 0.5620886593814227 0.5000000000000000
0.5000000000000000 0.6242396124550644 0.5000000000000000
0.3924347054930378 0.5620886593814227 0.5000000000000000
0.3924347054930378 0.4379113406185772 0.5000000000000000

Alternatively, the above benzene molecular structure can also be retrieved from the Pubchem public repository ², and then converted to the POSCAR format for uploading on our platform through any online converter, such as the OpenBabel Open Source Chemistry Toolbox ³, which allows to convert between nearly all the chemical data formats.

Create Benzene Molecule Entry in Materials Collection¶

The chemical structure for Benzene can readily be imported from the Materials Bank into the account-owned collection, if it is not already present there.

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

Open Materials Designer¶

We start with opening an instance of the Materials Designer Interface for creating and designing new Materials structures on our platform.

Create a Gold Surface¶

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

The instructions contained in this page should then be followed in order to create a surface of Gold, with normal vector oriented along the [211] axis, using our surface creator in Materials Designer, starting from the original gold crystalline sample.

Order of structures is important

The gold surface has to be created first in order for it to appear first in the list of materials shown on the left-had items list sidebar of the Materials Designer interface, so that its cell is used when later combining the two materials together.

Import the Benzene Molecule into Materials Designer¶

The Benzene molecule should now be imported into the current Materials Designer session, from the account-owned collection of materials.

Once imported into Materials Designer, the benzene molecule will appear as a new distinct entry item within the list of structures shown on the left-had items list sidebar of the Designer interface, besides the previously-generated gold surface.

Care should be taken by the user to remove any other material structure entry listed in the sidebar, besides benzene and the gold surface being considered here, that may have been loaded by default initially at the moment of the opening of Materials Designer.

Open Multi-Materials 3D Editor¶

After both the benzene molecule and the gold surface have been created as two separate structural items in the current session of Materials Designer, the user should now open an instance of the Multi-Materials 3D Editor via the "View" Menu, located within the header bar of the Materials Deigner Interface.

Combine the Two Materials¶

The Multi-Materials 3D Editor allows the two materials under investigation, the benzene molecule and the gold surface, to be combined together into a new unified materials entity.

Care should be taken by the user to place the molecule on top of the surface in as "symmetrical" a way as possible, for example by positioning the center of the benzene ring on the central portion of the surface. Relocation of the benzene molecule position can be done by following the instructions contained in this page, after selecting the benzene atom components under the "Scene" sidebar list of the 3D Editor interface.

Since in this example the plane of the 2D benzene molecule and the gold (211) surface are already parallel to each other, a simple translation of the benzene atoms on top of the surface should suffice.

Exit Multi-Materials 3D Editor¶

After the correct desired positioning of the benzene molecule on top of the gold surface, the user should now exit the Multi-Materials 3D Editor, and return to the original Materials Designer interface.

The user will notice that a new material entry, called "New Material" by default, has now been created automatically and is listed within the left-had items list sidebar of the Materials Designer interface. It contains the combined benzene-gold surface crystallographic structure, as a new single material entity.

Toggling of Orthographic Camera

The user is recommended to toggle the use of the Orthographic camera functionality, accessible via the 3D Editor interface of Materials Designer, in order to verify the correct alignment and centrality of the benzene molecule over the surface.

This new entry should first be renamed to a more memorable form, and should finally be saved via the "Input/Output" Menu located at the top-left corner into the account-owned materials collection, as a new material structure entry which is distinct from both the original isolated benzene molecule and gold structure.

Resulting Material¶

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

Run Further Analysis¶

The user is now free to use the newly generated benzene-gold surface system, in order to perform its further analysis, such as studying the adsorption energy.

The Nudged Elastic Band (NEB) method can be used for reaction energy profile calculations. We offer two alternative approaches for implementing the NEB method on our platform, based on the use of the VASP or Quantum ESPRESSO modeling engines, which are narrated in two separate tutorials accessible here and here respectively.

Animation¶

We demonstrate the above-mentioned steps which lead to the creation of a combined benzene molecule/gold surface crystallographic system, made possible via the functionalities of the Materials Designer Interface of our platform, in the following animation.

In this example, we consider a 3x3x3 slab supercell of the primitive unit cell of gold as a surface approximation (larger supercell dimensions should be envisaged for a more realistic surface representation). We also place the benzene molecule over the gold surface such that the molecule-surface distance is approximately 3.6 Angstroms, as measured by the difference in the z coordinates of the positions of the benzene atoms and gold surface atoms.