Adsorption Locator tutorials

The following tutorials illustrate how to utilize the Adsorption Locator's capabilities.
Determining the location of SO2 on the Ni(111) surface with Adsorption Locator
Modeling inhibitor adsorption onto a Pigment Red crystal face

Determining the location of SO on the Ni(111) surface with Adsorption

2
Locator
Purpose: Introduces the use of Adsorption Locator to study the adsorption of different types of
adsorbates onto substrates of different nature.

Modules: Materials Visualizer, Adsorption Locator, Forcite

Time:

Prerequisites: Sketching a benzamide molecule Visualizer Tutorial

Background
This tutorial is inspired by a paper on "Density functional theory investigation of the structure of SO
2
and SO on Cu(111) and Ni(111)" by Harrison et al. (2006). The importance of the adsorption of SO and
3 2
SO molecules relates to the necessity of scrubbing such environmental pollutants from power station
3
emissions. The paper presents DFT calculations on a number of geometries of the adsorbed SO
2
molecules.
Adsorption Locator can be used as a preparatory and screening tool in two ways:
to generate adsorbed configurations automatically, which can subsequently be used as starting
points for further DFT studies such as in the above paper.
to use the forcefield method to obtain a ranking of the energies for each generated configuration,
thereby indicating the preferred adsorption sites.
This tutorial will concentrate on the case of SO on Ni(111), and covers:
2
Getting started
To prepare the structures
To set up the Adsorption Locator calculation
To analyze the results
Summary
Note: In order to ensure that you can follow this tutorial exactly as intended, you should use the
Settings Organizer dialog to ensure that all your project settings are set to their BIOVIA default values.
See the Creating a project tutorial for instructions on how to restore default project settings.
1. Getting started
Begin by starting Materials Studio and creating a new project.
Open the New Project dialog and enter Ni_SO2 as the project name, click the OK button.

The new project is created with Ni_SO2 listed in the Project Explorer.

Page 2 | Materials Studio • Modules Tutorials

2. To prepare the structures
In this section of the tutorial you will prepare the structures of the Ni(111) surface and the SO
2
adsorbate. First prepare the SO molecule.
2

Select File | New... from the menu bar to open the New Document dialog, double-click on 3D
Atomistic. Using the sketching tools, build an SO molecule defining both S-O bonds as double
2
bonds, click the Clean button . Select File | Save from the menu bar and save the structure as
SO2.xsd.

The SO molecule should be optimized before adsorbing it onto the Ni surface you will construct.
2
Select Modules | Forcite | Calculation from the menu bar to open the Forcite Calculation dialog. On
the Setup tab, change the Task to Geometry Optimization and the Quality to Fine.

Select the Energy tab and change the Forcefield to COMPASS. Click the Run button.

When the job has completed the optimized structure is created in SO2 Forcite GeomOpt/SO2.xsd.
Now you will construct a Ni(111) surface.
Select File | Import... from the menu bar to open the Import Document dialog. Navigate to
Structures/metals/pure-metals and import Ni.msi.

Select Build | Surfaces | Cleave Surface from the menu bar to open the Cleave Surface dialog.
Change the Cleave plane (h k l) to 1 1 1 and press the TAB key. Increase the Fractional Thickness to
6.0 and press the TAB key. Click the Cleave button and close the dialog.

The number of layers in the structure should be chosen so that the depth of the surface is greater than
the non-bond cutoff used in the calculation. The choice of the cutoff will always be a trade off between
the accuracy and the time required for the calculation. Using 6 layers of Ni atoms gives a sufficient depth
that the SO molecule will only be involved in non-bond interactions with Ni atoms in the layers of the
2
surface, without increasing the calculation time unreasonably.
Next you will build a 2×2 supercell in order to expose a more realistic surface area for docking the SO
2
molecules.
Select Build | Symmetry | Supercell from the menu bar to open the Supercell dialog. Increase the
values of U and V to 2 and click the Create Supercell button. Close the dialog.

This structure should be converted to have 3D periodicity. As 3D periodic boundary conditions are used,
it is important that the size of the vacuum is great enough that the non-bond calculation for the sorbate
does not interact with the periodic image of the bottom layer of atoms in the surface. The vacuum
depth should be based on the non-bond cutoff and the shape of sorbate molecule. This should
generally be over-estimated to ensure that the sorbate interacts only with the surface.
In this case, a distance of 15 Å between the Ni surface layer and the next layer beyond the vacuum is
sufficient to prevent any non-bond interactions between the next repeat unit and either the Ni surface
or the SO molecule.
2

Adsorption Locator tutorials | Page 3

 Select Build | Crystals | Build Vacuum Slab... from the menu bar to open the Build Vacuum Slab
Crystal dialog. Set the value of Vacuum thickness to 15.0 and click the Build button.

To display the Ni atoms more clearly the ball and stick display style should be used.
Select View | Display style from the menu bar to open the Display Style dialog. On the Atom tab,
change the Display style to Ball and stick, then close the dialog.

3. To set up the Adsorption Locator calculation

You are now ready to set up the Adsorption Locator calculation, you will define the settings for the
quality and the forcefield and the method for selecting the location of the sites that the calculation will
probe.

Click the Adsorption Locator arrow on the Modules toolbar and select Calculation from the
dropdown list to open the Adsorption Locator Calculation dialog. Ensure that Ni(1 1 1).xsd is the
active document.

On the Setup tab set the Quality to Fine. Select SO2 Forcite GeomOpt/SO2.xsd from the Adsorbate
dropdown list. Set the value of Loading to 1.

On the Energy tab select COMPASS from the Forcefield dropdown list.

On the Location tab check the Surface region defined by atom set checkbox.

When the Quality of the calculation is set to Fine many simulated annealing cycles with many steps per
cycle will be used, so that good statistics are obtained.
Now you need to select the atoms that define the surface region.
Select the top layer of Ni atoms, this will display them in yellow.

Tip: If you are not familiar with selecting atoms refer to the Opening and viewing 3D documents
visualizer tutorial.

On the Location tab of the Adsorption Locator Calculation dialog, click the Add button to include the
selected atoms in the TargetAtoms set for the adsorption calculation. Check the Set maximum
adsorption distance checkbox, and enter a value of 5.0.

The region defined by the specified maximum distance from the selected target atoms will be sampled
for adsorbate inclusion. A value of 5.0 allows the system to develop new configurations of SO adsorbed
2
onto the Ni surface. If the maximum adsorption distance is too short some configurations will not be
accessible, and if it is too long no new configurations will be added.

Page 4 | Materials Studio • Modules Tutorials

Ni(111) after defining the TargetAtoms set
The fixed energy window is used to select which configurations are reported, so all configurations which
differ from the lowest configuration by less than 100 kcal/mol will be returned. In initial calculations it is
useful to use a wider energy window, as this ensures that no significant configurations are missed.
On the Properties tab check the checkboxes for all properties. Select the radio button for Fixed
energy window and enter a value of 100 kcal/mol.

You are now ready to run the calculation.

Click the Run button and close the dialog.

4. To analyze the results

When the calculation begins Materials Studio will create a new folder called Ni (1 1 1) Adsorption Anneal.
Once the calculation has completed, all results will be returned to this folder.
Open the 3D Atomistic document Ni (1 1 1) Fields.xsd.

This file displays a field of adsorption sites, higher density of points showing more likely locations.
Right-click in the document and select Display Style from the shortcut menu to open the Display
Style dialog. On the Field tab click the Color by field values radio button and select the Volume
display style. Close the dialog.

Now the more likely adsorption areas are shown in green and less likely sites appear red.
Open the study table Ni(1 1 1).std.

This contains the structures and energies of the lowest energy configurations. Compare the one found
here with the lowest one found in the paper.

Adsorption Locator tutorials | Page 5

 Repeat the Adsorption Locator calculation using Cu in place of Ni.

5. Summary
Your Adsorption Locator calculations should yield results similar to the following.

Schematic view of two possible bonding sites

Tip: To improve the view of the energy fields over the Ni surface, select all of the non-surface Ni atoms
and, on the Atom tab of the Display Style dialog, set their display style to None.
Because the Monte-Carlo approach has a statistical component your results may be slightly different. To
obtain results that are consistent between repeated calculations, it is necessary to run longer, more
accurate simulations.
For SO on Ni, the bridge site was found to be the lowest one in energy, in agreement with the paper by
2
Harrison et al. They also reported no appreciable difference in energy between the bridge and the hollow
sites for SO on Cu.
2
This is the end of the tutorial.
"Density functional theory investigation of the structure of SO and SO on Cu(111) and Ni(111)" by M. J.
2 3
Harrison, D. P. Woodruff , and J. Robinson, Surface Science, 600, 1827, (2006)

Page 6 | Materials Studio • Modules Tutorials

Adsorption of CO onto a Pd(110) surface
Purpose: Introduces the use of CASTEP for calculating the adsorption energy of a gas onto a metal
surface.

Modules: Materials Visualizer, CASTEP

Time:

Prerequisites: Using the crystal builder Visualizer Tutorial

Background
In this tutorial you will examine the adsorption of CO on Pd(110). The Pd surface plays a crucial role in a
variety of catalytic reactions. Understanding how molecules interact with such surfaces is one of the first
steps to understanding catalytic reactions. In this context, DFT simulations can contribute to this
understanding by addressing the following questions:
Where does the molecule want to adsorb?
How many molecules will stick to the surface?
What is the adsorption energy?
What does the structure look like?
What are the mechanisms of adsorption?
You will focus on one adsorption site, the short bridge site, as it is known to be energetically preferred at
fixed coverage. At 1 ML coverage the CO molecules repel each other preventing them from aligning
exactly perpendicular to the surface. You will calculate the energy contribution of this tilting to the
chemisorption energy by considering a (1 × 1) and (2 × 1) surface unit cell.

Pd bulk and a top view on the Pd(110) surface. The (110) cleave plane is highlighted in blue. a is the bulk lattice
0
constant, also known as the lattice parameter.

CASTEP tutorials | Page 39

Introduction
In this tutorial, you will use CASTEP to optimize and calculate the total energies of several different
systems. Once you have determined these energies, you will be able to calculate the chemisorption
energy for CO on Pd(110).
This tutorial covers:
Getting started
To optimize bulk Pd
To build and optimize CO
To build the Pd(110) surface
To relax the Pd(110) surface
To add CO to the 1 × 1 Pd(110) surface and optimize the structure
To set up and optimize the 2 × 1 Pd(110) surface
To analyze the energies
To analyze the density of states (DOS)
Note: In order to ensure that you can follow this tutorial exactly as intended, you should use the
Settings Organizer dialog to ensure that all your project settings are set to their BIOVIA default values.
See the Creating a project tutorial for instructions on how to restore default project settings.
1. Getting started
Begin by starting Materials Studio and creating a new project.
Open the New Project dialog and enter CO_on_Pd as the project name, click the OK button.

The new project is created with CO_on_Pd listed in the Project Explorer.
This tutorial consists of five distinct calculations. To make it easier to manage your project, you should
begin by preparing five subfolders in your project.
Right-click on the root icon in the Project Explorer and select New | Folder, repeat this four more
times. Rename the folders Pd bulk, Pd(110), CO molecule, (1x1) CO on Pd(110) and (2x1) CO on Pd
(110).

2. To optimize bulk Pd
The crystal structure of Pd is included in the structure library provided with Materials Studio.
In the Project Explorer, right-click on the Pd bulk folder and select Import... to open the Import
Document dialog. Navigate to Structures/metals/pure-metals and import Pd.msi.

The bulk Pd structure is displayed. You can change the display style to ball and stick.
Right-click in the Pd.xsd 3D Viewer and select Display Style to open the Display Style dialog. On the
Atom tab, select Ball and stick and close the dialog.

Now optimize the geometry of the bulk Pd using CASTEP.

Click the CASTEP button on the Modules toolbar then select Calculation or select Modules |
CASTEP | Calculation from the menu bar.

This opens the CASTEP Calculation dialog.

Page 40 | Materials Studio • Modules Tutorials

CASTEP Calculation dialog, Setup tab
Cell optimization of crystals requires more accurate calculations than those performed with default
settings.
Change the Quality from Medium to Fine.

To maintain consistency across the calculations that you are going to perform, you should make some
changes on the Electronic tab.
Select the Electronic tab and click the More... button to open the CASTEP Electronic Options dialog.
On the Basis tab check the Use custom energy cutoff checkbox and make sure that the field value is
570.0 eV. This ensures that all calculations in the tutorial use the same energy cut-off.

The default values for geometry optimization do not include optimization of the cell.
Change the Task from Energy to Geometry Optimization. Click the More... button to open the
CASTEP Geometry Optimization dialog. Check the Optimize cell checkbox and close the dialog.

Click the Run button. A message dialog about conversion to the primitive cell is displayed. Click the
Yes button.

The job is submitted and starts to run. You should proceed to the next section and build the CO
molecule but return here when the calculation is complete to display the Lattice Parameters.
When the job has finished, you must convert the primitive cell result back to a conventional cell
representation in order to proceed with building the Pd(110) surface in step 4.
In the Project Explorer, open Pd.xsd located in the Pd CASTEP GeomOpt folder. Select Build |
Symmetry | Conventional Cell from the menu bar.

You should now save your project files.

CASTEP tutorials | Page 41

 Select File | Save Project, then Window | Close All from the menu bar. In the Project Explorer, re-
open the optimized Pd.xsd.

Right-click in the 3D Viewer and select Lattice Parameters.

This opens the Lattice Parameters dialog. The value of a should be approximately 3.962 Å, compared
with the experimental value of 3.89 Å.
Close the Lattice Parameters dialog and Pd.xsd.

3. To build and optimize CO

CASTEP will only work with periodic systems. To optimize the geometry of the CO molecule, you must
put it into a crystal lattice.
In the Project Explorer, right-click on the CO molecule folder and select New | 3D Atomistic
Document. Rename the new document CO.xsd.

An empty 3D Viewer is displayed. You will use the Build Crystal tool to create an empty cell and then add
the CO molecules to it.
Select Build | Crystals | Build Crystal... from the menu bar to open the Build Crystal dialog. Choose
the Lattice Parameters tab and change each cell Length a, b, and c to 8.00. Click the Build button.

An empty cell is displayed in the 3D Viewer.

Select Build | Add Atoms from the menu bar to open the Add Atoms dialog.

The C-O bond length in the CO molecule has been determined experimentally as 1.1283 Å. By adding the
atoms using Cartesian coordinates you can create your CO molecule with exactly this bond length.
Select the Options tab and ensure that the Coordinate system is set to Cartesian. On the Atoms tab
click the Add button.

A carbon atom is added at the origin of the cell.

Change the Element to O, leave the x and y values as 0.000. Change the z value to 1.1283. Click the
Add button and close the dialog.

You are now ready to optimize your CO molecule.

Open the CASTEP Calculation dialog.

The settings from the previous calculation have been retained. However, you do not need to optimize
the cell for this calculation.

Page 42 | Materials Studio • Modules Tutorials

 Open the CASTEP Geometry Optimization dialog. Uncheck the Optimize cell checkbox and close the
dialog.

On the Properties tab of the CASTEP Calculation dialog check the Density of states checkbox. Change
the k-point set to Gamma and check the Calculate PDOS checkbox. Click the Run button.

When asked about converting to higher symmetry, click the No button to proceed with the current
symmetry.

The calculation starts. You can move onto building the Pd(110) surface as you will analyze the energy at
the end of the tutorial.
4. To build the Pd(110) surface
This section of the tutorial uses the optimized Pd structure from the Pd bulk part of the tutorial.
Select File | Save Project, then Window | Close All from the menu bar. Open Pd.xsd in the Pd
bulk/Pd CASTEP GeomOpt folder.

Creating the surface is a two step process. The first step is to cleave the surface and the second is to
create a slab containing the surface and a region of vacuum.
Select Build | Surfaces | Cleave Surface from the menu bar to open the Cleave Surface dialog.
Change the Cleave plane (h k l) from -1 0 0 to 1 1 0 and press the TAB key. Increase the Fractional
Thickness to 1.5. Click the Cleave button and close the dialog.

A new 3D Viewer is opened containing the 2D periodic surface. However, CASTEP requires a 3D periodic
system as input, this is obtained using the Vacuum Slab tool.
Select Build | Crystals | Build Vacuum Slab... from the menu bar to open the Build Vacuum Slab
Crystal dialog. Change the Vacuum thickness from 10.00 to 8.00 and click the Build button.

The structure changes from 2D to 3D periodic and a vacuum is added above the atoms. Before
continuing, you must reorient the lattice.
Open the Lattice Parameters dialog and select the Advanced tab, click the Re-orient to standard
button. Close the dialog.

You should also change the lattice display style and rotate the structure so that the z-axis is vertical on
the screen.
Open the Display Style dialog and select the Lattice tab. In the Display style section, change the Style
from Default to Original. Close the dialog.

Press the UP arrow key twice.

The 3D view shown below is displayed:

CASTEP tutorials | Page 43

The Pd atom with the largest z-coordinate will be called "the uppermost Pd layer".
Later in this tutorial, you will need to know the bulk interlayer spacing d . You can calculate this using
o
the atom coordinates.
Select View | Explorers | Properties Explorer from the menu bar. Select the Pd atom with
FractionalXYZ x = 0.5 and y = 0.5. Note the z value of this atom from the XYZ property.

The z value should be 1.401 Å and this is the interlayer spacing. This z value refers to the Z coordinate
from the (Cartesian) XYZ property and not FractionalXYZ.

Note: For an fcc(110) system, d can be calculated as .

0
Before you relax the surface, you must constrain the Pd atoms in the bulk as you only need to relax the
surface.
Hold down the SHIFT key and select all the Pd atoms except the uppermost Pd layer. Select Modify |
Constraints from the menu bar to open the Edit Constraints dialog. Check the Fix fractional position
checkbox and close the dialog.

The bulk atoms have been constrained. You can see the constrained atoms by changing their display
color.
In the 3D Viewer, click anywhere to deselect the atoms. Open the Display Style dialog and select the
Atom tab. Change the Color by option to Constraint.

This 3D view is now displayed:

Page 44 | Materials Studio • Modules Tutorials

 Change the Color by option back to Element and close the dialog.

This structure is needed for the Pd(110) surface relaxation and also as a starting model for (1x1) CO on Pd
(110) optimization.
Select File | Save As... from the menu bar. Navigate to the Pd(110) folder and click the Save button.

Hold down the CTRL key and drag the document into the (1x1) CO on Pd(110) folder. Rename the
document (1x1) CO on Pd(110).

Select File | Save Project, then Window | Close All from the menu bar.

5. To relax the Pd(110) surface

Now you are ready to optimize the Pd (110) surface.
From the Project Explorer, open Pd(110).xsd in the Pd(110) folder. Open the CASTEP Calculation
dialog and then the CASTEP Geometry Optimization dialog. Ensure that the Optimize cell checkbox
is unchecked and close the dialog.

You should also calculate the density of states for the system.
Select the Properties tab on the CASTEP Calculation dialog. Check the Density of states and Calculate
PDOS checkboxes and change the k-point set to Fine.

You are ready to run the calculation.

Click the Run button and close the CASTEP Calculation dialog.

When asked about converting to higher symmetry, click the No button to proceed with the current
symmetry.

The calculation will take some time to run and so you will perform the analysis at the end. You should
move on and construct the next set of surfaces.
Select File | Save Project then Window | Close All from the menu bar.

CASTEP tutorials | Page 45

6. To add CO to the 1 × 1 Pd(110) surface and optimize the structure
Now you are going to work with the structure in the (1x1) Co on Pd(110) folder.
In the Project Explorer, open (1x1) CO on Pd(110).xsd in the (1x1) CO on Pd(110) folder.

Now add the CO molecule above the short bridge position. You will make use of the fact that for CO on
Pd(110), bond lengths have been experimentally determined.

Geometry of CO on Pd(110) in the yz-plane. Hatched atoms are not displayed in Lattice: Original display mode.
The first step is to add the carbon atom. The Pd-C bond length (denoted above as d ) should be
Pd-C
1.93 Å. When you use the Add Atom tool you can enter either Cartesian or fractional coordinates but in
this case you will use fractional coordinates, x , y , and z . x and y are simple as y = 0.5 and x = 0.
C C C C C C C
However, determination of z is slightly more difficult. You will construct it from the two distances z
C Pd-C
and z
Pd-Pd.
z is simply the lattice parameter a divided by √2 (it should be 2.80 Å).
Pd-Pd 0

z is obtained from the formula (it should be 1.33 Å).

Pd-C
Add z and z to obtain z (it should be 4.13 Å). Now convert this distance into a fractional length.
Pd-C Pd-Pd C
You do this using the Lattice parameters.
Right-click in the 3D Viewer and select Lattice Parameters from the shortcut menu. Note the value of
c.

To calculate the fractional z coordinate, you divide z by the c lattice parameter (you should obtain
C
0.382).
Open the Add Atoms dialog and choose the Options tab. Check that the Coordinate system is
Fractional. On the Atoms tab change the Element to C, change a to 0.0, b to 0.5, and c to 0.382. Click
the Add button.

If you want to confirm that you have set up the model correctly, use the Measure/Change tool.

Page 46 | Materials Studio • Modules Tutorials

 Click the Measure/Change arrow on the toolbar and select Distance from the dropdown list.
Click on the Pd-C bond.

The next step is to add the oxygen atom.

On the Add Atoms dialog, change the Element to O.

Experimentally, the C-O bond length has been determined as 1.15 Å. In fractional coordinates this is
0.107, adding this value to the fractional z-coordinate of carbon (0.382), the z-coordinate of oxygen is
0.489.
Change the value of c to 0.489 and click the Add button. Close the dialog.

The calculations for the Pd surface model were carried out using P1 symmetry. However, the system has
a higher symmetry, even after the addition of the CO molecule. You can find and impose symmetry,
using the Find Symmetry tool, to speed up further calculations.

Click the Find Symmetry button on the Symmetry toolbar to open the Find Symmetry dialog.
Click the Find Symmetry button then the Impose Symmetry button.

The symmetry is PMM2.

Open the Display Style dialog and select the Lattice tab. Change the Style to Default. On the Atom
tab, select the Ball and stick display style and close the dialog.

The structure should look similar to this:

Before you optimize the geometry of the structure, you should save it in the (2x1) CO on Pd(110) folder.
Select File | Save from the menu bar to save the 1x1 system. Then also select File | Save As... from
the menu bar, navigate to the (2x1) CO on Pd(110) folder and save the document as (2x1) CO on Pd
(110).xsd.

You are now ready to optimize the structure.

CASTEP tutorials | Page 47

 Select File | Save Project, then Window | Close All from the menu bar.

In the Project Explorer, open (1x1)CO on Pd(110).xsd in the (1x1)CO on Pd(110) folder.

Open the CASTEP Calculation dialog.

The parameters from the previous calculation should have been retained.
Click the Run button and close the dialog.

Once again, you can move onto building the final structure while the calculation progresses.
7. Setting up and optimizing the 2 × 1 Pd(110) surface
The first step is to open the 3D Atomistic document in the (2 × 1) CO on Pd(110) folder.
In the Project Explorer, open (2x1) CO on Pd(110).xsd in the (2x1) CO on Pd(110) folder.

This is currently a 1 × 1 cell so you need to use the Supercell tool to change it to a 2 × 1 cell.
Select Build | Symmetry | Supercell from the menu bar to open the Supercell dialog. Increase B to 2
and click the Create Supercell button and close the dialog.

The structure should look like this:

(2 × 1) Cell of CO on Pd(110)
Now tilt the CO molecules with respect to each other. To simplify this operation, identify the CO
molecule at y = 0.5 as molecule A and the one at y = 0.0 as molecule B.
Select the carbon atom of molecule B. In the Properties Explorer, open the XYZ property and subtract
0.6 from the X field. Repeat this for the oxygen atom of molecule B but subtract 1.2 from the X field.

Now repeat this for molecule A.

Select the carbon atom of molecule A. In the Properties Explorer, open the XYZ property and add 0.6
to the X field. Repeat this for the oxygen atom of molecule A but add 1.2 to the X field.

The view down the z-axis of the molecule should look like this:

Page 48 | Materials Studio • Modules Tutorials

However, you will notice that the Pd-C and C-O bond lengths have changed from their original values.
Select the carbon atom in molecule A and use the Properties Explorer to change the Z field of the
FractionalXYZ property to 0.369. Repeat this for molecule B.

This corrects the Pd-C bond length. You can use the Measure/Change tool to correct the C-O bond
length.

Click the Measure/Change button on the Sketch toolbar and select Distance from the
dropdown list. Click on the C-O bond for molecule A.

Choose the 3D Viewer Selection Mode tool on the 3D Viewer toolbar and select the monitor. In
the Properties Explorer, change the Filter to Distance.

Change the Distance property to 1.15 Å. Repeat this for molecule B.

Now recalculate the symmetry of the system.

Open the Find Symmetry dialog and click the Find Symmetry button then the Impose Symmetry
button.

The symmetry is PMA2. The view of the unit cell changes from 3 CO molecules on the Pd surface to only
2. You are now ready to optimize the geometry of your system.
Open the CASTEP Calculation dialog and click Run.

The calculation starts. When the calculation finishes, you will need to extract the total energy of the
system as detailed in the next section. You can move onto the next section to extract the energies from
the previous calculations.
8. To analyze the energies
In this section you are going to calculate the chemisorption energy ΔE . This is defined as:
chem

Allowing the CO atoms to tilt against each other, hence reducing the self repulsion of the CO molecules,
should result in a gain in energy. The repulsion energy can be calculated from:

CASTEP tutorials | Page 49

To calculate these properties, you need to extract the total energies from CASTEP text output
documents for each simulation.
In the Project Explorer, open CO.castep in the CO molecule/CO CASTEP GeomOpt folder. Press CTRL
+ F and search for Final Enthalpy. Note down the value that appears in that line. Repeat the
procedure to find the total energies of the other systems and so complete the table.

Simulation Total Energy (eV)

CO molecule
Pd(110)
(1×1)CO on Pd(110)
(2×1)CO on Pd(110)
Once you have the energies, simply use the above equations to calculate ΔE and ΔE . These
chem rep
should have values of approximately - 1.79 eV and - 0.06 eV, respectively.
9. To analyze the density of states (DOS)
Next, you will examine the changes in the density of states (DOS). This will allow you to obtain an insight
into the bonding mechanism of CO on Pd(110). To do this, you need to display the density of states of
the isolated CO molecule and of (2x1) CO on Pd(110).
In the Project Explorer, open CO.xsd in the CO molecule/CO CASTEP GeomOpt folder.

Click the CASTEP button on the Modules toolbar, then select Analysis to open the CASTEP
Analysis dialog.

Select the Density of states. Click the Partial radio button and uncheck the f and sum checkboxes.
Click the View button.

A chart document is displayed showing the PDOS for the CO molecule.

PDOS of CO molecule

Page 50 | Materials Studio • Modules Tutorials

 Repeat the above for (2x1) CO on Pd(110).xsd.

PDOS of (2x1) CO on Pd(110)

It is clear that the electronic states of the isolated CO molecule at approximately -20, -5, and -2.5 eV are
considerably lowered in energy as the CO binds to the surface.
Note: The default pseudopotential for Pd, Pd_80.otfg, treats 4s and 4p semicore states as valence.
This results in sharp peaks in the calculated DOS at about -84 and -49 eV. The chart above excludes
those states; this can be achieved by using Properties Explorer to change the maximum and
minimum values along X and Y axes.
As an independent exercise you can analyze PDOS further by investigating contributions to the PDOS of
the adsorbate complex that arise from the C and O atoms.
Hold down the SHIFT key and select all C and O atoms in the (2x1) CO on Pd(110).xsd document.
Generate PDOS - it shows the effect of hybridization with Pd states which manifests itself as
broadening of the energy levels and their general shift towards lower energies.

This is the end of the tutorial.

CASTEP tutorials | Page 51