Atomic Layer Deposition

Tutorial Created with Software Release: 2025-4
Topics: Catalysis & Reactivity, Energy Capture & Storage, Metals, Alloys & Ceramics, Thin Film Processing
Methodology: Molecular Quantum Mechanics, Periodic Quantum Mechanics
Products Used: MS Maestro, MS Surface, Quantum Espresso

Tutorial files

350 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

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Abstract:

 

In this tutorial, we will learn to use enumeration tools and adsorption/desorption workflows based on periodic DFT in MS Maestro to study reaction mechanism and determine the thermodynamics of the reactions of gaseous precursors as they nucleate onto a substrate during atomic layer deposition.

 

Tutorial Content

  1. Introduction to Atomic Layer Deposition

  1. Creating Projects and Importing Structures

  1. Building the Substrate Slab

  1. Molecular Adsorption

  1. Surface Reactions: Dissociative Adsorption

  1. Surface Reactions: Molecular Desorption of By-Products

  2. Surface Reactions: Associative Desorption of By-Products

  1. Visualizing the Reaction Energies

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Atomic Layer Deposition

Atomic layer depositiona type of chemical vapor deposition that relies on self-limiting chemical reactions to control the number of deposited layers on a surface. (ALD) is a type of chemical vapor deposition (CVD) technique that can be used to produce high quality thin films. While CVD encompasses a large class of gas-surface processes that deposit a desired product, the ALD process specifically relies on a cycle of self-limiting chemical reactions for a large degree of control over the thickness, purity, uniformity and conformality of deposited layers. As a result, ALD processes are indispensable in many fields, though especially for the fabrication of devices in the semiconductor industry.

Since ALD depends on self-limiting surface chemistry, detailed understanding of these chemical reactions is needed in order to change an ALD process or develop a new one, potentially including the introduction of new precursor chemicals. Precursor synthesis, characterization, film deposition, process optimization and scale-up are expensive and time consuming in a lab setting, and so computational modeling in this area is very beneficial. Computational techniques can be used to determine the ability of potential precursors to adsorb onto the surface, undergo self-limiting reactions, and cleanly release volatile by-products. A similar set of reactions can be studied for atomic layer etching. Computing the likelihood of these reaction steps at various temperatures and pressures reveals under what conditions an ALD cycle is viable and whether competing reactions (such as CVD) are taking place.

In this tutorial, we demonstrate how to simulate reaction steps during the deposition of a germanium-based film onto an SiO2 substrate. We evaluate reaction free energies as a function of temperature for the organometallic Ge precursor by computing molecular adsorption, reaction of ligands with surface hydroxyl groups, and desorption of protonated ligands as by-products. These reactions are typical of the first step in nucleation and growth onto the substrate. We first model the adsorption of the GeMe3(F) precursor containing the fluoro and methyl (Me = CH3) ligands. Then we explore how the ligands dissociate at the surface, react with hydroxyl and desorb as HF or CH4.

One result from this study is determining the chemical identity of the fragments of germanium precursor that - in an ideal ALD process - will saturate the surface at the end of the germanium pulse.  These stable intermediates can be used as the starting point for a similar study of the adsorption and elimination reactions of the second ALD reagent, e.g. water as an oxygen source for the deposition of germanium oxide. In this way, the chemistry of the entire ALD cycle can be computed.

Surface structures will be built with the Adsorption Enumeration and Desorption Enumeration panels and optimized using machine learning force field (MPNICE) and periodic DFT (Quantum ESPRESSO) via the Adsorption Energy panel, followed by analysis with the Thermochemistry Viewer and Reaction Profile Viewer panels. An outline of the workflow followed in this tutorial is shown in Figure 1, below. For more information on using periodic DFT to model surface reactions, see our tutorial on Modeling Surfaces.

Figure 1: Modeling the energetics of an ALD process consisting of molecular adsorption of precursors, dissociation to fragments that chemisorb and/or undergo H-transfer to form the by-product HF, and then desorption of the by-product.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved. in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project., which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data.. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/ald.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved. for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to ald_tutorial, click Save
    • The project is now named ald_tutorial.prj

Figure 2-3. Importing the structure that will be used as the adsorbate throughout the tutorial.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files and select Section_02 > GeMe3F.maegz and click Open

Note: The structure of this complex can be created from scratch using the Single Complex Builder panel. See the Organometallic Complexes tutorial and the Building Small Molecules video.

3. Building the Substrate Slab

In this section we will prepare the substrate slab by importing a SiO2-OH slab from a previous literature study, see Rozanska, et. al.  Alternatively, any surface of any crystalline material can be generated using the Surface Energy panel, as detailed in our tutorial on Modeling Surfaces.

Figure 3-1. Importing the substrate slab.

  1. Go to Tasks > Materials > Structure Builders > Import Slabs
    • Alternatively you can search for the panel in the Tasks menu
    • The Import Slabs panel opens
  2. From the list of options, select the SiO2-OH_Rozanska_101-1 entry
    • We choose this slab because the original publication shows that this (1 0 1) surface is stable under typical ALD conditions and because the unit cell is small enough to simulate with DFT
    • See the For Further Reading section for a link to the paper related to this slab
  3. Click Add
    • The table at the bottom of panel should populate with information about the slab
  4. Check the citation agreement option
  5. Click Import Table
    • A new entry is added named SiO2-OH_Rozanska_101-1
  6. Close the Import Slabs panel

Figure 3-2. Elongating the slab unit cell via the Redefine Lattice panel.

In order to make room for the adsorbates we need to elongate the unit cell of the slab.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. and includethe entry is represented in the Workspace, the circle in the In column is blue. the SiO2-OH_Rozanska_101-1
  2. Go to Tasks > Materials > Tools > Redefine Lattice
  3. Click Anchor to Origin in the bottom left corner of the panel
    • This brings the slab towards one end of the cell, making it easier to visualize and manipulate the structures later in the tutorial
  4. In the Set new cell parameters section, change the length of the c direction to 25 Å
    • The transformation matrix will automatically update
  5. In the Transformation mode section select the option for Frame (only cell dimensions may change)
    • We are not trying to change the structure of the slab itself, just increase the space above the slab to have plenty of room for our surface simulations
  6. Click Run
    • This calculation requires a CPU host and will finish almost instantaneously
    • A new entry is added

Figure 3-3. Updated substrate entry.

  1. Close the Redefine Lattice panel
  2. Rename the new entry to SiO2-OH_substrate by double clicking on the entry name

4. Molecular Adsorption

Adsorption reactions are described as ‘molecular’ when the adsorbate remains intact at the surface:

surf-OH + GeMe3F(g) → surf-OH⋯GeMe3F

In this section, we will use the Enumerate Adsorbates panel in order to create initial guesses for the adsorbate geometries. Then we will use the Adsorption Energy Calculations panel to optimize the structures of the adsorbate geometries using machine-learning force fields and periodic quantum mechanics and calculate the adsorption free energies of the systems at various temperatures and pressures. We will use the computed free energies when comparing molecular adsorption to other modes of adsorption in later sections.

An alternative way to generate geometries of molecular adsorbates is the Adsorption Site Finder panel, which uses OPLS or MLFF force fields in Monte Carlo simulated annealing to randomly translate and rotate the adsorbate molecule over a fixed substrate (see the Locating Adsorption Sites on Surfaces tutorial).

Figure 4-1. The enumeration settings for the substrate.

  1. Make sure the SiO2-OH_substrate entry is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries.
  2. Go to Tasks > Materials > Enumeration > Adsorption
  3. In the Substrates section of the panel, for Load structures from choose Selected entries and click Load
    • The table is updated
    • While we load just one substrate in this case, note that it is possible to load multiple substrates
  4. Select H from the Reactive atom filter
    • This tells the panel which atom(s) in the substrate structure will be reacting with the gas molecules in the adsorption process
  5. Select the option for Include surface atoms within
  6. Change the distance to 4.5 Å of the reactive atom
    • This selects two of the four surface hydrogens as possible reactive atoms

Figure 4-2. The enumeration settings for the gas molecule (adsorbate).

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the GeMe3F entry
  2. In the Gas molecules section, ensure Select entries is chosen for Load structures from
  3. Click Load
    • The table is updated
    • While we load just one gas molecule in this case, note that it is possible to load multiple molecules
  4. Ensure Molecular is selected for the Adsorption
  5. Change the Reactive atom filter to F
    • Make sure that the reactive atom in GeMe3F updates to the fluorine atom
  6. Change the Job name to enum_adsorbates_ molecular
  7. Adjust the job settings as needed
    • This job requires a CPU host and should finish almost instantaneously

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_04 >  enum_adsorbates_molecular > enum_adsorbates_molecular-out.maegz
    • The completed job should have resulted in a new group with two new entries
  2. Close the Enumerate Adsorbates panel

Note: If any of the entries appears in a group labeled ‘Bad contacts’ you need to edit the geometry of the adsorbate structure so that the proposed adsorption does not interfere with the structure of the surface slab.

Note: If the slab is too small in the x or y directions to accommodate the adsorbing molecule, you can extend the substrate cell by using the ‘extents’ option and ‘Make P1 cell’ tool in the periodic structure toolbox. You could also use the Redefine Lattice panel.

There is the option to use any molecular adsorbate structure above as input for the Adsorption Site Finder panel, randomly translating and rotating the adsorbate so as to sample more configurations (see the Locating Adsorption Sites on Surfaces tutorial). The output resulting from that panel can be used as input for Adsorption Energy calculations below, in just the same way as we will directly use the output from Enumerate Adsorbates.

Having built candidate adsorbate structures, the following steps show how to set up an adsorption energy calculation for these structures. We will first do a coarse optimization of the geometries with a machine learning force field (MLFF), followed by a finer optimization with density functional theory (DFT). We will also calculate the thermochemistry over a range of temperatures. Our aim is to find the most thermodynamically-favorable mode of adsorption.

Figure 4-3. The Adsorption Energy Calculations panel.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the two adsorbate entries from the enumeration
  2. Go to Tasks > Materials > Quantum Mechanics > Workflows > Adsorption Energy
    • The Adsorption Energy Calculations panel opens
    • This panel will be used multiple times throughout this tutorial; for easier access, click the star next to the panel name in the Tasks menu to have the panel appear as an option in the favorites toolbar above the workspace
  3. Make sure that Use adsorbate structures from is selected and shows Project Table (2 selected entries)
    • Geometries of the gas molecule and substrate will be generated using instructions in the adsorbate entries from the enumeration
  4. In the Adsorption energy at 0 K and 1 atm section, select Machine learning force field
    • If this option does not exist or is greyed out for you, you do not have access to the MS Force Field Applications license. We recommend jumping to step 30 to import the results directly.
  5. Click MLFF Options
    • The MLFF Options - Adsorption Energy dialog box opens
  6. Select the Hybrid_MPNICE force field from the dropdown menu
  7. Set Maximum steps to 350
  8. Set Convergence criteria to Loose
  9. Tick Use special measures to prevent convergence failure
  10. Untick Use symmetry
  11. As an Additional keyword enter intopt=0 so as to use Cartesian coordinates
  12. Click OK
  13. Change the Job Name to adsorption_energy_molecular_mlff
  14. Adjust the job settings () as necessary
    • This job requires a CPU host
    • With 12 CPUs this job should complete in about 2 minutes

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_04 > adsorption_energy_molecular_mlff > adsorption_energy_molecular_mlff-out.maegz

In this workflow for adsorption, the initial geometries are sometimes far from the minimum and the optimization process may not converge first time. Unconverged entries are flagged ‘Failed’ in the output group. They can be run again with the Restart option, possibly adjusting the MLFF optimization settings, or the partially-optimized geometries can be used as input for DFT in the next step.

Using the ‘Hybrid_MPNICE’ MLFF, we have obtained geometries and adsorption energies that suggest that molecular adsorption is favorable. In the next step we will use these geometries as input for higher-accuracy (but more time-consuming) DFT calculations. Our tests show that starting from the geometries that are pre-optimized with MLFF reduces the number of cycles required in subsequent DFT optimizations by 20-60%.

Figure 4-4. Selecting the job to restart.

  1. Return to the Adsorption Energy panel, select Restart job
    • The Locate Adsorption Energy Job dialog opens
    • If the dialog does not open, click on Select Job
  2. Select Manually locate job directory, click Browse, and navigate to the downloaded job (Section_04 > adsorption_energy_molecular_mlff)
  3. Click OK
    • The Locate Adsorption Energy Job dialog closes

Figure 4-5. Selecting the subjobs to restart with Quantum ESPRESSO.

  1. Select all five entries in the table
    • Any failed entries are automatically ticked, but we tick all entries because we wish to run DFT on all of the MLFF structures
    • The ticked entries will be used as initial geometries for optimization
  2. In the Adsorption energy at 0 K and 1 atm section, select Periodic with Quantum ­Espresso

You can learn more about setting up periodic DFT calculations with Quantum ESPRESSO in the Installing and Configuring Quantum ESPRESSO documentation.

Figure 4-6. Theory settings for the periodic DFT calculations.

  1. Click Advanced Options
    • The Adsorption Energy Calculations - Advanced Options dialog box opens
  2. Make sure the following options in the Theory tab are selected:
    • For Density functional type select GGA and for Density functional select PBE, as we need the accuracy of a gradient-corrected functional
    • For Dispersion correction select DFT-D3 because including dispersion is likely to be important for molecules at surfaces
    • Set the Grid plane distance to 0.1/Å - a fairly wide spacing like this is appropriate for non-metallic systems 

Figure 4-7. SCF settings for the periodic DFT calculations.

  1. Go to the SCF tab
  2. Click Update from pseudopotentials
    • The cutoffs should be automatically set to 40.0 Ry and 200.0 Ry for the wavefunction and charge density, respectively. Change the cutoffs to these values if they are not what you see.
    • If your pseudopotentials do not come with energy cutoffs, change these values manually
  3. Set the Max steps in SCF to 200

Figure 4-8. Optimization settings for the periodic DFT calculations.

  1. Go to the Optimization tab
  2. Set the Number of steps to 350 so as to avoid the optimization ending prematurely
  3. Click Save

Figure 4-9. Adjusting the adsorption free energy calculation settings.

  1. Check the box for Adsorption Free Energy
  2. Set the temperature start to 373.15 K
  3. Set the number of temperature steps to 3
  4. Set the temperature step increment to 100 K
  5. Change the pressure to 0.013 atm which is 10 Torr
  6. Click to set the Jaguar Options that will be used for the thermochemical corrections

Figure 4-10. Adjusting the settings for the Jaguar optimization calculations.

  1. Change the Theory to B3LYP-D3 where the D3 dispersion correction may be significant for molecules at surfaces
  2. Change the Basis set to LACV3P** which is a large basis set that covers many elements
  3. Increase the Maximum iterations of SCF cycles to 100
  4. Increase the Maximum steps for the optimization to 200 so that the optimization does not stop prematurely
  5. Click OK

 

Note: See the Modeling Surfaces tutorial for more information about this panel and differences between Jaguar and Quantum ESPRESSO calculations.

Figure 4-11. Running the adsorption calculation.

  1. Change the Job Name to adsorption_energy_molecular_dft
  2. Adjust the job settings () as necessary
    • This job requires a CPU host
    • We recommend allocating for 3 simultaneous subjobs as calculations will be run on the 2 adsorbate slabs and the substrate slabs. The gas molecules will also be optimized but these will be comparatively fast.
    • With 24 CPUs for each subjob, this run should complete in about 12 hours

For each system, the Adsorption Energy panel generates structures of substrate and a gas molecule, and optimizes them along with the adsorbate slab using periodic DFT, combining the resulting total energies to calculate the adsorption energy. The panel also carries out vibrational analysis of the gas molecule with molecular DFT and uses the resulting thermochemical data to approximate the free energy of adsorption at the specified temperatures and pressures.

Figure 4-12. Selecting the new entry group.

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_04 > adsorption_energy_molecular_dft > adsorption_energy_molecular_dft-out.maegz
  2. After importing, you should see a new entry labeled adsorption_energy_molecular_dft (5). This should have the two optimized adsorption structures as well as optimized structures for the gas adsorbate and the substrate.
  3. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the whole group by clicking on the group entry name
  4. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Thermochemistry Viewer

Figure 4-13. Thermochemistry viewer panel loaded with the results of the DFT adsorption energy calculations.

  1. The Series and Axes buttons can be used to customize the plot. For instance, try the temperature axis ranging 0 to 580 K and free energy range -15 to +5 kcal/mol; also untick Update axis ranges.
  2. The specific values can be found by opening the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. and looking at the Adsorption Energy (kcal/mol) and Adsorption Free Energy columns. There should be an Adsorption Free Energy column for each temperature and pressure combination specified in the panel.
  3. Close the panel when finished analyzing the results
 

The adsorption energies at T=0 K (dots) are -11.9 and -12.5 kcal/mol. The negative values mean that the complex GeMe3F molecule interacts favorably with the SiO2-OH surface. Consistent with this, the optimum geometries indicate that there is H-bonding between F and one or two surface hydroxyls. There is however an entropy penalty for adsorption, which leads to positive free energies of adsorption (lines) across this range of temperatures and pressures. This means that the adsorbed molecule is metastable against desorption, unless another chemical reaction intervenes first.

Figure 4-14. Gathering key results for visualization.

 

Finally, we gather together the key DFT results of this section for use in Section 8:

  1. Select the group  adsorption_energy_molecular_dft
  2. Open the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. and find the Etot (Ry) property that records the DFT energy
  3. Looking at the two Substrate entries in this group, select the entry with the more negative value of Etot (Ry), meaning that it is the more stable isomer
  4. Duplicate that entry into a new group at the end of the table named energy_profile_dft
  5. Rename the substrate entry to SiO2-OH_substrate
  6. Select the gas_1 entry in the group, duplicate it into the existing group energy_profile_dft and rename it GeMe3F
  7. Select the more stable of the two Adsorbate entries on the basis of Etot (Ry), duplicate that entry into the existing group energy_profile_dft and rename it molecular_adsorption

5. Surface Reactions: Dissociative Adsorption

In this section we will explore how to simulate the ALD surface reaction often described as ‘ligand exchange.’ During the ALD of oxides and nitrides, this involves the elimination of protonated ligands.  For instance, the ligands of the GeMe3F precursor may be eliminated as HF and CH4.  At this point, the by-products will be left in the simulation cell to ensure that the stoichiometry of the reaction stays consistent between calculations; we will investigate by-product desorption in Section 6.

surf-OH + GeMe3F (g) → surf-O-GeMe3⋯HF

surf-OH + GeMe3F (g) → surf-O-GeMe2F⋯CH4

The ligand elimination reaction can also be viewed as the dissociation of a ligand from a previously-adsorbed precursor molecule, combined with bonding that ligand to a proton from the surface site. For instance, when F is dissociated it binds with a proton and the remaining precursor fragment GeMe3 then bonds to an oxygen site that has lost a proton. In the same way, dissociation of a Ge-C bond can lead to CH4 production. Therefore, in a general sense, this ALD reaction falls into the category of dissociative adsorptionthe process by which a molecular species dissociates and then one of the fragments adsorbs onto the active site of a surface. In the example shown in this tutorial, the creation of the active site - the breaking of the O-H surface bond - was also part of the dissociative adsorption process.. This section demonstrates the functionality in the Adsorption panels for simulating dissociative adsorptionthe process by which a molecular species dissociates and then one of the fragments adsorbs onto the active site of a surface. In the example shown in this tutorial, the creation of the active site - the breaking of the O-H surface bond - was also part of the dissociative adsorption process..

Figure 5-1. Setting up the Enumerate Adsorbates panel for dissociation.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. the SiO2-OH_substrate that was generated in Section 3
  2. Go to Tasks > Materials > Enumeration > Adsorption
  3. Reset the panel
  4. Click Load in the Substrates section of the panel
  5. Select H from the Reactive atom filter
  6. Select the option for Include surface atoms within
  7. Set the distance to 6.0 Å of the reactive atom
    • This selects the four surface H’s that are geometrically slightly different from each other
  8. In the section of the panel for the Gas Molecules, select the Dissociative option
    • Only one gas molecule is permitted to be loaded at a time
  9. Load the GeMe3F gas into this section of the panel and change its Reactive atom filter to Ge
    • Adsorbing fragments will be generated by breaking each bond to the reactive atom, i.e. Ge-C and Ge-F
  10. Tick Remove symmetry equivalent structures
  11. Change the Job name to enum_adsorbates_dissociative

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_05 >  enum_adsorbates_dissociative > enum_adsorbates_dissociative-out.maegz
  2. Close the Enumerate Adsorbates panel

Figure 5-2. The structures that are generated for dissociative adsorption.

A new group is created that contains sub-groups for Ge-C (Adsorbate_0) and Ge-F (Adsorbate_1) dissociation, each sub-group containing the original adsorbate molecule and the 12 possible arrangements for adsorbing the two fragments on the four OH groups.

  1. In the Adsorbate_0 sub-group, select the entry GeMe3F_on_GeMe3F_on_SiO2-OH_substrate_top-41_top-43 and rename it to GeMe3F_Me_dissoc_on_SiO2-OH for ease of reference later
  2. In the Adsorbate_1 sub-group, select the entry GeMe3F_on_GeMe3F_on_SiO2-OH_substrate_top-42_top-41 and rename it as GeMe3F_F_dissoc_on_SiO2-OH for ease of reference later

It is evident from this enumeration that there are many different potential ‘isomers’, because the fragments may be located on various combinations of surface sites. As in the previous section, we will now do a coarse optimization of the candidate adsorbate structures using MLFF, so as to save time in subsequent DFT optimization - in this case reducing the number of DFT cycles by 45-65%.

Figure 5-3. The Adsorption Energy Calculations panel.

  1. Select the entire group enum_adsorbates_dissociative-out (26)
  2. Unselect the two entries for the GeMe3F molecules, leaving 24 slab entries selected
  3. Go to Tasks > Adsorption Energy > Quantum Mechanics > Workflows > Adsorption Energy
  4. Reset the panel
  5. Use the same settings as in Section 4 (steps 18 to 29)
  6. Change the Job Name to adsorption_energy_dissoc_mlff

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_05 > adsorption_energy_dissoc_mlff > adsorption_energy_dissoc_mlff-out.maegz

We have used MPNICE to pre-optimize the geometries of the adsorbate structures. The corresponding adsorption energies from MLFF total energies are recorded in the Project Table and range from -18 to +51 kcal/mol. Because we are looking at chemical reactions on which the MPNICE force field was not trained, the absolute values of the MPNICE adsorption energies are unlikely to be reliable. The next step is therefore to refine the optimization with DFT and obtain DFT adsorption energies. To illustrate the procedure, we will choose just one isomer for HF and one for CH4, but best practice would be to perform an Adsorption Energy calculation at DFT level on all distinct isomers of interest.

Figure 5-4. Restarting the DFT job from the MLFF optimized structures.

  1. In the Adsorption Energy panel, select Restart job and click on Select Job
    • The Locate Adsorption Energy Job dialog opens
  2. Select Manually locate job directory, click Browse, and navigate to the downloaded job (Section_05 > adsorption_energy_dissoc_mlff)
  3. Click OK
    • The Locate Adsorption Energy Job dialog closes
  4. In the table, tick the following two adsorbate entries GeMe3F_Me_dissoc_on_SiO2-OH and GeMe3F_F_dissoc_on_SiO2-OH
  5. Also tick the gas entry gas_1 and the four substrate entries
  6. In the Adsorption energy at 0 K and 1 atm section, select Periodic with Quantum Espresso
  7. Make sure the Advanced Options still match those outlined in Section 4
  8. Tick Adsorption free energy and make sure that the settings in this section match those in Section 4
  9. Make sure the Jaguar Options match those used in Section 4
  10. Change the job name to adsorption_energy_dissoc_dft
  11. Adjust the job settings () as necessary
    • This job requires a CPU host
    • This job requires a CPU host and takes around 1 day on 25 CPUs

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_05 > adsorption_energy_dissoc_dft > adsorption_energy_dissoc_dft-out.maegz

Figure 5-5. Output structures from GeMe3F calculations.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the entries named periodic_dft_GeMe2F_Me_dissoc_on_SiO2-OH_0_relax_0 and periodic_dft_GeMe3_F_dissoc_on_SiO2-OH_0_relax_0
  2. Use the Periodic tools to Translate to First Unit Cell, Recalculate Connectivity, and Recalculate Bond Orders
  3. Includethe entry is represented in the Workspace, the circle in the In column is blue. each entry in turn and examine their structure in the workspace

In both optimum structures, the bonding of Ge to a surface-O has caused its H to be donated to neighboring surface-O within the H-bonding network at the surface, ultimately replacing the H that has protonated the dissociated ligand. The ligand has thus been turned into by-products CH4 or HF, which are now distinct molecules. The geometries show no sign of significant chemical bonding between CH4 and the surface, whereas HF seems to be participating in the H-bonding network. The newly-formed Ge-O bond indicates that the precursor remnant has been chemisorbed.

Figure 5-6. Visualizing the results in the thermochemistry viewer.

Look in the Gas and Substrate sub-groups to check that the Ge precursor gas and SiO2-OH substrate are still the reference systems against which the energetics are measured. This means that the computed free energies are for dissociative adsorptionthe process by which a molecular species dissociates and then one of the fragments adsorbs onto the active site of a surface. In the example shown in this tutorial, the creation of the active site - the breaking of the O-H surface bond - was also part of the dissociative adsorption process. of that gas at the chosen gas pressure and temperature.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the whole group by clicking on the group entry name
  2. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Thermochemistry Viewer
  3. The Series and Axes buttons can be used to customize the plot. For example, try the temperature axis ranging 0 to 580 K and free energy range -30 to 0 kcal/mol; also untick Update axis ranges.

Figure 5-7. Gathering key results for visualization.

 

To gather together the key DFT results of this section for use in Section 8:

  1. Select the group  adsorption_energy_dissoc_dft
  2. Select the sub-group Adsorbate (2) with two entries, one from Ge-Me dissociation and one with from Ge-F dissociation
  3. Duplicate the sub-group into the existing group energy_profile_dft and rename it dissociative_adsorption

The adsorption energies at T=0 K are -18 and -27 kcal/mol for dissociation of Ge-F and Ge-CH3 respectively. Comparing these to the molecular adsorption energy (-12 kcal/mol, Section 4) shows that precursor dissociation and formation of both by-products is energetically favorable on this substrate. While this shows that thermodynamics favor CH4 over HF, kinetics may tell a different story (the tutorial Activation Energies for Reactivity in Solids and on Surfaces shows how to compute activation energies).

The adsorption free energies increase with temperature in parallel to one another, because they are calculated relative to the same Ge precursor. The adsorption free energies remain negative over temperatures up to 573 K (300°C), indicating that it would not be thermodynamically favorable for the precursor to re-form as a molecule and desorb.

6. Surface Reactions: Molecular Desorption of By-Products

In this section, we will run further DFT calculations to determine how thermodynamically likely it is for the by-product molecules HF and CH4 to desorb from the surfaces computed in the previous section.

surf-O-GeMe3⋯HF → surf-O-GeMe3 + HF (g)

surf-O-GeMe2F⋯CH4 → surf-O-GeMe2F +CH4 (g)

Desorption is the reverse reaction of adsorption and so the approach followed here has many similarities to what we have already done for adsorption in previous sections.  The main difference is that we need to specify a molecule for desorption and then find an intact version of that molecule within the surface adsorbate.

Figure 6-1. Viewing HF in the workspace.

The first step is to define the gas molecules that should be desorbed from the surface.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files and select Section_06 > by-products.maegz and click Open
    • The HF and CH4 molecules can also be drawn using the 2D Sketcher

Figure 6-2. Configuring the Desorption Enumeration calculation.

  1. Go to Tasks > Materials > Enumeration > Desorption
  2. From from the calculations of Section 5, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the optimized adsorbate entries named periodic_dft_GeMe2F_Me_dissoc_on_SiO2-OH_0_relax_0 and periodic_dft_GeMe3_F_dissoc_on_SiO2-OH_0_relax_0
  3. Click Load to import the optimized Adsorbate structures into the upper Adsorbates section of the panel
  4. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the HF and CH4 entries
    • The structures inputted into this panel do not have to be DFT optimized, as the panel will do that
  5. Check that they have the expected bonds when viewed in the Workspace
    • The panel will look for the same atoms and bonds at the surface so as to find intact molecules to desorb
  6. In the lower Gas molecules section of the panel select the Molecular option
  7. Click Load to import the two molecules into the Gas molecules section
  8. Leave Ignore hydrogen atom when searching for adsorbed gas molecules unchecked
  9. Change the job name to desorption_enumeration_HF_CH4
  10. Adjust the Job Settings as needed
    • This job requires a CPU host and finishes in just a couple of minutes

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_06 > desorption_enumeration_HF_CH4 > desorption_enumeration_HF_CH4-out.maegz
    • Compared to the adsorbate that was inputted, the structures outputted by the panel are identical but with the desorbing molecule highlighted

As in previous sections, it is possible to use the Machine learning force field to pre-optimize the new slab structures where the desorbing molecules have been removed. This is recommended in cases where the new structures are far from optimum, as described in Section 7 below. In the current case however, the adsorbate structures have been optimized previously with DFT and are perturbed very little by desorption of the by-product molecules. MLFF pre-optimization is therefore not needed.

Figure 6-3. Settings for the Adsorption Energy calculation.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the desorption_enumeration group
  2. Go to Tasks > Adsorption Energy > Quantum Mechanics > Workflows > Adsorption Energy
  3. Select Use adsorbate structures from
    • Geometries of the gas molecule and substrate will be generated using instructions in the adsorbate entries from the enumeration
  4. In the Adsorption energy at 0 K and 1 atm section, select Periodic with Quantum Espresso
  5. Make sure the settings for the Advanced Options are the same as in the previous two sections
  6. Ensure that Adsorption free energy is selected and that the settings match those of the previous two sections
    • Note that the pressure and temperature now refer to the desorbing gases, HF and CH4
  7. Ensure that the Jaguar Options are the same as those in the previous two sections
  8. Change the Job name to adsorption_energy_desorb_HF_CH4
  9. Adjust the Job Settings as needed
    • This job requires a CPU host and takes about 1 day on 32 CPUs

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_06 > adsorption_energy_desorb_HF_CH4 > adsorption_energy_desorb_HF_CH4-out.maegz
  2. Close the Adsorption Energy Calculations panel

Figure 6-4. Viewing the desorption free energy in the project table.

After importing you should see the new group adsorption_energy_desorb_HF_CH4 with a total of 8 entries; the two substrate entries show the structure of the surface after desorption of the by-product molecules

  1. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Thermochemistry Viewer
  2. The Series and Axes buttons can be used to customize the plot. For instance, try the temperature axis ranging 0 to 580 K and free energy range -10 to +20 kcal/mol; also untick Update axis ranges.
  3. The specific values can be found by opening the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. and looking at the Desorption Energy (kcal/mol) and Desorption Free Energy columns; the desorption energies are +3.4 and +17.3 kcal/mol for CH4 and HF respectively
  4. Close the panel when finished analyzing the results

Figure 6-5. Gathering key results for visualization.

 

To gather together the key DFT results of this section for use in Section 8:

  1. Select the group  adsorption_energy_desorb_HF_CH4
  2. Select the gas_1 and gas_2 entries by Ctrl-clicking, duplicate them into the existing energy_profile_dft group and rename them to CH4 and HF
  3. Select the sub-group Substrate (2) with two entries, duplicate it into the energy_profile_dft group and rename as follows:
    • Substrate → molecular_desorption
    • substrate_1 → desorbed_CH4
    • substrate_2 → desorbed_HF

Positive desorption (free) energies mean that the molecule is stable against desorption from the surface. The values computed here indicate that CH4 is weakly bound (ΔEdes=+3.4 kcal/mol at T=0 K) and desorbs at elevated temperature (ΔGdes<0). By contrast, a high desorption energy is computed for HF, which means that it remains bound to the surface at all temperatures (ΔGdes>0), under the specified vapor pressure of 0.013 atm = 10 Torr. This is consistent with the observation in Section 5 of a hydrogen-bonding network between HF and surface hydroxyl. It is therefore possible that HF persists at the surface for a long enough time to undergo reverse reactions, such as H-transfer and generation of Ge-F or Si-F species.

7. Surface Reactions: Associative Desorption of By-Products

In section 4 we found structures for the molecular adsorption of the precursor onto the substrate. In sections 5 and 6 we computed dissociation onto various sites and subsequent molecular desorption of the intact by-product molecules that formed when ligands reacted with substrate hydroxyl groups. An alternative approach for studying the same reactions is presented in this section. Starting from the molecularly-adsorbed precursor of section 4, we will investigate how the various hydroxyl groups on the surface can donate protons to its ligands and associate into a desorbing by-product molecule. As this functionality is restricted to one molecule at a time, we consider just the HF by-product in this section. Repeating the steps for CH4 would be straightforward.

surf-OH⋯GeMe3F + surf-OH → surf-OH + surf-O-GeMe3 + HF (g)

The workflow consists of specifying a molecule for desorption and then finding fragments within the surface adsorbate that can form that molecule. The energy required to remove these fragments is computed as the desorption energy.

Figure 7-1. Creating zero-order bonds between the adsorbate and the surface.

In the following, either use the HF entry from Section 6 in the group by-products, or go to File > Import Structures, navigate to where you downloaded the tutorial files, select Section_07 > HF.mae and click Open

  1. From the molecular adsorption calculations of Section 4, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the two DFT-optimized Adsorbate entries in the group adsorption_energy_ molecular_dft and duplicate them as ungrouped entries
  2. Rename the duplicated entries as GeMe3F_on_SiO2-OH_A and GeMe3F_on_SiO2-OH_B
  3. Includethe entry is represented in the Workspace, the circle in the In column is blue. GeMe3F_on_SiO2-OH_A and open the 3D Builder.
  4. In the workspace, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. both the Ge atom and an O atom on the surface.
  5. In the 3D Builder panel, click the button to add a bond between the atoms
  6. Now decrease the bond order to a zero-order bond by clicking the button
    • This is to ensure that the surface hydroxyls are not mistaken as being equivalent
  7. Follow the same procedure for the entry GeMe3F_on_SiO2-OH_B

Figure 7-2. Opening the Desorption Enumeration panel.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the two entries GeMe3F_on_SiO2-OH_A and GeMe3F_on_SiO2-OH_B
  2. Go to Tasks > Materials > Enumeration > Desorption
  3. Click Load to import the two adsorbate structures into the upper Adsorbates section of the panel.
  4. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the HF entry
  5. In the lower Gas molecules section of the panel click on the Associative (1 molecule) option
  6. Click Load to import the HF molecule into the Gas molecules section
  7. Leave Ignore hydrogen atom when searching for adsorbed gas molecules unchecked
  8. Change the job name to desorption_enumeration_assoc
  9. Adjust the Job Settings as needed
    • This job requires a CPU host and finishes in just a couple of minutes

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_07 > desorption_enumeration_assoc > desorption_enumeration_assoc-out.maegz
    • 34 new entries are generated, 17 for each adsorbate input
    • Compared to the adsorbate that was inputted, the structures outputted by the panel are identical but with the desorbing fragments highlighted
  2. Close the Desorption Enumeration panel

There are 17 H atoms and 1 F atom in the inputted slabs, which means that there are 17 ways to form HF from each slab, presented as 17 enumerated outputs. Any of these can be chosen for further calculations, depending on the research question that is to be answered. To investigate ALD reactions in the current case, we ignore H-transfer from the bottom face of the slab and from the methyl groups.

Figure 7-3. Selecting the subgroup of entries with surface hydroxyls.

  1. From the desorption_enumeration_assoc group, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the eight entries numbered 5, 11, 14 & 17 for both the A and B slabs, verifying that H atoms of surface hydroxyls on the top face are highlighted
  2. Duplicate the selected entries into a new group entitled desorption_enumeration_assoc_subset and select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. that group
  3. Reopen the Adsorption Energy Calculations panel

Figure 7-4. Running a pre-optimization with MLFF.

We will now perform a pre-optimization with MLFF.

  1. Reset the panel
  2. Use the same settings as in Section 4 (steps 18 to 29)
  3. Change the Job Name to adsorption_energy_desorb_assoc_mlff

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_07 > adsorption_energy_desrob_assoc_mlff > adsorption_energy_desrob_assoc_mlff-out.maegz

Figure 7-5. Job settings for the Adsorption Energy calculation with DFT.

  1. Select the entry group adsorption_energy_desorb_assoc_mlff
  2. In the Adsorption Energy panel, select Restart job and click on Select Job
    • The Locate Adsorption Energy Job dialog opens
  3. Select Manually locate job directory, click Browse, and navigate to the downloaded job (Section_07 > adsorption_energy_desorb_assoc_mlff)
  4. Click OK
    • The Locate Adsorption Energy Job dialog closes
  5. In the table, tick all 18 entries
    • Any failed entries are automatically ticked, but we tick all entries because we wish to run DFT on all of the MLFF structures
  6. In the Adsorption energy at 0 K and 1 atm section, select Periodic with Quantum Espresso
  7. Make sure the Advanced Options still match those outlined in Section 4
  8. Tick Adsorption free energy and make sure that the settings in this section match those in Section 4
    • The pressure and temperature now refer to the desorbing gas HF
  9. Make sure the Jaguar Options match those used in Section 4
  10. Change the job name to adsorption_energy_desorb_assoc_dft
  11. Adjust the job settings () as necessary
    • This job requires a CPU host
    • This job requires a CPU host and takes around 1 day on 32 CPUs

We will now import typical results for this job.

  1. Go to File > Import Structures, navigate to where you downloaded the tutorial files and Open Section_07 > adsorption_energy_desorb_assoc_dft > adsorption_energy_desorb_assoc_dft-out.maegz

Sometimes, some of the DFT optimizations will fail due to a lack of convergence within the maximum number of steps. This is not surprising when studying chemical reactions, as they often cause widescale reorganization of the surface, resulting in slow optimization of the geometry. The usual course of action is to use the partly-optimized geometries to restart the failed runs.

Figure 7-6. Thermochemistry viewer panel loaded with the results of the DFT energy calculations.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the new entry group adsorption_energy_desorb_assoc_dft
  2. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Thermochemistry Viewer
  3. The Series and Axes buttons can be used to customize the plot. For instance, try the temperature axis ranging 0 to 580 K and free energy range -2 to +12 kcal/mol; also untick Update axis ranges.
  4. The specific values can be found by opening the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. and looking at the Desorption Energy (kcal/mol) and Adsorption Free Energy columns. There should be a Desorption Free Energy column for each temperature and pressure combination specified in the panel.
    • Remember that these free energy curves are for desorption of gaseous HF, unlike those for the adsorption of GeMe3F in Section 4 and Section 5
  5. Close the viewer panel when finished analyzing the results

Figure 7-7. Gathering key results for visualization.

 

To gather together the key DFT results of this section for use in Section 8:

  1. Select the group  adsorption_energy_desorb_assoc_dft
  2. Open the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. and find the Etot (Ry) property that records the DFT energy
  3. Looking at the eight Substrate entries in this group, select the entry with the most negative value of Etot (Ry), meaning that it is the most stable isomer
  4. Duplicate that entry into the existing group energy_profile_dft and rename the entry associative_desorption

In this section we have used the Associative Desorption functionality to study the first elimination of one ligand (HF) from the molecularly-adsorbed precursor. The Desorption Energy ranges from +7.7 to +10.9 kcal/mol. These positive values mean that energy is required to eliminate the protonated ligand from the molecularly-adsorbed precursor. The spread of values indicates how proton transfer is affected by the location and orientation of hydroxyl groups.

The procedure can be repeated for the first elimination of other ligands (CH4) or for the elimination of the second or third ligands from the remaining precursor fragment. Once a model for the fragment-covered surface has been obtained, reactive adsorption of the co-reagent in the other ALD pulse can be investigated in the same way.

8. Visualizing the Reaction Energies

In this section, we will use the Reaction Profile Viewer to visualize the potential energy profile for the entire sequence of ALD reaction steps that were modeled in this tutorial.

Figure 8-1. Setting up the reactions in the Reaction Profile Viewer.

  1. Go to Tasks > Quantum Mechanics > Molecular Quantum Mechanics > Reaction Profile Viewer
  2. Select option for Quantum ESPRESSO
  3. Navigate to the group energy_profile_dft that has been populated with the DFT results from each section
  4. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. the two entries SiO2-OH_substrate and GeMe3F and use the Selected Entries button in the panel to import them as Reactant
  5. To look at HF as the by-product, select the two adsorption entries molecular_adsorption and periodic_dft_GeMe3_F_dissoc_on_SiO2-OH_0_relax_0 and click on Import to New Steps in the panel
    • Alternatively, to study CH4 formation, import molecular_adsorption and periodic_dft_Ge3Me2F_Me_dissoc_on_SiO2-OH_0_relax_0
  6. Click on Add New Step, select the desorption entry desorbed_HF and the HF entry, and click on Selected Entries to import them for the new step
    • Alternatively, import desorbed_CH4 and CH4 into a new step
  7. Click on Add New Step, select the desorption entry associative_desorption and HF, and click on Selected Entries to import them for that new step
  8. Rename the steps as desired by double-clicking on Reactant or Product
  9. Click Plot

Figure 8-x. Reaction energy profile for reactive adsorption of GeMe3F with by-product HF

The reaction energy profile is a convenient way to display and interpret the computed energetics across the sequence of reactions. Here we can see that adsorption of molecular GeMe3F and H-transfer to HF are energetically favorable, and while there is an energy cost for desorbing HF at T=0 K, the overall reaction is still slightly favorable relative to the reactants. There is close agreement between the ligand elimination energy computed step-by-step (-7.1 kcal/mol relative to reactants) and that computed via one associative desorption step (-5.1 kcal/mol).

Figure 8-x. Reaction energy profile for reactive adsorption of GeMe3F with by-product CH4

Comparing this energy profile with the previous one illustrates that elimination of the methyl ligand as CH4 is more energetically favorable than elimination of HF. This is consistent with the methyl ligand being more strongly basic than fluoro, and with CH4 interacting less strongly than HF with the hydroxylated silica surface.

These differences ΔE in electronic energy (or internal energy) tell us about the intrinsic chemistry of bonds being made and broken, independent of experimental conditions. The effect of temperature or pressure on the free energy (ΔG) of adsorption or desorption at each step has been computed with the Adsorption Energy panel in previous sections.

9. Conclusion and References

In this tutorial, we learned how to simulate the atomic-scale structures and thermodynamics of the elementary steps of reactive adsorption of a precursor gas and reactive desorption of by-product molecules, which constitute the chemical mechanism of atomic layer deposition (ALD). Similar reactions take place in atomic layer etching (ALE) and chemical vapor deposition more generally.  Heterogeneous catalysis is another field of application that depends on gas-surface reactions of this sort.

The main panels used were:

We computed the reactive adsorption of a heteroleptic germanium precursor, GeMe3(F), during the nucleation of a germanium-based film onto a hydroxylated silica (SiO2) substrate. The precursor initially formed a metastable molecular adsorbate, which could either desorb again or undergo ligand dissociation during H-transfer from substrate OH groups to form a strongly-bound surf-O-GeMe3 intermediate. The new O-Ge bond is evidence for deposition of germanium oxide at this interface. The growth of oxide is thus driven by the elimination of ligands in protonated form, i.e. as HF and/or CH4, and the energetics of these reactions were computed, both in terms of intrinsic bonding and in terms of free energies at realistic process temperatures and pressures.

These adsorption and desorption tools can be used to study further aspects of this ALD process - for instance, computing the elimination of second, third and fourth ligands during the precursor pulse, or computing the reactive adsorption onto a precursor-saturated surface of a co-reagent such as water or ozone in the other ALD pulse.

It is important to remember that these results are the thermodynamics of production of surface intermediates. If desired, the reaction path between these surface intermediates can be computed with the nudged elastic band approach (see the Activation Energies for Reactivity in Solids and on Surfaces tutorial), so as to yield the activation energy for each elementary step, and hence determine the kinetics of the reaction. When all relevant reactions for an ALD process have been discovered, and their activation energies have been computed or estimated, the reaction network can be used in a microkinetic model (see the Microkinetic Modeling tutorial) to determine the overall growth per cycle and sticking coefficient under experimental conditions.

For further learning:

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For some related practice, proceed to explore other relevant tutorials:

For further reading:

10. Glossary of Terms

Atomic layer deposition - a type of chemical vapor deposition that relies on self-limiting chemical reactions to control the number of deposited layers on a surface.

Associative desorption - the process by which two adsorbed species react together and then desorb as a single molecule from a surface. For example, two co-adsorbed hydrogen atoms can desorb as gas-phase H2.  Associative desorption is the reverse of dissociative adsorption.

Dissociative adsorption - the process by which a molecular species dissociates and then one of the fragments adsorbs onto the active site of a surface. In the example shown in this tutorial, the creation of the active site - the breaking of the O-H surface bond - was also part of the dissociative adsorption process.

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Included - the entry is represented in the Workspace, the circle in the In column is blue.

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data.

Reductive decomposition - a reaction in which species such as a metal center is reduced by electron transfer from leaving groups. For example, one can model the reductive decomposition of the surface-OGeIVMe3 intermediate of this tutorial via the desorption of two methyl groups (2CH3-) as neutral C2H6, producing surface-OGeIIMe.

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project.

Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries.

Working Directory - the location where files are saved.

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed.