Atomistica WORKSHOPS

Workshop A-SIDE

WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONS
Task 3 - Adsorption of hydrogen molecule

About this task

In this task consisting of three parts, you will investigate how a hydrogen molecule (H₂) interacts with three different graphene-like adsorbers:

  • Coronene, which represents a flat fragment of graphene,
  • Nitrogen-modified coronene, where one carbon atom is replaced by nitrogen to study the influence of electronic modification, and
  • Sumanene, a curved, bowl-shaped polycyclic aromatic molecule that introduces the effect of surface curvature.

These compact molecular models are computationally efficient yet chemically meaningful. Together, they allow you to explore how surface topology (flat vs curved) and electronic character (pure vs N-doped) influence the adsorption of small molecules such as hydrogen.

Why coronene?

Coronene (C₂₄H₁₂) is a flat polycyclic aromatic molecule often used as a molecular approximation of graphene. For small adsorbates like H₂, its central rings capture the local physics of adsorption while minimizing edge effects that would otherwise appear in smaller aromatic systems. It is therefore ideal for simulating molecular-level interactions on extended carbon surfaces.

Orientations of H₂

In your calculations, you will test two canonical orientations of H₂ above each adsorber surface:

  • Parallel to the π-surface
  • Perpendicular to the π-surface

This will allow you to observe how molecular orientation influences both interaction energy and equilibrium distance between the H₂ molecule and the adsorbing surface.

Electronic tuning via N substitution

Next, you will examine N-substituted coronene, in which one carbon atom in the aromatic framework is replaced by nitrogen. This substitution alters the local electron density and polarity of the surface, potentially modifying how strongly H₂ interacts with it. This part of the study demonstrates how chemical modification of graphene-like materials can be used to fine-tune their adsorption behavior.

Effect of curvature: sumanene

Finally, you will explore sumanene, a bowl-shaped polycyclic aromatic hydrocarbon (PAH) that introduces positive curvature to the carbon framework. Curvature redistributes the π-electron cloud and affects how adsorbates approach and interact with the surface. By comparing the results obtained for flat coronene and curved sumanene, you will see how molecular geometry influences adsorption strength and preferred orientation.

Learning objectives

Through this task, you will:

  • Visualize and quantify the interaction between H₂ and carbon-based adsorbers.
  • Understand how orientation, electronic modification, and surface curvature affect adsorption.
  • Apply concepts of molecular modeling and energy analysis to interpret adsorption trends on atomistic surfaces.

What You’ll Need for This Task

To successfully complete this task, you will need the molecular structures and the excel table available in the following archive file: Task 3 – Molecular structures and table.zip

The mentioned archive file contains all molecular structures, both single molecules and complexes, necessary for calculations. These structures serve as starting geometries for your adsorption studies.

Adsorption Energy Equation
You will calculate the adsorption energy using the following relation:

Eads=Esurface+H₂−Esurface−EH₂

where Esurface+H₂ is the total energy of the adsorber with the hydrogen molecule, EsurfaceE_{\text{surface}} is the total energy of the clean adsorber, and EH₂E_{\text{H₂}} is the total energy of the isolated hydrogen molecule.

Note: A negative adsorption energy indicates that the process is energetically favorable (H₂ binds to the surface).

A Note on Energy Units

The xTB code reports all total energies in Hartree units (Eh). However, in the literature and most adsorption studies, binding (adsorption) energies are often expressed in kilocalories per mole (kcal mol⁻¹).

To make your results easier to interpret, the provided spreadsheet file automatically converts Hartree values into kcal mol⁻¹.
In general, to convert manually: 1 Hartree (Eh) = 627.509474 kcal/mol

Thus, to express an energy difference (for example, Eads) in kcal mol⁻¹, simply multiply its value in Hartree by 627.509474.

For example: 0.010 Eh × 627.509474 = 6.28 kcal/mol

This conversion helps you discuss adsorption strengths in commonly used chemical energy units.

Part 1 - H2 adsorption by Coronene

In this part, you will examine the interaction between a hydrogen molecule (H₂) and coronene, which represents a small flat fragment of graphene.
You will perform geometry optimizations for each individual molecule (H₂ and coronene) and then for the combined system (coronene + H₂).
Only one orientation, parallel H₂ above the coronene plane – will be considered here.

Step 1. Optimization of H₂ molecule

  1. Open Atomistica Online 2025 and select the calculator “xTB & g-xTB” under the Calculators section in the left menu.

  2. Upload the H₂ structure (H2.xyz).

  3. In the General Settings section:

    • Set Task to Optimization.

    • Set Method to GFN2-xTB.

  4. Click the “RUN XTB” button. The optimization will finish in a few seconds.

  5. Once completed, open the Output file text area and scroll near the end to find the line containing “TOTAL ENERGY.”
    Record this value (and its units) in your spreadsheet in the row for H₂ molecule.

  6. You can also view the optimized structure using the “View optimized structure” button to confirm that the H-H bond length is reasonable (~0.74 Å).

Step 2. Optimization of coronene

  1. Return to the xTB & g-xTB tool.

  2. Upload the coronene structure (coronene.xyz).

  3. In General Settings, again choose:

    • Task: Optimization

    • Method: GFN2-xTB

  4. Run the calculation by pressing “RUN XTB.”

  5. After the optimization is finished, find the “TOTAL ENERGY” at the end of the output file and record it in your spreadsheet in the row for COR.

  6. Visualize the optimized geometry, you should see a perfectly planar aromatic structure with a symmetrical honeycomb arrangement of carbon atoms.

Step 3. Optimization of the H₂-coronene complex

  1. Upload the combined structure of coronene + H₂ (parallel orientation) that you prepared earlier.

  2. In General Settings, again select:

    • Task: Optimization

    • Method: GFN2-xTB

  3. Press “RUN XTB.”
    The optimization will take slightly longer since more atoms are present.

  4. When finished, scroll to the end of the Output file and locate the “TOTAL ENERGY” value.
    Record this energy in your spreadsheet under the “COR_H2 parallel” entry.

  5. View the optimized geometry you will likely notice that the H₂ molecule moves slightly closer to the surface (around 2.8–3.2 Å), aligning itself with the π-cloud of coronene.

Step 4. Calculation of adsorption energy

Now use the total energies you have recorded to calculate the adsorption energy using the equation:

 

Eads=Ecoronene+H₂−Ecoronene−EH₂

 

 

where all energies must be in the same units (xtb code reports in units of Eh).

  • If Eads is negative, the adsorption is energetically favorable – H₂ binds weakly to coronene.

  • If Eads is positive, the configuration is unstable, and the H₂ molecule does not adsorb significantly.

Record the calculated Eads value in your spreadsheet.

Step 5. Repeat for perpendicular orientation

After completing the steps above for the parallel orientation, repeat the same workflow (Steps 1–4) for the perpendicular orientation of H₂ above the coronene surface.
This means performing a new optimization for the coronene + H₂ (perpendicular) structure, recording its total energy, and calculating a new adsorption energy value.
By comparing the two results, you will determine how the orientation of H₂ affects its interaction with the graphene-like π-surface.

Part 2 - H₂ Adsorption on N-Substituted Coronene (Modified Flat Surface)

In this part, you will investigate how the adsorption of a hydrogen molecule (H₂) changes when the adsorbing surface, coronene, is modified by a nitrogen atom.
By replacing one carbon atom in the aromatic network with nitrogen, the local electron density and polarity of the surface are altered.
You will perform geometry optimizations for each individual molecule (H₂ and N-coronene) and then for the combined system (N-coronene + H₂).
As before, begin with the parallel orientation of H₂ above the molecular plane.

Step 1. Optimization of H₂ molecule

(If you have already optimized the H₂ molecule in Part 1, you can reuse the same energy value here. Otherwise, repeat this step.)

  1. Open Atomistica Online 2025 and select the calculator “xTB & g-xTB” under the Calculators section in the left menu.

  2. Upload the H₂ structure (H2.xyz).

  3. In the General Settings section:

    • Task: Optimization

    • Method: GFN2-xTB

  4. Click “RUN XTB.” The optimization finishes in a few seconds.

  5. Scroll near the end of the Output file to find the line containing “TOTAL ENERGY.”
    Record this value (and its units) in your spreadsheet in the row for H₂ molecule.

  6. Confirm that the optimized bond length is approximately 0.74 Å.

Step 2. Optimization of N-coronene

  1. Return to the xTB & g-xTB tool.

  2. Upload the N-coronene structure (N_coronene.xyz), where one carbon atom has been replaced by nitrogen.

  3. In General Settings, choose:

    • Task: Optimization

    • Method: GFN2-xTB

  4. Press “RUN XTB.”

  5. When the calculation finishes, find the “TOTAL ENERGY” near the end of the output file and record it in your spreadsheet in the row for N-COR (nitrogen-modified coronene).

  6. Visualize the optimized geometry — the structure remains nearly planar, but the region around the nitrogen atom may show a slightly different bond arrangement or charge distribution.

Step 3. Optimization of the H₂–N-coronene complex

  1. Upload the combined structure of N-coronene + H₂ (parallel orientation) that you prepared earlier.

  2. In General Settings, select:

    • Task: Optimization

    • Method: GFN2-xTB

  3. Press “RUN XTB.”
    The optimization will take a little longer due to the larger number of atoms.

  4. Once complete, scroll to the end of the Output file and locate the “TOTAL ENERGY” line.
    Record this value in your spreadsheet under the “COR_N_H2 parallel” entry.

  5. View the optimized geometry – check if the H₂ molecule has shifted closer to or farther from the doped region compared to Part 1.

Step 4. Calculation of adsorption energy

Use the same equation as before to calculate the adsorption energy:

Eads=EN-coronene+H₂−EN-coronene−EH₂

All energies must be in the same units (Eh).

  • A negative Eads means adsorption is energetically favorable.

  • A positive Eads  indicates that the configuration is unstable.

Record the calculated Eads  in your spreadsheet under the N-coronene section.

Step 5. Repeat for perpendicular orientation

Repeat the same procedure (Steps 1–4) for the perpendicular orientation of H₂ above the N-coronene surface.
Perform a new optimization for the N-coronene + H₂ (perpendicular) structure, record its total energy, and calculate a second adsorption energy value.
This will allow you to compare how both orientation and nitrogen substitution affect H₂ binding.

Part 3 - H₂ Adsorption on Sumanene (Curved Surface)

In this part, you will investigate how surface curvature affects the adsorption of a hydrogen molecule (H₂).
Sumanene is a bowl-shaped polycyclic aromatic hydrocarbon: its concave side (inside the bowl) and convex side (outside) provide different local π-environments compared to flat coronene.
As before, you will optimize each individual molecule (H₂ and sumanene) and then the combined system (sumanene + H₂). Start with the parallel orientation of H₂ relative to the local π-surface.

Step 1. Optimization of H₂ molecule

(If you already optimized H₂ in Part 1, you may reuse that energy here. Otherwise, repeat this step.)

  1. Open Atomistica Online 2025 → Calculators → “xTB & g-xTB.”

  2. Upload/Import H2.xyz.

  3. General Settings:

    • Task: Optimization

    • Method: GFN2-xTB

  4. Click “RUN XTB.”

  5. In Output file, scroll near the end to find “TOTAL ENERGY”; record the value (with units) in the H₂ row of your spreadsheet.

  6. (Optional) View optimized structure to confirm H–H ≈ 0.74 Å.

Step 2. Optimization of sumanene

  1. Upload your sumanene structure (sumanene.xyz).

  2. General Settings:

    • Task: Optimization

    • Method: GFN2-xTB

  3. Press “RUN XTB.”

  4. After completion, find “TOTAL ENERGY” at the end of the Output file and record it in the SUM (sumanene) row of your sheet.

  5. Visualize the optimized geometry to confirm the bowl shape.

Step 3. Optimization of the H₂-sumanene complex (parallel)

  1. Upload your combined sumanene + H₂ (parallel orientation) structure.

  2. General Settings:

    • Task: Optimization

    • Method: GFN2-xTB

  3. Click “RUN XTB.” (This may take a bit longer due to more atoms.)

  4. When finished, scroll to the end of the Output file and record “TOTAL ENERGY.”
    Save it under “SUM_H2 parallel” in your spreadsheet.

  5. View optimized structure to see the relaxed H₂ position relative to the bowl center.

Step 4. Calculation of adsorption energy

Use the same expression as before:

Eads=ESumanene+H₂−ESumanene−EH₂

  • Keep units consistent (xTB reports Hartree, Eh).

  • Negative Eads → favorable adsorption (physisorption). Record Eads for parallel in your table.

Step 5. Repeat for the perpendicular orientation

Repeat Steps 3–4 for the perpendicular orientation of H₂ above the concave side.

  • Upload sumanene + H₂ (perpendicular), optimize, record TOTAL ENERGY, and compute a new Eads

Results and Discussion

Eventually, after completing all calculations for Parts 1–3, you should obtain numerical results similar to those presented in the table below. These values represent the binding (adsorption) energies of the hydrogen molecule on three different carbon-based adsorbers, coronene, N-substituted coronene, and sumanene, in two orientations: parallel and perpendicular.

Remember that the xTB code reports total energies in Hartree (Eh), while adsorption energies are often expressed in kcal mol⁻¹. The provided Excel spreadsheet automatically performs this conversion using the relation: 1 Eh = 627.509474 kcal/mol.

The table below summarizes typical adsorption energy results obtained for the studied systems.

H₂ Adsorption Energies (kcal/mol)

Negative values indicate stronger (more favorable) adsorption.

Surface Orientation Adsorption Energy (kcal/mol)
Coronene Parallel −0.92
Coronene Perpendicular −1.00
N-Coronene Parallel −1.03
N-Coronene Perpendicular −0.73
Sumanene Parallel −1.51
Sumanene Perpendicular −1.69

Now, after this table is finished, try to analyze the results and try to give answers the following questions and reflect on the observed trends.

1. Orientation Effects

  • Compare the adsorption energies for the parallel and perpendicular orientations of H₂ on each surface.
    Which orientation leads to a stronger interaction (more negative adsorption energy)?
  • What can you infer about how the alignment of H₂ relative to the π-electron cloud of the surface influences the adsorption strength?

  • Why does the perpendicular orientation generally result in slightly stronger binding on aromatic surfaces like coronene?

2. Electronic Modification Effects (Nitrogen Substitution)

  • Compare the results for coronene and N-coronene in the same orientations.
    How does introducing nitrogen into the carbon framework affect the binding energy?
  • What does this tell you about how surface electronic structure (charge distribution and polarity) influences H₂ physisorption?

  • Would you expect nitrogen substitution to increase or decrease electron donation or withdrawal from the surface? How could this affect future material design for gas adsorption?

3. Curvature Effects (Sumanene)

  • How do adsorption energies on sumanene compare with those on flat coronene or N-coronene?
  • Does the curved surface enhance or weaken H₂ adsorption?
  • How might curvature modify the distribution of π-electron density or the effective contact area between H₂ and the surface?
  • From a design perspective, what does this suggest about the role of molecular curvature in tailoring adsorption strength in carbon-based materials?

Follow-up session

If you enjoyed completing these exercises and want to discuss your results in more detail, I invite you to reach out at office@atomistica.online for a follow-up session.

During the session, we can go through your answers, interpret your results together, and explore deeper insights into atomistic modeling of energy materials.

Whether you are a beginner or already familiar with computational methods, this is a great opportunity to strengthen your understanding and learn how tools like Atomistica Online can be used for real research applications.