Atomistica WORKSHOPS

Workshop A-SIDE

WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONS
Task 2 - Geometry Optimization and Equilibrium Structure

This task has two parts. In the part 1, you will visualize how a molecule relaxes from a highly distorted geometry into its stable, equilibrium structure. This task demonstrates the direct connection between molecular geometry and energy, the most stable molecular structure corresponds to the lowest (minimum) energy. In the part 2, you will compare distorted and optimized geometries and draw some very important conclussions.

For this task you will need: 

Distorted molecular structure of ibuprofen (.xyz): Task 2 – ibuprofen_distorted.zip

Part 1 - Geometrical optimization

Step 1. Download the structure of ibuprofen

Download the provided .xyz file containing the intentionally highly distorted molecular structure of ibuprofen. The file can be downloaded using the button below this section.

Step 2. Visualize the starting structure

On the left-side menu, click the “View starting structure” button.
The model that appears represents a deliberately distorted ibuprofen molecule.
You will notice unrealistic bond lengths, angles, and dihedral orientations, the atoms are positioned far from their natural arrangement.

This structure is not in equilibrium; its internal energy is very high.
To bring it to a stable, physically meaningful geometry, we need to perform a geometry optimization, a process in which the program systematically adjusts atomic coordinates to find the configuration where the total energy of the molecule is minimal.
You will perform that in the next step.

Step 3. Select the task

To perform a geometry optimization, you must tell the program what type of calculation to run.
In the “General Settings” section, locate the “Select task” dropdown menu and change the current task to “Optimization.”
This instructs the program to search for the lowest-energy geometry by adjusting all atomic positions.

Step 4. Choose the computational method

We will use the GFN2-xTB method because it is both fast and reliable for small organic molecules such as ibuprofen.
In the “Select method” dropdown menu, choose “GFN2-xTB.”
This method uses a semiempirical method developed by Prof. Stefan Grimme and co-workers and provides a good balance between accuracy and computational efficiency.

Step 5. Run the optimization

Once the task and method are selected, everything is ready.
Click on the “RUN XTB” button to start the optimization.
The calculation will finish in just a few seconds. During this process, Atomistica automatically updates the atomic coordinates until the forces acting on each atom are minimized.

Step 6. Review the output and optimized structure

When the xTB calculation is complete, two text areas will be populated:

  • “Output file” – contains the content of the output file generated by xTB, including details about each optimization step and the final energy value.

  • “Optimized structure” – contains the new atomic coordinates of the molecule in its equilibrium geometry.

These coordinates correspond to the lowest-energy (ground-state) structure of ibuprofen, the configuration the molecule naturally adopts.

Step 7. Visualize the optimized structure

From the left-side menu, click the “View optimized structure” button.
This will open the molecular viewer and load the optimized ibuprofen geometry.

You will immediately notice a huge difference: bond lengths and angles now look realistic, dihedral angles are properly aligned, and the overall structure appears balanced and natural.
This optimized geometry represents the true ground state — the molecule is now relaxed and physically meaningful.

Step 8. Download the optimized structure

Click the “Download optimized geometry” button to save your final structure.
Keep this file, you will need it later for Part 2.

Step 9. Compare and reflect

Try switching back and forth between the “View starting structure” and “View optimized structure” buttons several times.
Observe how drastically the geometry changes, this visual exercise helps you understand how molecular systems adjust to minimize their energy.

Part 2 - Energy comparison

Compare the total energies of the distorted and optimized geometries of ibuprofen. At the beginning of the page, you already have the distorted structure, while the optimized one was generated in Step 8.

Run single-point energy calculations (Energy in the “Select task” dropdown menu) for both geometries using the same computational method (for example, GFN2-xTB).
Record the obtained total energies and calculate the difference between them.

Questions for discussion:

  • Which geometry has the higher energy – the distorted or the optimized one?
  • How much lower is the energy of the optimized geometry compared to the distorted one?
  • How do your findings relate to the fundamental physical principle that all systems in nature tend to move toward a state of minimal energy?

This comparison quantifies how much stabilization occurs when the molecule reaches its equilibrium geometry. It also demonstrates the universal principle that stability corresponds to the lowest possible energy state, a concept that applies to molecules, materials, and all physical systems alike.