Optimize Your Molecular Structure: Avogadro User Guide

Avogadro is an advanced molecule editing and visualization tool developed for use in fields such as computational chemistry, molecular modeling, bioinformatics and materials science. It stands out with its flexible structure, high-quality visualization options and powerful plugin support (1). Avogadro, which can run on Windows, Linux and Mac OS operating systems, can be downloaded from the following address:

https://sourceforge.net/projects/avogadro/files/latest/download

When the program opens, the user is first greeted by the opening screen given in Figure 1.

Figure 1. Avogadro program opening screen.

When we look at the tools in the Avogadro program:

1-) Draw Tool: Allows you to add the desired atoms with a right click and create bonds between these atoms.

2-) Navigation Tool: Allows you to rotate, move and zoom the molecule.

3-) Bond Centric Manipulation Tool: Allows you to change the bond lengths and angles in the molecule.

4-) Manipulation Tool: Allows you to move atoms by selecting and dragging them.

5-) Selection Tool: Used to select atoms, residues and molecular parts.

6-) Auto Rotation Tool: Allows you to rotate atoms around the x, y and z axes in a specified manner.

7-) Auto Optimization Tool: Continuously optimizes molecule geometry using molecular dynamics methods.

8-) Measurement Tool: Helps determine bond lengths and angles between atoms.

9-) Align Tool: Aligns molecules around a specific reference axis (x, y or z).

As an example, the isopropanol (C₃H₈O) molecule will be used. The optimization process will be performed by applying a force field on this molecule. In this way, it is aimed to reach the most stable geometric structure of isopropanol.

Step 1: First, carbon, hydrogen and oxygen atoms are added using the Draw Tool. In Figure 2, the gray atoms represent carbons, the white ones represent hydrogens and the red atom represents oxygen.

Figure 2. Drawing of the isopropanol molecule.

Step 2: In the Auto Optimization Tool, enter the Settings section. UFF (Universal Force Field) is selected as the Force Field and Steepest Descent is selected as the algorithm. The energy optimization is updated every four steps. After the necessary settings are made, the Start button is pressed and the process is completed. (The force field and algorithms can be changed according to the purpose of the study.)

Figure 3. Auto Optimization settings for the isopropanol molecule.

Step 3: After the optimization was completed, the isopropanol molecule reached the most stable state in terms of bond lengths and angles. When evaluated numerically, the energy of the molecule was calculated as E = 26.8496 kJ/mol.

Figure 4. Optimized version of the isopropanol molecule.

Step 4: The optimized isopropanol molecule is now ready to be saved in the desired format. To save, open the "File" tab in the upper left corner of the Avogadro program and use the "Save As" option. If you want to save the molecule in PDB (Protein Data Bank) format, select PDB (*.pdb) as the "Save Type" in the "Save As" window and save the file.

Figure 5. Saving the molecule in the desired format.

By following these steps, the creation, optimization and saving of the isopropanol molecule in the desired format with the Avogadro program has been completed. This process is one of the basic building blocks in molecular modeling and computational chemistry studies and allows for more comprehensive analyses using different molecules and force fields. Thanks to the flexible tools offered by Avogadro, you can easily perform geometric and energy optimizations of molecules and make your work more efficient.

REFERENCES

1. https://avogadro.cc/