Avogadro Molecule

Posted on by

1.1 Avogadro and Adobe Illustrator

I am currently working on a figure for a publication which requires the chemical structure of paranitrophenylphosphate, C6H6NO6P. I use Adobe Illustrator to create my publication figures, but creating chemical structures in Illustrator is time consuming and prone to error. Avogadro is an open source molecular editor that can be downloaded here: https://avogadro.cc/. My workflow to create molecular graphics in Avogadro and export them to Illustrator is outlined in the following subsections:

1.2 Ball and Stick Structure(s) in Avogadro

The Avogadro constant has the same numerical value as the Avogadro number, but they differ in the unit which will be explained later in this article. Perrin defined the Avogadro number as the number of atoms in one gram of hydrogen (one gram-molecule). This definition was later revised to the number of atoms in 12 grams of carbon-12 (12 C). Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering framework and a powerful plugin architecture. Avogadro is an application purely for scientists and students that have to draw three-dimensional molecular compositions that showing a molecule from every conceivable angle and perspective. It works across platforms and is used in computational chemistry, molecular modeling, bio informatics, material science and other related areas. Avogadro’s number is an absolute number: there are 6.022×10 23 elementary entities in 1 mole. How many protons and neutrons in oxygen. This can also be written as 6.022×10 23 mol-1. The mass of one mole of a substance is equal to that substance’s molecular weight. For example, the mean molecular weight of water is 18.015 atomic mass units (amu), so one mole of water weight 18.

After downloading Avogadro, open a new document. The drawing tool will be selected by default. To draw C6H6NO6P, start with the benzene ring, a refresher on drawing chemical structures can be found in any organic chemistry textbook. Ensure you select a double bond order for the benzene ring. Click to create a carbon atom, four hydrogens will be automatically added to maintain electroneutrality. Click and drag from the center of the first carbon atom to the desired location of the second carbon atom then release. Repeat for the four remaining carbons. Change the bond order to single and the element to nitrogen to begin the nitro functional group. Continue for the remaining bonds in the nitro and phosphate groups.
Figure 1. Sequential construction of the benzene ring in pNPP using the Ball and Stick Display

1.3 Optimize Geometry of the Structure(s)

After completing all of the bonds on your structure you should optimize the interactions between the atoms using Extensions > Optimize Geometry. The default settings are appropriate for most molecules, but for more complex structures there are additional force field options available in the tool settings panel.
Avogadro Molecule

Figure 2. Optimized atomic interactions for the completed pNPP molecule.

1.4 Change Display Type

One of the benefits to drawing molecules in Avogadro is the ability to change the display of the molecule between the numerous presets. It is possible to customize and combine display types, but that is beyond the scope of this post. To change from ball-and-stick to a space filling model use the Van der Waals Spheres check box in the display types panel.

1.5 Export to SVG

2. then select SVG from the dropdown menu

1.6 Import SVG to Illustrator and Save as Symbol

(a) File > Open..
3. Open the symbols panel
4. Drag and drop the molecule into the symbols panel
6. Save the custom symbols panel for future use in all Adobe products

1.7 Tips

1. If incorporating multiple molecules into a single figure:
(a) View > Align View To Axes before exporting to SVG to ensure all atoms are properly scaled
2. To load custom symbols in another Adobe program or instance of Illustrator
(a) Window > Symbol Libraries > Other Libraries..
Avogadro
Written by TPS Fellow Parker Evans

1.8 References

Who Was Avogadro

1. Cornell, T. & Hutchison, G. Avogadro Documentation. Avogadro (2015). Available at:https://avogadro.cc/docs/.