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:

 

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

 

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 3. Space filling model of pNPP