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Drawing Chemical Structures on the Computer

There are several programs available that allow drawing of chemical structures.  These programs tend to be fairly similar in usage, and a general overview of procedures for using these programs is given below.  Following this is a brief overview of how to save pictures from the web-based programs.


General Procedure

Generally, to draw a structure, perform the following steps.

  1. Move the pointer to the position where you want the first carbon atom to be located.
  2. Press and hold the left mouse button, then drag the pointer to the position for the second carbon atom. Release the mouse button, and the bond will be drawn.
  3. To change elements, select the desired element from the menu, then click on the position where you would like this element to be located. Generally, it is best to draw a carbon bond first, then change a carbon atom into the desired element.
  4. Multiple bonds are drawn by either selecting the double-bond tool, or by drawing a second bond between two existing atoms.



Most of these molecular drawing programs default to line-bond drawings (stick pictures). This means that H atoms (and C-H bonds) are not usually shown, and carbon atoms are not labeled (although C-C bonds are shown).

These programs usually have an option to "clean-up" a structure.  While this often gives "better" pictures, unexpected changes often result from this.  Usually it is best to clean the structure first, then add labels, change elements, or make other changes/additions later.

Save your work often.  While complex molecules can be drawn somewhat rapidly, it can be a tedious process to get a structure exactly how you like it.  These programs are somewhat prone to crashing, resulting in loss of all unsaved work.



ChemDoodle is a web-based program that uses HTML5.  This program requires a "modern" web browser, but does not require java or any other plugins. To save images, it is best to use Firefox or Google Chrome as your web browser.  With an appropriate browser, if you "right-click" on the drawing window, you have the option to "Save Image As...", which will allow you to save your structure as a .png graphics file that can be read by a wide number of programs.  This does NOT appear to work with all browsers.

Saving images with ChemDoodle


Programs to Install on your computer

The following programs can be downloaded and installed on your computer.  In general, these programs are a bit more stable, and saving files and pictures is much simpler.  If you don't mind downloading a program that will only be used occasionally, any of these may be good options.


  • JChemPaint - A freely available Java program for drawing structures.
  • WinPLT - For computers running Microsoft Windows
  • BKChem - A freely available program for drawing chemical structures.  (Images saved in .SVG format).

Commercial Program - Free after registration