The most important part of a chemical structure editor is to create quality graphics, and ChemDoodle does this with excellence.

A focus on control and creativity

ChemDoodle’s main focus is to draw chemical structures, and it does that well. You can create graphics in ChemDoodle that you cannot match in any other program. Whether using the Optimize Zone, or changing stroke styles, or searching with the MolGrabber widget, you will see that ChemDoodle has the best tools for creating chemical graphics.

Intuitive Controls

ChemDoodle’s drawing controls are made to clearly model the atoms and bonds they manage. Copious visual feedback is provided. There are also many options for customizing the drawing tools to your preference.

24 Bond Types

24 different bond types are provided to create any type of chemical representation. No other program compares.

Superior Bond Graphics

Bond graphics will join into each other and merge to create the most aesthetic figures.

Advanced Labels

In addition to the standard elemental labels, you can input any custom label you desire. ChemDoodle will automatically chemically interpret and format them. You can also directly control text formatting. Labels can be expanded to full atom models and full atom models can be automatically collapsed into labels based on your abbreviation library or a custom label.

Atomic Notations

ChemDoodle is the only chemical drawing tool to contain superscript and subscript merge formatting in text fields to easily create atomic notations and other chemical text.

Custom Element Color Sets

In addition to the predefined Jmol, Rasmol, PyMOL and CDK color sets, you can also manually define your own color set to apply to molecule rendering.

Automatic Atom/Bond Tagging

If you need to tag atoms or bonds by increments, ChemDoodle provides powerful tools to do this. Simply click on the atom or bond to tag them and the next tag is automatically incremented. Tag by alphabet, number, roman numeral or greek letter.

Implicit Hydrogens

Implicit hydrogens will be added for you to your drawings. You have the ability to turn them off as well for single atoms or globally or override them as appropriate.

Auto-layout of Attributes

ChemDoodle will automatically place your charges, radicals, stereo center labels and other attributes for you in an aesthetic manner. You can override these decisions at any time by holding down and dragging the mouse during placement.

Arbitrary Ring and Crown Ethers

In addition to standard ring tools and templates, ChemDoodle provides special arbitrary ring and crown ether tools for quickly building advanced ring systems.


Atomic and molecular orbital graphics are easily added to figures. These are completely customizable just like the rest of ChemDoodle, so you can customize color, stroke styling, fill type and more!


Easily highlight parts of your structures for emphasis and attention.

Lewis Dot Structures

ChemDoodle provides you with all the tools to build perfect figures of Lewis Dot Structures. Draw them yourself, or have ChemDoodle automatically create the Lewis Dot Structures for you!

Perspective Structures

Easily create 3D effects in figures by using protruding and bold bonds. ChemDoodle will automatically merge them for optimal appearance. Bonds in the foreground will buffer intersecting bonds in the background.

Query Structures

An advanced query structure system for defining sets of molecules and for searching partner services. Both beginner and advanced tools are provided for quickly and intuitively building these rules.

Carbon Nanotube Builder

Several tools are provided to help you quickly build complex 3D geometries, including carbon nanotube and prism builders. Armchair, zigzag and chiral nanotubes can be built. Use the Rotate in 3D tool to change the 3D perspective of the drawn structure.

Stroke styling

Choose from 7 different stroke styles to add a bit of character to your figures. Perfect for use in group meetings and in presentations.

Publishing Style Sheets

ChemDoodle comes with preset publishing style sheets including ACS Document 1996 to easily create figures for publications.

Clean Structures

Complex algorithms have been implemented to automatically lay out chemical structures aesthetically. Select only part of a structure to clean only that part, leaving the rest untouched.

3D Coordinate Generation

Generate 3D coordinates for your drawn structures.


ChemDoodle can detect the aromaticity and anti-aromaticity of your rings and display the number of pi electron contributors. You can also force aromatic ring recognition using all resonance bonds.


ChemDoodle can perceive stereochemistry for drawn 2D structures. CIP stereochemistry is determined for chiral centers and double bonds. Common cis/trans stereochemistry can also be determined for double bonds.

IUPAC Naming

ChemDoodle is one of the few tools that can generate IUPAC names for your drawn structures. ChemDoodle can also parse IUPAC names into structures for you. Use updating labels to continuously name your structures as you draw them!

Chemical Warnings

ChemDoodle will double check your work for you and notify you when it finds chemistry issues, such as overbalanced atoms, or incorrectly drawn stereocenters.

Cheminformatics Functions

Quickly access powerful functions to help modify your graphics: saturation, Kekulization, label expansion, ring perception, distance geometry embedding, and more.