Best Freeware, Online Tools For Drawing Chemical Structures

In the ever-evolving world of chemistry, digital tools have emerged as essential companions for professionals and enthusiasts alike.

From visualising complex molecular structures in 3D to seamless conversions between file formats, we delve into four leading chemical drawing software options, showcasing their unique offerings. Dive in to see which tool aligns with your needs.

Online Tools For Drawing Chemical Structures

Software NameKey Features
ChemDraw– Visualizes 2D & 3D structures 
– Converts to multiple file formats 
– Integrates with databases like PubChem
– Handles complex reactions
ChemSketch– Freeware with 2D & 3D visualization
– Drag-and-drop sketching
– Access to chemical database
– File compatibility, including ChemDraw
MolView– Creates 2D & 3D structures
– Converts 2D sketches to 3D
– Comprehensive database
MarvinSketch– Offers 2D & 3D visualisation
– Integrates with renowned databases
– Multiple file format support
– Freeware with advanced tools


ChemDraw allows researchers and students to draw chemical structures with ease. ChemDraw has earned a significant reputation in the chemistry development community due to its functionality and user-friendly interface.

To get started, users open the sketcher interface, where a toolbar filled with various atomic symbols and bonds is present.

To draw a chemical structure, one simply needs to select an atom from the toolbar and drag it into the main workspace.

To create bonds, click and drag between two atoms. The tool allows for the visualisation of both 2D and 3D molecular structures.

For a more in-depth look, users can also rotate the structure, viewing molecules in wireframe, Van Der Waals spheres, or other 3D graphics rendering modes.

One hidden gem in ChemDraw is its capability to convert drawn structures into various file formats. It’s not just limited to the common ‘mol’ or ‘smile’ formats; there’s support for numerous proprietary and chemical research relevant formats.

This becomes invaluable, especially when integrating your work with scientific databases like PubChem or RCSB.

Best Freeware, Online Tools For Drawing Chemical Structures

Moreover, ChemDraw also supports complex chemical reactions as well as simpler molecular structures. With a built-in database, it can recognise and auto-complete the structural formula of many common compounds.

A bonus for those working on their thesis or academic projects is its energy minimisation function, which offers insight into the most stable conformation of a molecule.

For those who prefer online tools for drawing chemical structures, various web-based alternatives exist, but ChemDraw’s desktop application remains a favourite for many.

Chemsketch – Free Software

ChemSketch, a prominent freeware, is an indispensable tool in chemistry development. It empowers users to draw chemical structures with finesse, bridging the gap between complex chemical compounds and their graphical representation.

Going beyond just 2D sketches, ChemSketch also allows users to visualise molecular structures in both 2D and 3D, providing an immersive experience.

Utilising ChemSketch is rather straightforward. At its core, it’s a sketcher, allowing users to drag atoms and bonds onto a canvas, making the task of drawing the chemical structure a breeze. 

Its toolbar boasts a plethora of built-in tools for drawing chemical structures, from basic molecules to more intricate compounds. Users can also tap into ChemSketch’s database, accessing a spectrum of pre-existing molecules and chemical data.

One of the distinguishing features of ChemSketch is its compatibility. Beyond just rendering structural formula, the software also supports a variety of file formats, including:

  • Spectrus
  • EZChrom
  • Atlas
  • and more

If ChemDraw is your go-to, fret not. ChemSketch can convert and load files in ChemDraw format seamlessly.

For those who prefer online tools for drawing chemical structures, several web-based alternatives like ChemDoodle and MolView offer similar functionality.

Yet, ChemSketch remains a reliable desktop solution with its comprehensive features, from viewing to advanced searches. Whether you’re drafting a thesis or conducting chemical research, ChemSketch has you covered.

Molview – 2D Format Sketcher

MolView tool has emerged as a pivotal player in the digital landscape of chemistry. This online tool allows users to effortlessly sketch chemical structures, ensuring a streamlined approach for both novices and seasoned chemists.

Chemsketch and ChemDraw have long dominated the realm of free software for structure drawing. However, MolView, as an advanced chemical drawing tool, brings together functionality for creating both 2D and 3D molecular structures in a user-friendly format.

The heart of MolView lies in its intuitive sketcher. On loading the platform, users are welcomed with a canvas. With various menus, users can select different:

  • Bond types
  • Cyclic compounds
  • and many other elements especially those commonly used in organic chemistry. 

A standout feature? Its ability to convert a 2D sketch into a 3D model with a simple click, giving depth to the chemical structure using advanced rendering techniques.

Best Freeware, Online Tools For Drawing Chemical Structures

But MolView is not just about drawing; it houses a vast database. By entering terms like e.g ‘methyl propane,’ users can search, visualise and transform complex chemical compounds, or protein structures.

Once a molecule is on-screen, its 3D model can be rotated, providing comprehensive viewing angles. 

For those seeking deeper insights, the built-in search allows users to delve into molecules’ nuances, from structural formulae to atomic details.

In essence, MolView isn’t merely another Chemdoodle in the chemistry development toolbox. It’s a dynamic web-based platform, merging the worlds of chemical research, drawing tools, and 3D graphics.

MarvinSketch – Chemistry Structure Drawing Tool

MarvinSketch is a premier sketcher tool tailored for chemists and professionals in the chemical industry. It offers a versatile platform for users to draw chemical structures, molecular compositions, and reactions.

Being one of the go-to online tools for drawing chemical structures, its user-friendly interface and vast range of functionalities cater to both novice and expert users.

A prominent feature is its capability to represent a chemical structure in both 2D and 3D formats.

By just a few clicks, users can seamlessly convert a 2D chemical structure into a 3D model, enhancing the depth and detail of molecular visualisation.

The tool also allows users to rotate and view 3D models with molecule editor, offering a comprehensive view of molecules and polymer, whether it be complex chemical compounds or simpler structures.

Beyond simple drawing, MarvinSketch is packed with advanced features. For instance, its built-in database functionality aids in loading, searching, and visualising chemical data from renowned sources like:

  • PubChem
  • ChemSpider
  • RCSB

The sketcher is also equipped with a toolbar that houses a myriad of drawing tools, from basic atoms and bonds to more complex objects and pathways.

Another intriguing facet is its compatibility. The tool supports multiple file formats, ensuring easy integration with other chemical drawing software like ChemDraw and ChemDoodle.

Users can also use MarvinSketch to perform substructure and advanced searches, aiding in chemical research and database exploration.

Lastly, for those concerned about pricing, MarvinSketch stands out as a freeware. This means it offers its vast suite of tools for drawing chemical structures without any cost, making it a valuable asset in the chemistry development world.

Wrapping Up: More Than Just Chemsketch

This post highlights four pivotal chemical drawing tools: ChemDraw, ChemSketch, MolView, and MarvinSketch. Each software offers unique functionalities, from intricate 3D visualisations to vast molecular databases.

As the need for efficient chemistry software grows, understanding the capabilities of these tools is paramount for both professionals and novices. Which is your preferred choice? 

The Author

Dr Andrew Stapleton has a Masters and PhD in Chemistry from the UK and Australia. He has many years of research experience and has worked as a Postdoctoral Fellow and Associate at a number of Universities. Although having secured funding for his own research, he left academia to help others with his YouTube channel all about the inner workings of academia and how to make it work for you.