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Free Online Tools to Draw Chemical Structures

If you are a science’s student you may require to insert a chemical structure in the report or assignment. Drawing it with paint is not an easy task. What people normally do is search the structure using google image. Copy-paste it, then you are done. You are lucky if you could found the chemical structure. Even if you are lucky, the image is not at high resolution. There are actually plenty of free online tools for drawing chemical structures.


MolView is a powerful web-tool to search through various scientific databases. Drawing chemical structure using MolView is very convenient. In fact, we can get the structure of any chemical and protein compounds by searching using its names. MolView uses PubChem, RSC Protein Data Bank, or Crystallography Open Database to retrieve the structures. The chemical structure is of high quality with 2-D and 3-D visualization. Importantly, a 3-D view of the chemical structure looks great compared to other web-tools. We can rotate the structure as we please for best viewing. Of course, the representation of the chemical structure could be changed to ball & stick, ribbon, cylinder & plate, B-factor tube, C-alpha trace, wireframe, line, or van der Waals spheres. For those who are working with protein structure, Viewing protein structure with MolView definitely stunning.

Draw chemical structure with free software
Figure: Chemical structure representation using MolView.
Figure: Catalase structure in MolView.

Additionally, Molview can retrieve chemical data from PubChem and NIST chemical webBook. This feature is indeed useful for those who are looking for chemical or physical properties of a specific chemical structure. Apart from that the mass spectrum and infra-red spectrum could be retrieved as well. The spectrum can be downloaded as a PNG image or JCAMP data.

MolView is loaded with other good features such as various calculations (bond dipoles, charge, energy minimization, etc) and measurements (distance, angle, and torsion). This is the best free web-tool to draw chemical structure so far. It offers plenty.


Chem-space is a specialty chemical provider. They provide a high quality of compounds for new drug discovery or medicinal chemistry. They claim to have 1.3 billion of chemical compounds in their stocks. To make things easier to browse their catalog, they provide chemical search features by drawing its structure. What you need to do is using their online tool for drawing the chemical structure. Once done you can search in their database a chemical with an exact match, it substructure, or any similar structure. This feature is very helpful if we are searching for a complex chemical structure.

Draw a chemical structure by using Chem-Space online tool
Figure: Draw a chemical structure by using Chem-Space online tool.

Drawing structure using a chem-space online tool is very easy. We can draw almost any chemical structure with different shapes including hydrocarbons, aromatics, cyclic, charged compounds, polymers and etc. The tool allows us to view the chemical structure in the form of wires or ball & stick. There is also a setup function to view the lone pair, carbon number, and explicit hydrogen of the chemical structure. You can save the chemical structure in various formats such as SMILES, MOL File, InChlKey, etc. and in the form of an image as well. However, the chemical structure images could only be saved as JPEG and PNG. The best part is you can save the chemical structure images without the background.


ChemSpider is a chemical search engine own by the Royal Society of Chemistry. Similar to Chem-space, ChemSpider provides an online tool to search billion of chemical structures. Searching a unique chemical structure using it’s the online tool is much more easy and accurate rather than remembering its complex and long name. Almost any chemical structure can be drawn by using the ChemSpider online tool, however, I found that Chem-space is much more responsive and user friendly, but it does the job quite well.

Draw a chemical structure by using ChemSpace online tool
Figure: Draw a chemical structure by using ChemSpace online tool.

I notice that we can draw the bond in an upward or downward direction to illustrate the chemical structure in a 3-D view. The unique feature of ChemSpider that I like is that we are able to protonate or deprotonate the chemical structure. The save function is rather limited, we only allow to save the chemical structure file in the format of SMILES and MOL File. Sadly, we could not save the chemical structure as pictures.format