MolView: An App to View Structural Formulas and Models


What is the best way for students to visualize compounds? From the traditional physical ball and stick models to the various online simulations the objective for all of these tools is to provide one with a visual for the different structures and patterns. This summer while facilitating a workshop, the participants and I discussed this question and while reviewing various representations we came across MolView.

In July of 2014 a Dutch undergrad student, Herman Bergwerf, launched the Chrome app MolView with the objective for users to visualize various molecular and ionic structures. MolView is comprised of two main parts, a structural formula editor and a 3D model viewer. The user can draw a compound or choose from a selection of compounds from three databases. Once a compound has been selected the user can click the 2D to 3D button to convert the molecule into a 3D model which is then displayed in the viewer, located on the right side of the screen.

"it helps users identify that each type of solid has different structures and patterns."

In addition to the 3D viewer you can also use the app to distinguish between atomic, molecular, and ionic solids by clicking on the crystallography model tab. What I love about this function of the app is that it helps users identify that each type of solid has different structures and patterns.

Other features of the current version of MolView include spectroscopy graphs, dipole tools, angle calculations, as well as color-coded electrostatic potential maps that measure the electron distribution in the molecule. If you want to export any of these 3D images MolView can do that as well. 

Although there are a lot of features to MolView my recommendation is to dive right in and try it out. If you are overwhelmed refer the User Manual or the corresponding You Tube videos. I was told by the creator that a new version is being developed so if you have a question for the creator, the contact information is provided as well.

Also, if you have any ideas in regards to how you would use MolView in your classroom share them with our ChemEdX community in the comments section below. 

Publication information
Pick Attribution: 

Author: Herman Bergwerf

Twitter: @molview 

Publication Date: 
Monday, August 8, 2016
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Comments 2

Tracy Schloemer's picture
Tracy Schloemer | Fri, 12/30/2016 - 21:08

Hi Michelle-

There are some cool lessons in the Smells Unit within the Living by Chemistry curriculum - my students got WAY more out of the lessons that focused on larger molecules than with physical models. Happy you shared this! 

Joseph Lomax's picture
Joseph Lomax | Sat, 12/31/2016 - 13:16

All maps are to some extent, or they would be reality.  It is useful to tell students this and remind them of it often.  Every map should emphasize certain aspects, such as roads, and should deemphasize or eliminate  other aspects, such as vegetation or altitude.  In the same way, molecular models should match their function.  Which is more important, the atoms or the bonds?  Philosophically, it is a ridiculous question because the bonds do not exist without atoms and atoms are not in a molecule without the connections of the bonds.  But in mapping out a molecule the distinction becomes crucial.  Space-filling models are closer to reality, but they often shape of the atoms obscures much of the molecule.  Bond-only representations are particularly useful with large organic molecules, but are mysterious to those who have not had a good deal of familiarization with the 'rules of road'.  Ball and stick models are useful compromise, but my favorite is the space-filling molecules with a color-coded (blue-positive, red-negative) electrostatic potential surface (reference above).  They combine the shape and polarity of molecules in one.  The challenge is to show many a 'map' and convince the students they are looking at the same 'land'.