Modmol: an App for the study of molecules

Theoretical and Computational Chemistry Institute (IQTC)

Chemistry students, or more widely, students of disciplines in which understanding the structure of a molecule plays a significant role often can find difficulty in understanding the implications of a certain chemical structure. This is particularly true for students in early stages, to which visualizing those molecules interactively can be greatly beneficial.

To aid the didactic efforts of teachers in such disciplines (mainly chemistry, but also biochemistry, materials science, nanotech, etc.), the Theoretical and Computational Chemistry Institute of the University of Barcelona has developed Modmol©, an application for mobile devices that allows the visualization and edition of molecules within an environment of augmented reality by using the most ubiquitous electronic device nowadays: smartphones.

 

ModMol: a tool to learn and study molecules and their properties

ModMol © generates a molecular representation of the structure in three dimensions for organic, inorganic and biomolecular systems, as well as general information about them (name, formula, properties and so forth). ModMol creates a three-dimensional molecular representation of organic and inorganic systems and biomolecules.

ModMol promotional presentation video.

Initially launched with a repertoire of 115 molecules, the database would henceforth be updated regularly to include an increasing number of meaningful examples in each group. Among numerous other molecules, it features the structure of the acetic acid, cholesterol and caffeine, as well as polymers, molecular organic frameworks (MOFs), carbon nanotubes and proteins.

In addition to the natively available structures, the application is capable of opening files containing a Cartesian coordinate structure (.xyz) stored on the mobile device. This allows to view and manipulate external molecules of interest to the user. Other than molecule viewing, ModMol also allows molecular edition using any element of the periodic table as well as a library of pre-built standard fragments and functional groups that can also be used in the edition process.

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Screenshots of the ModMol app welcome and tutorial.

The app allows elements and molecules to be linked to build new compounds, which can then be saved and exported from the mobile phone to another device in a format compatible with standard molecular visualization programs. An advantage of the app if compared with long-standing specialized software is that it enables to manipulate and view the molecules using via the phone touchscreen, a particularly intuitive and convenient approach for students not yet familiar with more specialized tools.

ModMol is designed to be a repository capable of helping chemistry, chemical engineering, biology and pharmacy students to visualize molecular structures, with special emphasis on aspects such as stereochemistry, an area of chemistry involved in the study of the specific three-dimensional arrangements of atoms in molecules and the implications thereof.

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Ascorbic acid (Vitamin C) superposed with natural sources of this nutrient, via the ModMol app using the phone camera.

With ModMol, students will be able to observe 3D structures of different molecules and nanostructures while studying their chemical-physical properties and reactivity, in this way complementing the other teaching materials available to them.

On the other hand, researchers who want to visualize a compound on which they are working can do so easily and conveniently, also having the possibility of modifying, editing and saving it from their own mobile device.

The project has been carried out thanks to the aid received by the “Maria de Maeztu Units of Excellence” 2017 program, funded by the Ministry of Science and Innovation and the State Research Agency, and developed by Visyon, belonging to the Mediapro Group focusing on innovation via emergent technologies. The app is available at the GooglePlay Store and App Store.

 

Image credits:

Snapshot of menus re-used with permission from original release by IQTCUB.

Snapshot of composition with ascorbic acid molecule and apple and citrus fruits generated via the ModMol app.

Ongoing collaboration