What are the shapes of molecules, and why? How do they move? How do proteins bind DNA to read the genetic information coded in it? How do we even work out molecular structures? Learning – and teaching – chemistry is often complicated because of the abstract nature of its many concepts. If we can’t see actual atoms or molecules in everyday life, how can students then imagine, and teachers communicate, the molecular shapes, interactions, and mechanisms behind chemistry and biology? Ordinary teaching materials like books make extensive use of static, two-dimensional graphics, which often fail to communicate complex topics especially about 3D shapes and motions.
Physical three-dimensional molecular models provide very intuitive ways to understand the spatial arrangement of the atoms in a molecule, or the different ways that the molecule itself moves in space. But even such models are limited: they are only useful for working with molecules but can’t represent other parts of chemistry such as molecular orbitals and surfaces, and also can’t comprehensively represent large biological molecules; besides, physical models are limited in the number of atoms and atom types available in the kit, and users need to build the models themselves, which, among other problems, becomes difficult for large molecules.
Novel technologies to assist chemistry and biology education
Modern technologies based in virtual (VR) and augmented reality (AR) can get the best of the computer simulation and physical worlds to enable teachers and students to work with virtual objects that they can manipulate as if they were real. However, most teaching content available in these formats is expensive and may require hardware such as VR goggles. And in many cases, the tools consist of static visualizations with no interactivity.
Now, Luciano Abriata and Fabio Cortes, two scientists with the lab of Matteo Dal Peraro at EPFL’s School of Life Sciences have designed a website with numerous interactive AR teaching activities in chemistry and biology, which teachers and students can use on regular laptops, tablets, and smartphones.
Users choose an activity through their web browser, and show their webcam AR markers that have been printed beforehand on a regular printer. Each activity displays virtual objects onto the markers, and the user can then move them around in space to inspect their shapes and make them interact through the screen, overlaid onto the real world. The activities available at the moment are tailored to chemistry and biology courses at the level of high school and the first two or three years of university courses: molecular shapes, atomic and molecular orbitals, molecular conformations and dynamics, acid-base equilibria, chirality and enantiomerism, protein structures, and macromolecular biological assemblies.
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The “star” activity acts as a virtual alternative to plastic modeling kits where users can build any molecule or load it from a database and manipulate it in three dimensions, aided by several controls that go beyond what a conventional plastic model can do. Users can easily inspect complex 3D structures, see how molecules move, compare chiral centers, test interactions, and more.
Other activities allow users to load different molecules that represent the main types of molecular shapes, atomic orbitals, or even the molecular orbitals of simple molecules. These activities support two AR markers that act independently, which makes it easy to directly compare the 3D objects in the user’s space. This is important for understanding the origin of different molecular shapes and chemical reactivity by comparing pairs of molecules or orbitals.
A special set of activities allow students to experience dynamic equilibria, hydrogen bonding, and acidity/basicity, with molecules that exchange hydrogen atoms upon interaction. The server also features two special modules of activities dedicated to biological macromolecules and assemblies, ranging from structures that can be inspected in atomic detail to learn about protein structure and protein-DNA interactions, to 3D representations of experimentally determined structures of whole viruses.
The website, developed as part of a Spark grant from SNSF, is now freely available, without registration, at https://molecularweb.epfl.ch in English, French, German Italian, Spanish, and Portuguese. “We now hope to hear the experiences of Swiss students and teachers using the website, and to collaborate especially with teachers to possibly create new activities tailored to their curricula, or even allow them to create their own AR activities,” says Abriata, adding “[…] the barrier to use is minimal: just access a webpage, print a marker and show it to the webcam. We hence think that the website can permeate deeply into schools and modern learning, being particularly suitable for online teaching too.”
Since its early versions were introduced for EPFL’s Portes Ouvertes event and other outreach events that took place in 2019, the website has been accessed more than 10,000 times, showing high engagement from students, fostering interest in chemistry and, interestingly, also promoting interest in web programing. “When we showed this at the Lycée Cantonal de Porrentruy, some students, realizing that this was coded as web pages, asked us to see the code, which you can do – as they well knew – right in the web browser itself, allowing you to experiment with the code right there and thus learn about programming,” says Abriata.
The tool’s developers, a Chemistry PhD and a webXR Engineer, are now reaching out to educators to hear about their experiences, to measure the actual pedagogical effect of the tool on chemistry education, and to hear their requests for new activities. They invite teachers and professors of chemistry and biology to try the website in their classes, and stress that the modest hardware requirements easily allow individual use, at school and at home.
Check https://molecularweb.epfl.ch for more information.