Domhnall OShaughnessy
Introduction
Students love hands-on learning experiences. In undergraduate chemistry courses, students often learn through laboratory work. However, many aspects of chemistry cannot be seen with the naked eye or held in a student’s hand. New advances in technology allow for students to transcend these barriers and understand chemistry and science in new and exciting ways. In particular, the use of AR and VR technolo- gies allow students to investigate atomic level molecules and hold individual atoms.
Several important topics in introductory chemistry courses rely heavily on an understanding of three-dimensional systems (Desseyn, Herman, & Mullens, 1985;
Donaghy & Saxton, 2012; Stieff, Ryu, Dixon, & Hegarty, 2012). These systems include, but are not limited to, molecular geometries (Harle & Towns, 2011; Tuckey, Selvaratnam, & Bradley, 1991) and atomic orbitals (Hoogenboom, 1962). Molecular model kits have long been used in the chemistry classroom to give students an appreciation for the structure of chemicals. Models for the structure of chemicals have evolved from models made from cork and glass rod (Minne, 1929), to vinyl covered wires (Larson, 1964), to do-it-yourself models (Birk & Foster, 1989), to traditional commercially available models (Ghaffari, 2006). Models have dramati- cally improved since the cork and vinyl versions, but commercially available mod- els are expensive, particularly more elaborate models.
Molecular models are known to aid in student understanding of chemical struc- tures in undergraduate chemistry courses. In the 1970s some scientists questioned the usefulness of molecular models. Petersen investigated the use of models in education and research despite push back against their continued use (Peterson, 1970). Tuckey et al. found that students gained deeper understanding of chemical structures by
D. OShaughnessy (*)
Department of Chemistry, Shenandoah University, Winchester, VA, USA e-mail: [email protected]
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exploring these geometries using models (Tuckey et al., 1991). To this day, models are considered useful tools to promote visualization of atoms and molecules (Mohamed- Salah & Alain, 2016; Stull, Gainer, Padalkar, & Hegarty, 2016), and students indicate models are useful for understanding in their chemistry courses. (Hageman, 2010).
However, molecular models do not provide the entire picture necessary for deep understanding of chemical structures. The structure of atomic orbitals and their influences on bonding angles are critical to the understanding of the geometries of molecules (Martins, 1964). Many students have difficulty perceiving the geometry of atomic orbits as these are somewhat difficult to represent on paper or on projector screens (Fowles, 1955; Lambert, 1957). While some models attempt to incorporate atomic orbitals, these models have some key deficiencies.
Presently educators use commercially available model kits and molecular mod- eling software in their classes to explain geometries. More recently 3D printing (Griffith, Cataldo, & Fogarty, 2016; Robertson & Jorgensen, 2015) and virtual and augmented reality (Cai, Wang, & Chiang, 2014; Merchant et al., 2012) have been used to aid students’ understanding of the geometries in lectures. Most of the options available today have shortcomings (Vögtle & Goldschmitt, 1974). For example, a basic commercial model kit will contain plastic spheres, which represent atoms.
These atoms have connectors where sticks, representing bonds, are inserted. The connectors are in a fixed location and, therefore, only allow for particular angles to be produced. Real molecular geometries may vary in their angles and arrangements.
The available bonds in these models have fixed lengths. However, in reality, many combinations of bond lengths may occur.
An alternative is molecular modeling software. This software is designed to mathematically solve angles and bond lengths as accurately as possible. The soft- ware produces a three-dimensional representation of molecular geometries dis- played on a two-dimensional screen. However, it has been shown that concrete models are more beneficial to student learning (Stull, Barrett, & Hegarty, 2013).
3D printing is an option that allows educators to reap the benefits of the accuracy afforded from software while allowing a student to hold a concrete object. However, 3D printing remains an expensive option, both in up-front costs in buying a 3D printer and in producing models for each student in a class.
Augmented Reality (AR) can be used as a solution in these cases. Using a similar approach used to create 3D printed models, an AR version of the model may be produced. Once it has been produced and stored in the cloud, it can be shared with an unlimited number of students. Students may refer to these models during class and again in their own time while studying. Students are able to manipulate AR models using a tracker behind a mobile device. Hence, AR gives the promise of replicating the effect of concrete models. Students are able to see instant movement on the screen in front of them simulating an actual object.
In this chapter, I will describe a method for producing molecular models in AR technology that have an appearance similar to the commercially available models but provide more realistic molecular geometries. I will also explore options for cre- ating representations of atomic orbitals, which currently rely on expensive models made from materials such as wood or on 3D printing technology. I will discuss methods of incorporating these models into classroom instruction.
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Methods
Molecular Models
Students investigate a variety of molecular geometries in introductory chemistry courses. In order to give a broad view of these geometries, eight particular mole- cules were created for students to investigate. In particular, AR models were created for water, ammonia, carbon dioxide, dichloromethane, sulfur tetrafluoride, iodine chloride, sulfur trioxide, and phosphorus trichloride.
The first step was to create the molecule in molecular modeling software.
Avogadro ver. 1.2.0 (Hanwell et al., 2012) was used to create models. Figure 10.1 shows methane in the software. Avogadro allows the user to select particular atoms and drag them into the workspace. For methane, a user can click on carbon and place it in the workspace. The software will automatically add the four hydrogen atoms in this case. However, a user can select other atoms to change the molecule.
A user can specify particular angles for the geometries. However, the software uses mathematical modelling methods to calculate the correct structure as well. This makes creating models straightforward. The software is free and has the ability to export a file compatible with 3D processing software.
After the molecules were created, the file was exported in a Virtual Reality Modeling Language (VRML) format. These files were then imported into Blender (www.blender.org). Figure 10.2 shows the methane molecule moved from Avogadro to Blender. Blender is a free and open source 3D creation suite. It allows for creating 3D images. Blender was used to clean up the 3D models. When the molecules are imported into Blender from Avogadro, the molecules lose some roundness. Blender
Fig. 10.1 A screenshot of Avogadro software used to create models 10 Visualization of Molecular Structures Using Augmented Reality
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has a function to smooth the edges for use in AR. Molecules also required adjust- ments to color. For example, Avogadro exported models with bonds colored in two different colors, half from each atom color. The bond colors were replaced with a black bond to make the bonds stand out from the atoms. Blender was also used to brighten colors making the molecules more aesthetically pleasing. Blender was a required step in order to create files accessible by AR software.
The final step in creating the models was to import them to the Augment website (augment.com). Augment is a website that allows users to interact with three- dimensional models in augmented reality. Blender allows for a variety of export formats. Several of these formats were experimented with and it was found that either .DAE or .OBJ would preserve the colors created in Blender. These file types are common in 3D visualization and printing. These two types allow for animation and color to be preserved where other file types do not. Once files are imported into Augment, the user is prompted to choose a particular size for the model. The models were sized to be comparable to traditional molecular modeling sets.
Atomic Orbitals
Atomic orbits were modeled using Mathematica (https://www.wolfram.com/math- ematica/). Electrons within an atom can be found at varying energy levels around the nucleus of the atom. Atomic orbitals represent a volume where the probability of finding the electron is highest. These areas are solved using quantum mechanical techniques. The calculations can be complex; so software is used to calculate and
Fig. 10.2 Screenshot of Blender used to edit files and adjust color
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display the results. For these models, I used Mathematica. However, others have used online freeware software (Griffith et al., 2016) with similar results. The book Molecular physical chemistry: A computer-based approach using Mathematica and Gaussian (Teixeira, 2017) has Mathematica code useful for creating atomic orbit- als. The code required some adjustments to model the required orbital shapes.
Figure 10.3 shows examples of two atomic orbitals as displayed in Mathematica.
Models can then be exported in .DAE format. This is the same format previously imported into Augment. However, unlike previous attempts, color data were lost when files were directly imported into Augment. Hence, the same method used for molecular models was repeated to add color to the orbitals. Hence, the models were smoothed, and color was re-added in Blender. This is shown in Fig. 10.4. After this step, the models where exported into Augment and sizing adjustments were made in the same manner as for the molecular models.
Implementation
Once all files are uploaded to Augment, they are available in the cloud. Free education accounts for Augment are available for both students and teachers. To make use of the models in augmented reality, students require a smartphone or tablet. The Augment application is available free to download for both Android and iOS. To allow for manipulation of models, trackers are used. A tracker is a unique physical object that links the virtual and real worlds. It allows the software to know where to display the
Fig. 10.3 Atomic orbitals as displayed in Mathematica
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virtual models. In Augment, trackers can take numerous forms. For example, a dollar bill can be used. Augment also has a universal tracker available to download, which is shown in Fig. 10.5. It is also possible to create unique trackers that are linked directly to a given model. When these are scanned, the connected model appears.
The universal tracker can be downloaded in various sizes, from letter size to pocket size. I have found that the pocket size tracker works the best for this applica- tion and produced a much more stable tracker than using dollar bills or the other options available. I also found that unique trackers are difficult to make. After creat- ing the unique trackers, they are uploaded to Augment. Augment will decide if the tracker was sufficiently different from existing trackers and would regularly reject trackers I made. Hence, this method was abandoned as it became cumbersome.
Even if a unique tracker was successfully created, the process needed to be repeated for each model and multiple trackers must be printed for the students.
A better alternative was to use the QR codes Augment supplies for each model.
QR, “quick response”, codes are used as an easy way for a smartphone to connect to particular information, such as text, a website, or a model. An example of a QR code is given in Fig. 10.6, and more examples are available in the appendix. The QR code in Fig. 10.6 links to a model of water. A student can scan the QR code within the Augment application on their smartphone or tablet. The student must then hold their tracker in view of their camera on the smartphone or tablet. The model will appear on the tracker as shown in Fig. 10.7. Students are then able to twist and turn the tracker and see the model from various angles.
Initial rollout to students was made by way of adapting an existing worksheet on molecular geometries to include QR codes printed on the sheet. Students were also
Fig. 10.4 Atomic orbital displayed in Blender undergoing coloring
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supplied with the traditional model kits and allowed to work on the required models and compare the augmented reality with traditional models.
Atomic orbitals were not previously included in the worksheet. AR allowed the opportunity to include atomic orbitals and add a basic introduction to the topic. The shape of s orbitals is simple spheres, and 2p orbitals are shaped like dumbbells.
Animations were created for the p orbitals to show how the orbitals look together and separated. The p orbitals consist of three dumbbells arranged along the x, y, and z axes. For clarity, images in textbooks are typically drawn as separate diagrams. To aid with students’ understanding that these orbitals exist in shared space (i.e., over- lapping), animations were used for visualization. A QR code with the link to the animations is shown in Fig. 10.8. These animations gave students the opportunity to investigate the orbitals from a variety of viewpoints. The animation starts with the orbitals overlapping, and the orbitals slowly move apart so students can see what
Fig. 10.5 Augment universal tracker
Fig. 10.6 QR code linked to a model of a water molecule stored in Augment. (This code links to a working model)
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they look like when overlapped and when separated out. This method helped stu- dents understand that these orbitals do not occupy their own unique location in space.
Problems were encountered with the initial worksheet. These worksheets con- tained multiple QR codes on a single sheet, and this resulted in difficulty for the students knowing which QR code had been scanned. Alternative approaches could include using less QR codes per page, printing the QR codes separately, labeling them, and providing them in an envelope or Ziploc bag. Displaying QR codes on a screen at the front of the class was also attempted. This method did work and even led to some fun moments as students gathered at the front of the class to try and get a better view of the QR code. Students interacted with each other and the models, discussing coursework. If this congregation of students at the front of the class is problematic, varied placement of the code and sizing them larger would make it feasible for scanning from their seats.
Fig. 10.7 Screenshot of Augment showing tracker and superimposed water molecule
Fig. 10.8 QR code links to an augmented reality representation of 2p orbitals. This augmented reality model is animation to aid in student’s comprehension of the three-dimensional arrangement of these orbitals. (This code links to a working model)
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