Chemical Exploration with Virtual Reality in Organic Teaching

Jul 23, 2019 - Detailed description of the hardware and software setup (PDF, DOCX). Tabulated survey results (PDF, DOCX). Notes for instructors (PDF, ...
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Chemical Exploration with Virtual Reality in Organic Teaching Laboratories Jonathon B. Ferrell,† Joseph P. Campbell,† Dillon R. McCarthy, Kyle T. McKay, Magenta Hensinger, Ramya Srinivasan, Xiaochuan Zhao, Alexander Wurthmann, Jianing Li,* and Severin T. Schneebeli* Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States

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S Supporting Information *

ABSTRACT: While virtual reality (VR) is emerging as an interactive tool for chemical education, its application and assessment for chemical education are still limited. Thus, an educational VR activity based on interactive molecular dynamics in virtual reality (iMD-VR), which allows for realtime, immersive interactions with a dynamic molecular world, was now designed and executed to demonstrate chemical concepts and engage students in exploring molecular structures, motions, and interactions. There were 70 students in the first semester of an introductory organic chemistry course asked to complete an example task to pull a methane molecule through a carbon nanotube with iMD-VR software originally designed for research purposes by Glowacki and coworkers. Our assessments of this activity have shown valuable motivational impacts and measurable learning gains. The VR activity can be further tailored to many different levels by varying the topics and tasks, with affordable hardware and software. KEYWORDS: Multimedia-Based Learning, Second-Year Undergraduate, Interdisciplinary/Multidisciplinary, Organic Chemistry, Cheminformatics, Computer-Based Learning, Hands-On Learning/Manipulatives, Inquiry-Based/Discovery Learning, Computational Chemistry

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interactive molecular dynamics in virtual reality (iMD-VR) by Glowacki and co-workers15,19 further increases immersion and understanding (in particular of dynamic aspects) by giving physically realistic, dynamic feedback to user interactions. While, iMD-VR has been successfully employed for other applications,19,20 it has still remained a priority to assess whether utilizing VR technology in the classroom (and iMDVR in particular) is indeed able to help motivate university students and potentially even lead to measurable learning gains. In this paper, we describe the results of executing a prototypical iMD-VR activity with 70 students in eight organic teaching laboratories in the first semester of an introductory organic chemistry course at the University of Vermont (UVM). For the iMD-VR activity, students were asked to pull a methane molecule (Figure 1) through a carbon nanotube, which is one of the four iMD-VR tasks described by Glowacki and co-workers.15,19 In what follows we utilize iMD-VR for undergraduate teaching and see the statistical improvement of this experience for chemical education, in a well-defined group of 70 students participating in eight sections of an organic chemistry laboratory. We emphasize

ince the chemical properties of molecules are largely determined by their structural features and dynamic interactions, it is essential for chemistry, materials science, and health-sciences students to understand molecular structures, interactions, and motions in a realistic, interactive environment.1,2 Thus, model kits have been used for students to build and manipulate simple molecular structures since the late 19th century.3 In the past decade, an increasing use of computer-based models have been applied to visualize molecular structures and demonstrate chemical concepts.4 However, most of the chemical models (either tangible or virtual) currently used for education only provide a limited demonstration of the important dynamic aspects of molecules, such as bond vibrations, diffusion, reactive collisions, kinetics, etc. Thus, new chemical models need to be applied that are both dynamic and interactive at the same time, allowing for exploratory educational activities in chemistry that are known5−14 to enhance independent learning. Virtual reality (VR) technology15 is well-suited to fill this need for chemical education for the following reasons: (i) With its enhanced immersive and interactive space, VR allows for an intuitive understanding of chemical systems. (ii) With the recent arrival of accessible virtual reality (VR) equipment as well as VR software15,16 for chemical systems, the technology is now starting to mature into a state where it can be integrated17,18 into chemical education. (iii) The specific development of © XXXX American Chemical Society and Division of Chemical Education, Inc.

Received: January 24, 2019 Revised: June 8, 2019

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DOI: 10.1021/acs.jchemed.9b00036 J. Chem. Educ. XXXX, XXX, XXX−XXX

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Figure 1. Screen shots of what is seen with the VR goggles when pulling a methane molecule through a carbon nanotube. Reprinted from ref 15. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

Some of the first attempts in this direction are described herein.

the assessment of potential motivational enhancements as well as potential learning gains of the students in the iMD-VR activity. The goals of our iMD-VR activity were to (i) demonstrate the spatial structures of simple and complex molecules, (ii) illustrate typical noncovalent interactions with molecules in motion, and (iii) engage the students to visualize the microscopic world and independently explore basic chemical concepts. Overall, VR represents15,16 an interactive tool for chemical education, which allows students to manipulate dynamic molecules within the virtual space. Furthermore, iMD-VR, which couples19 regular VR with real-time, rigorous molecular dynamics (MD) simulation engines, enables realtime, immersive interactions with a dynamic molecular world, that is otherwise inaccessible to the students. Compared to traditional modeling kits and 2D computer models, the immersive, dynamic experience of iMD-VR can allow students to better observe molecules in motion, promote understanding of molecular interactions, and help connect the molecular views with macroscopic properties. In addition, students can study simple molecules (typical examples from textbooks or traditional chemical education), as well as complex structures like supramolecular assemblies, biological macromolecules, etc., which greatly expands the depth and breadth of chemical understanding for students with various interests at different levels. Notably, recent advances in computing and gaming hardware have provided affordable options for activities in a classroom or a laboratory, while a number of software programs (Nano Simbox,15 Nanome,16 Molecular Rift,18,21 MEL Chemistry VR,22 VRMC,23 Narupa,19 etc.) are available either for free or at an educational price. Moreover, the implementation of VR software developed by companies like MEL Science22 and EduChem VR18,24 has shown promise as practical educational tools. However, the successful utilization of VR (and iMD-VR in particular) for chemical education is still uncommon and requires further practice and assessment.

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THE ACTIVITY The activity was carried out in eight laboratory sections of Introductory Organic Chemistry (CHEM141) at UVM in the Fall of 2018. Students were mainly sophomores with nonchemistry majors. The setup includes a desktop computer with a VR-ready graphics processing unit (GPU), a headmounted display (HMD), and two wireless controllers from HTC VIVE. The local computer runs the iMD-VR program described by O’Connor et al.15 (now officially succeeded by Narupa, an open-source community software package19), which interfaces with the HTC VIVE with MD simulations performed on a cloud-mounted remote server. The nanotube/ methane task was chosen for students to pull a methane molecule through the center of a C60 nanotube, in a time limit of ca. 5 min. Both the methane and nanotube molecules were created and loaded before the exercise. In a one week time period, a total of 70 students in eight different sections of the organic teaching laboratory for Organic Chemistry I (Chem141) at UVM were given the opportunity to experience the technology. While waiting for gas chromatographic analysis, the students tried out the iMDVR activity to experience how a molecule’s size and “bulkiness” can be experienced effectively in the iMD-VR environment. The concept of “bulkiness” was familiar to the students, as all of them had participated in a molecular model lab by this point in the semester. After a brief tutorial of how to use the controls of the VR equipment, and an introduction of the task by the facilitator (the TA of the laboratory), the students were outfitted, one by one, with the VR HMD. If students opted not to experience the iMD-VR (e.g., due to concern of potential motion sickness) they were still given the questionnaire as part of the control group. Only three students chose this option, and while some students reported feeling disorientated, no students specifically reported feelings of motion sickness. B

DOI: 10.1021/acs.jchemed.9b00036 J. Chem. Educ. XXXX, XXX, XXX−XXX

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Figure 2. (a) Question used to assess the spatial recognition/imagination capability of the students. (b) The students’ answers to the question of panel a. Correct answers (see Figure 3) are marked with a green tic; incorrect ones are marked with a red cross. The control group of students did not participate in the iMD-VR activity. Error bars were calculated from a set of five different experiments, each carried out in a different Chem 141 laboratory section. Overall, the iMD-VR activity was executed eight times in different laboratory sections, and the assessment results of the smaller laboratory sections (with less than 10 students) were grouped together to afford the five distinct data sets. The total number of students in the iMD-VR group was 70. The total number of students in the control group (which did not participate in the iMD-VR activity) was 85.

in detail in the Assessment section, students reported that with iMD-VR they could get a more accurate depiction of the size and shape of complex molecules while also noting how they sterically interact with one another.

The iMD-VR environment placed the students into a virtual room that shows a real-time MD simulation of the carbon nanotube and the methane molecule. This gave students the opportunity to interact with more accurate representations of (i) space occupied by molecules, their bonds, and the electronic fields that are associated with them as well as (ii) different space filling models to more accurately determine how bulky some of these molecules were. The main iMD-VR activity was the challenge of manipulating15 the methane through the center of the carbon nanotube using the “skeletal” orientation. To meet this challenge, students would inherently experience different interactions between the molecules. After the initial attempts using a skeletal representation, the students could cycle through different representations and repeat the exercise which led to varying degrees of success. As described

Assessment of the Activity

Students were given a simple questionnaire (see the survey instrument provided in the Supporting Information) which asked their opinion of the lab and petitioned them to assess the likelihood of three different molecules going through a carbon nanotube. This questionnaire was distributed to all eight sections participating in the iMD-VR experiment (a total of 70 students) as well as to 85 students acting as controls in other sections. The experimental group was also provided questions directly relating to the VR activity. C

DOI: 10.1021/acs.jchemed.9b00036 J. Chem. Educ. XXXX, XXX, XXX−XXX

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Figure 3. Minimized (OPLS2005 force field25) molecular models (carbons in green and magenta, hydrogens in white) showing that only the methane and the long linear hydrocarbon chain, but not the branched hydrocarbon chain, can fit through the nanotube provided in the assessment question of Figure 2. (a) Model of methane molecule inside of the carbon nanotube. Both front and side views are shown for clarity. (b) Model of the branched hydrocarbon getting stuck when trying to move through the carbon nanotube. (c) Model of the long linear polymethylene chain (side and front views) moving through the carbon nanotube.

Of the questions provided, the first three assessed (i) the students’ opinion of the lab for that day, (ii) how they felt it changed their interest, and (iii) the value of the lab in understanding the material. From those questions we see a significant positive outcome for students who participated in the VR activity, compared to those who did not. On the question specifically assessing the usefulness of the lab in understanding the material presented, the number of students who strongly agreed with the statement increased by 58.8% over control (p-value of 1.86 × 10−25; all data analysis in this section used a χ2 test). The following two questions, which assessed interest in organic chemistry in general as well as in carbon nanomaterials, also saw an increase of 89.7% and 53.1%, respectively (p-values of 2.44 × 10−16 and 4.66 × 10−16, respectively). The last question (Figure 2a) assessed the students’ understanding of the relative size of molecules and showed a marked decrease (Figure 2b) of −65.8% (p-value of 7.53 × 10−41) in selection of an obvious (Figure 3) incorrect answer for those that used iMD-VR compared to those who did not. The relatively large error in the selection of the long linear hydrocarbon stems from two potential sources: (i) the students were interacting with a much narrower nanotube in iMD-VR than what is shown in the drawing, and (ii) students did not read the “CIRCLE ALL” comment and thought that they could only select one answer instead of multiple ones. Overall these findings clearly represent a nontrivial increase in both student enjoyment and understanding, both perceived and actual.

Supporting Information. In regard to visualization it was clear that iMD-VR was widely considered a superior visualization tool as students noted the following: “You can actually see and move the 3D shapes, other computer programs try to create this, but they end up being more frustrating than helpful.” “Virtual reality enhanced my perspective of how molecules are visualized more than conventional textbook structures as it allowed visualization around the entire molecule, allowing me to be able to see how stereochemistry matters and how molecules actually interact.” “It was very interesting to see the size and shape of the molecules using the VR. Typically, it is difficult to compare molecules from a textbook picture since all images are relatively similar in size. The VR was a great tool for visualizing the way molecules would actually act.” The visualization aspect was viewed as the greatest benefit. Students overwhelmingly said that “visualization” and “understanding 3D concepts” would be greatly beneficial to students. One student noted the following: “There are only benefits to using VR as a visual tool because textbooks can only show flat images. Even using dashes and wedges can only be so helpful, whereas VR allows for better spatial representations.” Finally, the notion of using iMD-VR as a conventional tool in a beginner organic chemistry course received substantially positive feedback. When students were asked if their outlook of the material and overall course would change if they used iMD-VR throughout the semester, their written responses indicated that this recent advance in spatial visualization could change not only how students would learn but also how the material would be perceived with students noting the following:

Activity Impact and Student Feedback

We collected student feedback in the form of comments with respect to thoughts on visualization, inherent benefits, and overall outlook of organic chemistry courses if iMD-VR were to be incorporated regularly. From this feedback we garnered 29 responses, which were all scanned and included in the D

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“It would add a new element of understanding to organic chemistry. It would expand the visualization of molecules, from being printed on a page to model kits to VR. This would create more excitement learning these difficult concepts and allow for a better understanding of organic chemistry.” “I think I would be more interested in organic chemistry... It would be easier to learn concepts and view structures, stereochemistry, or mechanisms first hand.” “OH MY GOD, it would help me understand those concepts (Stereochemistry, Fisher Projections, Newman Projections, Mechanisms) so much better! It would be like a molecular modeling kit but even better. I would get much better exam grades.” The overall student feedback was encouraging as many students confirmed that using the iMD-VR technology was helpful in learning about spatial interactions. Furthermore, the students’ general responses to the spatial questions showed that there was a better understanding of spatial interactions after using the iMD-VR, while a preliminary analysis of midterm grades even seemed to indicate an overall positive impact26 on the students’ learning experience.

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ASSOCIATED CONTENT

* Supporting Information S

The Supporting Information is available on the ACS Publications website at DOI: 10.1021/acs.jchemed.9b00036. Detailed description of the hardware and software setup (PDF, DOCX) Tabulated survey results (PDF, DOCX) Notes for instructors (PDF, DOCX) Survey instrument (PDF, DOCX) Scanned student comments (PDF)

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: severin.schneebeli.uvm.edu. ORCID

Jianing Li: 0000-0002-0143-8894 Severin T. Schneebeli: 0000-0002-9511-9922 Author Contributions †

J.F. and J.P.C. contributed equally.

Notes

CONCLUSIONS

The authors declare no competing financial interest.

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An iMD-VR enabled activity, which continues to be freely available in its open-source version, Narupa, with enhanced features as detailed by Glowacki and co-workers,19 has been assessed in an educational setting to demonstrate chemical concepts and engage students to explore molecular structures, motions, and interactions in the first semester of introductory organic chemistry at UVM. The activity has started to advance discovery-based learning of dynamic chemical concepts, where students explore and discover fundamental chemical principles on their own. There were 70 students who participated in the iMD-VR activity, and our assessment results show valuable motivational and learning gains. iMD-VR can be further tailored to many different levels by varying the topics and tasks, with affordable hardware and software. All of the studies described in this paper are now available as part of the free, open-source, and customizable iMD-VR framework Narupa,19 which includes several key enhancements including the ability (i) to run custom simulations and (ii) for multiple users to cohabit the same VR environment. With these custom simulations we are currently expanding the iMD-VR activity to different courses at UVM. For example, in organic chemistry, we are starting to engage students in more complex concepts like chiral outcomes in asymmetric synthesis, the understanding of complex transition states, or memory of chirality. Furthermore, in physical chemistry, we are investigating water cluster structures with iMD-VR to help students better understand the concept of entropy, while in biochemistry, students are able to interact with protein structures and place small molecules into the drug binding pockets with iMD-VR. Furthermore, we will also start to apply VR to K−12 outreach, e.g., to reveal the dynamic aspects of polymerization kinetics and molecular machinery containing advanced supramolecular and interlocked components to the general public.

ACKNOWLEDGMENTS The authors thank Ms. Rosie Brown from Interactive Scientific; Profs. William Geiger, Christopher Landry, and Rory Waterman at the University of Vermont for helpful discussions; as well as all of the CHEM141 TAs and students who participated in this activity. This work was supported by the National Science Foundation (Grant CHE-1609137 awarded to S.T.S.). Partial support was also provided by the ACS Petroleum Research Fund (Grant 58219-DNI6 awarded to J.L.).

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iMD-VR activity rose to 7% (midterm 3) above the class average. These preliminary results suggest that our iMD-VR activity might indeed be able to translate into academic improvements in the short term due to motivational gains, which might have helped the students to stay more focused on studying for the third midterm examination.

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DOI: 10.1021/acs.jchemed.9b00036 J. Chem. Educ. XXXX, XXX, XXX−XXX