A Collaborative, Wiki-Based Organic Chemistry Project

ARTICLE pubs.acs.org/jchemeduc

A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web Michael J. Evans and Jeffrey S. Moore* Department of Chemistry, University of Illinois, Urbana
Champaign, Illinois 61801, United States

bS Supporting Information ABSTRACT: In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chemistry software for the creation of interactive chemistry content on the Web. Using currently available software, students are able to design, build, and describe computational molecular models with a high degree of independence. For a second-semester organic chemistry course with biochemistry applications, we designed and implemented a wiki-based project that involved student development of Web pages presenting the mechanism of action of a molecule of their choice. Student feedback supports the value of the project as a means to help students apply course content to biochemical applications. Organic chemistry instructors may benefit from the experience we gained while designing and implementing an organic chemistry wiki project. KEYWORDS: Second-Year Undergraduate, Curriculum, Organic Chemistry, Collaborative/Cooperative Learning, ComputerBased Learning, Internet/Web-Based Learning, Bioorganic Chemistry, Computational Chemistry, Student-Centered Learning

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n organic chemical education, emphasis over the last few decades has shifted from content-centered, rote-memorization approaches toward conceptual approaches. Although conceptcentered approaches present obvious advantages for students, overly abstract course material may cause students to disengage unless they gain an appreciation for the generality and applicability of concepts. At this university, the organic chemistry curriculum for nonmajors is rooted in a physical organic conceptual framework, relying, for instance, on a generalized classification of elementary mechanistic steps in terms of the frontier orbital interactions involved.1 Keeping in mind the danger of “overabstraction”, we initiated course reforms to help students appreciate the generality of the concepts by applying them to biochemical topics aligned with their long-term interests. Both nonmajor organic chemistry courses involve a significant online component, which presents both advantages and challenges.2 The traditional lecture has been replaced by three interactive online discussion sessions per week, at which time students solve problems individually using Web-based chemistry software. A consequence of our online mode of delivery is that student
student interactions have been limited. It has been recognized for nearly three decades that increased student
student interaction can improve student motivation and encourage critical thinking.3 Thus, improving the social environment of our courses by fostering student
student interaction through collaborative learning became a second goal of our course reforms. Introducing collaboration in the context of Web-based chemistry software seemed a natural extension of our approach. Educators from diverse fields have recognized the benefits of collaborative learning for many years.4 The interdependence Copyright r 2011 American Chemical Society and Division of Chemical Education, Inc.

encouraged by learning situations in which students must collaborate with one another to solve problems mirrors well the interdependence of professional scientific specialists tackling complex problems. Theories of collaborative learning have been adapted to online projects,5 and a number of examples from this Journal have illustrated the advantages of collaborative chemistry projects.6
9 Many of these projects took advantage of electronic resources and software available at their times of publication. We identified recent Web 2.0 technologies (such as wikis) and open source chemistry software (vide infra) as relatively untapped resources for collaborative chemistry projects. Wikis, collaborative Web pages that can be edited by a large number of users, are becoming common in educational settings as a framework for publishing the work of student teams.10 In the physical sciences, wikis have been used for problem-based learning assignments,11 collaborative technology simulations,12 and other activities.13
15 Using a common wiki page, students are able to collaborate with one another over large distances and at any time. By examining wiki page histories, instructors can trace the development of a page from start to finish and gauge the contributions of individual team members. Commenting tools facilitate collaboration between groups and offer a means for formative assessment of projects throughout the semester. Thus, wikis solve many of the problems that plague traditional group projects.16 Additionally, the potential for wiki pages to reach a broad audience can enhance the quality of student work and provide motivation beyond simply getting the grade.17 Wiki Published: March 18, 2011 764

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Table 1. A Survey of Software Available for Construction, Viewing, and Manipulation of Chemical Structures Softwarea

Type Structure-drawing Programs

Three-dimensional Molecular Viewers Web-based Computational Chemistry Interfaces a

Description

MarvinSketch

Web- or desktop-based, Java structure or reaction drawing software

JME

Web-based drawing software for chemical structures only

ChemDraw

Desktop-based structure drawing software

Jmol

Open-source molecular viewer with some editor capabilities

PyMol

High-quality molecular viewer, advanced animation options

WebMO

Open-source interface for computational chemistry calculations on the Web

Programs students used for the Molmodac project are displayed in bold.

Table 2. Checkpoints for the Molmodac Wiki Project Due Date

Table 3. Examples of Molmodac Project Topics and Corresponding Well-known Effects

Checkpoint

Molecule

Effect

Tuesday, Week 3

Creation of Student Teams

Friday, Week 3

Wiki Pages Created

Cocaine

Drug Addiction

Monday, Week 7

Preliminary Topic Selection

Hyaluronic Acid

Bee Stings

Friday, Week 9

Final Topic Selection

2-Phenylethylamine

Aphrodisiac Effects of Chocolate

Wednesday, Week 12 Friday, Week 14

Visualization Checkpoint Initial Submission of Wiki Page

Humulone

Beer Skunking

Lidocaine

Numbing of Tissues

Wednesday, Week 15

Peer Commenting Deadline

VX Nerve Agent

Nerve Gas Toxicity

Friday, Week 15

Final Submission of Wiki Page

Vardenafil

Treatment of Erectile Dysfunction

Alpha-thujone Warfarin

Absinthe Intoxication Anticoagulation

Chitin

Formation of Insect Exoskeletons

projects can be highly structured and expansive in scope, as long as instructors provide an adequate template from which students can build.18 Because of these advantages, we saw the wiki format as an excellent way to address our course’s past challenges and developed a semester-long project, Molecular Mode of Action (“Molmodac”), using the wiki format as a foundation for student work. Because the project uses primarily free software and readily available technologies such as Java and JavaScript, it can be carried out at any university that hosts a wiki server for faculty and student use. Until recently, educational wikis have been limited primarily to media exhibiting a limited degree of interactivity, such as text, static images, and videos. However, several existing wiki projects support the notion that student creation of highly interactive content on the Web is no longer unrealistic.19,20 Chemical education in particular has benefited from the development of a variety of free and opensource software tools for chemistry. Some of these tools are surveyed in Table 1; programs our students used for the Molmodac project are displayed in bold. The Molmodac project relies heavily on free and open-source chemistry software for student creation of content, an exercise with well-known benefits to learning.21 While actively contributing to a wiki, the role of the student shifts from passive observer to active creator, and all of the benefits of active learning accompany this transition. The next generation of educational wikis will almost certainly take this into account and incorporate software with high educational value.

’ WIKI PROJECT DESIGN We designed the Molmodac project to help students connect course material to real-world applications of organic chemistry. The project proceeded in three major stages. First, teams of three or four students chose a small molecule with an effect well-known to the general public and carried out a literature search to identify how organic chemical change in the key small molecule leads to its well-known effect. The key molecule defined each team’s “topic”. At the topic selection stage, we pointed students to a variety of

database resources to aid their search, including PubChem,22 the Protein Data Bank,23 KEGG,24 and specialty compound databases such as SuperScent.25 The aim of the literature and databases searches was to establish a central literature reference on which the wiki page would be based (however, supporting references were strongly encouraged). Second, with a topic and a key literature citation in hand, teams created wiki pages describing the topical molecule’s mechanism of action, visualized using the software in Table 1. Each group created a 5-min video segment to describe the contents of their page. Finally, with their pages in nearly finished form, students provided comments on other teams’ pages, offering advice on content or presentation. Throughout the semester, course instructors and teaching assistants used commenting to provide technical advice and suggest creative uses of the chemistry software. We established a number of checkpoints throughout the semester to ensure that wiki pages were under continuous development and to aid the grading process (see the Supporting Information for a full copy of our grading rubric, which includes both the required checkpoints and guidelines for page content and presentation). The checkpoints and their corresponding due dates are listed in Table 2.

’ PROJECT IMPLEMENTATION During the topic selection stage, teams identified a process they were interested in that could be traced to the mechanism of action of a small organic molecule: examples included the skunking of beer, a bee sting toxin, cancer chemotherapeutics, and medications for the treatment of erectile dysfunction. In consultation with course instructors, teams then developed a key question or problem related to the mechanism they had identified. Some examples of student-chosen molecules and their corresponding effects are listed in Table 3. Once teams had identified key literature references related to the mechanism of action of their topic, they turned their attention to the second 765

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stage of the project, bringing their references to life on their Web pages through creative use of free, Web-based chemistry software. Students developed their wiki pages based on a template (https://wiki.cites.uiuc.edu/wiki/display/CHEM332Molmodac/MolmodacþEntryþTemplate, also available in the Supporting Information) and example page (https://wiki.cites. uiuc.edu/wiki/display/CHEM332Molmodac/CyclicþAdenosineþMonophosphate, also available in the Supporting Information) that we provided. Additionally, we provided student teams with a number of activities related to their topics that directly involved the use of free or open-source chemistry software. These included • Depicting chemical change with curved arrows in MarvinSketch • Calculating the molecular orbitals of the topical molecule or related molecules using WebMO • Calculating reaction progress or transition state geometry using WebMO • Comparing the geometry-optimized conformation of a free ligand to its conformation while bound to a protein • Constructing the electrostatic potential energy surface of a ligand or protein active site • Depicting frontier molecular orbital interactions with Jmol • Highlighting noncovalent interactions in proteins using Protein Data Bank entries and Jmol To describe their molecular mechanisms on the wiki, student teams summarized the results of these activities and created interactive visualizations (Jmol and MarvinSketch applets) to illustrate the important features of their mechanistic model. Because these applets are information rich, they represent objects

Figure 1. A simple student-built MarvinSketch applet. Advantages of MarvinSketch applets over images of chemical structures and reactions are highlighted.

of significant value to end-users. Figure 1 shows a simple studentbuilt MarvinSketch applet and lists some of the advantages of using applets for displaying molecular structures in place of images. Figure 2 depicts an interactive Jmol applet created by a group exploring the mechanism of action of vanillin. When the user clicks on the buttons associated with the Jmol applet, different amino acids appear and the view shifts to emphasize interactions of the ligand with the newly displayed residues. Although the positions and connectivity of atoms were provided by structural data from the Protein Data Bank, students designed the buttons and their associated views themselves, and built the applets using a graphical user interface for Jmol that we developed (http://butane.chem.illinois.edu/jsmoore/Experimental/ mpjmols/JManip.aspx) after hearing feedback from students that scripting with Jmol was too difficult. The Molmodac Jmol interface can be used to create Jmol applets for a variety of purposes and is described in more detail in the Supporting Information.26 Clougherty and Wells have noted that wikis are particularly well suited to the process of peer review.11 In this vein, we encouraged teams to offer constructive criticism on each other’s pages through the wiki’s commenting tool (the third stage of the project). Throughout the project, we also encouraged collaboration between teams to develop the presentation aspects of their wiki pages; however, it was not until the final two weeks of the project, when most of the pages were filled with content, that our students embraced the commenting function of the wiki. This may have been because we did not draw attention to the requirement associated with the peer commenting checkpoint until close to the end of the semester. In any case, the high volume of comments on the wiki at the end of the project was an indication that students valued the ability to discuss their pages with others and comment on the pages of other groups.

’ STUDENT FEEDBACK ON THE MOLMODAC PROJECT To evaluate student response to the Molmodac project, we conducted an informal survey at the end of the semester. We also held a focus group involving 10 student volunteers to ascertain student opinions on issues not covered by the survey and to discuss future directions for the project. Student feedback indicated that the project was a useful exercise for connecting course content to real-world applications, although difficulties with using the technology were its primary limitation. Despite the difficulties many students had with using Web-based chemistry software (particularly Jmol), the majority concluded that

Figure 2. An interactive Jmol applet highlighting the interactions of catalytically active residues with vanillin in Protein Data Bank entry 2VSS. 766

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Journal of Chemical Education Molmodac was a step toward making our course more relevant, engaging, and social. One student remarked, “This project really helped me to get to know my classmates and instructors better than I would have expected for an online class.” The formation of student study groups due to the project was also apparent. Open-ended responses on our survey revealed student difficulties with the technological aspects of the project. “The complexities of learning [Jmol scripting] and producing visualizations take away from learning organic chemistry,” said one student. The time demands associated with purely technical tasks were substantial: “we would end up spending an hour and a half just trying to figure out how to put up a Jmol, which took away from the learning behind it,” said one student. Another student suggested, “Some extra computer training would be helpful.” We held an hour-long focus group with 10 students to further explore student response to the Molmodac project. Students were chosen from an excess of volunteers to represent a variety of grade levels on the project. Most student concerns were related to the processes of topic selection and creating visualizations. Some students felt that the literature-searching component of the topic selection process was too vague, which led to the discovery of topics with little or no useful literature very late in the topic selection process. Additionally, because many students were new to primary literature searching, a great deal of consultation with the course instructors was often necessary. This suggested that future incarnations of the project should both clarify our expectations of the literature search and provide guidelines for students to effectively carry out searches. One idea brought up in the focus group, which was implemented in the summer of 2010, was to center each wiki page on a particular literature reference addressing an aspect of the mechanism of action of the chosen topic. Our survey and focus group results indicate a number of directions for improvement. First and foremost, we must work to facilitate the creation of visualizations and develop help pages so that the technical knowledge required to build interactive models does not overpower what it can teach our students about chemistry. This prompted a significant investment in the development of a new, user-friendly Jmol interface beyond the prototype that was in place during the inaugural semester. We plan to develop how-to resources with the help of students who have completed the project in the past. We also need to clarify the process of topic selection and inform students about what constitutes an effective search of the literature. Reflecting as instructors, we identified an interesting trend among students as they developed their pages. Many of the mental operations that practicing chemists do regularly—adding implied hydrogens, considering ionization state, and visualizing orbitals, to name a few—were overlooked by our students as they carried out the Molmodac project. It may be that the automation inherent in chemistry software gives students the mistaken impression that electronic tools provide the final word on organic chemistry—not true in the slightest! We had to remind students regularly to interpret computational results and evaluate their reliability. Students too often treated a computer-generated model or the results of a calculation as ends in themselves, rather than as means to an end.

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wide variety of processes and are benefiting from increased interaction with each other and with course instructors and teaching assistants. Our experience with Molmodac shows that students stand to benefit from the creation of materials grounded in course content, especially when these tasks are applied to a topic of their interest. The project has exposed our students to important aspects of the scientific process (primary literature searching, construction and development of models, and peer review), which prepares them to become better professionals. Student awareness of available and open-source chemistry software has increased as a result of the project; however, work remains for us to lower the technological barriers that impeded many of our students. It is our hope that our example encourages other chemical educators to embrace the use of chemistry software and collaborative work in their courses.

’ ASSOCIATED CONTENT

bS

Supporting Information A copy of the grading rubric, including the checkpoints and guidelines for page content and presentation; wiki-page template and example; description of the Molmodac Jmol interface. This material is available via the Internet at http://pubs.acs.org.

’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected].

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’ CONCLUSIONS The Molmodac Project has transformed our course. Through Molmodac, students have seen how organic chemistry relates to a 767

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(18) Reo, R. Scaffolding Student Collaboration for Group Wiki Projects. In Using Wikis in Education [Online]; Mader, S., Ed.; Chapter 4, p 34
40. https://wiki.doit.wisc.edu/confluence/download/attachments/19922950/UsingWikiInEducation_StewartMader.pdf (accessed Mar 2011). (19) Hodis, E.; Prilusky, J.; Martz, E.; Silman, I.; Moult, J.; Sussman, J. L. Genome Biol. 2008, 9, R121. (20) Tracy, H. J. J. Chem. Educ. 1998, 75, 1442. (21) Krathwohl, D. R. Theor. Pract. 2002, 41, 212. (22) Wang, Y.; Xiao, J.; Suzek, T. O.; Zhang, J.; Wang, J.; Bryant, S. H. Nucleic Acids Res. 2009, 1. (23) Berman, H.; Hendrick, K.; Nakamura, H. Nat. Struct. Mol. Biol. 2003, 10, 980. (24) Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M. Nucleic Acids Res. 2010, 38, D355. (25) Dunkel, M.; Schmidt, U.; Struck, S.; Berger, L.; Gruening, B.; Hossbach, J.; Jaeger, I. S.; Effmert, U.; Piechulla, B.; Eriksson, R.; Knudsen, J.; Preissner, R. Nucleic Acids Res. 2009, 37, D291. (26) Instructors who wish to use Jmol Interface for their own courses are freely available to do so, and may contact J.S.M. (jsmoore@illinois. edu) or M.J.E. ([email protected]) for additional information.

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