ARTICLE pubs.acs.org/jchemeduc
Design and Implementation of a Self-Directed Stereochemistry Lesson Using Embedded Virtual Three-Dimensional Images in a Portable Document Format Jeremy A. Cody,* Paul A. Craig, Adam D. Loudermilk, Paul M. Yacci, Sarah L. Frisco, and Jennifer R. Milillo Department of Chemistry, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
bS Supporting Information ABSTRACT: A novel stereochemistry lesson was prepared that incorporated both handheld molecular models and embedded virtual three-dimensional (3D) images. The images are fully interactive and eye-catching for the students; methods for preparing 3D molecular images in Adobe Acrobat are included. The lesson was designed and implemented to showcase the 3D virtual images and determine whether the use of virtual 3D images should be permanently included with the stereochemistry lesson. A group of students completed the lesson and provided positive feedback on the incorporation of the embedded virtual 3D images. KEYWORDS: Second-Year Undergraduate, Curriculum, Organic Chemistry, Computer-Based Learning, Hands-On Learning/Manipulatives, Multimedia-Based Learning, Enantiomers, Stereochemistry rotate, spin, pan, zoom, walk, fly, and return to the default setting (see Figure 1 for a screen shot). In this article, a description of how the interactive sets of 3D molecular structures in the pdf format were created and the results of the experience in the classroom are presented.
C
hemistry is often brought to life by viewing threedimensional (3D) images of molecules using a computer. Computer visualization has been available for over a decade, but this often involves added software expense for programs such as Spartan; even when these concepts can be communicated with freeware, such as ChemSketch or Jmol, there is a significant learning curve for the software, both for the instructor and the student. Furthermore, the freeware products provide only community support. To circumvent these problems and provide universal access to 3D chemical models, virtual 3D images can now be embedded in the portable document format (pdf); these 3D images can then be viewed with the latest version of the freely available Acrobat Reader,1 arguably the most ubiquitous digital imaging format. The use of this technology in chemical education has great promise for delivering learning in a format that is familiar and comfortable to this generation of students. Visualization has been recognized as an important component for learning chemistry for many years;2,3 this is especially true for the study of stereochemistry. The extensive variety of ideas and articles on teaching stereochemistry indicate the complexity and importance of the subject matter. Articles have been published about using different techniques to teach stereochemistry such as drawing,2 transparent sheets,3 word games,4 one’s hands,5 and stick figures,6 as well as the popular Darling molecular models. The challenge of teaching stereochemistry results in part from the limited ability of some students to visualize molecular structures in three dimensions. A series of 3D pdf files have been created that can be used for teaching and assessing learning of stereochemistry in an organic chemistry sequence for majors. The virtual 3D molecular structure images may be viewed as ball and stick, wire, or spacefill. When the students view interactive 3D structures, they can Copyright r 2011 American Chemical Society and Division of Chemical Education, Inc.
’ METHODS FOR GENERATING EMBEDDED VIRTUAL THREE-DIMENSIONAL IMAGES Creating the documents with embedded virtual 3D images may be accomplished by using the following procedures (Figure 2 and Additional Notea). 1. Using either ACD ChemSketch 11.0 Freeware7 or CambridgeSoft ChemDraw,8 the required two-dimensional (2D) structures were drawn. 2. The 2D structure was then optimized into 3D with the 3D conversion tools found in ChemSketch. 3. The 3D molecules were saved to the MDL molfile (*.mol) format. The files were then converted from a mol format to a pdb (Protein Data Bank) format, which is the format recognized by the Adobe software, using Open Babel Graphical User Interface v2.2.09 with the default settings. 4. Three views (wire, balls and sticks, and spacefill) of the 3D molecule were then prepared using Adobe Acrobat 3D Toolkit 8.1.0. 5. A pdf template was opened with Adobe 3D and the virtual 3D images were added using the 3D tool. 6. Often it was desirable to match the interactive 3D image with a traditional 2D static image. The addition of 2D Published: October 25, 2011 29
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Figure 1. Screen shots of a ball and stick representation of (A) D-( )-tartaric acid, (B) meso-tartaric acid, and (C) L-(+)-tartaric acid. Key: C is black, O is red, and H is white.
Table 1. Student Itinerary for the Stereochemistry Lab Session 1. Asked to read prelab (pre-lab pdf) before lab session 2. Worked through self-guided lab manual (lab manual pdf) with 2D structures and embedded virtual 3D images on the computer using molecular-model kits 3. Completed the lab exercise document (lab exercise pdf) on the computer. The students were given 2D drawings, molecular-model kits, and virtual 3D images to complete the exercise 4. Completed the lab quiz (lab quiz pdf) on the computer with only the use of 2D drawings 5. Completed a survey (survey pdf)
Figure 2. A general schematic showing the processes for embedding virtual three-dimensional images in pdf’s.
more challenging topics in the organic chemistry sequence. Stereochemistry has traditionally been taught by first presenting the 2D structures to students in the classroom, then asking them to convert those 2D images into 3D models using handheld molecular-model kits. However, as modern technology plays a larger role in education, the addition of virtual 3D molecular images can supplement or replace the use of handheld models. The pilot study was conducted to gain initial feedback on whether the use of virtual 3D images in teaching stereochemistry should be pursued. An organic chemistry class composed of mainly biochemistry and chemistry majors was given the instructions listed in Table 1 during their laboratory session in week 5 of the 30 week long organic chemistry sequence. The lab session was held in a personal computer classroom and each student used a computer to access the online lessons. The self-guided discovery documents were designed to engage the students in learning stereochemistry as a supplement to the lectures with hands-on work with stereochemical tools to develop their spatial ability skills and understanding of the stereochemistry of organic molecules. The students had the use of handheld molecular-model kits and pdf documents containing both the embedded virtual 3D images and the static 2D images. The students worked at their own pace and most required the majority of the 4-h lab period to complete all of the tasks. The self-guided lab manual required the most time and allowed the students to learn and correct their answers to questions. Once the lab manual was completed, the students were asked to complete the lab exercise consisting of 10 questions designed to test their stereochemistry knowledge. During the lab exercise, the students had access to the virtual 3D images in addition to the 2D drawings, and molecular models. After each
images was completed by opening the ChemSketch (sk2) file and saving it as a TIFF Bitmap file (*.tif) and opening the file in Microsoft Paint 5.1 to convert to JPEG (*.jpg). The 2D file was then placed in the pdf using the TouchUp Object Tool. The file was then saved as an Adobe pdf file (see Additional Noteb). Documents containing the embedded virtual 3D images are available in the RIT Digital Media Library10 for free download for educational purposes. The technology has also been further utilized to create self-directed exercises in topics such as dipole moments and conformations of n-butane and cyclohexane.
’ VIEWING EMBEDDED VIRTUAL 3D IMAGES The pdf files that contain embedded 3D images can be viewed using either Acrobat Reader version 10.0.3 or newer or Acrobat Professional version 10.0.3 or newer on either the Mac or Windows environments. For Mac users, these files cannot be viewed in Preview, which is the default pdf viewer on most Mac OS computers. Viewing these pdf files with either Safari or Firefox using the Adobe plug-in on the Mac can be spotty and inconsistent. The files should be created or downloaded and opened directly in either Acrobat Reader or Acrobat Professional. ’ STEREOCHEMISTRY LESSON The classroom experience reported in this article centers around the use of a self-directed computer-based lesson embedded with virtual 3D images as a tool to assist in teaching the stereochemistry of organic compounds during a laboratory period. Stereochemistry of organic compounds is one of the 30
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Table 2. Survey Resultsa Question
Strongly Agree
Agree
(%)
(%)
Disagree Strongly Disagree (%)
(%)
1. Were the virtual 3D images easy to interact with?
39
61
0
0
2. Do you think the virtual 3D images would be helpful in learning other topics in organic chemistry? In other
39
61
0
0
courses?
a
Added to
Detracted from
Question
the Lab
the Lab
Both/Indifferent
4. Do you feel that the addition of the virtual 3D images added to or detracted from the effectiveness of the lab?
91
0
9
See Additional Notec
question in the lab exercise, the students were asked to identify which stereochemical tool(s) they used to answer the question. Students were then asked to complete a 10-question stereochemistry lab quiz using only 2D drawings. At the end of the lab period, students were then asked to complete a short survey aimed at determining their feelings and thoughts about the virtual 3D images (see Additional Notec).
responses, the students used a stereochemical tool, either handheld molecular-model kits, virtual 3D images, or both, 37% of the time when completing the problems in the exercise. Of the times that the students used an additional tool, the virtual 3D images were used 74%, handheld molecular-model kits were used 20%, and both were used 6%. Therefore, when the students felt they needed the use of an additional stereochemical tool, the majority of the time they relied on the virtual 3D images. Problems 3, 5, and 8 of the lab exercise can be most logically solved with higher spatial reasoning, which would be greatly assisted with handheld molecular models, or virtual 3D images, so intuitively one could assume the students would use the tools provided to obtain the correct answer (Table 3). In Table 3, the percentage of the students who got the question correct is listed in parentheses. For example, in problem three, 89% of those who used the virtual 3D images chose the correct answer, compared to 50% when students used only the handheld molecular kit and 23% when students used neither tool.
’ RESULTS The results include the students’ answers to a survey of which stereochemical tool they used in answering questions in the exercises (handheld molecular-model kits, virtual 3D images, both, or neither), an attitude survey at the end of the lab session, and instructors’ observations. Survey of Study Group: What Did the Students Think?
The students completed the survey at the end of their laboratory session and a summary of the questions pertaining to the virtual 3D images can be seen in Table 2 (see Additional Notec). The students seem in agreement that the virtual 3D images were easy to use. In answering question four, none of the students thought that the virtual 3D images detracted from the lab and 91% thought that the images added to the lab. The students demonstrated by their answers to survey questions two and four an acceptance of the virtual 3D images and an overall positive impression (Table 2). Another point worth discussing is the ease of use of the virtual 3D images and the fatigue associated with extensive handheld molecular-model building. Question one of the survey demonstrates that the students are comfortable with the simplicity of using the virtual 3D images and during the lab sessions very few questions were a result of navigating the documents or using the images. During the 4-h lab, students did suffer from fatigue and several of them made comments to this effect in their surveys. Two survey comments are
Instructor Observations
It is important to note some observations from the lecture and laboratory instructors. Two observations were made during the lab periods. First, the students were thoroughly engaged in the lab with the right amount of discussions between individuals. The computer seemed to captivate the students’ attention. Therefore, having the self-directed documents available on the computer was largely responsible for engaging the students.11 Second, the students complained of hand fatigue due to building molecules with the handheld molecular model kit. Later in the lab period, molecules built by the students were often incomplete.
’ CONCLUSIONS Two-dimensional drawings of molecules will remain the general symbolic representation of molecular structures for the foreseeable future. One of the tasks as chemistry instructors is to equip students with the ability to mentally convert a 2D representation of a molecule into 3D and back to a 2D structure. Mastering this skill enables the students to relate structure to function and to envision potential interactions for that structure in 3D space. The embedded virtual 3D images in the readily accessible portable document format (pdf) have the potential to make 3D molecular modeling accessible to anyone who has a computer and connection to the Internet. Instinctively, we believe that our students are growing more oriented toward learning in virtual online environments and we are committed to refining our materials and assessment tools to identify approaches and audiences that will receive the greatest benefit from this approach.
“...but 4 straight hours of packing stereochemistry into your brain is a bit much, ...” “I relied more on the 3D images just because it was so much work to put the hand kits together. Also, they were better in the sense that they were already loaded and could rotate them without worry about messing up.” Lab Exercise Results
During the stereochemistry exercise, after each question, the students were asked whether he or she used handheld molecularmodel kits, virtual 3D images, both, or neither to answer the previous question (see Additional Notec). On the basis of their 31
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Table 3. Students' Responses to Three Laboratory Exercise Questions
a
Number in parentheses is percent that got the question correct using the respective teaching tool.
’ ACKNOWLEDGMENT The authors would like to thank Michael Coleman and Christina Collison for allowing us to use their laboratory sections for a trial run of our stereochemistry lessons. This work was supported by grants from the College of Science, the Office of the Provost and Office of the Vice President for Finance and Administration at RIT.
On the basis of this experience, the students found the virtual 3D images useful and were successful in using them to solve problems in the exercises. The application of the embedded virtual 3D images in studying stereochemistry of organic molecules is intuitive and has the potential for increasing student learning and interest in organic chemistry. Initially, the focus has been on stereochemical understanding, but the use of embedded virtual 3D images could easily be extended to other structural aspects of chemistry.
’ ADDITIONAL NOTE a Detailed instructions with screen shots have been included in the Supporting Information.
’ FUTURE PLANS Further development of the 3D materials can add depth to any online courses or online course work for general, organic, and biochemistry courses, but should not be limited to those disciplines. Handheld models are extremely useful in research, one’s own learning, and in teaching, but the virtual 3D images are already prepared for the students and are not as cumbersome or limited by the quantity of atoms as are handheld molecular model kits. On the basis of the positive feedback from the students, the stereochemistry lab has been added to the curriculum and development of other self-directed learning exercises (e.g., virtual 3D images of molecules such as cyclohexane in higher energy conformations) using the virtual 3D images to enhance visio spatial learning in the organic chemistry and biochemistry courses has begun.
b
The 2D structures (step 1) could also be extracted from structure images in NCBI’s PubChem Project12 in a number of formats (InCHI, IUPAC International Chemical Identifier, and SMILES, Simplified Molecular Input Line Entry Specification) that Chemsketch can use to generate the desired structure. Using the “Clean Structure” Tool is often useful for optimizing bond angles and lengths. c
A copy of the document has been included in the Supporting Information.
’ REFERENCES
’ ASSOCIATED CONTENT
(1) Kumar, P.; Ziegler, A.; Ziegler, J.; Uchanska-Ziegler, B.; Ziegler, A. Trends Biochem. Sci. 2008, 33, 408–412. (2) Haudrechy, A. J. Chem. Educ. 2000, 77, 864–866. (3) Shine, H. J. J. Chem. Educ. 1957, 34, 355. (4) Neeland, E. G. J. Chem. Educ. 1998, 75, 1573. (5) Beauchamp, P. S. J. Chem. Educ. 1984, 61, 666–667. (6) Starkey, L. S. J. Chem. Educ. 2001, 78, 1486. (7) ACD ChemSketch 11.0 Freeware. http://www.acdlabs.com/ resources/freeware/ (accessed Oct 2011). (8) CambridgeSoft ChemDraw. http://www.cambridgesoft.com/ software/ChemDraw/ (accessed Oct 2011). (9) Open Babel Graphical User Interface v2.2.0. http://www.openbabel. sourceforge.net (accessed Oct 2011).
bS
Supporting Information Copies of the detailed instructions for creating virtual 3D molecular images in a portable document format; prelab, lab manual, lab exercise, lab quiz, and survey form. This material is available via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION Corresponding Author
*E-mail:
[email protected]. 32
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(10) RIT Digital Media Library. https://ritdml.rit.edu/handle/ 1850/11865 (accessed Oct 2011). (11) Hays, T. A. J. Educ. Comput. Res. 1996, 14, 139–155. (12) NCBI’s PubChem Project. http://pubchem.ncbi.nlm.nih.gov (accessed Oct 2011).
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