Technology for the Organic Chemist: Three ... - ACS Publications

In the Classroom

Technology for the Organic Chemist: Three Exploratory Modules John J. Esteb, LuAnne M. McNulty, John Magers, Paul Morgan, and Anne M. Wilson* Department of Chemistry, Butler University, Indianapolis, Indiana 46208 *[email protected]

The use of computer-based technology in chemistry is essential. Although undergraduate students arrive on campus with significant computer skills, the literature suggests that students overestimate their computer knowledge (1) and educators often assume that students have the computer literacy required. Google has developed tutorials for the use of its search engine for educators (2). However, general Internet searches may provide scientific information of imperfect quality or authenticity (3), and general searches do not develop the proficiency most appropriate for a professional chemist. Rather than postpone the introduction of such skills to upper-level courses or fold these skills into a research or library course (4), undergraduate programs should incorporate computer skills across the curriculum. Herein, we describe our efforts to include computer-based technology into the first-semester organic chemistry course through three modules that can be used in the classroom or laboratory setting. Background Undergraduate students arrive on campus with the impression that any and all information is available somewhere on the Internet and that the information retrieved in this way is accurate. The incorporation of appropriate computer-based learning into courses has been gradual, and the results of these adaptations have been seen in the literature (5-17). It is now the responsibility of chemical educators to teach students to find scientifically correct information using Web-based resources. Online resources provide a variety of specific Web-based activities for courses throughout the curriculum. A few of these include the molecule of the day (5); statistical resources through the National Science Foundation Educational database (6); large-scale incorporation of cheminformatics into an entire curriculum (7); and managing access to current literature utilizing a RSS feed in advanced courses (8). We are interested in introducing topic-specific computer-based technology into appropriate chemistry courses (e.g., plotting software in general chemistry; advanced plotting software in analytical chemistry and biochemistry; molecular modeling software in physical chemistry). Topic-specific computer-based examples have been described. Several examples of using Excel Solver for kinetics data are available (9) for use in general chemistry, analytical chemistry, and biochemistry. Use of the Cambridge Structural Database (10) and use of an Excel workbook to generate X-ray structures (11) for inorganic chemistry have been developed. A computer-based quantum mechanics laboratory has appeared (12). Contributions have come from the area of biochemistry and molecular biology, ranging from use of 3D graphics programs (13) to bioinformatics (14). Organic chemists are fond of chemical drawing 1074

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software (15) and tools such as 13C NMR prediction programs packaged with the drawing software (16), and some courses have been able to incorporate database searching into the undergraduate organic experience (17). Previously, our organic chemistry laboratory utilized a ChemDraw computer-based laboratory in the first semester. Recently, our university purchased a site license for this software, allowing students to load it onto their personal computers, obviating the need for us to run this experiment in the computer laboratory. This provided the opportunity to enhance the computer-based experience, and following are the results of these developments. Overview The computer-based exercise was divided into three modules: (i) research tools, (ii) database tools, and (iii) a chemical drawing program. The first module on research tools utilizes chemically appropriate Web-based resources rather than culturally popular search engines (i.e., Google) or information sites (i.e., Wikipedia). The second module on database tools works with scientific databases. The final module provides the opportunity to utilize ChemDraw as well as online versions of American Chemical Society journals. These modules can be mixed and matched as needed. Other modules, such as use of SciFinder Scholar or molecular modeling, could easily be envisioned if the institution has appropriate access to the software. Our institution's site license for SciFinder Scholar only allows two users access at a time, so a module utilizing this software is inappropriate for our large (240 students) organic chemistry series. Molecular modeling has been extensively utilized in our physical chemistry and inorganic laboratory series and inclusion in the general chemistry course is under development. Rather than duplicate efforts, we have chosen to focus on the three modules addressed here. As our students are prepharmacy, prephysician's assistant, premed, biology, and chemistry majors, the modules chosen here provide translatable skills to any area of study pursued by students who complete our organic chemistry series. All three of these modules are performed in a single laboratory period in a computer classroom, but we could easily envision incorporating these modules into the classroom setting. Module 1: Research Tools ChemINDEX (18), Sigma-Aldrich database (19), and the Spectral Database for Organic Compounds (SDBS) site maintained by the National Institute of Advanced Industrial Science and Technology (AIST), Japan (20) have been chosen as the chemically appropriate research tools. These resources allow a

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Vol. 87 No. 10 October 2010 pubs.acs.org/jchemeduc r 2010 American Chemical Society and Division of Chemical Education, Inc. 10.1021/ed100362d Published on Web 07/30/2010

In the Classroom

Figure 1. Procedure for module 1, online resources. Figure 2. Procedure for module 2, database searching.

search by chemical or compound name or Chemical Abstracts number. A known compound1 (aspirin) and a compound chosen by the student2 (a prescription medication, a known toxin, etc.) are evaluated via ChemINDEX and Sigma-Aldrich. Both ChemINDEX and Sigma-Aldrich provide information on physical properties (melting point, molar mass, etc.). Students utilize these resources to obtain information required in later laboratories in the semester and year. The MSDS sheets are examined for any hazards, safe handling procedures, LD50 data, key information on toxicity and reactivity, and chronic exposure data. The SDBS Web site provides spectral data for a large number of organic molecules. This is especially useful in the second-semester laboratory sequence for identification of solid and liquid unknowns. This introductory exercise allows insight into the large number of compounds available for a given structural formula. By entering a given molecular formula, a list of structural isomers along with spectroscopic data (mass, FT-IR, proton and carbon NMR, Raman, and ESR) is generated. Whereas each compound may not have all the spectroscopic data, students can obtain data for many common structures. These three online sources allow the organic student to explore scientifically correct chemical information. Students are expected to know how to obtain basic physical property data, spectral data, and where to find toxicity information. Colleagues in other science areas can also have the same expectations of our students. An abbreviated in-class procedure is shown in Figure 1. The complete procedure for our exercise is included in the supporting information. Faculty members should evaluate the online resources available and the skills most appropriate to their classroom prior to implementation. We chose to emphasize the use of online resources for scientifically correct information. Module 2: Database Tools Database searching is required of any student wishing to perform research effectively. Identifying the correct database to search is crucial to narrow the search to the appropriate original literature. The introductory exercise detailed in this laboratory uses PubMed, Toxline, and a third database of the student's choosing. PubMed is one of the most widely available databases utilized by the sciences. A search of aspirin3 yields an unwieldy number of citations. Students narrow the results using an appropriate modifier (e.g., aspirin synthesis; aspirin uses; aspirin history). Students are asked to evaluate the modifier choice they

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have utilized as well as evaluate the retrieved articles. A second search on aspirin using Toxline is performed. The number of articles, type of reference, and presentation style in Toxline are compared to the same information obtained from PubMed. Students are asked to critically evaluate each of the databases. A third, nonscientific, database (EBSCO, FirstSearch, Gale, Academic Universe, LISTA, etc.) is investigated and evaluated utilizing a search of aspirin. The three database tools are compared and the utility of multiple database searches can be determined. Lastly, the American Chemical Society (ACS) publications database (21) is employed and aspirin is searched in ACS journals. The students evaluate the subset of articles obtained in this database against the searches in the more inclusive PubMed and Toxline databases. Finally, the students perform a search on their compound of choice from module 1 using the database of choice. An abbreviated in-class procedure is shown in Figure 2. The complete procedure for our exercise is included in the supporting information. Faculty members should evaluate the databases available at their institution and the skills most appropriate to their chemistry program prior to implementation. We chose to include PubMed and Toxline databases as these are the most commonly used by all our science students. Module 3: A Chemical Drawing Program Chemical drawing programs, both free and licensed, are available to all scientists (22). Depending on one's discipline, the requirements and specifics of the types of drawings are varied. Regardless of drawing tool used, expectations are that professional publications, correspondence, and presentations utilize computer-aided representations of molecules. Students must produce such drawings on all formal laboratory assignments in our department. ChemDraw is used, but any program could be utilized for this module. The students must retrieve the appropriate settings to use from the ACS Journal of Organic Chemistry (23). The ACS publications settings are available options for ChemDraw, but student verification is the purpose of this portion of the exercise. The students draw several compounds and evaluate their work. The students are encouraged to change the settings on ChemDraw. These settings must include a change in font choice and bond length; other changes are up to the student. These changes are evaluated and the preferred settings are used to draw compounds from a previous laboratory.

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Acknowledgment Special thanks to the CH 351 students in 2007, 2008, and 2009 for helpful comments in revising these exercises. Notes 1. We chose aspirin. It is well-known to the students and is a wellcharacterized molecule. 2. Student choice of compound is key for generating student interest in these modules. 3. We chose aspirin. It generates a large number of “hits” and the list is easily narrowed using scientific modifiers.

Literature Cited

Figure 3. Procedure for module 3, using a chemical drawing program.

An abbreviated in-class procedure is shown in Figure 3. The complete procedure for our exercise is included in the supporting information. Faculty members should evaluate the drawing program available at their institution, if any, or obtain one of the free drawing programs available. Skills most appropriate to their chemistry program should be defined prior to implementation of this module. We utilize ChemDraw as our institution has a site license for all interested science students. Student Discussion and Response In-class discussion can revolve around the searches for aspirin (What is an MSDS?; What is an LD50?; Does the data match regardless of source?; How much information is “out there”?; etc.). Particularly fruitful discussions can take place around the students' compound of choice (Why did they choose this compound?; What did they learn that was unexpected?; Were there any new terms that they learned?; How do you get to the literature?; What is a “good” literature source?; etc.). Although not lending itself to formal discussion, student manipulation of the chemical drawing program led them to understand that it did require some practice and just because it can be drawn with the program does not make a structure chemically correct. This series of three modules have been well received. The students' favorite portion of the laboratory was searching for their choice of compound. The diversity of compounds, from medications to natural products, shows the wide variety of interests of our student population. A partial list of the students' compounds is included in the supporting information. Summary Organic chemistry-specific computer-based skills have been successfully integrated into first-semester organic chemistry. Students learned the correct use of online resources, utilized databases, and gained practical experience with a chemical drawing program. Students utilized this skill set throughout the rest of the academic year in lecture, laboratory, and when writing formal lab reports. As computer-based technology continues to evolve, the teaching modules will be updated to reflect such changes. 1076


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1. Tesch, D.; Murphy, M.; Crable, E. Inf. Syst. Educ. J. 2006, 4 (13), 3–11. 2. Google for Educators. http://www.google.com/educators/ p_websearch.html (accessed Jul 2010). 3. (a) Minol, K.; Spelsberg, G.; Schulte, E.; Morris, N. Biotechnol. J. 2007, 2, 1129–1140. (b) Voorbij, H. J. J. Am. Soc. Inf. Sci. 1999, 50 (7), 598–615. 4. (a) Hollenbeck, J. J.; Wixson, E. N.; Geske, G. D.; Dodge, M. W.; Tseng, T. A.; Clauss, A. D.; Blackwell, H. E. J. Chem. Educ. 2006, 83, 1835–1843. (b) O'Reilly, S. A.; Wilson, A. M.; Howes, B. J. Chem. Educ. 2002, 79, 524–526. (c) Ridley, D. D. J. Chem. Educ. 2001, 78, 557–560. 5. Scharberg, M. A.; Cox, O. E.; Barelli, C. A. J. Chem. Educ. 1997, 74, 869–870. 6. Wink, D. J. J. Chem. Educ. 1999, 76, 1479. 7. Borkent, H. ChemInform Devel. 2004, 203–217. 8. (a) Denton, P. J. Chem. Educ. 2000, 77, 1524–1525. (b) Harris, D. C. J. Chem. Educ. 1998, 75, 119-121 and references therein. 9. Davis, T. V.; Zaveer, M. S.; Zimmer, M. J. Chem. Educ. 2002, 79, 1278–1280. 10. Pence, L. E.; Pence, H. E. J. Chem. Educ. 2008, 85, 1449–1452. 11. Taylor, M. R. J. Appl. Crystallogr. 2000, 33, 975–976. 12. Ramos, M. J.; Fernandes, P. A.; Melo, A. J. Chem. Educ. 2004, 81, 72–75. 13. Booth, D.; Bateman, R. C., Jr.; Sirochman, R.; Richardson, D. C.; Richardson, J. S.; Weiner, S. W.; Farwell, M.; Putnam-Evans, C. J. Chem. Educ. 2005, 82, 1854–1858. 14. (a) Bednarski, A. E.; Elgin, S. C. R.; Pakrasi, H. B. Cell Biol. Educ. 2005, 4, 207–220. (b) Boyle, J. A. Biochem. Mol. Biol. Educ. 2004, 32 (4), 236–238. (c) Centeno, N. B.; Villa-Freixa, J.; Oliva, B. Biochem. Mol. Biol. Educ. 2003, 31 (6), 386–391. (d) Feig, A. L.; Jabri, E. Biochem. Mol. Biol. Educ. 2002, 30 (4), 224–231. 15. Li, Z.; Wan, H.; Shi, Y.; Ouyang, P. J. Chem. Inf. Comput. Sci. 2004, 44, 1886–1890. 16. Wang, H. J. Chem. Educ. 2005, 82, 1340–1341. 17. (a) Christensen, S. B.; Franzyk, H.; Frølund, B.; Jaroszewski, J. W.; Stærk, D.; Vedsø, P. J. Chem. Educ. 2002, 79, 765–768. (b) Rosenstein, Ian J. J. Chem. Educ. 2005, 82, 652. 18. ChemINDEX Home Page. http://chemindex.cambridgesoft.com/ (accessed Jul 2010); ChemINDEX, previously ChemFinder.com, is available as a site license at a nominal cost from CambridgeSoft. 19. Sigma-Aldrich Home Page. http://www.sigmaaldrich.com/ united-states.html (accessed Jul 2010). 20. Spectral Database for Organic Compounds SDBS. http://riodb01.ibase. aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng (accessed Jul 2010).


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In the Classroom

21. ACS Publications; Advanced Article Search. http://pubs.acs.org/ search/advanced (accessed Jul 2010). 22. CambridgeSoft; Life Science Enterprise Solutions. http://www. cambridgesoft.com/software/ChemDraw/ (accessed Jul 2010). (b) Bio-Rad; Chemical Structure Drawing-ChemWindow. http://en.bio-soft.net/chemdraw/ChemWindows.html (accessed Jul 2010). (c) Symyx; Isis/Draw. http://www.symyx.com/ products/software/decision-support/isis-draw/index.jsp (accessed Jul 2010). (d) Advanced Chemistry Development; ACD/ChemSketch 12.0 Freeware. http://www.acdlabs.com/products/draw_nom/draw/


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chemsketch (accessed Jul 2010). (e) ChemInnovation Software, Inc.; Network Science-NetSci, Chemistry 4-D Draw. http://www. cheminnovation.com/products/chem4d.asp (accessed Jul 2010). 23. ACS Publications. http://pubs.acs.org/loi/joceah (accessed Jul 2010).

Supporting Information Available The complete procedure for the exercise; a partial list of the students' compounds. This material is available via the Internet at http://pubs.acs.org.


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Technology for the Organic Chemist: Three ... - ACS Publications

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