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Resources edited by
Cost-Effective Teacher
Harold H. Harris University of Missouri–St. Louis St. Louis, MO 63121
Making Student-Acquired Spectra Available via a Web Browser
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Jennifer L. Muzyka* Department of Chemistry, Centre College, Danville, KY 40422; *
[email protected] Ian M. Kaster Departments of Chemistry and Computer Science, Centre College, Danville, KY 40422 Lucas W. Hatcher Department of Computer Science, Centre College, Danville, KY 40422
Spectroscopy is one of the most important topics for introductory organic chemistry students (1). Thus, it is important for students to gain experience solving practice spectral problems and even more important for them to have opportunities to analyze spectra of products that they have prepared in the laboratory. Instructors use a variety of approaches to provide their students with access to spectra. These approaches include online practice problems (2–5), homework assignments (6), spectral simulation (7, 8), access to FIDs that students process to obtain spectra (9, 10), remote access to and printing of spectra (11, 12) and remote acquisition of spectra (13–18). Rationale for This Approach In our department, second-year students in organic chemistry begin using our 300 MHz FT–NMR during the second week of lab in the first semester. We follow a gradual approach similar to that previously described (19). By the end of the first semester of organic lab, the students have enough experience that they can acquire spectra of their products with minimal instructor supervision. They typically acquire their spectra outside of their assigned three-hour laboratory period. With 50–70 students taking an organic chemistry course in a given term, sometimes students must wait to access the instrument. We observe that students tend to spend more time zooming, integrating, and printing spectra than they do actually acquiring them. Thus, we wanted to facilitate the processing part of the task in order to alleviate the bottleneck associated with student access to the instrumentation. Our approach is to make student-acquired spectral data available via a Web browser. In this way, we avoid the need for students to learn how to use additional processing software, for example, NUTS from Acorn NMR (20). Other solutions to this problem have been described. These include: additional Linux workstations with the instrument manufacturer’s software (12), the use of remote access software (21) to access the manufacturer’s software residing on the instrument’s workstation (11), and using the manufacturer’s software on networked computers accessing shared directories (15). Our approach is most like that described by Cancilla (15), except that our shared directories are available via a Web www.JCE.DivCHED.org
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browser from any computer, rather than only on computers with the shared directory explicitly installed. Thus, we have avoided the additional IT labor involved in installing shared directories on computers distributed around campus. Additionally, we have avoided the expense involved with the purchase of additional software or computers. System Logistics We began our work by searching for a way to display JCAMP spectral data through a Web site (22). At the time, we were using the Chemscape Chime plug-in to display the spectra of unknowns for students to gain practice solving spectra of unknowns problems (23). A significant limitation of the Chime plug-in is its inability to show spectra using anything except the Windows OS. We sought a solution that would be equally effective for any operating system and browser. We discovered the SourceForge JCAMP-DX project (24), but it involves a body of code too large to be encompassed in a Java applet. JSpecView was not yet available (25). Thus, our first task was to create a Java applet to display the spectra interactively. An applet was desirable to avoid the need for a plug-in or other specialized software. The freely available Java Runtime Environment (JRE) is likely to be installed on most computers already and it functions using nearly any operating system. Desirable features for the applet included: ability to zoom; display of axes; integrals in 1H NMR (but not 13C NMR or IR); ability to decompress data; display of cursor position to determine peak positions; ability to print spectra; conversion between absorbance and transmittance in IR; ability to copy to the clipboard; ability to save the spectrum as an image file; and the ability to save the JCAMP data. Some of these features (print, copy, save image) required the use of a signed applet due to security concerns. When an unsigned applet is used, certain security restrictions are placed on it, thereby limiting the applet’s access to the client machine. Two of the restrictions that had to be overcome were write access to the local file system (for saving data) and access to system properties (printer access and system clipboard). Another important consideration was that we needed all of this functionality in an applet that is quick and responsive. We used JavaScript as an interface with Java to prevent the applet from
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reloading every time a new spectrum was opened, thus improving response time. Centre College organic chemistry students have been using this Java applet since August 2005 in our Spectral Zoo application (26). The fact that our IR and NMR spectrometers can both save data in the standardized JCAMP format led us to develop an approach to enable students to see their own spectra in a Web browser as well. An important consideration in this project was that the system would need to be maintained by a faculty member (JLM) whose expertise is in chemistry rather than IT, as her undergraduate collaborators graduated in May 2006. We created custom experiments on each of the instruments in order to automatically save the data in the JCAMP format into a directory on the Web server. The computer controlling the infrared spectrometer (Nicolet Avatar 360 with EZ OMNIC 7.2) uses Windows XP Professional. The computer controlling the NMR spectrometer (JEOL Eclipse 300 with Delta NMR v4.3.4) uses Red Hat Linux 7.2. Thus, different approaches were required to share the data from the two different instruments. Samba—an open-source implementation of the file- and print-sharing services used by Microsoft Windows—was used to enable the shares between the Web server (Linux Red Hat Enterprise running Apache’s Web server) and the IR controller (Windows XP Professional), while the native network file system was used to enable the shares to the NMR controller (Linux Red Hat 7). PHP, a powerful Web scripting language, was used to generate the list of JCAMP files from these shares onto the Web site. Outcomes During the first few weeks after the new system was implemented at the beginning of our Spring 2006 term, students encountered problems accessing their spectra. Most of these problems were caused by not having JRE installed on their computers. We created a Web page with answers to frequently asked questions, which has been effective in helping students use the application successfully (27). Students in our instrumental analysis and physical chemistry classes rapidly adopted this tool in their laboratories as well. They used it to access data after completing the experiment and to copy their spectra for use in laboratory reports. The students found it helpful to be able to access their spectra from the network instead of having to come back to the laboratory. The files for this Web-based application (28) include the Java applet as well as the PHP script. Both of these are available in the Supplemental Material.W This approach can be readily adapted for use on other campuses. Users will need to modify experiments on their instruments to export data in the JCAMP format and to enable shares between the instrument computers and their Web server. W
Supplemental Material
A number of files for making student-acquired spectra accessible to students via the Web are available in this issue of JCE Online.
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Literature Cited 1. Alexander, C. W.; Asleson, G. L.; Doig, M. T.; Heldrich, F. J. J. Chem. Educ. 1999, 76, 1294–1296. 2. Merlic, C. G.; Fam, B. C.; Miller, M. M. J. Chem. Educ. 2001, 78, 118–120. 3. Kandel, M.; Tonge, P. J. J. Chem. Educ. 2001, 78, 1208– 1209. 4. Young, P. R. Organic Chemistry OnLine. http:// www.chem.uic.edu/web1/OCOL-II/WIN/HOME.HTM (accessed Aug 2007). 5. Buser, J. Y.; McDoughal, O. M. Chem. Educator 2004, 9, 216– 219. 6. Hart, A. N.; McDougal, O. Chem. Educator 2004, 9, 374– 377. 7. Rummey, J. M.; Boyce, M. C. J. Chem. Educ. 2004, 81, 762– 763. 8. Lundberg, P. J. Chem. Educ. 1997, 74, 1489–1490. 9. Swartz, J. E.; Vojta, G. M.; Erickson, L. E. J. Chem. Educ. 1994, 71, 1069–1070. 10. Vaughn, J. B., Jr. J. Chem. Educ. 2002, 79, 306–307. 11. Dyer, D. Instructions for Remote Access to the NMR from the Chemistry Computer Lab. http://www.science.siu.edu/chemistry/chem343/nmr.html (accessed Aug 2007). 12. Otter, A. NMR News 2004-02. http://nmr.chem.ualberta.ca/ nmr_news/2004-02.htm (accessed Aug 2007). 13. Benefiel, C.; Newton, R.; Crouch, G. J.; Grant, K. J. Chem. Educ. 2003, 80, 1494–1496. 14. Baran, J.; Currie, R.; Kennepohl, D. J. Chem. Educ. 2004, 81, 1814–1816. 15. Cancilla, D. A. J. Chem. Educ. 2004, 81, 1809–1813. 16. James, C. R.; McCann, M. P. J. Chem. Educ. 2003, 80, 221. 17. The EMSL Collaboratory Home Page. http://collaboratory. emsl.pnl.gov (accessed Aug 2007). 18. Grushow, A.; Brandolini, A. J. Chem. Educator 2001, 6, 311– 312. 19. Alexander, C. W.; Asleson, G. L.; Beam, C. F.; Doig, M. T.; Heldrich, F. J.; Studer-Martinez, S. J. Chem. Educ. 1999, 76, 1297–1298. 20. Acorn NMR Home Page. http://www.acornnmr.com/ (accessed Aug 2007). 21. Tatham, S. PuTTY: A Free Telnet/SSH Client. http:// www.chiark.greenend.org.uk/~sgtatham/putty/ (accessed Aug 2007). 22. IUPAC CPEP Subcommittee on Electronic Data Standards. http://www.jcamp-dx.org/ (accessed Aug 2007). 23. MDL Chime. http://www.mdl.com/products/framework/chime/ (accessed Aug 2007). 24. JCAMP-DX Summary Page. http://sourceforge.net/projects/ jcamp-dx (accessed Aug 2007). 25. Lancashire, R. J. JSpecView Applet Specification. http:// jspecview.sourceforge.net (accessed Aug 2007). 26. Muzyka, J. L.; Kaster, I. M. Spectral Zoo. http://web.centre.edu/ muzyka/organic/jmol10/table/JcampIndex.htm (accessed Aug 2007). 27. Muzyka, J. L. ChemServ FAQ’s. http://web.centre.edu/muzyka/ organic/lab/chemServFAQ.htm (accessed Aug 2007). 28. Muzyka, J. L.; Kaster, I. M. Hatcher, L. W. ChemServ. http:// chemserv.centre.edu/ (accessed Aug 2007).
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