News from Online: What's New with Chime?

molecules, and giant macromolecules—all can be viewed in several formats, including ball-and-stick and spacefilling. Create your own Web pages. Use ...
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Chemical Education Today edited by

Reports from Other Journals

Carolyn Sweeney Judd

News from Online: What’s New with Chime?

Houston Community College Houston, TX 77004

by Liz Dorland

Interactive Molecules Using the Chime Plugin The Chime plugin (pronounced like the bells) provides a simple route to presenting interactive molecular structures to students via the Internet or in classroom presentations. Small inorganic molecules, ionic structures, organic molecules, and giant macromolecules—all can be viewed in several formats, including ball-and-stick and spacefilling. Create your own Web pages. Use some of the many student tutorials that are already online. Highlight regions of a protein. Click on a peak on an IR spectrum and relate it directly to a vibration in a molecule. Access databases of structures in the .pdb file format used by Chime. Whether you want to illustrate visual concepts such as molecular geometry, stereochemistry, organic reaction mechanisms, or protein and DNA structure, Chime has something for you! Chime Resources If you are new to Chime, the best place to start is with some of the Chime resource pages that describe how to manipulate structures with the mouse (a skill your students will need to have as well). Try William McClure’s Chime Features Demo using the ATP molecule as an example (1). To develop your own Chime Web pages, visit Harry Unger’s extensive Chime Web site (2) with basic Chime instructions plus tutorial exercises for organic chemistry students and instructions for developers. Eric Martz has a Web site (3) with a list of biochemistry tutorials such as protein secondary structure as well as information for programmers on how to develop with Chime. The Online Macromolecular Museum (4), developed by David Marcey and his students at Kenyon College and California Lutheran University, has directions for using and developing with Chime plus a collection of biochemical structures arranged by type. Enter the Hall of DNA, or perhaps the Hall of Virology to see the structure of HIV-1 protease. The Chime plugin was developed at MDL Information Systems (MDLI), based on the program Rasmol written by Roger Sayle. Go to the MDLI Web site (5) to download the plugin and to find additional links and tutorials using Chime. Materials for Student and Classroom Use Since their beginnings in the mid-90s, tutorials for students based on Chime have increased in number and complexity. My own Chemistry Tutorial and Resource Page (6) was created in September 1996, and many links have been added since then. The links are organized by major content: organic, biochemistry, and general chemistry. Most of the links discussed in this article and many more can be found on this page. There is also a link to the Beginner’s Guide to Chime that I wrote as a reference guide while I was learning to use Chime, so that I could refer back to it over time. I’ll

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Side-by-side Chime windows to compare amino acid structures by Duane W. Sears, http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tw-amn/tabs-standard-frames.htm (accessed May 2002).

describe some of my favorite tutorials, but there are so many good ones that it is hard to choose. For introductory and general chemistry students, an excellent VSEPR tutorial can be found at John Nash’s site (7). He has written other tutorials, including a unit on coordination chemistry. The site also contains a library of crystal structures showing the unit cell and extended crystal structure of several ionic compounds and covalent molecules (8). Many tutorials are directed toward organic chemistry students. Dan Berger has a tutorial that uses Chime structures to illustrate the use of molecular model kits (9). Frank Gorga’s tutorial (10) includes isomerism, chirality, and absolute configuration. Explore mirror images by rotating structures in side-by-side windows. Concepts of conformation, stereochemistry, reaction mechanisms, and spectroscopy are illustrated with structures and animations on Jennifer Muzyka’s Web site (11). Hans Borkent at the University of Nijmegen in the Netherlands (12) has one of the largest Chime-based organic chemistry Web sites: it has more than 20 topics with Chime structures and animations. In addition, a student can use a molecular editor to construct animations of reactions and their corresponding energy plots. Robert Lancashire (13a) and Paul Lahti (14) have Web pages that utilize Chime to display an organic molecule and then link it to an IR spectrum. Clicking on a peak in the spectrum causes the molecular structure to vibrate in the proper mode. Biochemistry students will find extensive sets of tutorials and biochemical macromolecules at the Web pages of Charles Grisham (15) and Eric Martz (3). Martz’s Protein Explorer allows a student to isolate and examine various regions of the protein structure, viewing them in various formats including backbone and ribbons for primary and secondary structure. Duane Sears (16) uses side-by-side Chime windows to compare amino acid structures. His extensive tutorial includes hemoglobin, enzymes, nucleic acids, and a quiz function.

Journal of Chemical Education • Vol. 79 No. 7 July 2002 • JChemEd.chem.wisc.edu

Chemical Education Today

Reports from Other Journals

Structure library with multiple viewing options by Robert Lancashire, http://wwwchem.uwimona.edu.jm:1104/spectra/PDBIndex.html. (accessed May 2002).

Organic molecules displayed with physical data by Paul R. Young, http://www.chem.uic.edu/web1/OCOL-II/WIN/LIBRARY/ FRAMES.HTM (accessed May 2002).

Structure Libraries

structures. Flick Coleman’s alphabetical listing of molecules (21) includes small inorganic molecules and ions as well as organic structures. Some structure libraries have molecular viewers with more extensive features. Paul R. Young’s Organic Chemistry Online (22) includes control buttons for the structure display as well as physical data and NMR spectra. Robert Lancashire (13b) has four types of viewers depending on your browser and computer’s capability. William McClure’s Molecules for Modern Cell Biology (1) includes DNA, RNA, and proteins. Each of these has buttons to interactively illustrate structural features.

One final type of Chime site is the database or structure library. Molecular coordinate text files in the .pdb format can be downloaded. The Chime plugin provides the visual display. Gerard Depuis (17) and Scott Wherland (18) have lists of inorganic compounds and complex ions suitable for illustrating bonding and VSEPR concepts. Another great site is Dave Woodcock’s Molecular Models from Chemistry (19), which has more than 1400 molecules organized by organic functional group. A. C. Pratt’s Molecular Viewing Gallery (20) has side-by-side windows for comparison of two organic

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Journal of Chemical Education • Vol. 79 No. 7 July 2002 • JChemEd.chem.wisc.edu

Chemical Education Today

Reports from Other Journals Conclusion Whether you use only the already available tutorials and structure libraries for your students, or write your own materials, both you and your students will benefit. Chime is at present compatible with Netscape 4.x (not 5.x) and Internet Explorer 5.x (not 6.x). Check the MDLI Web site (5) for the latest compatibility information and the most recent version of Chime. Enjoy! Liz Dorland is in the Physical Science Department, Me s a C o m m u n i t y C o l l e g e , Me s a , A Z 8 5 2 0 2 ; [email protected]

World Wide Web Addresses

Crystal Structure Library from Visualization and Problem Solving by John Nash and William R. Robinson, http://www.chem.purdue.edu/ gchelp/ (accessed May 2002).

Chime Resources

a) http://wwwchem.uwimona.edu.jm:1104/spectra/iranim/

2. Harry Unger, Cabrillo College http://c4.cabrillo.cc.ca.us/

b) http://wwwchem.uwimona.edu.jm:1104/spectra/ PDBIndex.html

3. Eric Martz, University of Massachusetts http://www.umass.edu/microbio/chime/ 4. David Marcey, California Lutheran University http://www.clunet.edu/BioDev/omm/gallery.htm 5. MDL Information Systems, MDLI http://www.mdlchime.com/chime/ 6. Liz Dorland, Mesa Community College http://www.mc.maricopa.edu/~dorland/chime.html Materials for Student and Classroom Use Introductory and General Chemistry 7. John Nash, Purdue University http://www.chem.purdue.edu/gchelp/ 8. William Robinson, Purdue University http://www.chem.purdue.edu/gchelp/crystals/ Organic Chemistry 9. Daniel J. Berger, Bluffton College http://www.bluffton.edu/~bergerd/Models/

14. Paul Lahti, University of Massachusetts http://www.chem.umass.edu/~nermmw/Spectra/ vibtutor.htm Biochemistry 15. Charles M. Grisham, University of Virginia http://cti.itc.Virginia.EDU/~cmg/ 16. Duane W. Sears, University of California, Santa Barbara http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/ tw-amn/tabs-standard-frames.htm Structure Libraries Inorganic 17. G. Dupuis, Lycée Faidherbe de Lille http://www.faidherbe.org/site/cours/dupuis/ banque.htm 18. Scott Wherland, Western Washington State http://www.wsu.edu/~wherland/wwwlist01.htm Organic and biochemistry

10. Frank Gorga, Bridgewater State College http://webhost.bridgew.edu/fgorga/Stereochem/ default.htm

19. Dave Woodcock, Okanagan University http://people.ouc.bc.ca/woodcock/molecule/ molecule.html

11. Jennifer Muzyka, Centre College http://web.centre.edu/~muzyka/organic/organic.htm

20. A. C. Pratt, Dublin City University http://www.dcu.ie/~chemist/pratt/JGallery/ JGallery.htm

12. Hens Borkent, University of Nijmegen http://www.cmbi.kun.nl/wetche/organic/

access date for all sites: May 2002

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13. Robert Lancashire, University of the West Indies

1. William McClure, Carnegie Mellon http://info.bio.cmu.edu/Courses/BiochemMols/

21. Flick Coleman, Wellesley College http://www.wellesley.edu/Chemistry/Flick/molecules/ newlist.html 22. Paul. R. Young, University of Illinois, Chicago http://www.chem.uic.edu/web1/OCOL-II/WIN/ LIBRARY/FRAMES.HTM

Journal of Chemical Education • Vol. 79 No. 7 July 2002 • JChemEd.chem.wisc.edu