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2006 Spring ConfChem: Web-Based Applications for Chemical Education: Experiences and Visions

05/05/06 to 06/20/06
Robert E. Belford Department of Chemistry University of Arkansas at Little Rock Little Rock, AR 72204-1099 Robert M. Hanson Department of Chemistry, St. Olaf College 1520 St. Olaf Ave, Northfield, MN 55057
Web-based applications have had, and will continue to have, a profound impact on chemical education.  This online conference will bring together a variety of presentations representing recent work in this important field of chemical education.Paper 1A
Schedule of Papers
Paper 1A. Are chemistry instructors and students ready for an internet-based text?
Mark Bishop
(Monterey Peninsula College)
Paper 1B. Progress towards a holistic web: integrating open-source programs, semantic data, wikis and podcasts
Henry Rzepa (Imperial College London)

Marion Cass
(Carleton College)

Paper 2A. JSpecView: Developing spectroscopic representations on the web
Robert John Lancashire
(University of West Indies, Mona)
Paper 2B. Jmol: Open-source molecular visualization and analysis
Robert M. Hanson
St. Olaf College)

Egon Willighagen
(Cologne University Bioinformatics Center)

Nicolas Vervelle, Timothy Driscoll

Miguel Howard
(Jmol Project

Paper 3A. ChemPrep: Self-paced OWL preparation for first semester general and organic chemistry
Beatrice Botch, Roberta Day, William Vining, Stephen Hixson, Peter Samal, Barbara Stewart, David Hart
(University of Massachusetts, Amherst)

Kenneth Rath, Alan Peterfreund

Paper 3B. BestChoice, a model for interactive web-based teaching
Sheila Woodgate and David Titheridge
(University of Auckland)
Paper 4A. Creation of an online stoichiometry course that melds scenario based leaning with virtual labs and problem-solving tutors
David Yaron, Jordi Cuadros, Mike Karabinos
(Carnegie Mellon University)
Paper 4B. JChemPaint viewer and editor applets: Interactive 2D molecular diagrams
Stefan Kuhn, Tobias Helmus, Egon Willighagen and Christoph Steinbeck
(Cologne University Bioinformatics Center)
Paper 5A. Using InterChemNet for lab curriculum development and evaluation
Barbara Stewart, Robert Kirk, Francois Amar, and Mitchell Bruce
(University of Maine)
Paper 5B. The Science of Spectroscopy: Collaborative curriculum development using a wiki
Stewart Mader (Brown University)
Paper 6A. Tools for performing organic reaction mechanisms over the web
ohn Penn
(West Virginia University)

Christoph Steinbeck
(Cologne University)

Ada Casares
(Richard Stockton College)

Paper 6B. The Green Chemistry Assistant: a new concept in web applications
Robert M. Hanson
(St. Olaf College)
Paper 7A. WebMO: Web-based, state-of-the-art, and cost-effective computational chemistry
William F. Polik and Jordan R. Schmidt
Paper 7B. GEMs for chemists: a community-based approach to develop greener education materials
Julie Haack
(University of Oregon)

Irvin Levy
(Gordon College)

Paper 8A. Improving safety comprehension through hypertext: the MSDS HyperGlossary
Robert Toreki (Interactive Learning Paradigms, Inc.)
Robert E. Belford  (University of Arkansas at Little Rock)
Paper 8B. Teaching chemistry with Moodle
Fred Senese
(Frostburg StateUniversity)
Paper 8C. Expanding the role of the organic chemistry teacher through podcasting, screencasting, blogs, wikis and games
Jean-Claude Bradley (Drexel University)

Conference Articles

Abstracts of Papers:

Henry Rzepa
Imperial College London

Marion Cass
Carleton College


The way educators typically use the Web to support their teaching in 2006 is arguably a regression from many of the ideals first anticipated in 1994. Time pressure, a reluctance to learn "difficult HTML", and pressure from the publishing industry has allowed the Web to retreat into "shrink-wrapped" black holes known as Acrobat files. An ever greater reluctance (by both authors and publishers) to appreciate the importance of deploying meta-data in a meaningful manner means that most often, these Acrobat files represent the bones lying in an information graveyard, stripped of any "reusability" and really fit only for printing (e-books have yet to take off in any significant sense). In our article (we hesitate to perpetuate the above by calling it a "paper"!) we discuss two particular themes. Firstly, how a greater emphasis on data capture and its re-usability, together with the use of open-source software such as the remarkable Jmol, can result in a much more meaningful and future-proofed way of presenting chemical knowledge to students. We illustrate this via two resources, one designed to introduce symmetry to chemistry students, the other a dynamical introduction to pseudorotation in fluxional molecules. These can be viewed at and Secondly, we address the issue of how to create holistic resources and to overcome the reluctance of stressed and pressured academics by discussing two recent phenomena, that of the "Wiki" and the "Podcast". The Wikipedia is perhaps the best known illustration of how a community can coalesce and produce something far greater than the sum of its parts. Podcasting, which seems to be taking off in chemistry, focuses on audio and video content, but seems divorced from other forms of content, and is currently rather less than holistic. Currently, these two broad themes about how the Web should evolve are more or less developing independently. The prospects of coalescence are discussed.

Prof Robert John Lancashire
Department of Chemistry, University of the West Indies, Mona Campus, Kingston 7, JAMAICA Email


In 1997, we began collaboration with MDL Information Systems Ltd and incorporated our spectroscopy (JCAMP-DX) viewer code into MDL Chime. By 2005, when the contract ended, MDL had had over 2 million downloads of the free version of the browser plug-in. In 2006, we followed up with the release of JSpecView (, a JAVA based spectroscopy viewer, which can be run as an applet from a web page or as a standalone application. There are several expected uses of JSpecView, and in this presentation I will demonstrate examples where the applet can be used in a teaching environment for the interpretation of IR, MS and NMR spectra, delivery of spectral unknowns and in a laboratory setting in combination with Jmol and another JAVA applet for characterisation of visible spectra with Tanabe-Sugano diagrams.

Robert M. Hanson
St. Olaf College

Egon Willighagen
Cologne University Bioinformatics Center

Nicolas Vervelle, Timothy Driscoll

Miguel Howard
Jmol Project


Jmol ( is free software for displaying interactive 3D molecules. It is designed as a component that can be used as a standalone application, as an applet within the context of a web page, or as a display subsystem within a more sophisticated software package. Because it is written in Java and requires no special graphics hardware, Jmol runs on all major operating systems and web browsers. Jmol has been developed as a collaborative project using standard open-source software development methodologies and procedures. All source code is publicly available under the GNU licenses, facilitating experimentation, testing, public contributions, and peer review. Rendering representations can be controlled using an extended version of the RasMol scripting language. The Jmol applet allows web content developers to display interactive 3D representations of molecules within web pages, providing an upgrade path for users of the Chime web browser plugin. New capabilities are being added to Jmol on an ongoing basis. As Jmol has matured over the past few years, it has become an increasingly popular component in computer based molecular visualization. We expect Jmol's popularity to continue to grow as we continue to build into it additional new features, many of which will be demonstrated in this presentation.

Beatrice Botch, Roberta Day, William Vining, Stephen Hixson, Peter Samal,
Barbara Stewart Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003

Kenneth Rath, Alan Peterfreund
Peterfreund Associates, Amherst, MA 01003

David Hart Department of Computer Science
University of Massachusetts Amherst, Amherst, MA 01003


Two self-paced chemistry courses were written to help improve student preparedness for first semester General and Organic Chemistry. These courses are delivered over the web using the OWL (Online Web-based Learning) system developed at the University of Massachusetts. The courses are designed to take ten to twenty hours to complete and are offered prior to the start of the semester. ChemPrep/General Chemistry covers topics such as matter, algebra, significant figures, nomenclature and dimensional analysis. ChemPrep/Organic Chemistry covers concepts such as Lewis structures, formal charge, geometry, hybridization and acid/base theory. Evaluation studies of the Spring 04 and Fall 04 semesters show that for those students who completed more than half of the ChemPrep units, course grades and retention rates in the subsequent chemistry courses were higher. The content, implementation, and evaluation of the ChemPrep courses is discussed.

Sheila Woodgate and David Titheridge
The University of Auckland, Auckland, New Zealand


The BestChoice online tutorial system designed by the authors has been used since 2002 in New Zealand to support both first-year university students and high school students in their learning of chemistry (4000 active users in 2005). 80 modules with content appropriate to the above cohorts have been written. In total there are 2500 screen views and 6000 possibilities for interaction generating feedback available. A selection of these can be viewed at by clicking on the DEMO MODE link.

The primary focus of BestChoice modules is interactive teaching using a programmed learning approach. We have made major strides in developing methods to simulate on screen pen-and-paper solutions to multistep problems. The paper will describe
factors taken into account in the design and implementation of BestChoice
our experience incorporating use of BestChoice into first year university and high school courses
how evaluation by over 8000 users has provided validation of the approach taken in BestChoice modules as well as useful insights for future work

David Yaron, Jordi Cuadros, Mike Karabinos
Carnegie Mellon University)


This paper will discuss an online review course in stoichiometry aimed at students who are about to enter college chemistry and need a review of this important foundation material. The course uses the ChemCollective's virtual lab ( and the course delivery and problem solving tutor tools of Carnegie Mellon's Online Learning Initiative ( The course is set in the context of arsenic contamination in the groundwater of Bangladesh. This scenario highlights the utility of stoichiometry concepts in a real world problem and allows us to, as the course progresses, shift the theme to the challenges facing modern analytical chemistry. The course contains 15 modules ranging from the mole and molecular weight up through reaction stoichiometry, empirical formula and limiting reagents. Modules typically start with a video explaining the concepts followed by a few simple tutors that serve as interactive worked examples and then either a virtual lab or more extensive problem solving tutor. Our experiences with creating and evaluating this course will be discussed.

Fred Senese
Frostburg State University


Moodle ( is a free, open-source course management system that emphasizes community building, critical reflection, and collaborative work. It provides a powerful array of tools not found in many commercial course management systems. It includes facilities for web publishing, equation typesetting, content management, adaptive prelabs and lessons, parameterized and hierarchical homework banks, Flash and SCORM learning objects, assessment, detailed student tracking, and record-keeping. Moodle is under active development, and is supported by a large community of system administrators, teachers, researchers, instructional designers and developers. Being open source, the code can easily be modified to suit specific needs, and Moodle can run on any server capable of running PHP and MySQL.

Moodle has been used to teach chemistry at all levels of the curriculum at Frostburg State University for the last two years. In this paper, I'll outline the tools and features of Moodle, and demonstrate their application in our general chemistry, physical chemistry, and environmental chemical analysis courses. I'll also discuss the impact that Moodle has had on classroom dynamics and pedagogy in laboratory, lecture, and workshop settings.

Stefan Kuhn, Tobias Helmus, Egon Willighagen and Christoph Steinbeck
Cologne University Bioinformatics Center, Germany


JChemPaint ( is an open-source 2D structure editor for which recently two applet versions have been developed. One is a smaller viewer-only applet; the other is a larger editor applet. Based on the Chemistry Development Kit (CDK), the applet is quite rich in features, including 2D rendering of molecules and reactions, popup labels on atoms, structure diagram generation (diagram cleanup), optional use of templates, input/output capability including Chemical Markup Language (CML), SMILES, MDL molfile and many others, undo/redo capability, and much more. An installation of the editor applet is available on The NMRShiftdb application ( uses both the editor and the viewer applets. Being open-source, the JChemPaint applet can be customized for specific educational applications. Application scenarios in education as well as access information for interested users and potential contributors will be provided.

Barbara Stewart, Robert Kirk, Francois Amar, and Mitchell Bruce
University of Maine


InterChemNet (ICN, is a web-based laboratory management and curriculum delivery system that incorporates spectroscopic instrumentation, student choice, and assessment of student learning. Data from studies evaluating spectroscopy curriculum modules in terms of assessment of student learning are presented. We discuss the use of ICN as a tool for action research in the laboratory setting, focusing on two modalities that can be facilitated with this technology: parallel curriculum improvement cycles and multi-campus assessment.

Stuart Mader


A wiki can be thought of as a combination of a web site and a Word document. At its simplest, it can be read just like any other web site, with no access privileges necessary, but its real power lies in the fact that groups can collaboratively work on the content of the site using nothing but a standard web browser. The wiki is gaining traction in education, as an ideal tool for the increasing amount of collaborative work done by both students and teachers. Students might use a wiki to collaborate on a group report, compile data or share the results of their research, while faculty might use the wiki to collaboratively author the structure and curriculum of a course, and the wiki can then serve as part of each person's course materials. Recently I've converted The Science of Spectroscopy, a well-known educational web site (, into a wiki so that the growing number of readers can now become writers and collaboratively build a richer and more useful tool. I'll demo the site, give a brief online tutorial on how to edit it, and provide any CONFCHEM participant an account to edit the wiki.