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2014 Fall Newsletter

Each Fall the CCCE hosts online discussions of recent work of relevance to the use of computers in chemical education. The authors of each paper are available to discuss their work with the community on the days assigned to their papers, and both the papers and discussion are archived on our site. You do not need to be a member of ACS, CHED or the CCCE to participate in these discussion, but need to set up a free account by contacting the site moderator, Bob Belford at  

 Discussion Schedule

Nov. 4-8              OrganicERs a Growing Online Community, Justin Houseknecht and Jennifer Muzyka

Nov. 10-12          ChemEd X: An Interactive Hub for Chemistry Teachers, Deanna Cullen
Nov. 13-15          CheMarkup Slides and Notes: A Presentation Container for the Virtual Molecular Model Kit, Otis Rothenberg & Thomas Newton

Nov. 17-19          From Demonstrations & Clicker Questions to Guided-Inquiry Activities: Resources for Integrating PhET Chemistry Simulations into Your Course, Emily Moore
Nov. 20-22          Organizing Chemical Safety Information to Support Lab Safety, Ralph Stuart

Nov. 24-26          IYCr2014: Spreading the Word About Crystallography in an International Year, Brian McMahon & Michele Zema
Nov. 27-29          Thanksgiving

Dec. 1-3              The Advantages of Electronic Laboratory Notebook Use in Research Laboratories and Best Practices in Implementation, Jeremy Miller & Earl Beutler
Dec. 4-6              Proteopedia: A Powerful Tool for Biomolecular Communication and a 3D Web Encyclopedia of Biomolecules,  Jaime Prilusky & Joel Sussman

Dec. 8-10            Transforming the Chemistry Lab Notebook with ElementsTM, Layne Morsch
Dec. 11-13          The ChemWiki: A Free Online Substitute for Commercial Chemistry Textbook
Delmar Larsen and Ronald Rusay

The CCCE Newsletter is a free service of the CCCE to the chemical education community and new participants are welcome.


Robert E. Belford

Newsletter Articles

Abstracts of Papers

 Justin Houseknecht and Jennifer Muzyka

The organicERs community ( has been organized to provide an online site where college-level instructors of organic chemistry can share curricular materials and network.  With sponsorship from the NSF-funded Chemistry Collaborations, Workshops and Communities of Scholars program (cCWCS,, we have led two-day workshops in 2013 and 2014.  Workshop leaders and participants have contributed tests, quizzes, syllabi, etc. to the site.  Other organic chemistry faculty members have joined the community, which includes access to discussion forums and an abundance of materials used at a wide variety of institutions

Deanna Cullen

The Chemical Education Xchange (ChemEd X, is an online presence serving mostly high school and community college chemistry instructors. The Journal of Chemical Education hosted some online resources for that group of teachers for many years. The resource was called JCE Online. In 2010, JCE entered into an agreement with American Chemical Society Publications, but JCE Online was left out of that agreement. JCE editors considered alternative housing for the well used resources. They also wanted to use a more interactive platform that would allow for a more dynamic resource hub. ChemEd X went live in 2012 and has been growing ever since.


Otis Rothenberger, Illinois State University; Thomas A. Newton, University of Southern Maine

The Virtual Molecular Model Kit (VMK) was designed as a classroom presentation tool that could provide greater versatility than a classic wooden or plastic model kit. During the development phase of the VMK, the authors of this paper have focused on the technical aspects of the kit, including a recent conversion from Java Jmol to HTML5/JavaScript Jmol (JSmol). In this current paper, the authors get back to VMK basics. The VMK is a communication tool for discussing molecules. This paper describes CheMarkup, a presentation container for the VMK that allows the VMK to become a more complete communication tool. CheMarkup makes use of HTML5 Local Storage to allow the creation of presentations that contain editable slides, VMK models, JME structures, images, and more. Entire presentations can be distributed to students in text format that comes to life when loaded into browser memory via the CheMarkup browser application. The editable presentations are retained in local browser memory until deleted by the browser user.

Emily B. Moore, Yuen-ying Carpenter, Robert Parson, and Katherine Perkins
University of Colorado Boulder

The PhET Interactive Simulations project at the University of Colorado Boulder ( develops interactive simulations in science and mathematics, including over 30 simulations designed for introductory chemistry courses. The PhET project supports teachers in their use of the simulations by providing general and discipline-specific teacher resources. In the summer of 2013, the PhET project organized a diverse working group of five chemistry faculty from four institutions in the United States, each experienced using PhET simulations in different classroom contexts. In collaboration with the PhET project, this working group created classroom resources based on their use of PhET simulations in their introductory chemistry courses (General Chemistry, Preparatory Chemistry, and Physical Science for non-majors). Resources include: 1) Interactive Lecture Demonstration Guides, 2) Clicker Questions, 3) Annotated Presentation Slides, and 4) Guided-Inquiry Activities. Here, we introduce these resources to the community by highlighting a specific example from each category. Each resource is designed to be flexible for teachers to use and adapt to their course needs.

Ralph Stuart, CIH, CCHO
Chemical Hygiene Officer, Keene State College
Secretary, ACS Division of Chemical Health and Safety

The Internet provides easy access to a wide variety of information sources relevant to answering chemical safety questions in the laboratory. However, this information is found in a wide variety of formats with varying audiences and intents. This often means that the quality of the information is difficult to evaluate, organize and use to support risk assessment of laboratory work with hazardous chemicals. The ACS Division of Chemical Health and Safety and Division of Chemical Information are partnering to address this concern by developing a chemical safety ontology, or structured vocabulary of terms associated with chemical hazards and risk assessment and management. The goal of this ontology will be to enable the organization of chemical safety information in a sustainable, scalable, and transferable way. This paper will describe the conceptual basis of this work, including the key stakeholders involved, the information channels they use, and their roles in conducting and overseeing the chemical risk assessments in the laboratory.

Brian McMahon, R&D Officer, International Union of Crystallography
Michele Zema, IYCr2014 Coordinator, International Union of Crystallography

The United Nations declaration of 2014 as the International Year of Crystallography (IYCr2014) provides world-wide opportunities to celebrate and promote crystallography. This is a science spanning many traditional disciplines. It offers incredibly precise analytic techniques and profound understanding into the nature of solid materials. With a long history, it is still producing many Nobel Prizes. The UN proclamation stresses that education about and the application of crystallography are critical in addressing fundamental challenges. However, fundamental courses on crystallography are disappearing from chemistry degree curricula and are almost absent in the developing countries. Among the major goals of IYCr2014 are capacity-building in the developing world, and efforts to promote public outreach and stimulate curriculum development. This article will summarize the activities of IYCr2014 to date, with a particular emphasis on their educational mission, and will relate these to the activities of the International Union of Crystallography.

Jeremy Miller, Earl Beutler and Michelle Driessen

Laboratory Notebooks are an important component and vital tool in the laboratory classroom, where observations, experiments and results are recorded.  For hundreds of years, lab students have employed paper notebooks to maintain their research data and information, but with improved technology and the evolution of data from analog to digital, there has been a migration to digital versions. Electronic Lab Notebooks (ELN) provide an overall digital management solution, while allowing the teachers and TAs to manage, engage, monitor and evaluate their students lab work, all at a lower cost than a traditional paper lab notebook and in real-time.

Electronic lab notebooks have proven to increase student interest, engagement and overall performance in the lab. Results show that students who use electronic lab notebooks are more likely to share with lab partners for better assignment completion; at the same time enhancing the instructor/TA to student communication process, progress monitoring and grading. Additionally, students come to lab more prepared so that more work can be done, and instructors have reported an improvement in lab reports. No more collecting, storing, and distributing paper notebooks.

With the movement from paper to digital, lab classrooms around the world have been experiencing the benefits of upgrading to digital technologies.  ELN’s can also be used as a digital publishing platform for course content.  Instructors have seen the benefits of migrating the publication of their courseware (i.e. lab manual) to within the ELN to create a hybrid lab manual and lab notebook, taking a fraction of the time, cost and effort required to produce traditional paper courseware, while allowing for updates or corrections to content at any time during the course.

To help demonstrate how quick and easy it is to use your existing course assets to create, publish, monitor and grade your lab courses with a simple change from paper to an ELN, we will cover the full life cycle of a course as viewed by both the instructor and their students.   

Jaime Prilusky & Joel L. Sussman,
Weizmann Institute of Science,
Rehovot, Israel

Proteopedia is an interactive resource that facilitates understanding the role of 3D protein structures have in their biological function (Fig. 1). Proteopedia is widely used in scientific research, in the preparation of papers for publication and teaching from secondary level to post-graduate.


Two main facts explain the popularity of Proteopedia in the teaching community: pages specifically designed for and by educators (Teaching Scenes, Tutorials, and Educators' Pages) and the exclusive Proteopedia’s Scene Authoring Tool that enables the creation of rich Jmol 3D scenes with zero learning effort.


Dr. Layne A. Morsch The University of Illinois Springfield, Department of Chemistry, MS HSB 314, One University Plaza, Springfield, IL 62703

We have been using Elements™ in organic chemistry lab to increase engagement and interaction with undergraduate students. Elements™ is a modular and cloud-based scientific collaboration platform. It allows for facile template construction by lab instructors to disseminate laboratory procedures. The sharing of notebooks between students and instructors allows for information exchange, submission of work and grading all in one package. The web-based platform works across devices and allows for uploading of spectra, images, videos, spreadsheets, pdfs and integration of text editing and structure drawing. Student attitudes relating to integration of this new technology will be presented.

Delmar Larsen (UC Davis) and Ronald Rusay (Diablo Valley College), Gregory Allen (UC Davis), Alberto Guzman (UC Davis), Marco Molinaro (UC Davis)

The ChemWiki (http:/ is the largest component of the UC Davis (UCD) STEMWiki Hyperlibrary with six other pseudo-independently operating and interconnected “STEMWikis.” The ChemWiki focuses on augmenting post-secondary chemistry education with the primary goal of developing and disseminating viable online textbook alternatives within a central environment that is both vertically (from advance to basic level) and horizontally (across different fields) integrated and provides students with high quality cost-free textbooks. The project is developed by a consortium of students and faculty across multiple campuses and countries and grows monthly.