Visualization in Chemistry and Education

Chemistry is a multi-dimensional and dynamic world. Yet, it is still taught within the confines of static 2-dimensional media (books, blackboards...). Chemistry is also notorious for its use of abstract concepts and mathematical formalisms. Effective multimedia visualizations can greatly enhance the teaching and learning experience in chemistry.

  “… chemical education demands so much from students. It requires them to understand abstract theories, (sometimes two to explain one phenomenon!), to have mathematical skills, to have experimental skills, … and to visualize in three dimensions given information in two dimensions. And that is just the start.”

D. J. Waddington, “Molecular Visualization in Science Education”, NSF workshop report, 2001.
 

Organic Chemware/ Flashware | Biocomputing | PostDock | News Releases | Publications/Presentations/Conferences

Organic ChemWare

adobe animate logoWe develop innovative web-based interactive learning objects for teaching and learning chemistry using Adobe Animate™ technology. Our Organic ChemWare is the definitive visual solution for learning organic chemistry, bridging the gap between the static imagery of textbooks and the real dynamic world of organic chemistry. Organic ChemWare is a comprehensive collection of 220 interactive learning objects to help visualize chemical structure, organic reaction mechanisms, orbital interactions, and other topics. Designed for both individual study and classroom usage, Organic ChemWare empowers learners while redefining the lecture experience. The collection is 100% HTML5 compliant and runs seamlessly on computers and mobile devices without any third-party plugin. It is available as a web-based subscription, for individual and institutional use through Nelson Education.

chemware sample 1 chemware sample 2

 

Ogilvie textbook coverOrganic ChemWare has been integrated in the new textbook Organic Chemistry: Mechanistic patterns (Ogilvie, Ackroyd, Browning,Deslongchamps, Lee, Sauer, 1st Ed., Nelson Education, 2017, ISBN 017650026-X), the very first introductory organic chemistry title that holistically focuses on a mechanistic approach; an approach that has proven to achieve a deeper understanding of chemical reactivity. This mechanistic approach visualizes reactivity as a collection of patterns in electron movement, making it possible for students to describe why a reaction occurred.

Over 185 ChemWare learning objects are linked to the textbook margins and available for online access.

 

 

 

Flashware

flashwareOrganic Chemistry Flashware was a legacy collection of 135 learning objects for studying organic chemistry created with Adobe Flash™ technology. With an emphasis on the arrow-pushing notation, reaction mechanisms, and orbital interactions, the Flashware collection is still available as a web-based subscription, for individual and institutional use at: http://flashchem.nelson.com

Subsets of the OCF package are electronic supplements to the textbook "Chemistry: Human Activity, Chemical Reactivity" 1st and 2nd Eds. by P. Mahaffy et al.

Biocomputing in drug design

biocompBiocomputing in Drug Design is a series of undergraduate courses that bridge the disciplinary gap between chemistry and computer science, with a focus on computer-assisted drug design.
Designed for classes comprising both science and computer science undergraduate students, the courses comprise web-based interactive multimedia courseware, computer-based molecular modelling and simulation laboratories. To date over 60 biocomputing Flashware animations have been developed for these courses.

 

 

PostDock

postdockPostDock is a new visualization tool for the analysis of molecular docking, an important component of computer-assisted drug design. It processes a numeric database of docking results into an interactive 3D image of multiple ligand docking poses. Both docking energies and docking poses are visually encoded for rapid assessment (energies: transparency scale ; poses: color scale). Written in SVL, PostDock has been integrated into MOE (Chemical Computing Group Inc.) and is used for ligand-protein docking and “reverse-docking” design applications.

 

News Releases

 

Publications/Presentations/Conferences

  • “Organic ChemWare - HTML5 interactives for teaching and learning organic chemistry”, G. Deslongchamps, 100th Canadian Chemistry Conference, Halifax, NS, May 28-June 1, 2017.
  • “Visualizing VB orbital interactions in organic chemistry”, G. Deslongchamps, 98th Canadian Chemistry Conference, Ottawa, ON, June 13-17, 2015.
  • “Organic Chemistry Flashware 2.0 - "Think Tetrahedral”, G. Deslongchamps, 23rd IUPAC International Conference on Chemical Education, Toronto, ON, July 13-18, 2014.
  • “Lab3D.me: Visualizing Organic Chemistry Reactions Online”, M. Burger, M. Corrin, G. Deslongchamps, J. Jenkinson, 23rd IUPAC International Conference on Chemical Education, Toronto, ON, July 13-18, 2014.
  • “Lab3D (www.lab3d.me): A New Web-Based Resource of Interactive, Animated Organic Chemistry Reactions”, M. Burger, M. Corrin, G. Deslongchamps, J. Jenkinson, American Chemical Society, DivCHED CCCE: Committee on Computer in Chemical Education, Fall Newsletter, Nov. 25-27, 2013 (http://www.ccce.divched.org/P10Fall2013CCCENL).
  • “Textbook treatments of electrostatic potential maps in general and organic chemistry” Hinze, S. R., Williamson, V. M., Deslongchamps, G., Shultz, M. J., Williamson, K. C., & Rapp, D. N. J. Chem. Educ. 2013, 90, 1275-1281.
  • “When do spatial abilities support student comprehension of STEM visualizations?“ Hinze, S. R., Williamson, V. M., Shultz, M. J., Williamson, K. C., Deslongchamps, G., & Rapp, D. N.  Cognitive Processing – The International Quarterly of Cognitive Science 2013, 14, 129-142.
  • “Beyond the ball-and-stick: Students’ processing of novel STEM visualizations”, S. R. Hinze, D. N. Rapp, V. M. Williamson, M. J. Shultz, G. Deslongchamps, K. C. Williamson, Learning & Instruction, 2013, 26, 12-21.
  • “Identifying Student Use of Ball-and-Stick Images versus Electrostatic Potential Map Images via Eye Tracking” Williamson, V. M., Hegarty, M., Deslongchamps, G., Williamson, K. C., Shultz, M. J. J. Chem. Educ., 2013, 90, 159-164.
  • “The role of prediction tasks and spatial abilities in the use of macroscopic and particulate representations” S. R. Hinze, V. Williamson, K. C. Williamson, M. J. Shultz, G. Deslongchamps, D. N. Rapp, Abstract, 2012 Biennial Conference on Chemical Education, Penn State, PA, July 29 -Aug. 2, 2012.
  • “Electrostatic potential maps: How are these visualizations used in general and organic chemistry textbooks?” V. Williamson, S. R. Hinze, G. Deslongchamps, M. J. Shultz, K. C. Williamson, D. N. Rapp, Abstract, 2012 Biennial Conference on Chemical Education, Penn State, PA, July 29 -Aug. 2, 2012.
  • “Organic Chemistry Flashware 2.0 - a preview”, G. Deslongchamps, 22nd International Conference on Chemical Education, 11th European Conference on Research in Chemical Education, Rome, Italy, July 15-20, 2012.
  • “Organic Chemistry Flashware – Lessons from the GRC on visualization in science and education” G. Deslongchamps. Abstract, 243rd American Chemical Society, National meeting, San Diego, CA, March 25-29, 2012.
  • “Spatial Abilities Influence the Use of Dynamic Chemistry Visualizations.” S. Hinze, D. N. Rapp, V. M. Williamson, M. J. Shultz, K. C. Williamson, G. Deslongchamps, Annual Convention of the Association for Psychological Science, Washington D.C, 2011.
  • “Unlocking potential: Individual differences in the use of concurrent scientific visualizations.”, S. R. Hinze, D. N. Rapp, V. M. Williamson, M. J. Shultz, K. C. Williamson, G. Deslongchamps, G., Proceedings of the Annual Conference of the Cognitive Science Society, 2011.
  • “What visualizations are students able to use successfully?” V. M. Williamson, S. R. Hinze, K. C. Williamson, M. J. Shultz, G. Deslongchamps, D. N. Rapp. 241st American Chemical Society, National meeting, Anaheim, CA, March 27-31, 2011.
  • “Identifying Representational Competence with Multi-Representational Displays”, M. Stieff, M. Hegarty, G. Deslongchamps, Cognition & Instruction, 2011, 29(1), 123-145.
  • "Organic Chemistry Flashware – A closet developer's story" G. Deslongchamps ,Purdue University ,Lafayette, IN, Dec. 1, 2010.
  • "Nelson Education presents: Organic Chemistry Flashware – Bring learning to life and life to learning" G. Deslongchamps, 93rd CSC Conference, Toronto, ON, May 29 – June 2, 2010. Sponsored by CSC and Nelson Education Inc.
  • "Organic Chemistry Flashware – Visualizing and Interacting with the Unseen", Association of Atlantic Universities Teaching Showcase, Acadia U., Oct. 24, 2009.
  • “Animating localized orbital interactions with organic chemistry Flashware” G. Deslongchamps. 238th ACS National Meeting, Washington, DC, Aug. 16-20, 2009.
  • "Visualization in Science and Education", Gordon Research Conferences, July 26-31, 2009, Oxford University, UK, conference vice-chair.
  • “PostDock: A Novel Visualization Tool for the Analysis of Molecular Docking”, E. A. Wiley, G. Deslongchamps, Computing and Visualization in Science, 12, 1-7, 2009.
  • IM2.4, “Image and Meaning” forum, Harvard University, USA, Oct. 25-26, 2007, participant.
  • "Visualization in Science and Education", Gordon Research Conferences, July 1-5, 2007, Bryant University, RI, USA, invited workshop coordinator.
  • "Organic Chemistry Flashware: an academic closet developer’s story” G. Deslongchamps, 28th National McGraw-Hill Ryerson Teaching, Learning & Technology Conference, Saskatoon, SK, Nov. 1-3, 2006.
  • "Image and Meaning 2: Discovering new visual expressions for science and technology", June 23-25, 2005, Getty Center, Los Angeles, CA, invited participant.
  • “Animating localized orbital interactions with organic chemistry Flashware” G. Deslongchamps. PacifiChem 2005, Honolulu, HI, December 15-20, 2005.
  • "Visualization in Science and Education", Gordon Research Conferences, July 3-8, 2005, Oxford University, UK.
  • "Visualization in Chemistry for the Major and the Non-Science Major", Pacifichem 2005, December 15-20, Honolulu, HI.
  • “The Visualization of Linear Algebra Algorithms In Apt Apprentice”. Andrews, C., Cooper, R., Deslongchamps, G., Spet, O., Proceedings of the International Conference on Computational Science 2005 , V.S. Sunderam et al. (Eds.), LNCS , Vol 3514, pp. 1011-1018, Springer-Verlag, Berlin, 2005.
  • “Animating orbital interactions in Flash”, G. Deslongchamps, Gordon Research Conference: “Visualization in Science and Education”, Queen’s College, Oxford, UK, July 3-8, 2005.
  • “Organic Chemistry Flashware: Animating reaction mechanisms and orbital interactions in Flash”, G. Deslongchamps, Department of Chemistry, University of Wisconsin-Madison, WI, April 25, 2005;
  • “Organic Chemistry Flashware: Animating reaction mechanisms and orbital interactions in Flash”, G. Deslongchamps, Beloit College, WI, April 26, 2005, Invited lecturer
  • "Methodology development with MOE: PostDock, Reverse-Docking, SPLASH and LGA-Dock” G. Deslongchamps, 1st North American User Group Meeting, Chemical Computing Group Inc., Montreal, May 26-28, 2004.
  • "Animating reaction mechanisms and orbital interactions in Flash”, G. Deslongchamps, Gordon Research Conferences: “Visualization in Science and Education”, Queen’s College, Oxford, UK, July 20-25, 2003.
  • "PostDock: A Novel Visualization Tool for the Analysis of Molecular Docking”, E. A. Wiley and G. Deslongchamps, Gordon Research Conferences: “Visualization in Science and Education”, Queen’s College, Oxford, UK, July 20-25, 2003.
  • "Macromedia Flash”, G. Deslongchamps, Pre-Conference Workshop, Gordon Research Conference: “Visualization in Science and Education”, Queen’s College, Oxford, UK, July 18-20, 2003Invited workshop.
  • “Visualisations scientifiques avec multimedia Flash" Département de Chimie, Université Laval, March 20, 2003.
  • "Web-Based Chemistry Flashware: transparent teaching and learning tools", G. Deslongchamps, Department of Chemistry, University of Pittsburgh, PA, February 18, 2003.
  • "Web-Based Chemistry Flashware: transparent teaching and learning tools", G. Deslongchamps, National Science Foundation, Arlington, VA, December 16, 2002.
  • "Biocomputing in Drug Design: Bridging the Disciplinary Gap with Web-Based Interactive Multimedia Courseware”, C. Andrews, A. Deschênes, R. Cooper, and G. Deslongchamps, Gordon Research Conference: “Computational Chemistry”, Colby College, NH, June 30-July 5, 2002.
  • "Biocomputing in Drug Design: Visualization of cross-disciplinary topics with web-based Flash multimedia courseware", C. Andrews, A. Deschênes, R. Cooper, and G. Deslongchamps, Abstract,85th   CSC Conference, Vancouver, BC, June 1-5, 2002.
  • "Biocomputing in Drug Design I: Bridging the disciplinary gap with MOE and web-based interactive multimedia courseware", C. Andrews, M. Castonguay, A. Deschênes, D. Norman, G. Deslongchamps and R. Cooper, Abstract, Cambridge Healthtech 2nd Annual Conference on "Structure-Based Drug Design", Cambridge, MA, April 18-19, 2002. view poster
  • "Biocomputing in Drug Design I: Visualization of cross-disciplinary topics with web-based Flash multimedia courseware", G. Deslongchamps, 6th Annual Atlantic Universities Teaching Showcase, Mount Allison University, NB, Oct. 27, 2001.
  • "Biocomputing in Drug Design I: Bridging two disciplines with MOE, Flash and Maple" , Deslongchamps, G., R. Cooper, Gordon Research Conferences: “Science Education and Visualization: International”, Mt-Holyoke College, MA, Aug. 5-10, 2001.

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