Computation and Visualization
for Chemistry Educators and Students
at the Institute for Chemistry Literacy
Through Computational Science (ICLCS)
Jay Mashl
National Center for Supercomputing Applications
GK-12 Workshop
August 11, 2009
Goals of the ICLCS
* Strengthen rural high school teachers' and students' understanding
of chemistry within the context of 21st-century research.
+ medicinal chemistry (biomedicine)
+ materials science, including nanotechnology
+ agricultural chemistry
+ computational aspects of molecular-level chemistry
* Increase teachers' use of, and comfort with, computational and
visualization tools.
* Create a cadre of teacher-leaders who will become advocates for
excellence in science education.
* Promote institutional change in the university and school district
partners.
* Expansion to less-rural school districts
....thereby promoting sustainability
Quick Facts
93 rural Illinois school districts
~100 high school chemistry teachers
~3,750 students
Basic High school curriculum (as relates to this talk)
geometries of small compounds
2-D representations; 3-D in 2-D; hand-built 3-D models
types of bonds
polarity of molecules
intermolecular forces
physical properties (e.g. surface tension, boiling point trends)
atomic orbitals
molecular orbitals
thermodynamics (e.g. heats of formation)
Design and Approach
We provide access to and training with modern computational
and visualization tools
Use of free software when possible
ICLCS Fellows incorporate tools into their (existing) curricula
to stimulate students' computational thinking.
Student can use the tools for inquiry-based learning about
the world around them.
Tools
1. Spreadsheets (Microsoft Excel/OpenOffice Calc)
2. ChemSketch
3. WebMO
4. Molecular Workbench
5. VenSim
6. Boltzmann 3D
Web Resources
7. Instit. for Chem. Literacy through Comput Sci (ICLCS)
-- Molecular Animations
8. Computational Science Educ Ref Desk (CSERD)
9. National Science Digital Library (NSDL)
Tools Matrix (part 1)
Http: /// iclcs.uiuc.edu / gk12 / ToolsMatrix.pdf
Tools Matrix (part 2)
Http: /// iclcs.uiuc.edu / gk12 / ToolsMatrix.pdf
1. Spreadsheets (Microsoft Office, or openoffice.org)
A table of values that are related through forumlas.
Examples of use:
a. Generate visual representations of data
(data plots, bar graphs, etc.)
b. “Slider bars” allow the user to adjust interactively
the value of a variable with a range.
Sample uses:
Stoichiometry, Equilibrium, Reactions,
Integrated rate laws, limiting reagents
2. ChemSketch
(http :// www. acdlabs. com / download )
http://www.acdlabs.com/download/
--- Free(ware) for educational use
Draw molecules in 2D
Manipulate and visualize molecules in 3D
Name structures according to IUPAC
Export complex structures for use in other
programs (e.g., WebMO)
3. WebMO
(http :// webmo. ncsa. uiuc. edu; also www. webmo. net)
* Draw molecules
* Compute molecular properties using fundamental quantum
mechanical methods
* Compute IR (vibrational) and UV-Vis spectra
* Visualize geometries and properties in 3D
* Make connections between molecular structure & properties
+ inquiry-based molecular design (e.g., dyes, indicators,
sunscreens)
+ insight into biological cell receptor function (i.e., polarity)
+ computational insights into contemporary issues
(e.g., greenhouse gases, energy content of food & fuels)
Requirements: Web browser, JavaScript, Java(*), Internet access
(or local WebMO server install (advanced))
*NOTE: some sysadmins block Java
4. Molecular Workbench
(http :// mw . concord . org )
* A repository of applets in the areas of chemistry, biology,
molecular biology, physics, materials science, engineering,
technology
Go to http :// mw . Concord . Org
→ Download
(What to click may depend on operating system;
we'll work with you.)
* Requires Java, but a fully offline version is possible
* Some applet are editable
* Instructors & students may create free accounts
* Instructors can create tests and collect and analyze student data
5. VenSim PLE
(http :// www . vensim . com )
* Allows graphical design and study of dynamic models
(for chemistry, e.g., one can follow the time progression of
species concentrations during a reaction)
6. Boltzmann 3D
(http :// www . chem . byu . edu / Site / Boltzmann3D
* hands-on kinetic theory demonstrator that show link between
molecular motion and macroscopic properties
* requires Java
Web Resources
7. Instit. for Chem. Literacy through Comput Sci (ICLCS)
http: // iclcs . uiuc . edu
Chemistry simulations provided→
http :// iclcs. uiuc. edu / simulations.html
• sodium
• chloride
• water
* Time progresses
A through D
Web Resources
8. Computational Science Educ Ref Desk (CSERD)
http :// www . shodor . Org / refdesk
9. National Science Digital Library (NSDL)
http :// nsdl . org
Workshop Resources
http :// iclcs . uiuc . edu / gk12
Try WebMO yourself: Http :// webmo.ncsa.uiuc.edu
Login: gk12_01, gk12_02, ..., gk12_30
Pw: password