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 WorkshopAugust 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

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 compounds2-D representations; 3-D in 2-D; hand-built 3-D modelstypes of bondspolarity of moleculesintermolecular forcesphysical properties (e.g. surface tension, boiling point trends) atomic orbitalsmolecular orbitals thermodynamics (e.g. heats of formation)

Quick Facts

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.

Design and Approach

Tools1. Spreadsheets (Microsoft Excel/OpenOffice Calc)

2. ChemSketch

3. WebMO

4. Molecular Workbench

5. VenSim

6. Boltzmann 3D

Web Resources7. Instit. for Chem. Literacy through Comput Sci (ICLCS)

-- Molecular Animations8. 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. ChemSketchhttp://www.acdlabs.com/download/

(http :// www. acdlabs. com / download )

--- Free(ware) for educational use

Draw molecules in 2DManipulate and visualize molecules in 3DName structures according to IUPACExport complex structures for use in other programs (e.g., WebMO)

* 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

(http :// webmo. ncsa. uiuc. edu; also www. webmo. net)3. WebMO

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 Resources7. 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 progressesA 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

Try WebMO yourself: Http :// webmo.ncsa.uiuc.edu

Login: gk12_01, gk12_02, ..., gk12_30Pw: password

Workshop Resources

http :// iclcs . uiuc . edu / gk12