Modern Applications in Chemistry:
Molecular Visualization
THIS PAGE was last revised: November 29, 2006


ANNOUNCEMENTS:

Welcome to chem 696, Section 600!

 Please finish all assignments by Dec. 15th or e-mail me to request an incomplete

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ASSIGNMENTS:
NOTE: A Form Confirmation Screen will appear after you submit your assignment. You can print this if you wish to save your responses.

 Assignment 1:   Survey- Do this before you begin any class activities

 Assignment 2:   Before 9/22 BUT AFTER doing assignment 1-the survey, read the following articles.

TEKS: The high school chemistry and IPC (Integrated Physics and Chemistry) sections of the state standards (click here for TEKS)

NSES: From the National Science Education Standards, chapter 6: Science Content Standards, read:

  • the content standard for K-12 , the unifying concepts and processes (click here)
  • the content standards 9-12 (click here) Especially note where chemistry comes into standards A-G.

Assignment 3:   Before 9/22 BUT AFTER doing assignment 1-the survey, read the following articles and do assignment #3.

Article 1: (click here for article 1)

Article 2:(click here for article 2)

You will need an adobe acrobat reader to view these articles. You can download one for free by clicking here.

Give your opinion of the program/plug-in/animation by completing this form as you are instructed. Click on Visualization Evaluation Form  You will use this throughout the course.  
 Assignment 4 (to be done following your 9/22-9/23 visit):   Consider the programs/plugins/animation collections that we used and your experiences here.

We used RasMol, Chime, J-mol, ISIS, CAP videos, MRA J-mol website, AND Animations from the HOLT CD, MoLE project (interactive animations), ISU/Greenbowe (animations/simulations), and the Collective (animation links).

Assignment 5 (Target Dates 9/25-10/2):   Use the Gelder CD, with the handout pages.  Your Assignment #5 is very similar to the assignment pages that were handed out.

Assignment 6: (Target Dates 10/3-10/9):

Read: Using Visualization Techniques in Chemistry Teaching by Williamson & Jose. 

Visit: http://www.copyright.gov concerning the use of animations, images, etc.

Also read: Is an Atom of Copper Malleable? by Ben-Zvi, Eylon, & Siberstein

Assignment 7: (Target Dates 10/10-10/16):

1) Using your HOLT CD, find a movie that you would use in your teaching.  Pull that movie to your hard drive and rename it.  Send it to me as an e-mail attachment. williamson@tamu.edu Be prepared to discuss the chemistry concept with which you will use the movie.

2)Download ISIS draw to your computer using the handout from the weekend.  Also download echem from the handout ( http://sourceforge.net/projects/echempp  ).  Create a NH3 molecule, a water molecule AND a CH4 molecule in each program.  Put the ones from ISIS draw into a word document and e-mail it to me as an attachment. Be prepared to compare the 2 drawing programs.  Do a Visualization Evaluation Form for e-chem.  (NOTE: we haven't been able to copy and paste from echem.  Try it for yourselves.)

3) Download J-mol to your computer from the handout sheets. Using the pdb file that you will be e-mailed, open the molecule in J-mol.  Copy it into a word document and e-mail it to be as an attachment.

4) Search on the Web and find a pdb file to download that you would use with your class.  Send it to me as an e-mail attachment, then be prepared to give the website and name/formula of the molecule.

5) Brush up on Lewis Dot.  ck out: http://www.pogil.org/downloads/HS/Lewis_Dot_Structures_of_Atoms_and_Ions_2.pdf#search='Lewis%20dot'

Assignment 8: (Target Dates 10/17-10/24):

Read thoroughly: 
1) The Effects of Computer Animation on the Particulate Mental Models of College Chemistry Students by Williamson & Abraham

2) The Use of Video Demonstrations and Particulate Animation in General Chemistry by Velaqquez-Marcano

Read entirely, then read your section in detail. Be prepared to discuss the main points in your section for this assignment AND at your next visit:

3) Exploring Visuospatial Thinking in Chemistry Learning by Wu & Shah

Sections:
**To What Degree Do Individual Differences in Visuospatial Abilities Predict Learning in Chemistry? (page 468) James, Casey
**To What Extent Do Conceptual Errors in Chemistry Arise From Difficulties in Comprehending, Translating, and Transforming Visual Representation? (pg 474) Travis, Rosalie
**To What Extent Can Visualization Tools, Ranging from Physical Models to Computer-Based Multimenia Software, Help Support Visuospatial Thinking in Chemistry Learning (pg 477) Tara, Lance
**General Discussion: Principles for Designing Visualization Tools (pg 481) Judy, Katie

Assignment 9: (Target Dates following your 10/27/28 visit):

This assignment is about your visit and the activities that we did while you were here. Do this as soon as possible.

Assignment 10: (Target Dates 11/1-11/15):

1) Download ChemSense (stand-alone version) to your computer from http://chemsense.org/download

2) Use ChemSense to make the animation that you are assigned.  You will receive your assignment via an e-mail from Katie. Then send your ChemSense animation to me at: williamson@tamu.edu.

3) Read the article: Enhancing Students' Conceptual Understanding of Chemistry through Integrating the Macroscopic, Particle, and Symbolic Representations of Matter by D. Gabel 
Please add the reference to your paper article:  This was printed   In N.J. Pienta, M.M. Cooper, & T.J. Greenbowe, (Eds) Chemists Guide to Effective Teaching, Volume 2. Upper Saddle Rive, N.J: Prentice Hall. 2005; pp 77-88.

Assignment 11: (Target Dates 11/15-11/30)

Read the following articles thoroughly:
1) Harrison, A. G. & Treagust, D.E. Modelling in Science Lessons: Are There Better Ways to Learn With Models
2) Singer, J. E., Tal, R., & Wu, H. Students' Understanding of the Particulate Nature of Matter
3) Wu, H., Krajcik, J.S., & Soloway, E. Promoting Understanding of Chemical Representations: Students' Use of a Visualization Tool in the Classroom

PROJECT ROUGH DRAFT (Target Dates 11/15-11/30)

Click here for the project details.

Prepare a ROUGH draft.  This means that pieces are missing.  You only need a backbone of your lesson or workshop. I will give you written feedback on your project.  This will be returned to you via FAX, attachment, or PDF.  IF I get this early, you may be able to get feedback from me twice before the final version comes in.

Click here for the required components of the Workshop

Click here for the required components of the Inquiry-Based Lesson

Submit a rough draft of either your workshop or lesson components as an attachment to:   williamson@tamu.edu
Assignment 12: (Target Dates 12/1-12/7):

Read the following articles thoroughly:
1) Barnea, N.,  & Dori, Y.J. High-School Chemistry Students' Performance and Gender Differences in a Computerized Molecular Modeling Learning Environment
2) Yezierski, E.J. & Birk J.P. Misconceptions about the Particulate Nature of Matter: Using Animations to Close the Gender Gap

PROJECT FINAL DRAFT (Target Dates 12/7-12/14)

Submit the final version of your workshop or lesson components as an attachment to:   williamson@tamu.edu

Assignment 14: (Target Dates 12/7-12/14):

Read the following article thoroughly:
1) Vermaat, H., Kramers-Pals, H., & Schank, P. The Use of Animations in Chemical Education

note that the proper citation is:

 Vermaat, H., & Kramers-Pals, H., & Schank, P. (2003). The Use of Animations in Chemical Education. Proceedings of the International Convention of the Association for Educational Communications and Technology, pp. 430-441. Anaheim, CA.

Assignment 15: SURVEY
When ALL of the above assignments are completed AND your final lesson is in: Complete this survey on teaching and learning.
Only a generic Form Confirmation Screen will appear after this assignment.

Assignment 16: SURVEY
When ALL of the above assignments are completed AND your final lesson is in: Complete this end of course survey.  It does not record a name and is an evaluation of the course.

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LINKS:

Click to go to the collective. You will find download info for visualization programs/plug-ins, a collection of animations by topics, and chemistry links to concept tests, periodic tables, humor, etc.

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SYLLABUS:

Click here for the syllabus.

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