ESM4714
Scientific Visual Data Analysis and Multimedia

Assignment #8:
Visualizing Structure-Property Relationships in Chemistry

Due: ______________________________

This assignment was written by, our last guest lecturer, T.L. Pickering, Assistant Director of the National Science Foundation Science and Technology Center on High Performance Polymers and Adhesives.

Part I (100pts):
Create images of electron orbitals

CONSTRUCT: an SDS_HDF file of your example. Also construct a text file that explains the images. In the past we have had difficulty is constructing these images therefore comment on any difficulties in creating these images.

GENERAL DIRECTIONS:

• Review the handout material and other sources, if desired, to determine the required molecular structure information for your problem.
• Calculate the atomic position coordinates for you molecule(s).
• Use the Boogie program to create the necessary input files.
• Transmit the job to the NCSA computer for image generation.
• Retrieve our image files.
• Experiment with your images to give the best (most meaningful to you) representation.

SOME HINTS:

• Don't try to use too many atoms in your image.
• Planar molecules are nice for multi-atom images, e.g. benzene, ethylene.
• Look at simple series to explore effect of atomic size, electronegativity, etc. for example , HF, HCl, HBr, or H2O, H2s, H2Se
• Look at various orbitals or energy levels in a simple molecule, e.g. CO, CO2, Ozone.
• "Dissociate" a molecule by varying the bond distance paramenter, e.g. HCL, HOOH (hydrogen peroxide).
• I use primarily organic structures and "common" elements like the halogens, alkali metals, etc. in simple molecules in my exploration of this program. They all worked. Transition metal compounds should work as well, But I haven't had the time to verify that yet.

POST YOUR RESULTS
Logon to username: homework, password: to be handed out in class. Create a directory with your lastname: (~homework.assign#8/lastname).

Put a copy of all your files in your lastname directory. Also put a copy of a text file lastname .txt with your comments on homework assignment#8. Print a copy of your files and also hand these copies in at class on the due date. Your grade will be based on your observations, conclusions and how well your file works. Your grade will not be based on your programing skills although brevity, clearity, and meaningful comment statements will be appreciated.