Chapter 2 Workshop

Computer Molecular Modeling Using Spartan

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This workshop is intended to familiarize you with the Spartan CD that comes with your textbook. It has two programs (SpartanBuild and SpartanView) that allow you to do numerous exercises and problems indicated in your textbook. The full program has many more capabilities and is available on the computers in the Chemistry Commons (SB1-221).

1. SpartanBuild - Creating Molecular Structures
Refer to Appendix 3 in your textbook and follow the instructions for creating propanal.
a) Practice with all of the following motions: rotate, translate, zoom, and rotate in plane.
b) View the molecule in all of the possible formats under the Model menu.
c) Minimize the energy and measure the bond distances for every C-C and C-H bond.
Describe and explain any trends you see.
d) Measure bond angles about the sp3 and sp2 carbons. Describe and explain any trends you see.
e) Measure dihedral angles. Describe and explain any trends you see.
f) Follow the instructions to create malonic acid and trans-1,4-diphenylcyclohexane as well.

2. SpartanView - Visualizing Molecular Structures and Properties
Quit SpartanBuild, open SpartanView, and open the file for Problem 1-68 (see textbook, p 56).
a) Click on each of the molecules in turn and note the names in the window titlebar.
b) Determine the magnitude and direction of dipole moments for each molecule.
c) Determine atomic charges for each atom in each molecule. Why don't they add to zero in some cases?
d) Click on each molecule in turn and view the potential map (solid) for each one.
Try the other views (mesh, transparent) as well. What information does this provide about the molecules?

Close all and open Appendix B.
e) Select ethylene and view the HOMO and LUMO.
f) Select butane and view the animation of conformational changes. Click one frame at a time.
Rotate the molecule for a Newman-type view of the conformational changes.
Select Energy and tabulate (graph) the energy changes as the conformation changes.

3) Spartan - Calculation of Molecular Properties Olympiad
Each of the computers in the Chemistry Commons has MacSpartan or PCSpartan installed.
a) Open the program and build any isomer of formula C3H6O . Minimize its energy.
b) Compare results from the group with respect to dipole moments, atomic charges, and stability.
c) Continue until the group is convinced it has made all possible isomers.
d) Identify the isomers that deserve gold, silver, and bronze in as many relevant categories as you can think of (e.g., most positive carbon). Try to determine what aspects of the structures makes these compounds winners in their categories.
e) Select any compound and set up a calculation for a potential surface.

4) Make sure you can do all of this on your own computer as well, then practice with the rest of Appendix 3.
You can now get the most benefit out of the computer exercises and problems in the chapters (identified with the CD icons).