C372: Molecular Modeling

Lecture Assignment 1

 

This assignment utilizes PCModel which is available at IUB on the Chemistry library computers and at IUPUI at the Computational Molecular Science Facility(LD 320)

 

  1. Start PCModel. 
    1. First you will draw propane

                                                     i.     Choose ÔDrawÕ from Tools pane

1.     Click anywhere in the screen to add atoms

2.     Subsequent clicks add bonds

3.     To add hydrogens to carbon backbone choose ÔH/ADÕ in Tools pane

    1. Next you will calculate the energy of the molecule you drew

                                                     i.     Under ÔForce FieldÕ choose ÔMMFF94Õ

                                                      ii.     Under ÔComputeÕ choose ÔSingle Point EnergyÕ

1.     Record the output

                                                        iii.     Under ÔComputeÕ choose ÔMinimizeÕ

1.     Record the output

 

  1. Which molecule had the higher energy? Why?
  2. Which terms in the energy changed the most? Explain.