Using PC Model, answer any two of the three questions below.

1. PCModel includes a number of substructure menus designed to facilitate the building of biopolymers. From the amino acid menu, construct the oligopeptide lys-lys-lys. In a biological system the C terminus would be deprotonated and the N terminus protonated, but let's not worry about that. The objective of this problem is to find the lowest energy conformation you can for this tripeptide. Presumably this will involve some internal hydrogen bonds. Grading will be based on the range of energies found (lower is better). When you have found what you think to be the lowest energy structure, print it out using the print option that includes the energy-try to orient your structure and choose the display option (e.g., ball-and-stick, tube, etc.) so as best to illustrate the actual conformation. [Note: On the Macintosh, some versions of PCModel will not send the PostScript file to the printer until you bring the Finder to the forefront, e.g., by touching the desktop.]

2. Use the dihedral driver option in PCModel to construct torsional potentials about the indicated bonds in the three molecules below. Construct the potentials over the range of 180 degrees taking points every 15 degrees (symmetry dictates that only 180 degrees are unique). Note that PCModel saves the 12 structures to a file, with their associated energies, so you can open any one of them to look at its energy and get the breakdown of that energy into its force field components by doing a single point. By analyzing the contributions of different force field terms to the total energy, provide a chemical explanation for any important differences you perceive between the three potentials.

3. Design a problem of your own that uses PCModel to illustrate some chemically interesting concept. Write down the problem, and then provide the answer. Note that you do not need to pick something that PCModel performs well for! However, if you create a problem where PCModel clearly gives the wrong prediction, provide some discussion in your answer of why the force field fails to be accurate. To get more of a feel for typical problems, feel free to drop by the website and look at first problem sets from previous years. Grading will be based on quality of the problem and originality.

Important note on resources: In addition to the computers in 176 Kolthoff, there are platforms in the IT Labs that are running PC Model. In principle, you have access to these machines (assuming you've been assessed the IT computer fee-if you have any trouble, let me know). Locations are EE/CSci 3-170 (M-Th 7 am - 2 am; Fr 7 am - midnight; Sa-Su 10 am - 2 am) and Physics 130 (M-Th 8 am - 10 pm; Fr 8 am - 6 pm; Sa 10 am - 6 pm; Su 4 pm - 10 pm). For output you will need a printer access card, which can be obtained in the lab itself.