2020

The final project for 2020 is a student-designed molecular modeling project that will lead to a journal article-style written report and an oral exam based on that report. Instructions can be downloaded at the following links. [2019 only]: The instructions do not mention this, but I am willing to entertain projects that apply calculated spectroscopic properties to problems of structure elucidation.

2020 final project instructions

2020 writing a research proposal (+ sample proposal)

[2020 post-covid update]

• The 2020 research project is optional. Let’s call it Plan A. If you opt for Plan A, you will still be responsible for 1) completing all homework assignments, 2) meeting the final deadline for your written report on your research project (see final project instructions), and 3) having a final conversation (“exam”) with me about your project and your report. Plan B is described in the bottom bullet.
• Project & Spartan modeling tips:
  • Have at least one conversation (probably more than one) with me about the suitability of your project plan. I can give you advice on what to calculate, what to avoid. Once the project is underway, I can advise you on what’s working, and what to try for things that don’t seem to be working.
  • Turn off (don’t just stop using, but turn OFF) all competing apps. Even when they are not in use, their windows may consume a lot of computer memory. Spartan needs the CPU and memory, both. Use Activity Monitor (on Macs) to see if Spartan is getting 90+% of CPU/memory when a calculation is running.
  • Set your computer to stay awake. You can turn off the display, but you can’t turn off the computer or put it to sleep. This will halt a calculation.
  • In general, run 1 Spartan job at a time. That way you will get the results from that calculation asap, and you’ll be able to decide what calculation to do next. If you know you need to run several jobs, save them for a time when you don’t need to use the computer (example: bedtime), and check on them when you wake up. You can check on the progress of Spartan calculations by choosing Options: Monitor to open the Monitor window. Click the > under Job Name and then click on the model label (example: M0001) to display an output summary file and the current model geometry. Right-click (secondary select) a job name to either Terminate a job that you want to stop, or to Start a job that is stuck in the Queue. Spartan is only working on the jobs with Status: Running.
• The alternative to Plan A is Plan B. This replaces the final project with a written final exam. The exam as currently planned will have 2 parts: Part 1) written Q&A much like the homework Q&A, Part 2) molecular modeling that will likely include construction/calculation/data report+analysis. Both parts will examine your ability to apply the material (concepts, tools) we have covered in class to mechanistic questions (particularly those applying to pericyclic reactions) and model use. Timing: The exam will likely be handed out sometime during or just after Reading Week, and will be due near the end of Finals Week. It will not be timed. If you opt for Plan B, you will still be responsible for 1) completing all homework assignments, as well as 2) completing both parts of the final exam.