Some of you may be planning a review of Chem 201 concepts before you take up the new challenges of Chem 202. Here are two short videos that review atomic structure and chemical bonding (note: this material is being taught by two very smart dogs).
As you prepare for Exam 3, make sure that you learn to quickly identify the roles that different molecules might play in a chemical reaction. The sooner you can decide that a molecule is probably an acid (or base, nucleophile, electrophile, solvent), and that certain atoms in the molecule are proton donors (or proton acceptors, electron donors, electron acceptors, or leaving groups), the sooner you can move on to solving the problem.
Lists of acidic functional groups have been provided, but how efficiently can you recognize basic functional groups? How about nucleophiles? (Sorrell Tables 6.2 & 6.3) Or aprotic and protic solvents? (Sorrell Figure 6.7) Sorrell’s chapters often end with a useful Reaction Summary (see p. 233-4). Here’s a link to a summary that I handed out to students in 2012. A tip for the future: as you study (this means work an activity, read the book, …), you should build your own summary of ‘things to know’. It isn’t enough to answer a couple of questions that illustrate a principle like primary RX react with Nu faster than secondary RX. You need to summarize this principle for yourself.
Mitsunobu Reaction. I didn’t say much about this reaction in class because I ran out of time, but you need to know the reaction (i.e., know how to ‘predict-plan-explain‘) for the next exam. You don’t need to know all of the subtleties of its mechanism, however. Just focus on these 3 points: What is the nucleophilic substitution step, SN1 or SN2? What is the ionization state of the Nu? What is the leaving group? There is considerable disagreement about the details of the mechanism, e.g., the steps leading to the formation of an OPPh3 leaving group. If you’re interested, compare Sorrell’s (poorly drawn) mechanism with alternative (and more plausible) mechanisms presented in Wikipedia and at the Organic Chemistry Portal.
Atomic force microscopy (AFM) is a imaging technique that works on a completely different principle from optical microscopes. Instead of magnifying light waves, an AFM device passes a needle-like probe over a surface and constructs an image of the surface based on subtle variations in the strength of probe-surface forces.
AFM and related imaging techniques generated lots of buzz in the 90’s by providing images of molecules, even individual atoms, on surfaces. AFM has returned to the front page with even higher-resolution images that track the pathways electrons take in chemical bonds, even hydrogen bonds. Compare the white tracks in the AFM image (left) with the pattern of covalent and hydrogen bonds expected from the structural formulas (right) (click image to enlarge).
For an easily digested description, see “Hydrogen Bonds Visualized” in C&ENews, 30 Sept, 2013. Or check out the original research article by J. Zhang et al, “Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy” (Science, 26 Sept 2013, DOI: 10.1126/science.1242603).
Here are links to all of the molecular modeling activities we have done in class (these links also can be found on the Classes page).
Links will be added as needed.
We are going to be building 5- and 6-carbon rings in class next week. I don’t have enough atoms in my bucket for more than a couple of rings so please bring your own.
The model kits that we used in class this week can be obtained from the Chemistry stockroom for a very modest fee. If you can get gently used models from a previous o chem student, that’s fine too.
Remember, you will want to have a model kit with you when you take the next short exam so why not get one now and start practicing with it?
Aaron Nilsen and I have been discussing how to make the transition from Chem 201 to Chem 202 (new schedule, new format, same book) as smooth as possible. One idea: share a short list of ‘things to remember from Chem 201’.
Aaron’s suggestions for things to review from Chem 201 can be downloaded here.
An essential aspect of SN1 and E1 reactions is the dissociation of the leaving group. These lecture slides from Day 16 (Oct 29-30) discussed the following phenomena and trends from an MO perspective:
I'm providing two documents for Day 14 of class: a reaction summary and my lecture slides. You can find additional summaries in Sorrell (see p.231-2 & 233-5 near end of chapter) and in my learning objectives. Summaries are highly useful ways of expressing the information that needs to be learned and I recommend that you write your own version. Use the 'predict-plan-explain' outline in the Day 14-15 learning objectives to guide what you do (and don't) write down. If your summary takes up more than 1-3 pages, it may be useful, but it isn't a summary.
Mitsunobu reaction alert. I didn't talk about this reaction in class because I ran out of time, but you need to know the reaction (i.e., know how to 'predict-plan-explain') for the next exam, but you don't need to know all of the subtleties of its mechanism. Just focus on the nucleophilic substitution step: is it SN1 or SN2? what is the ionization state of the Nu? what is the leaving group? There is considerable disagreement about the details of the mechanism. If you're interested, compare Sorrell's mechanism with alternative (and more plausible?) mechanisms presented in Wikipedia and at the Organic Chemistry Portal.
Exam alert. The next exam (Day 16) covers everything presented through Day 14, including the Mitsunobu reaction. The emphasis will be on Ch. 5 (acid-base), Ch. 6 (SNx reactions of alkyl halides), and only part of Ch. 7 (converting ROH into "RLg" and then RNu). The material from Day 15 will not be on the exam.
I showed a YouTube video in class last Wednesday, but didn't have time to show it to the Thursday class. The video presents the mechanism of the chemical reaction catalyzed by lysozyme enzyme, a chemical reaction that is also discussed in Sorrell 5.5.
You can watch the video (under 2 min) here. You can also get a copy of the lecture slides for this and other lectures by going to the Syllabus page and scrolling to Day 11.
Some interesting things about the video:
You can find a variety of things here as you prepare for next week's exam: