Chem 201 Archive – Alan Shusterman

Month: October 2012

  • Day 14 – Activating OH as a Leaving Group

    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.

  • All that stuff crawling around in my head: it's like musical chairs

    I recently wrote about the importance of carrying information forward. And I'm sure that you understand by now that the information we cover needs to be applied and not just regurgitated. But there's so much to learn. Is it possible that mere humans can learn organic chemistry?

    Yes. And here is why:

    (more…)

  • Lysozyme mechanism & video

    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:

    • energy, binding, and ring strain – while the video doesn't offer a reaction coordinate diagram, it gives you information about energy if you know where to look. When the substrate and enzyme bind to each other, their (combined) free energy decreases because bonding is always favorable. But even though binding occurs, the substrate is forced into an awkward conformation. This destablizes the bonds in this ring, making them easier to break. Still, the increase in substrate strain energy is more than offset by the overall drop in energy caused by substrate-enzyme binding.
    • acid-base chemistry & amino acid sidechains – the mechanism depicts proton transfers between the enzyme and the substrate. The reactive groups in the enzyme are amino acid sidechains. This is virtually always the case. Even though we may think of a single amino acid as containing a reactive amino group and a reactive carboxylic acid group, these groups have been converted into unreactive peptides (amides). An enzyme's catalytic properties are due to its amino acid sidechains.
    • curvy arrows – the video draws curvy arrows for the proton transfer that are incorrect. One arrow correctly shows electrons in the A-H bond moving towards A. The other arrow incorrectly shows H moving towards B. Come to think of it, the video's voice doesn't say these are curvy arrows, but if they were ….
    • electrophiles & nucleophiles – are these polar reactions? Do they form new bonds? Yes and yes. You should be able to identify electrophiles and nucleophiles for each step.