Reed chemistry alum and medical school student, Hassan Ghani ’08, just sent me this story from yesterday’s NY Times, “How to get an A- in Organic Chemistry” by Barbara Moran. Like so many others, Ms. Moran has decided a mid-life career change is in order, but her search for professional fulfillment has taken an unusual tack: at the tender age of 42, and with parental responsibilities for two small children, she finds herself enrolled in organic chemistry so that she can become a doctor.
Her story about the joys of “orgo” includes observations on the necessity of mastering electron pushing (draw a “zillion” curved arrows and you will eventually develop the kind of “intuition” that makes a poorly placed arrow seem as unpleasant as “ketchup on sushi”), similarities in the type of reasoning (“inductive generalization”) used by organic chemists and doctors, and the all-important life lesson that, even though our life compass points towards the Land of Perfection, it is not a place that we can ever visit.
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.
A few of you were unable to attend last night’s lab lecture. Here are slides from the lab lecture (bonus prize: GC data for a ‘standard’ mixture of isopentyl alcohol and isopentyl acetate):
Sapling sent this announcement to me today:
Sapling Learning is committed to providing the most effective online homework and the best support in higher education. We need feedback from you and your students to make sure that we are aware of where we can improve. As a token of appreciation for your time and feedback, each instructor who completes the survey will receive a $5 Starbucks gift card. As an incentive for students, we will be giving away an Apple iPad mini to 3 students randomly selected from those who complete the survey. The student survey must be completed and submitted by November 8, 2013 to be entered to win. Student winners will be announced on November 15, 2013.
Please share this link with your students: https://www.surveymonkey.com/s/studentfall2013
We thank you and your students in advance for taking 10 minutes to complete our survey.
You can download a copy of tonight’s lecture here.
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).
- Activity #1 – Build/sketch models with Spartan ’14
- Activity #2 – Potential maps, intermolecular interactions, hydrogen bonds
- Activity #3 – Orbital shapes (atomic, molecular), HOMO-LUMO gap, electron density surfaces, charge delocalization
Links will be added as needed.
The office hour scheduled for Monday, Sept 23, is canceled. I have a doctor’s appointment in NE Portland at that time. I will be on campus for lab on Monday and will answer questions that you bring there. Normal office hour schedule resumes on Wednesday, Sept 25, 10:30-11:30.
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?
The first short exam will be in-class Tue-Wed (Sept 17-18). It will run about 25 minutes. The brevity of the exam can make the experience feel a little intense so here are a few notes on how to prepare and what to expect: