Chem 201 - 202

Pity (or envy) poor Alice. In one book she falls down a rabbit hole. When she gets to her feet, she finds bits of food that demand to be eaten ("Eat me!"). And in the next book she steps through a looking glass only to find everything reversed. What is a girl to do?

Well, one thing scientists have always thought is that Alice should not eat any food while she visits the looking-glass universe. All of the protein in Alice's body is built from single enantiomers of chiral amino acids. This means these proteins, including her digestive enzymes, exist as single enantiomers, and they wouldn't be able to digest the mirror-image proteins that get cooked in a looking-glass kitchen. Worse, if she did eat looking-glass food, she might get a terrible stomach ache, and would definitely starve. According to the traditional view, there just isn't any biological value in looking-glass amino acids. A new study, however, turns this view on its head. If you would like to read about this, check out "Expanding Functionality Within the Looking-Glass Universe" (News Perspective, Science, 18 September 2009, 325, 1505-1506).

Slides from today's lecture can be viewed here.

Correction: I was gently informed after lecture that I was wrong about the behavior of CH3CN (acetonitrile) and water. They do mix. I had said they don't. In fact, mixtures of these solvents are routinely used as a solvent mixture for HPLC, a form of chromatography that is closely related to the procedure we will be using in lab next week. My mistake.

I didn't use PowerPoint on Wednesday, but I did show potential maps of several simple molecules that represent the functional groups covered in chapter 8. Slides of these potential maps can be viewed here.

As reported in lecture this evening, the lab report for this experiment will be due at the "end" of Monday, Nov 16. FYI "end" means before I arrive on Tuesday morning.

I forgot one vital piece of information concerning the lab report: what information needs to be printed out in your NMR spectrum.

I'm sure you are all familiar with the "placebo effect", the ability of an inactive substance to produce biological effects. The usual explanation is that the placebo substance activates the patient's "belief" that a treatment is being received and this belief, somehow, has restorative powers.

The placebo effect is too strong to ignore so when pharmaceutical companies test new drugs they divide the patients into two groups: one that receives the drug and one that receives a look-alike placebo. It isn't enough for the candidate pill to do something, it must actually be better than the placebo in order to receive FDA approval. The truly amazing thing is that, according to this recent Wired article by Steve Silberman, it appears as if placebos are getting harder and harder to beat.

The slides for last Friday's lecture, which covered the last part of Chapter 7 - the stereochemistry of chemical reactions - can be viewed here.

Today's lecture discussed how to name these classes of compounds: RX, ROH, RSH, ROR, RSR. An important point: the complexity of naming/drawing problems will be limited to compounds containing a single principal group.

Slides for today's lecture are located here.

Those of you who check the online lab calendar have probably wondered what is an NMR workshop?

Simple. It's classroom time devoted to studying Loudon, Chapter 13, Nuclear Magnetic Resonance (NMR) Spectroscopy.

The students in each lab session this week will spend 2.5-3 hours working on ChemActivities dealing with Nuclear Magnetic Resonance spectroscopy. This will prepare you to print out and interpret your NMR spectrum of isopentyl acetate in the final hour of the lab session. So, in short, we will be doing classroom work and computer work this week, but no wet lab work.

The Monday and Tuesday lab sections will meet in Rm. 105 at 1:10 PM. The Wednesday lab section will meet in Rm. 301 at 1:30 PM (there will be a Chem 101 conference finishing up around that time so we will wait in the hallway until they are finished). After the classroom work, each lab section will move to the computer lab (Rm. 203) during the final hour of the lab.

One or two students may also need to wrap up work on the synthesis of isopentyl acetate this week. I'd appreciate it if these students would remind me of their situation so the instructors and lab assistants can plan accordingly.

I just came across this in the Editor's Choice section of Science magazine (Oct 2, 2009, p. 19):

Getting a Grip on Nitrogen

Chirality is associated more with carbon than with nitrogen centers, as the latter atoms tend to invert their configurations fairly rapidly on account of their unbonded electron pair. Recently, relatively slow nitrogen inversion was observed in cyclic oligomers of four or six ... amino acids ... on account of hydrogen bonding among the substituents. Mocquet et al. now show that swapping in a single analogous [amino acid] residue that is chiral at carbon disrupts the collective inversion mechanism and thereby dramatically stabilizes the chrial nitrogen conformations throughout the ring.

Notice how the "editor" misuses the word "conformation" when referring to nitrogen "configuration"? Oh well. Probably a physicist.

Exam #2 has been graded and is available for you to pick up in Kathy Kennedy's office.

Kathy will be out of the office on Th-F during Fall Break so please stop by early in the week if you want your exam back. If you would like to meet with me, I will be here the rest of Monday afternoon and most of the day on Tuesday. I will be out of town from W-Su.