SN1!!!

Today we talked about the SN1 reaction, the second of our two substitution processes. There are significant differences between the SN1 and the SN2 reaction: in terms of stereochemistry, an SN1 gives racemization instead of inversion, for steric bulk it is better to have a highly substituted substrate for an SN1 reaction (instead of an accessible carbon like we needed for the SN2), etc. It is important to be able to recognize the difference in energy profiles for the two reactions -- an SN1 is two steps and an SN2 is one step.

There is also a major difference in solvent requirements: in an SN2 reaction, polar protic solvents surround and stabilize the negatively charged nucleophile, slowing the reaction. In an SN1 reaction, you must have a polar protic solvent to stabilize the intermediate carbocation otherwise the energy level is too high and the reaction will not take place.

The podcast for today's lecture has been posted and is available on iTunes. In iTunes, go to Advanced > Subscribe to Podcasts, then enter this URL: http://itech.dickinson.edu/blog/?feed=rss2&cat=765

On Friday I hope to cover both elimination reactions, allowing us to spend next Monday and Wednesday working problems in preparation for Friday's exam.

SN2!

Today was a day to learn about SN2 reactions. We pretty much covered it all, from nature of the mechanism to requirements for nucleophiles, leaving groups, substrates, and solvents. A few big points: There is only a single step (no intermediate) and the stereochemistry at the carbon of interest is inverted (the phenomenon is called a Walden inversion). On Wednesday we'll cover the other major substitution reaction, the SN1 (which, confusingly enough, has two steps).

Today's graphics have been assembled into a seven-minute podcast; it will be posted on Tuesday morning and will be available on iTunes.

Halogens, a rough day

Today was a tough one. We started out by finishing up the treatment of reactions by looking at reaction profiles (or reaction diagrams) and learning some new terminology. The big item: Know the difference between a transition state and an intermediate.

We then covered halogens, both the manufacture (which was heavy on radical chemistry) and one use of them (Grignard reactions). Along the way, we learned a few things about how lower energies for intermediates implies a lower activation energy and a better (faster) reaction, how hyperconjugation stabilizes a radical, and we re-visited allylic stabilization via resonance, but this time on an allylic radical instead of a cation or an anion.

Remember, a brief version of this lecture has been posted on iTunes as "Halides lecture."

The image is of Victor Grignard. An excellent mustache.

More on Reactions......

Today started with a group activity in which you had to show the curved arrows for a two-step reaction. This type of problem is central to the subject -- someone learning organic chemistry must learn to draw curved arrows to show the mechanism (electron movement) of a reaction. I showed some strategies for how to solved these problems. Essentially, it boils down to four basic rules: 1) find the Lewis base (anion, lone pair, multiple bond); 2) find the Lewis acid (cation, partial positive charge); 3) draw the curved arrow(s), which must start at the Lewis base and go to the Lewis acid; and 4) don't violate the octet rule! Hopefully, you are able to recognize the relationship between the kinds of arrows that we drew today and those we drew for the standard acid/base reactions that were the subject of the acid/base problem set a few weeks ago.

Exams returned and the start of organic reactions

OK, the return of the first exam was today, with a brief run-through to show where most of the problems seemed to occur. Check the key, come to me with questions if necessary. If you suddenly find that you are not performing up to your standards/expectations, you need to make sure that you are getting help -- either me, the group study sessions, or a tutor.

Today we started looking at Chapter 5, which deals with reactions. The main point was to show that we can look at reactive processes using the same methods as we used for resonance structures and acid/base reactions -- curved arrows, indicating electron movement.

We saw two kinds of electron movement in bond cleavages -- homolytic (both sides of a bond are treated the same way and each atom receives an electron; use "fish hook" arrows) and heterolytic (the sides are treated differently and one atom receives both electrons and the other is given none). The direction that the electrons flow in a heterolytic cleavage is governed by the polarity of the bond -- the electrons flow in the direction of the atom that is happier to have excess electrons. Generically, this is decided by electronegativity. The concept is made a bit simpler by the realization that nearly all heteroatoms (anything other than a C or H) attached to a carbon is more electronegative than the carbon and will grab the electrons from a carbon-heteroatom bond, leaving C with only six electrons and a more positive charge.

The picture is of a "rotating bomb combustion calorimeter," an instrument used to measure the energy contained within a compound. In this particular picture, it is being used to measure the differences between fuel oils containing differing amounts of heteroatom additives.

Diastereomers and Meso compounds

Today we started off with some practice at identifying (R) and (S) configurations -- and saw that there is still some work to be done. Remember, the substituent of priority number 4 MUST be going back for the CIP system to work. Futhermore, if you switch two substituents to get to that scenario, the act of switching has changed the stereochemistry to give you the opposite of the stereochemistry of the original compound.

We also looked at scenarios with more than one stereocenter and saw that there are a few possibilities that can come about. If every stereocenter is changed, then you have made the enantiomer UNLESS there is a plane of symmetry in the molecule. In that case, it is a meso compound and the mirror images are identical. If at least one but not all of the stereocenters are changed, then you have made a diastereomer of the original compound; the two compounds most likely have different physical attributes.

The image shows the addition of dioxygen to a compound to make a pair of diastereomers -- one is R, S, S, R and the other is R, R, R, R. The slash through the lower arrow shows that the pathway to the R, R, R, R compound does not happen.

Stereocenters

Yesterday was a day to learn about stereocenters. In organic chemistry, that essentially means a carbon with four different substituents attached to it. We was in class that such a carbon is not superimposable upon its mirror image -- we termed these things enantiomers. We also learned how to use the R and S descriptors for identifying the stereochemistry at a carbon center.

Exam Day!

Nothing like an exam to get the heart started. Hopefully it went well for everyone. I'll get a key posted this afternoon.

Also, the final two candidates for the BMB/Chem position will be on campus tomorrow (Tuesday) and Friday. As always, I am recruiting students to come to the research seminars and teaching seminars. I will send e-mails to each lab section with the details of each candidate's schedule. Thank you for the great responses that you've given me on the first two candidates and I hope that it will be repeated for the last two!

Chairs, chairs, chairs, and.......chairs

We spent the last two class periods learning how to draw chair conformations of cyclohexanes. Hopefully everyone has become reasonably proficient at it.

I sent an e-mail to everyone earlier today pointing out that it is OK (even advisable) to bring model kits to the exam. In fact, before you go to bed go ahead and assemble a cyclohexane.

I apologize for the lack of posts this week. Between preparing the exam, having our candidate on campus and preparing for the green-haired girl's birthday party I fell behind a bit. I promise to do better in the future.

See you tomorrow morning!

Conformers

Today was a day to look at conformers, in which we take a compound and manipulate it by rotating around bonds. Starting with ethane, we saw how to make STAGGERED and ECLIPSED conformations and looked at the relative energies of each. We moved up to butane and saw how the presence of different substituents can complicate the situation -- we saw GAUCHE and ANTI conformations. The main idea is that conformations are more stable (lower energy) when a molecule can get into a staggered orientation. It was also useful to note that there is a formal way of drawing these conformers, called a NEWMAN PROJECTION. It is worth your effort to become proficient at drawing these projections.

Also, group study sessions will be held on Tuesday and Thursday evenings from 7 - 9 pm.

Modeling exercise #1 is due in class on Wednesday; exercise #2 will be discussed in class.

Exam soon! If you haven't started to study, start now!

Strange prefixes, cyclic compounds and mashups

Today we learned some old prefixes that are often used as descriptors, especially on small molecules. These were "sec", "iso", "n" and "tert". All of these are ways of describing the organization of molecules (as different constitutional isomers). Although not as "official" as using IUPAC's numbered system, such prefixes are commonly used and we will have to come to grips with that.

We also looked at cyclic compounds and saw how we can have isomerism that is dependent on which side of the plan described by the ring contains substituents. If two substituents are on opposite sides of the plane we use the term trans, the same side leads to cis. We also mentioned that ring strain is an important factor, with small rings (three and four members) being unstable due to distortion away from the desired 109.5° angles.

The last topic was my latest obsession -- mashups -- and the first group mashup project has been posted. The link is to the left.

There is also a new problem set (#2), dealing with naming substituted alkanes.

Also, the problem with uploading podcasts has been solved and the second resonance podcast has been put in place.

The picture is of a strange thing someone did with mashed potatoes -- a mashed potato mashup, if you will.