Exam #2 answers

Exam #2 went quite well. You can pick up your exams from the box outside my office and download selected answers.

I apologize for the long delay in returning this exam. You know the main reason why everything got held up, but I regret the delay just the same.

A couple of comments beyond those in the answer sheet:

• The first step in problem #1 is quite difficult to think about. The other steps are more straightforward and everyone dealt with them more reliably. You are still having some problems with labels. Cycloadditions get [m+n], sigmatropic rearrangements get [m,n], and electrocyclizations get DIS/CON (and maybe number of electrons).
• The first step in problem #2 is nearly impossible to think about. Well, I exaggerate. You can think about it, but it is too difficult for an exam problem. Sorry. Interesting note: most of the remaining steps did not need to be analyzed because they duplicated steps in problem #1, but most of you analyzed these steps just the same. So it goes.
• Only one person built all four transition state models correctly. Two people built two models correctly. Two people were stumped or misled by the models that they had (which weren’t transition state models). I was hoping that the last problem on HW #8 would prepare everyone adequately for this exam problem, but I guess not. Is there something I could have done differently that would have helped?

Model #5 – Regiochemistry of 3+2 Cycloaddition

(First posted on April 30, 2008. This assignment and the resulting analysis illustrates the kinds of stuff you might base your final project on. Let me know if you have any questions about the following.)

The instructions for this assignment can be found here.

To summarize, you were asked to predict the regiochemistry of the following cycloaddition using FMO (note: the left and right-hand products will be referred to as meta and ortho, respectively):

Then you were asked to compare the FMO predictions to those based on calculated energy barriers. Finally, you were asked to look at other properties of the transition states (geometry, electron distribution) that might support the overall picture. My results follow …

Exam #2 – Download here

Exam #2 (3 page PDF). Due Monday, April 27, at 4 pm in my mailbox or my office (slip your exam under my door). Notice that you must also email models to me for one problem so that I can examine them.

Ground rules are the same as those for exam #1.

Important schedule updates

Since we didn’t have a full class today, and since several important items were discussed, I’m sending this out to everyone so that you have a clear idea of where we are going in the next two weeks.

Spin, angular momentum, and multiplicity

A previous post described how the ability of a molecule to absorb light can be expressed using a transition dipole moment integral (TDMI) between two quantum mechanical states, the ground state and the excited state. One part of the TDMI involved integration over electron spin coordinates and I want to explore the “spin integral” more deeply.

Re-Thinking Transition Probabilities

Today’s lecture contained three slides dealing with different aspects of transition probabilities: molecular geometry, electron spin, and orbital shape. I don’t think I made it very clear, however, how these aspects relate to one another. Let’s see if I can fix that.

Tying up today’s loose ends

I started my presentation of photochemistry in the last 10 minutes of today’s lecture – a questionable decision. Apparently, I had just enough time to say some really confusing things before it was time to stop talking completely. After chatting with Cameron after lecture, I thought it might be a good idea to try and set the record straight for everyone.

The two points that I want to review are 1) how thermal energy excites a molecule for chemical reaction, and 2) how photochemical energy excites a molecule for chemical reaction.

Paper #6 – Checking stereochemistry

A great discussion today of paper #6 – Synthesis of Tertiary α-Hydroxy Acids by Silylene Transfer to α-Keto Esters, OL, 2007, 4651. It was fun to have so many participants and so many ideas.

The take-home lessons stressed the importance of:

• asking yourself hard questions about unfamiliar reaction mechanisms (you know which questions to ask)
• acquainting yourself with unfamiliar technical terms (a frequent problem with organometallics because the reagents are not organic)
• not taking stereochemistry on faith

Going a bit farther with the third point …

Claisen Rearrangement: Chair v. Boat Transition State

(First posted Mar 25, 2008) After class, I built some models (B3LYP/6-31G*) of Claisen rearrangement transition states. The chair transition state is ~4 kcal/mol more stable than the boat when ZPE correction is included (ΔZPE ~0.3 kcal/mol).

ZPE corrections

Homework #6 instructs you to “include zero-point energy (ZPE) corrections” in your calculated energies, both the barrier and the reaction energy. Judging from some questions that have been sent by email and by comment (C. Bailey, 3/22), there are some mysterious parts to this procedure.

First, you need to build three models and obtain their energies. Second, you use the differences between these energies to estimate the reaction energy and barrier. Third, to get a molecule’s “energy”, you need to combine its “total” energy with its “zero-point” energy. We haven’t discussed the procedure for generating or using ZPE so let’s patch this hole right now: