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.

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).

Final project

We still have several major assignments ahead of us (homework, papers for discussion, and another take-home exam), but I am going to post the instructions for the final project now so that you can begin thinking about it.

Once you’ve read the instructions, you might want to go a little farther and start looking for a problem to study, but you can also afford to procrastinate for the next 2-3 weeks. It’s up to you.

Tomorrow’s class: modeling transition states

Tomorrow we will be in the computer lab learning how to build “true” transition state models (so far we have been building fake models). We will be looking at

• how computational chemists define a transition state mathematically as a particular location on a potential energy surface
• what methods are used to verify whether a model is a true transition state or not
• how to get better estimates of reaction barriers (and energies) by including zero-point energies (ZPE)
• and, if time permits, actually trying to construct some models of [1,n] H migration transition states

The “lecture” portion of tomorrow’s modeling session can be shortened? accelerated? made more meaningful? if you look at this three-page handout before class. Print copies can also be picked up from the box outside my door.

Allowed or Forbidden?

We’ve been looking at several tools that chemists have developed to answer the title question regarding concerted pericyclic reactions.

• Monday, Mar 2 – Fukui FMO & Woodward-Hoffmann Rules
• Wednesday, Mar 4 – Dewar-Zimmerman transition state aromaticity (you had to be there)
• Friday, Mar 6 – Transition state aromaticity & worksheet

These three sets of rules do not come close to exhausting …

Frontier MO analysis of transition states – Part II

Lecture notes for today’s (Wed, Pt II) lecture

Lecture notes for previous (Mon, Pt I) lecture

The Monday and Wednesday lectures tell a single story, namely, that the mainstream view of a molecule as a “carbon skeleton adorned by functional groups and modified further by substituents” can be described very nicely using molecular orbitals. In addition, the MO model that lets us construct MOs for molecules also lets us construct MOs for reaction transition states.

Some key points (some of which are further elaborated in HW #5):