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:

HW #2 – Answers and corrections

I did some really half-baked planning for this assignment.

First, both reactions in problem #1 contained errors. The correct reactions, my comments, and the journal articles that provided the information can all be found in the answers that I’ve posted online (I didn’t post answers to problems #2 and #3 because these were discussed in class). What is really humiliating here is that I discovered my mistake exactly one year ago, but I forgot to make a note in my files so I just shoved the wrong reactions out into the ether a second time.

Note on exo v. endo character of transition states: I found it rather hard to decide this issue. I noticed that nearly all of you predicted endo transition states (or were silent on this point) which is a reasonable guess provided that the endo transition states aren’t too strained. Here’s my question: did any of you make models of the transition states? If you didn’t, please try. Just try to build models of the transition states leading to the actual products. If you would like to save time, stop by my office and I’ll show you mine. I think constructing and/or examining these models is a really beneficial experience.

Second, relying on my amazing ability to mis-schedule assignments and lectures, I moved the due date for HW #2 to Monday evening and then gave the answers to problems #2 and #3 on Monday morning. So … if you were awake on Monday morning (and you all seemed very awake, probably because Dan let you sleep an extra hour), you were able to copy down the answers into your lecture notes and then go home and copy them again onto your homework.

This clever turn of events reminds me of something my Dad used to say to the neighbors, “my boys, all A’s in school (not true!), but when it comes to common sense, as dumb as the day they were born!” 40 years later and the shoe still fits. Sigh.

HW #7 and the Missing Lecture

The first problem on the homework assignment asks you to predict reaction products, but because I cut my lecture off before the final page of notes, I failed to give you some crucial information.

The final page of notes can be downloaded here. Please read it before you try to work the problem.

HW #3 – Modeling tips

When you generate a list of models, e.g., conformers, there are two ways to get information about them. One is tedious, but obvious. The other is very fast, but relies on obscure buttons.

Tedious & (perhaps) obvious

The obvious part: whenever you examine any model, you can always get its energy by selecting Display: Properties and you can always get the value of a dihedral angle by selecting Geometry: Measure dihedral (there is also a blue button you can use) and selecting 4 atoms.

The tedious part: you will have to repeat this for each molecule in your list. In addition, each energy and each angle will have to be written on a piece of paper and then (yawn) typed into Excel.

Very fast (uses obscure buttons)

First, select Display: Spreadsheet. To add relative energies, select the molecule that you think/know has the lowest energy, click the top of a blank column in the sheet, click Add…, and click rel. E (and kcal/mol). This adds a column of energy data to your sheet.

Second, use Geometry: Measure dihedral (or the blue button) to get the value of the dihedral angle that interests you. When this value is displayed, a little red-&-yellow “P” button will appear next to the value in the lower right-hand corner of the window. Click the “P”. This adds a column of dihedral data to your sheet.

Third, and the best part, click-drag in the sheet to select the data you want (you probably will need to drag the edges of the spreadsheet window to make it larger). Select Edit: Copy and then paste the data into Excel.

Ring Strain: CH2 v. O

Last Monday (Feb 11) we spent some time discussing ring strain in two bicyclic molecules: 2-norbornene and its 7-oxa analog. While several groups contribute to ring strain in these molecules, any difference in ring strain might be due to angle strain at position 7.

Spartan’s model database contains high-level models (MP2/6-31G*) of both molecules. The C-C7-C and C-O7-C bond angles are 93.9° and 95.6°, respectively. In our discussion, we had noted that the ideal angles for carbon were larger than those for oxygen ( 109° in CH4 v. 104° in H2O). Comparing the bond angles in the bicyclics with the ideal angles, we might predict that 2-norbornene is more strained. And this might actually be true. Using total energies from the model data, along with HF/3-21G ZPE energies, I have estimated that the following reaction is exothermic by -5.6 kcal/mol. This is consistent with strain release at atom 7.

You might wonder if CH4 and H2O are the best models for estimating ideal bond angles. These molecules contain H-Z-H combinations while the bicyclics contain C-Z-C. As it happens, the experimentally measured bond angles in CH3-Z-CH3 are 112.4° (Z = CH2) and 111.7° (Z = O) (note: the MP2 angles are in nearly perfect agreement with experiment). These angles are quite similar, although the COC angle is still smaller.