Chemistry 324 - Spring 2008

Today’s paper contains a number of interesting issues. Rather than take several days to create one big long post, I am going to slice my ideas into small chunks and invite your comments.

Here’s one issue: diastereoselectivity in the reactions of 8 with dienes (Table I). Since this reaction involves three distinct steps, there are multiple points at which to stop and ponder selectivity.

• Conversion of 8 (diazo ester) into a metal carbenoid
• Cycloaddition of carbenoid and diene making a divinylcyclopropane
• Tautomerization of divinylcyclopropane to benzofuran

Keep reading →

NMR - General

As we discussed in class, always use the very best data tables you can find to predict chemical shifts and coupling constant, but remember that spectral data + assignments for a structurally analogous compound are even better than data tables. Some places you can look for spectral data on specific compounds:

• The same paper. Chemists tend to make a series of analogous molecules, replacing a methyl with a phenyl here, or a proton with a methoxy group there. If one of these molecules possesses an easily interpreted spectrum, you might be able to apply this same interpretation to your molecule’s spectra.
• Books. The Reed library contains several compilations of NMR (1H and 13C) and IR spectra (and more). Two favorites of mine are the various Aldrich Libraries (also available online) and “Tables of Spectra Data for Structure Determination of Organic Compounds,” by Pretsch et al. (QC462.85 .T313 1983).
• Online Tables. The Sigma-Aldrich site lets you look at high quality spectra for many of the compounds they sell. You get the spectra, but no interpretation. Another excellent site that actually provides assignments is maintained by Prof. Hans Reich, U. Wisconsin-Madison. I have listed links to four of his data tables, but his site contains much, much more:
  • ¹H chemical shifts
  • HH coupling constants
  • ¹³C chemical shifts
  • CH coupling constants

I have also added some other useful links for organic chemists to the site’s side bar. Check them out before the Qual.

Keep reading →

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.

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). Keep reading →

Exam results were uniformly good. I have written comments on your exams and posted answers/comments on selected problems here. I don’t assign numerical scores to exams in this class, so if you would like additional feedback, please come see me.

Exam #1 (2 page PDF). Due Saturday, March 8, at 3 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.

The emphasis of my treatment of frontier MO theory has been on its application, not its theoretical foundation. When it comes to FMO, I hope that you will to be able to use it and read articles in which others refer to it.

Of course, I could say a lot more about orbitals if time permitted. If you feel like you would like to spend some extra time on this material (and this applies to everything that we cover), please come see me. Physical organic chemistry is one of my favorite subjects (nerd! nerd!) and I am more than happy to talk about any aspect of it.

Today’s PowerPoint (revised W, Feb 27)

HW #5 (due next Monday) is based on two reactions that appear in paper #5 (to be discussed on Friday). So, even though we will discuss the paper before the homework is due, it probably would make sense to try the homework first.

Authors often file additional material with their papers that does not get published in the journal proper. This material is referred to as supporting (or supplementary) information and often contains important additions to the basic paper.

For example, the experiment-based papers that appear in a rapid-publication journal like Organic Letters usually contain only summaries of the research. Detailed experimental procedures, spectroscopic data, and crystallographic data, are published on-line as supplements.

Nearly all journals expect computational chemists to provide supporting information for their papers. At the very least, the chemist is expected to provide lists of the atomic Cartesian coordinates for each model, but other model properties may be demanded too.

A coordinate list can serve two purpose. First, it makes it possible for another scientist to repeat the calculation and check it for errors. Also, and from our point of view more important, a coordinate list can be converted into a “3-D” model so we don’t have to rely solely on the small flat figures in the journal to see what is going on.

You can use Spartan to view published models if you know how to convert the data in the supporting info into a file format that Spartan recognizes. The conversion procedure that I followed for paper #4 can be briefly summarized as:

1. Download & open supporting information
2. Copy atom coordinates to clipboard
3. Paste atom coordinates into a text file
4. Save text file with .xyz extension
5. Open file in Spartan

Keep reading →

A few days ago I showed you how to model an energy profile for internal rotation. As part of that exercise, we tried (quickly) calculating a profile using AM1 and I said the results weren’t believable. I have also asked you to calculate some profiles using HF/3-21G. Are these more believable? Let’s see…

Truth = MP2/6-31G*

I have calculated energy profiles for internal rotation in 1,3-butadiene using 5 different tools: MMFF (a molecular mechanics force field), AM1 (semi-empirical QM), HF/3-21G and HF/6-31G (two versions of Hartree-Fock QM), and MP2/6-31G* (a post-Hartree-Fock QM tool). Of these, MP2 should give the most reliable results, so let’s just assume the results are reliable.

E relative (kcal/mol) vs. CCCC dihedral angle (^o) for MMFF, AM1, & MP2

MMFF energies are pretty good. AM1 are not. The AM1 curve is in the right ballpark, but all kinds of important details are incorrect: no skewed minimum, no cis (eclipsed) maximum, trans → skew barrier much too small.

E relative (kcal/mol) vs. CCCC dihedral angle (^o) for HF/3-21G, HF/6-31G* & MP2

The 3 models agree very closely. The agreement is especially good at large angles (180 > dihedral > 120), then subtle disagreements (error ~0.3 kcal/mol) appear.

The behavior of both Hartree-Fock models is very reassuring, but I have a sad fact to relate: the reliability of any approximate tool (and HF is definitely an approximation) varies from one molecule to the next. What works out so well for 1,3-butadiene, might or might not work for acrolein.