Structural motifs

A great deal of molecular modeling is spent, as it should be, on generating numbers (usually energies) that can be compared with experiment. The amount of time and effort spent in the inspection and analysis of molecular geometries pales by comparison. And yet, a number often means very little to us by itself. Inspiration comes from recognizing relationships and patterns. From seeing what is there.

This principle has been recognized by scientists for generations. Just think of Pasteur looking at chiral crystals of tartaric acid in his microscope, or of Galileo looking at Jupiter through his telescope, or of Pauling looking at molecular models of alpha-helices and beta-sheets. The list of important discoveries that were inspired by looking goes on and on, yet in our haste to complete assignments and produce publishable results, the idea of patient looking, of looking again, and of looking even more, strikes us as a luxury that no productive member of society can afford, and no modern multitasking individual can sit still for.

Here’s a story about two scientists that I came across in a book in the Reed College library called, amazingly enough, “One Dharma” (Ch. 7) by Joseph Goldstein:

Paper #3 – Instructions for analyzing transition state models

Paper #3 is “Stereoselectivity Control by Torsional Steering in an Intramolecular Diels-Alder Reaction of Vinyl Oxocarbenium Ions” by Robert Iafe and Kendall Houk (Org. Lett., 2006, 3469) (dx.doi.org/10.1021/ol061085x). Full reading instructions have been placed on the Papers page. This post covers item #2 in these instructions, namely, converting published transition state models into SPARTAN’08 models, studying their structures, and writing up your analysis.

Learning to Love ‘Energy Profile’ Calculations

Stupid @$#@!ing molecular models!!!!!

Yes, that’s exactly how I felt around 9 PM tonight after I had tried multiple times without success to generate a list of H2O2 conformations. Using a host of variations on the procedure that we had tried in class, I tried over and over again to get a list of 13 models with optimized geometries and evenly spaced dihedral angles, but it never worked. Just like you saw in class, I wound up with several models that failed to reach their equilibrium geometry and/or several models with the wrong dihedral angles. I was on the verge of quitting when it occurred to me: all of my attempts had started from one model. Maybe I needed to try something new right from the beginning?

HW #2 – More thoughts on today’s added problem

I’d like to clarify the problem that I added to the homework assignment due Wednesday.

I’m sure you all understand what to do: calculate HF/3-21G equilibrium geometries for three conformers of 1, 3-butadiene: planar s-trans, planar s-cis, and skew s-cis.

I suspect, though, that you are not so sure what to do after that. I said you should “rationalize” your results, but what does that mean?

HW #1 – comments

The homework assignments were very good. (Pat on back.) But there are still a couple of reasons to read the answers that I have posted online (see Homework page). Here are some of my favorites.

• Endo and exo labels used incorrectly.
• Endo and exo compounds drawn incorrectly. Note: the 3-membered ring cannot be wriggled up and down to make different stereoisomers.
• Diastereomeric ratio (dr) does not refer to endo/exo ratio.
• So what are all of the compounds in the product mixture? What are their relative amounts? One or more of these answers will surprise you.
• What are the mechanisms for #5 and #6?
• Did you ever overlook the stereochemistry in a Diels-Alder product? (Yes, all of you did, I think. In #5 and #6.)