Archive for June, 2013

Three interesting recent Angew. Chem. papers

A note here on a few recent Angew. Chem. articles of interest to readers of this blog. The first is a comment by Frenking1 concerning the “trilogue” by Shaik, Hoffmann and Rzepa2 which discusses the nature of C2, especially the notion that this molecules may possess a quadruple bond (see this post for a previous post on this article.) Frenking argues that the force constant associated with the C-C stretch in C2 is smaller than that in acetylene, so how can one argue that there is some quadruple bond character in C2? A reply from the original authors3 accompanies the comment by Frenking, and they respond by noting that the PES for bond stretching is unusually flat. I had the generally sense, though, that the authors of both articles were really talking past each other and that an opportunity for a more fruitful discussion has been missed.

The other article of note is an excellent review of de novo enzyme design as performed by the Baker and Houk labs.4 This review, authored by leaders of this effort, highlights their approach to this “holy grail” problem. The general notion is to use standard tools of computational chemistry to design a theozyme. Next, this theozyme is placed into known protein motifs with the attempt to have it fit without too much steric clash. The protein is then mutated one residue at a time to optimize the fit and binding of the theozyme to substrate. Lastly, the best targets are synthesized and tested. (The reader can see my post one of their projects: synthetic Diels-Alderase.)


(1) Frenking, G.; Hermann, M. "Critical Comments on “One Molecule, Two Atoms, Three
Views, Four Bonds?”," Angew. Chem. Int. Ed. 2013, 52, 5922-5925. DOI: 10.1002/anie.201301485.

(2) Shaik, S.; Rzepa, H. S.; Hoffmann, R. "One Molecule, Two Atoms, Three Views, Four
Bonds?," Angew. Chem. Int. Ed. 2013, 52, 3020-3033, DOI: 10.1002/anie.201208206.

(3) Danovich, D.; Shaik, S.; Rzepa, H. S.; Hoffmann, R. "A Response to the Critical Comments on “One Molecule, Two Atoms, Three Views, Four Bonds?”," Angew. Chem. Int. Ed. 2013, 52, 5926-5928, DOI: 10.1002/anie.201302350.

(4) Kiss, G.; Çelebi-Ölçüm, N.; Moretti, R.; Baker, D.; Houk, K. N. "Computational Enzyme Design," Angew. Chem. Int. Ed. 2013, 52, 5700-5725, DOI: 10.1002/anie.201204077.

Bond Dissociation Energy &Enzyme Steven Bachrach 24 Jun 2013 No Comments

Second edition of Computational Organic Chemistry

After much delay, the second edition of my book Computational Organic Chemistry has been sent off to the publisher! This edition is an update from the first, including many new examples of the major themes covered in the first edition. In addition there are some entirely new sections and chapters, extending the scope of the book into areas not mentioned in the first edition. There are also some new interviews of major players in the field. Comments from this blog where helpful in guiding my choices for what new materials to include in the book.

I suspect that editing of the book and making it all ready for print will take through the rest of the year. Later on this year I will discuss in the blog the new features of the book in some detail.

I intend to continue to blog on new papers through the publication of the second edition and beyond. So continue to monitor this blog for new papers and for information on where and when to purchase the second edition!

Uncategorized Steven Bachrach 10 Jun 2013 6 Comments