Addicoat and Mehta¹ have made a modification of the “Kick” algorithm. Recall, that the Kick method (discussed in this previous blog post) takes a collection of atom coordinates and applies a random kick to each atom. This creates a new initial configuration and a geometry optimization is performed starting form this configuration. If hundreds of such configurations are chosen, one hopes to locate most if not all reasonable structures. The new variation is to create fragments in which the atoms are held fixed. Then the kick is applied to the fragment as a whole.

Among the examples demonstrated in the paper, only one is of an organic species. They examined the structure of the Gly-Trp peptide associated with two water molecules. They used two conformations of the Gly-Trp dipeptide. The kick was supplied to one of these conformers and to the two water molecules. They ended up locating 22 structures with the first conformer and 46 with the second, spanning a range of about 0.5 eV. It must be pointed out that many of these configurations are clearly noncompetitive by not maximizing the degree of hydrogen bonding that can be obtained. Furthermore, many other conformers of the dipeptide would need to be examined to really map out the full PES and definitively locate all reasonable low-energy configurations. (it is not necessary that the gas-phase low-energy conformers yield the lowest energy configurations of the water complex.) Nonetheless, this modified kick procedure offers a “quick-and-dirty” means of generating a wide variety of initial conditions for locating structures.

References

(1) Addicoat, M. A.; Metha, G. F., "Kick: Constraining a Stochastic Search Procedure with Molecular Fragments," J. Comput. Chem., 2008, DOI: 10.1002/jcc.21026

A review of my book Computational Organic chemistry written by Christian Mück-Lichtenfeld, has appeared in Synthesis DOI: 10.1055/s-2008-1080541. A few things I particularly appreciate in the review is that Dr. Mück-Lichtenfeld recognized that the book in not intended to be a comprehensive review of computational organic chemistry but rather a survey of highlights, he mentions the book’s web site and blog, and favorably comments on the interviews that conclude each section.

I know this post is off topic for the blog, but yesterday’s New York Times simply raised my blood pressure.

The Book Review of the New York Times on Sunday March 30 has a review on the book Bonk. The book discusses sex research – and while that certainly is of interest – I want to focus on the associated artwork.

Now chemistry is not usually considered a particularly sexy subject, but its graphics can be fascinating. The periodic table might be the most widely known scientific graphic. The structure of DNA has captured the imagination of more than just scientists. And so it’s not unreasonable that the Times Book Review editors would choose to present some chemical (2-D) drawings. Given the subject of the book, one might have expected perhaps the structures of testosterone and progesterone. Instead, we get the following:

While these structures do not correspond to any known compound – not in and of itself a bad sin – the knowledge (or lack thereof) of chemistry displayed here is simply amazing. The graphic designer is certainly drawn to the preponderance of 6-member rings found in organic chemistry, but has taken this to an extreme! It seems that a random collection of atomic symbols were then willy-nilly added wherever the artist thought would be interesting. The result is simply absurd. One could only have hoped that some copy-editor with a chemistry background could have noticed some of the more glaring mistakes – oh, like five bonds to carbon! For the newspaper of record, these mistakes are simply unwarranted.

To make something good out of this, I am going to hold a contest with my first-semester organic students to identify the errors. The winner will get extra credit in the class – and I will post results here later on.

A review of my book Computational Organic Chemistry has appeared in the Journal of the American Chemical Society (DOI: 10.1021/ja077005h) The review by Donald E. Elmore of Wellesley College is very complimentary, pointing out many of the objectives I had hoped to achieve. Nonetheless, I am a bit disappointed in that he did not mention two of the more novel aspects of the book.

I am grateful that Elmore did mention the incorporation of the interviews with six leading theoreticians. However, he failed to mention the ancillary web site and this blog. Both of these electronic resources, I feel, greatly enhance the book. The ancillary web site includes links to all of the literature cited in the test, along with 3-D coordinates of all of the molecules with JMol for visualizing these structures. The blog provides a means for me to maintain the currency of the book. Blog posts extend the coverage of the book’s topics to the latest published research.

Is Elmore’s oversight reflective of a widespread belief that web enhancements offer little value to readers? Am I mistaken in believing that the web offers real opportunities to enhance a book (not just mine!)? I don’t view these web add-ons as “trivial” or “cute” or “trendy”.

I still believe that books offer many advantages to readers and scientists. But there are also limitations to what can be done on the printed page. I had hoped that the coupling of the printed book and the web enhancements would deliver the best of both worlds to my readers. I would enjoy hearing from you about whether these web resources are of value and if not, how do they fail? Are there other web-enabled resources I should explore?

In 2001, Pophristic and Goodman¹ initiated a controversy over the nature of the rotational barrier in ethane. Most organic textbooks argue that the barrier is due to unfavorable steric interactions in the eclipsed conformation. The Nature paper argues rather that the staggered conformation is favored due to hyperconjugative interactions between the C-H bond orbital on one methyl interacting with the anti-disposed antibonding C-H orbital of the other methyl group. Schreiner² wrote a follow-up essay where he was surprised by the response to this paper since he thought that the hyperconjugative explanation had been well-accepted within the community.

Now we have a nice review article by Mo and Gao³ that summarizes their recent investigation of the rotational barrier of ethane. Their main approach is to take advantage of the block localization method. Essentially, the methyl e-orbitals are localized to each methyl group, forbidding any hyperconjugation with each other. The energy difference then between the fully relaxed ethane and the block localized energy accounts for hyperconjugation – and this is about 0.76 kcal/mol, or about 25% of the barrier. The most important contributing factor to the barrier is the steric component – this is estimated by comparing the energies of the staggered and eclipsed conformers while freezing the π-like orbitals and removing the hyperconjugation effects. The estimate for the steric component is 2.73 kcal/mol. Mo and Gao conclude that the simple, traditional explanation, namely that steric interactions destabilize the eclipsed conformation, is in fact correct.

References

(1) Pophristic, V.; Goodman, L., "Hyperconjugation not Steric Repulsion leads to the Staggered Structure of Ethane," Nature 2001, 411, 565-568, DOI: 10.1038/35079036.

(2) Schreiner, P. R., "Teaching the Right Reasons: Lessons from the Mistaken Origin of the Rotational Barrier in Ethane," Angew. Chem. Int. Ed. 2002, 41, 3579-3582, DOI: 10.1002/1521-3773(20021004)41:19<3579::AID-ANIE3579>3.0.CO;2-S

(3) Mo, Y.; Gao, J., "Theoretical Analysis of the Rotational Barrier of Ethane," Acc. Chem. Res., 2007, 40, 113-119, DOI: 10.1021/ar068073w

The old EMSL Gaussian Basis Set Order Form (http://www.emsl.pnl.gov/forms/basisform.html) has now been updated to include a very nice interface. The new service is called Basis Set Exchange and is available at https://bse.pnl.gov/bse/portal.

This new service is built off of web 2.0 tools. Most critically, the basis sets are now stored in an XML format that builds upon Chemical Markup Language (CML). Not only can users get a wide variety of basis sets for most elements, basis set developers can upload their basis sets for curation and delivery. The design and implementation of this service is described in a recent article.¹

References

(1) Schuchardt, K. L.; Didier, B. T.; Elsethagen, T.; Sun, L.; Gurumoorthi, V.; Chase, J.; Li, J.; Windus, T. L., “Basis Set Exchange: A Community Database for Computational Sciences,” J. Chem. Inf. Model 2007, 47, 1045-1052, DOI: 10.1021/ci600510j.

Today I launch this blog – a blog to accompany my new book Computational Organic Chemistry. The book is officially released today – so go out and buy a copy before you get all tied up with the new Harry Potter!

This blog serves mainly to update the book. I will post on new articles and web sites that relate to topics covered in the book. It also serves as a mechanism to get feedback from you the reader. I welcome all comments, corrections, and suggestions.

I will also try to utilize new technologies within the post. Structures of molecules are available as xyz-coordinates and also directly within the blog using the JMol utility. I have added InChIs for most compounds. Articles are referenced by DOIs. Other technologies, like RDFa will be introduced in the future.

Enjoy!