Scientists write blogs for a variety of reasons. But these do probably not include getting tenure (or grants). For that one has to publish. And I will argue here that a blog is not currently accepted as a scientific publication (for more discussion on this point, see this article by Maureen Pennock and Richard Davis). For chemists, publication means in a relatively small number of high-impact journals. Anything more than five articles a year in such journals, and your tenure is (probably) secure (if not your funding).
To blog or to publish. That is the question.
February 9th, 2010The conformational analysis of cyclo-octane
January 31st, 2010In the previous post, I suggested that inspecting the imaginary modes of planar cyclohexane might be a fruitful and systematic way in which at least parts of the conformational surface of this ring might be probed. Here, the same process is conducted for cyclo-octane. The ring starts with planar D8h symmetry, and at this geometry (B3LYP/6-311G(d,p), DOI: 10042/to-3742) five negative force constants (corresponding to imaginary modes) are calculated. The most negative is non-degenerate, and gives directly the crown conformation of D4d symmetry (DOI: 10042/to-3738). The remaining four modes comprise two degenerate pairs. Following either of the E2u eigenvectors downhill leads to another conformation, D2d (DOI: 10042/to-3741), with a geometry which is noteworthy for exhibiting a pair of unusually close non-bonded H…H contacts (1.908Å). This value is about 0.3Å shorter than the sum of the Wan der Waals radii (DOI: 10.1021/jp8111556). We can debate whether such a close approach or inter-penetration of two hydrogens is a bond or not (an AIM analysis appears at the bottom of this post). Read the rest of this entry »
The conformation of cyclohexane
January 28th, 2010Like benzene, its fully saturated version cyclohexane represents an icon of organic chemistry. By 1890, the structure of planar benzene was pretty much understood, but organic chemistry was still struggling somewhat to fully embrace three rather than two dimensions. A grand-old-man of organic chemistry at the time, Adolf von Baeyer, believed that cyclohexane too was flat, and what he said went. So when a young upstart named Hermann Sachse suggested it was not flat, and furthermore could exist in two forms, which we now call chair and boat, no-one believed him. His was a trigonometric proof, deriving from the tetrahedral angle of 109.47 at carbon, and producing what he termed strainless rings.
Blisteringly bent (quadruple) bonds
January 23rd, 2010So ingrained is the habit to think of a bond as a simple straight line connecting two atoms, that we rarely ask ourselves if they are bent, and if so, by how much (and indeed, does it matter?). Well Hursthouse, Malik, and Sales, as long ago as 1978, asked just such a question about the unlikeliest of bonds, a quadruple Cr-Cr bond, found in the compound di-μ-trimethylsilylmethyl-bis-[(tri-methylphosphine) (trimethylsilylmethyI)chromium(II)(DOI: 10.1039/dt9780001314[cite]10.1039/dt9780001314[/cite]). They arrived at this conclusion by looking very carefully at how the overlaps with the Cr d-orbitals might be achieved.
Semantic Blogs
January 17th, 2010A Semantic blog is one in which the system at least in part understands about (some of the) concepts and topics that are in the content. The idea is that this content can be more intelligently (is that the correct word?) and importantly, automatically searched, harvested, and connected to the same or similar concepts found elsewhere in other blogs and the Web as whole. I am writing this blog using Firefox, having added a Firefox extension called Zemanta. As I write, the system offers suggestions for similar themes elsewhere that I could choose to link to the blog (and obviously the more one writes, or the more specific the terms one uses, the more sensible the suggestions become. At this precise moment, it is still offering fairly generic suggestions, one of which I have just chosen to add). My purpose in this particular post is to explore how the very process of writing a blog might be affected by such a product. I am also inferring (but cannot add detail at the moment) that all the (semantic) connections or links to other materials will be expressed in this blog using some form of formal declaration, such as e.g. RDF or RDFa.
Chemical intimacy: Ion pairs in carbocations
January 11th, 2010The scheme below illustrates one of the iconic reactions in organic chemistry. It is a modern representation of Meerwein’s famous experiment from which he inferred a carbocation intermediate, deduced from studying the rate of enantiomerization of isobornyl chloride when treated with the Lewis acid SnCl4.
How long will a blog last? ArchivePress
January 9th, 2010After around 40 posts here, I decided to take a look at the whole effort and ask some questions. For example
Read the rest of this entry »
Contriving aromaticity from S≡C Triple bonds
January 1st, 2010In the previous post, the molecule F3S-C≡SF3 was found to exhibit a valence bond isomerism, one of the S-C bonds being single, the other triple, and with a large barrier (~31 kcal/mol, ν 284i cm-1) to interconversion of the two valence-bond forms. So an interesting extension of this phenomenon is shown below:
Clar islands in a π Cloud
December 9th, 2009Clar islands are found not so much in an ocean, but in a type of molecule known as polycyclic aromatic hydrocarbons (PAH). One member of this class, graphene, is attracting a lot of attention recently as a potential material for use in computer chips. Clar coined the term in 1972 to explain the properties of PAHs, and the background is covered in a recent article by Fowler and co-workers (DOI: 10.1039/b604769f). The concept is illustrated by the following hydrocarbon: