In my first post on this theme, an ELF (Electron localization function) analysis of the bonding in the molecule HO-S≡C-H (DOI: 10.1002/anie.200903969) was presented. This analysis identified a lone pair of electrons localized on the carbon (integrating in fact to almost exactly 2.0) in addition to electrons in the CC region. This picture seems to indicate that the triple bond splits into two well defined regions of electron density (synaptic basins). In a comment to this post, I also pointed out that an NBO analysis showed a large interaction energy between the carbon lone pair and the S-O σ* orbital, characteristic of anomeric effects (in eg sugars). This latter observation gives us a handle on possibly tweaking the effect. Thus if the S-O σ* orbital can be made a better electron acceptor, then its interaction with the lone pair could be enhanced.
Author Archive
The nature of the C≡S Triple bond: Part 2
Saturday, December 5th, 2009The nature of the C≡S triple bond
Tuesday, December 1st, 2009Steve Bachrach has just blogged on a recent article (DOI: 10.1002/anie.200903969) claiming the isolation of a compound with a C≡S triple bond;
The Fine-tuned principle in chemistry
Sunday, November 29th, 2009The so-called Fine tuned model of the universe asserts that any small change in several of the dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). I suggest here that there may be molecules which epitomize the same principle in chemistry. Consider for example dimethyl formamide. The NMR spectra of this molecule reveal that at room temperature, the two methyl groups are inequivalent, indicating that the rate constant for rotation about the C-N bond has a very particular range of values at the temperatures at which most living organisms exist on our planet.
Mechanistic Ménage à trois
Wednesday, November 18th, 2009Curly arrow pushing is one of the essential tools of a mechanistic chemist. Many a published article will speculate about the arrow pushing in a mechanism, although it is becoming increasingly common for these speculations to be backed up by quantitative quantum mechanical and dynamical calculations. These have the potential of exposing the underlying choreography of the electronic dance (the order in which the steps take place). The basic grammar of describing that choreography tends to be the full-headed curly arrow for closed shell systems and its half-barbed equivalent for open shell systems. An effectively unstated and hence implicit rule for closed shell systems is that only one curly arrow is used per breaking or forming bond, i.e. electrons move around bonds in pairs. So consider the following reaction (inspired by a posting on Steve Bachrach’s blog)
The SN1 Reaction- revisited
Wednesday, November 11th, 2009In an earlier post I wrote about the iconic SN1 solvolysis reaction, and presented a model for the transition state involving 13 water molecules. Here, I follow this up with an improved molecule containing 16 water molecules, and how the barrier for this model compares with experiment. This latter is nicely summarized in the following article: Solvolysis of t-butyl chloride in water-rich methanol + water mixtures, which (for pure water) cites the following activation parameters
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Hypervalency: a reality check
Monday, October 5th, 2009We have seen in the series of posts on the topic of hypervalency how the first row main group elements such as Be, B, C and N can sustain apparent hypercoordination and arguably hypervalency. The latter is defined not so much by expanding the total valence shell of electrons surrounding the hypervalent atom beyond eight, but in having more than four well defined bonds to it, as quantified by AIM and ELF analysis. The previous post made the suggestion of how a compound involving hypervalent boron could also sustain a genuine bond to the rare gas helium. It is surely time to seek evidence that this type of bonding can be sustained in reality. Fortunately, a crystal structure of a reasonably analogous compound IS available (DOI: 10.1016/0022-328X(94)05089-T).
Uncompressed Monovalent Helium
Saturday, October 3rd, 2009Quite a few threads have developed in this series of posts, and following each leads in rather different directions. In this previous post the comment was made that coordinating a carbon dication to the face of a cyclopentadienyl anion resulted in a monocation which had a remarkably high proton affinity. So it is a simple progression to ask whether these systems may in turn harbour a large affinity for binding not so much a H+ as the next homologue He2+?
Pentavalent nitrogen and boron
Saturday, October 3rd, 2009The previous posts have seen how a molecule containing a hypervalent carbon atom can be designed by making a series of logical chemical connections. Another logical step is to investigate whether the adjacent atoms in the periodic table may exhibit similar effects (C2+ ≡ B+ ≡ N3+ ≡ Be ≡ O4+). So here are reported some results (B3LYP/6-311G(d,p) ) for boron, beryllium and nitrogen, for the general tetramethyl substituted system shown below
Full circle with carbon hypervalencies
Friday, October 2nd, 2009The previous post talked about making links or connections. And part of the purpose for presenting this chemistry as a blog is to expose how these connections are made, or or less as it happens in real time (and not the chronologically sanitized version of discovery that most research papers are). So each post represents an evolution or mutation from the previous one. To recapitulate, we have seen how the idea of cyclopentadienyl anion as a ligand for a dipositive carbon atom has evolved. Let us move in yet another direction; the cyclobutadienyl dianion. This ligand has recently been shown to bind Mg2+ (DOI: 10.1002/ejic.200800066), so why not He2+? And picking up again the previous theme, we will then protonate the bound complex. The result now is a monocation, and it has the C4v-symmetric structure shown below (DOI: 10042/to-2438). This bears some resemblance to pyramidane, a neutral C5H4 compound with hemispherical carbon reported in 2001 (DOI: 10.1021/jp011642r) which is also a stable minimum in the potential energy surface.