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Mechanistic Ménage à trois

Wednesday, November 18th, 2009

Curly 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)

Oxygen-nitrogen exchange between three nitrosonium cations

This is very much a hypothetical mechanism, or a thought-experiment if you will. Three nitrosonium cations decide to get together to swap their partners. Each diatomic molecule swaps e.g. one oxygen for another during this exchange reaction (it could easily be studied experimentally of course using isotopic substitution). Three sets of three curly arrows have been used, shown in different colours above.  One set of these arrows at least has plenty of analogy in the real world; representing a π2s+π2s+π2s cycloaddition reaction. The other two sets represents rotation of the  in-plane π-set and the in-plane σ-set. What about the choreography? Can all three sets move at the same time? If so, they would provide an exception to the rule above; three bonds would concurrently change their order from 3 to 0; the other three the reverse of 0 to 3.

What does quantum mechanics say about this? Well, a well defined, synchronous concerted transition state can indeed be found (B3LYP/6-31G(d), DOI:  10042/to-2905) It has one imaginary frequency (click on the above diagram to view the animation) which does indeed perform the bond transposition function required! It has the form of the so-called Kekule mode (deriving from a mode found in benzene which involves shortening of the lengths of three bonds, and lengthening of the other three, much in the manner of the resonance named after  Kekule; see e.g. DOI: 10.1039/B911817A for more details). Of course, describing it as a change in the bond orders 3 → 0/0 → 3 is simplistic; the bond order in the nitrosonium cation itself is almost certainly somewhat less than three.  But clearly, the implicit rule that  mechanistic arrow pushing should not involve more than one arrow departing from or arriving at any one bond can be broken. I will leave it to the reader of this blog to see what happens when you try to rearrange the choreography of the above reaction. Try pushing first one set of three arrows, then another and a final third. What do you get? (the why of the dance is almost certainly due to electrostatic repulsions between the three nitrosonium cations).

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The SN1 Reaction- revisited

Wednesday, November 11th, 2009

In 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

  • ΔH†283 = 23.0 kcal/mol
  • ΔG†283 = 19.7 kcal/mol
  • ΔS†283 = +11.1 cal/mol/K

But first, a word about how this new transtion state has been obtained. The DFT treatment used is quite standard (B3LYP/6-31G(d) ), and one can indeed locate a transition state using just this approach (this is how the previous model was obtained). One has to work very hard to orient the starting guess for the geometry so that as many hydrogen bonds between the waters themselves, and to the substrate, are created. The previous model took quite a few guesses and attempts! The solvent in such a model is simulated by the explicit water molecules themselves. Of course, the quality of the solvent then depends on how many water molecules are used. A proper solvent field using explicit water molecules is thought to require 100s of water molecules! But a reasonable approximation/compromise may well be 13.

So how can the model be improved? Well, in many ways, some of which include treating the dynamics of the system. But I will stick just to two.

  1. Firstly, we assume that the water molecules are used to form a bridge between the incoming nucleophile (another water) and the leaving group (the chloride). In the previous model, two such bridges were constructed using the 13 water molecules. But in fact, there is still space between two of the methyl groups to construct a third bridge. This takes the total solvent molecules to 16.
  2. Solvent can also be modelled as a continuum, in which a cavity which the substrate occupies is surrounded by a field generated by the continuum solvent. The problem with these cavity approaches in the past has been that it is not easy to optimize the geometry of the molecule contained within the cavity. Because the cavity was constructed by tesselation, the first derivatives of the energy of the molecule within the cavity were not regular, and as a result, geometry optimization (and particularly transition state optimization) would frequently meander and fail to converge. Darrin York and Martin Karplus came to the rescue (some time ago, it has to be said, DOI: 10.1021/jp992097l) by formulating a smoothed out solvation cavity where the first (and second derivatives) are stable and well behaved. This new algorithm has now been implemented in Gaussian09, and it now allows really easy transition state location within a solvent cavity

The result of this optimization is shown below (and can be seen in original form at the following DOI: 10042/to-2894).

Transition state for Sn1 solvolysis of tert-butyl chloride

Transition state for Sn1 solvolysis of tert-butyl chloride. Click for animation.

The model has not changed that much compared to before. The reaction (imaginary) mode still clearly shows formation of the C-O bond and cleavage of the C-Cl bond. Also as before, there is a lot of motion of the methyl groups, as the forming cation induces stereo-electronic alignment with the adjacent C-H bonds (and which explains the large secondary deuterium isotope effects measured for this reaction, kH/kD (298) = 2.39, see DOI: 10.1021/ja01080a004). The hydrogen bonding pattern is also retained (despite the surrounding solvent field!). But what of the predicted activation parameters

  • ΔH†298 = 17.4 kcal/mol
  • ΔG†298 = 18.7 kcal/mol
  • ΔS†298 = -4.4 cal/mol/K

The overall free energy is in great agreement with experiment! But the entropy is the wrong sign!! The calculation is predicting that the transition state is more rigid than the reactant. One can see how this might happen, since the greater ionic character produces very much stronger hydrogen bonds, which strengthen the three solvent bridges. It may be simply that the rigid-rotor-harmonic-oscillator approximation breaks down horribly for the entropy in this calculation. But it is encouraging that the activation barrier is reproducing experiment, which suggests the model cannot be completely wrong!

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Posted in Interesting chemistry | 7 Comments »

Uncompressed Monovalent Helium

Saturday, October 3rd, 2009

Quite 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+?

Inventing the Helium bond

Inventing the Helium bond

This possibility is explored with the series X=Be, B, C (tetramethyl substituted, resulting in neutral, +1 and +2 systems overall). The first two emerge as stable in terms of having all positive force constants for C4v symmetry; the last emerges as a transition state and is not discussed further. The specific system X=B has a B-He bond length of 1.317Å/B3LYP/6-311G(d,p), 1.305Å/B3LYP/Def2-QZVPP and 1.290Å/double-hybrid RI-B2GP-B2PLYP/TZVPP, which does seem as if it might be typical of a single bond between these two elements. The ρ(r)B-He AIM value (B3LYP/6-311G(d,p) is 0.069 au, and νB-He of 713 cm-1 (727 for Def2-QZVPP basis) makes it about one third the strength of a C-H bond. The disynaptic basin for the B-He region integrates to 1.99 electrons, whilst the four B-C basins correspond to 1.22 electrons each.

X Charge ρ(r) X-He C-B ELF
integration		 νX-He, cm-1 Repository
Be 0 0.031 1.10 484 10042/to-2443
B 1 0.069 1.22 713 10042/to-2444

10042/to-2446

10042/to-2453
C 2 0.026 – 136 10042/to-2445
AIM for X=B-He

AIM for X=B-He. Click for 3D
B-He vibrational stretching mode

B-He stretching mode. Click to vibrate

We can conclude that for X=B, this species exhibits not only a pentavalent boron atom, but a monovalent helium atom. The latter bond may indeed be amongst the strongest ever proposed for this element in a ground state, and indeed perhaps is even viable as a solid crystalline compound rather than merely existing in the gas phase. The Cambridge crystal database contains no entries for He or Ne, not even as an encapsulated clathrate (although crystal structures of such complexes for Kr and Ar are known). Theoretical studies of the rare gases in endohedral fullerene-like cages (DOI: 10.1002/chem.200801399) predict that under these compressed circumstances e.g. two helium atoms can approach each other to 1.265Å or less (see also DOI: 10.1002/chem.200700467) but these close approaches were not considered to be chemical bonds as we think of them. Perhaps Merino, Frenking, Krapp and co’s search for the chemistry of helium (they had found it earlier in the gas phase excited states of their molecules, DOI: 10.1021/ja00254a005) might be realised for the ground state of the system described here.

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Posted in Hypervalency, Interesting chemistry | 1 Comment »

Pentavalent nitrogen and boron

Saturday, October 3rd, 2009

The 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

Pentavalency across a series

Pentavalency across a series

X Charge X-C length, Å ρ(r) C-X ELF integration ν-Trampoline, cm-1 ν X-H, cm-1 Repository
N 2 1.616 .172 1.14 883 3417 10042/to-2439
C 1 1.580 .195 1.10 970 3291 10042/to-2438
B 0 1.649 .136 1.06 949 2746 10042/to-2440
Be -1 1.817 .064 0.98 797 1887 10042/to-2441

The systems H, C and B are stable in the sense that the C4v-symmetric calculated geometry has only positive calculated force constants (Be has a small negative frequency). All show bond critical points in the  X-C region (although these bonds are clearly  bent) and X-H region, and significant integrations for the X-C disynaptic basins in the  ELF analysis. The boron analogue is also of interest as being a neutral rather than a charged molecule, and therefore may be a worthy target for synthetic effort.

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Full circle with carbon hypervalencies

Friday, October 2nd, 2009

The 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.

C4-symmetric pentavalent carbon

C4-symmetric pentavalent carbon

Now, the apical C-C bonds have shrunk to 1.58Å, the trampoline mode is increased to 970 cm-1 and the apical C-H frequency to 3291 cm-1. The apical C-C value for the AIM bond critical point ρ(r) is up 0.195 au and the disynaptic basin integration in that region is now 1.1 electrons. Replacing the apical C-H by C-F further strengthens the system (DOI: 10042/to-2447); the apical C-C bonds contract slightly to 1.57Å, the bouncing castle/trampoline mode shoots up to ν 1595 cm-1 , ρ(r) reaches 0.201 au and the disynaptic basins 1.25 electrons. With this latter system, the C-F disynaptic basin contains only 1.08 electrons, suggesting it is similar in nature to the other four bonds surrounding the apical carbon, i.e. this carbon is surrounded by five more or less equivalent bonds. The pseudo-halogen CN can also replace the F (DOI: 10042/to-2449) to similar effect (ρ(r)C-C 0.190, ρ(r)C-CN 0.290).

AIM Analysis

AIM Analysis
ELF Basin centroids

ELF Basin centroids. Click for 3D

We are back to pentavalent, pentacoordinate carbon again, but we have gradually optimized the properties of the system for five short C-C bonds surrounding one carbon atom, and the largest electron density and disynaptic basin integration. Whilst the sentiments expressed by Hoffmann, Schleyer and Schaefer (DOI: 10.1002/anie.200801206) for more realism in predicting molecules must not be ignored, it is to be hoped that the original suggestions made here will lead to the discovery of realistic and makeable molecules exhibiting true C-C hypervalency.

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It’s Hexa-coordinate carbon Spock – but not as we know it!

Friday, October 2nd, 2009

Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about pentavalent carbon, one can identify a series of conceptual connections. The first, by  Matthias Bickelhaupt and co, resulted in the suggestion of a possible frozen SN2 transition state. They used astatine, and this enabled a connection to be made between another good nucleophile/nucleofuge, cyclopentadienyl anion. This too seems to lead to a frozen Sn2 transition state.  The cyclopentadienyl theme then asks whether this anion can coordinate a much simpler unit, a C2+ dication (rather than Bickelhaupt’s suggestion of a (NC)3C+ cation/radical) and indeed that complex is also frozen, again with 5-coordinate carbon, and this time with five equal C-C bonds. So here, the perhaps inevitable progression of ideas moves on to examining the properties of this complex, the outcome being a quite counter-intuitive suggestion which moves us into new territory.

The journey starts with the previous observation that the HOMO of the carbyliumylidene cation, shown in the previous post, has prominent electron density along the five-fold symmetry axis of the molecule;

The HOMO orbital

The HOMO orbital. Click for 3D

This suggests that the apical 5-coordinate carbon might actually be basic, and hence coordinate a proton to form a di-cation (below). So adding a proton results in the following stable (in the sense of having all positive force constants) structure, with apical C-C bond lengths of 1.7Å (compared to 1.8Å for the unprotonated system) and the bouncing castle/trampoline mode of  875 cm-1 (DOI: 10042/to-2435) is likewise increased (for the pentamethyl derivative of the structure shown below). The apical C-H stretch has the highest value of all the CHs in the molecule, 3208 cm-1. The calculated proton affinity of the parent compound is 134.2 kcal/mol. To put this into context, we can compare this value with a range of first and second proton affinities reported for carbon bases by Frenking (DOI: 10.1002/cphc.200800208). The highest second proton affinity there reported (ie protonation of an already positive system) is around 106 kcal/mol, which is a good deal less than that found here! So we might conclude that our value  must be a candidate for highest second proton affinity ever proposed for a carbon base.

Hexa-coordinate Carbon?

Hexa-coordinate Carbon?

The value of ρ(r) for the AIM bond critical point located for each of the five apical C-C bonds is 0.156 au, again up from the value for the unprotonated species. As before, the Cp ring itself shows no ring critical point. An ELF analysis (below) shows five disynaptic basins in the  C-C bond region, with the basin integrating to  0.75 electrons each. Together with the electrons in the apical C-H bond, 6.09 electrons are associated with basins surrounding this carbon atom. Both the AIM and the ELF concur in describing this carbon as not only hexa-coordinated, but hexavalent (although the bonds are not the conventional two-electron type, but perhaps more akin to a six-centre-four-electron interaction).

ELF Basins

ELF Basins. Click for 3D

So I suggest that simple protonation of a highly basic cation has resulted in a six-coordinate carbon atom, which exhibits six strong bonds coordinated around it. I suppose it is inevitable again that one ends this post with the question whether this species too might one day be made.

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It’s penta-coordinate carbon Spock- but not as we know it!

Wednesday, September 30th, 2009

In the previous two posts, I noted the recent suggestion of how a stable frozen SN2 transition state might be made. This is characterised by a central carbon with five coordinated ligands. The original suggestion included two astatine atoms as ligands (X=At), but in my post I suggested an alternative which would have five carbon ligands instead (X=cyclopentadienyl anion).

The Sn2 transition state

The Sn2 transition state

However, these five ligands are not all equal; far from it. Three form normal strength bonds to the central carbon, and two very weak (deci)bonds. So, could a molecule be made with five equal bonds all coordinated to a central carbon atom? Well, the inspiration for designing such a molecule comes with the report of a remarkable compound of silicon by Jutzi and co-workers (DOI: 10.1126/science.1099879). Examples with  Ge, Sn and  Pb are also known.

The silyliumylidene cation

The silyliumylidene cation

Using a large non-coordinating anionic counterion, a crystal structure could be determined for the pentamethyl derivative (Refcode: BIDLEG), which reveals the five-fold symmetry of the silicon coordination. The obvious mutation therefore is to see if the corresponding carbon compound might be stable.  A B3LYP/6-311G(d,p) calculation (DOI: 10042/to-2433) run with  C5 symmetry reveals this system to have only positive force constants, with five equal C-C bonds to the central carbon, each with the unusual length of 1.799Å. The bouncing castle vibrational mode involving the pentacoordinate carbon has a value of  767 cm-1

The carbyliumylidene Cation

The carbyliumylidene Cation

So, not only do we now have a clearly penta-coordinate carbon, all five bonds are of equal length! More unusual still, all five ligands occupy one hemisphere of the carbon coordination. Why might such a geometry be stable? Well, as with the silicon analogue, C2+ has only two valence electrons left. To elevate this to the standard octet, it must accept six electrons, and the cyclopentadienyl anion fulfils this role perfectly. The top three occupied molecular orbitals are shown below.

The HOMO orbital

The HOMO orbital. Click for 3D
The HOMO-1 (degenerate) orbital

The HOMO-1 (degenerate) orbital. Click for 3D

An AIM analysis (below) shows five equal bond critical points, with ρ(r) 0.13 au for each (see previous post for comparison), a value which probably can be described by the term bond. The ∇2ρ value of +0.07 au is similar to that quoted in the previous post. Noteworthy is the observation that no ring critical point (RCP, yellow dots) can be found for the cyclopentadienyl ring itself, only for the five three-membered rings to the pentacoordinate atom.

AIM (Atoms-in-Molecules) analysis

AIM (Atoms-in-Molecules) analysis

Can the species be made? Well, given that it seems the case that carbon and silicon chemistries are inverted, ie what is stable with silicon is unstable with carbon, and vice versa, the answer is probably no. But one never knows until one has tried!

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Capturing penta-coordinate carbon! (Part 2).

Wednesday, September 23rd, 2009

In this follow-up to the previous post, I will try to address the question what is the nature of the bonds in penta-coordinate carbon?

This is a difficult question to answer with any precision, largely because our concept of a bond derives from trying to define what the properties of the electrons located in the region between any two specified atoms are. Such a local picture is somewhat at variance with the idea of electrons being delocalized across the entire molecule. Two procedures for analyzing the local electronic behaviour which we have been using recently are AIM (Atoms-in-Molecules) and ELF (the topology of the Electron localization function). There are many useful published articles which elaborate these concepts; if you want to read some of them, start at DOI 10.1021/ct8001915 and follow the cited articles.

Firstly, the AIM analysis of the system below, where X=cyclopentadienyl anion and Y=CN.

The Sn2 transition state

The Sn2 transition state

This is shown below. If you click on the image, you will see a rotatable version of this diagram. The coloured (red, yellow and green) dots represent so-called critical points in the curvature of the electron density function ρ(r). The red dots are known as bond critical points, or BCPs. These (almost) always are found along the line connecting two atoms which we tend to refer to as a bond. You will see two that have been circled in the diagram below, and these appear to show a bond connecting the central 5-coordinate carbon atom and a carbon of each of the cyclopentadienyl rings (which themselves are revealed as rings by the presence of a yellow dot). Indeed, that central carbon atom does seem to have five red dots radiating out along lines connecting it to five carbon atoms.

AIM analysis (red = bond critical points, yellow = ring, green = cage)

AIM analysis (red = bond critical points, yellow = ring, green = cage)

So is the case proven for pentavalent carbon? Well, no. Firstly, one has to inspect the value of ρ(r) at the circled red dot. This has a (calculated) value of 0.022 au and a calculated bond length of ~2.7Å. We need to calibrate this against a real system as reported in DOI: 10.1021/ja710423d (below):

Hexa-coordinate carbon

Hexa-coordinate carbon. Click for 3D model

Here, the electron density ρ(r) was actually measured using X-ray diffraction, and found to be ~0.017 for bond critical points found connecting the central carbon and each of the four oxygen atoms. The length of these “bonds” was measured as  ~2.7Å. The agreement with our frozen transition state is quite striking.

One can go a little further and inspect the (2nd) derivative of the electron density at the bond critical point, termed the Laplacian, or ∇2ρ, which tells what kind of “bond” one might have. The measured value of ∇2ρ for the system above was ~0.06 au, and the calculated value for our pentacoordinate system is 0.04 au, which again suggests we are dealing with a very similar interaction in both systems (one hypothetical and calculated, the other real and measured). The use of the term  interaction was deliberate.  It is less loaded than the term  bond. Thus the value of ρ(r) for an undisputed C-C single bond is around 0.28 au, around ten times higher than our putative bonds. Since we do not really wish to grace a ρ(r) value of 0.022 with the term decibond (or any other fraction of a single bond) perhaps it is best to call it just an interaction, and leave open the question of how strong that interaction is! So, despite the  AIM analysis  finding a bond critical point, we shall settle for interpreting that merely as an interaction, and not a bond!  Well, is an interaction (or come to that, a decibond) worthy of counting towards a coordination?  Perhaps!

So AIM can provide information about the curvature and density of the electrons in the region of a bond/interaction. But it does not provide any information about another simple question which the term bond implies. How many electrons might be involved? Ever since  G. N. Lewis coined the term two-electron bond in 1916,  we have become used to interpreting bonds in terms of simple (often integer) numbers of electrons.  A carbon-carbon single bond shares two electrons; a double bond four electrons, and so on. We use this concept all the time in the technique known  as arrow-pushing, which helps us delineate mechanisms of reactions. Might it be possible to  identify how many electrons are involved in bonds/interactions of the captured  SN2 species above? Enter the ELF technique. It would not be appropriate to delve into the theory of this method here; suffice to say that  (approximately), the  bond-critical-point of the  AIM analysis in this case would map to a disynaptic basin for ELF. Thus a two-electron single bond will reveal a disynaptic basin (the centroid of which approximately matches the position of the  AIM BCP), which can be integrated to approximately two electrons. Shown below are the centroids of the disynaptic basins calculated for our SN2 species:

ELF basins (purple dots) for the SN2 system

ELF basins (purple dots) for the SN2 system. Click for 3D model

The most striking difference with the AIM analysis is that that the central carbon is surrounded only by three, not five disynaptic basins. The BCPs found for the two di-axial interactions have no counterpart in synaptic basins. Of course, that does not mean that there are no electrons that can be integrated in that region, just that the curvature of the density in that region is not sufficiently well defined to define a bounded volume of space which can be clearly integrated. Perhaps that condition is what we might mean by a bond!

The three disynaptic basins that do surround the central carbon integrate to a total of 7.85 electrons, which is close enough to 8 for us to say that this carbon is NOT hypervalent!

So what is our final conclusion? The frozen SN2 species is not hypervalent. It could reasonably be said to be coordinated by three bonds, and two diaxial substituents that interact with the central carbon weakly. Perhaps rather than penta-coordinate, the central carbon could be described as pentacoordinaloid!

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Capturing penta-coordinate carbon! (Part 1).

Tuesday, September 22nd, 2009

The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label, SN2. It is normally a slow reaction, with half lives often measured in hours. This implies a significant barrier to reaction (~15-20 kcal/mol) for the transition state, shown below (X is normally both a good nucleophile and a good nucleofuge/leaving group, such as halide, cyanide, etc.  Y can have a wide variety of forms).

The Sn2 transition state

The Sn2 transition state

This transition state is normally regarded as the only situation in which carbon can sustain penta-coordination (there are some exceptions), and this is often contrasted with the analogous situation for silicon, which demonstrates an abundance of stable penta- (and hexa-)coordinate (crystal) structures. Perhaps inevitably therefore, chemists have set themselves the goal of capturing a penta-coordinate carbon, not as a transition state with fleeting lifetime, but as a stable (and perchance crystalline) species.  The best strategy is to explore potential systems computationally, and the latest report of such an exploration has some suggestions for synthesis (Pierrefixe, S. C. A. H.; van Stralen, S. J. M.; van Strale, J. N. P.; Guerra, C. F.; Bickelhaupt, F. M., “Hypervalent Carbon Atom: “Freezing” the SN2 Transition State,” DOI: 10.1002/anie.200902125). Their suggestion corresponds to Y=CN and X=At (Astatine), a rather esoteric combination it has to be said.  In the manner of the blogosphere, Steve Bachrach has noted this report in his own blog, where a discussion has opened up on the origins of why carbon can be regarded as abnormal (at least compared to silicon), and more particularly whether such a species should be regarded as merely hypercoordinate, or as Bickelhaupt and co-workers suggest, hypervalent.

In fact, such reports are not new. As I note in the discussion of Steve’s blog, a crystalline structure of a hexa-coordinate carbon compound was reported in 2008 (DOI: 10.1021/ja710423d (below), and it is also tentatively described as possibly hexavalent near the end of the article! I shall return to this compound in the second part of this post.

Hexa-coordinate carbon

Hexa-coordinate carbon

The astatine system reported above is unusual, and it really only contains three carbon-carbon bonds surrounding the pentacoordinate carbon. The compound above contains only two such C-C “bonds”. It would be perhaps more interesting to ask if one could design a compound with five C-C bonds surrounding the putative pentacoordinate atom. Whilst mulling over Steve’s post, and pondering my contribution to that blog, a colleague in my department wandered into my office (my door is almost always open) and without saying a word, he wrote a structure on my blackboard (yes, I really do have such).  He then walked out (almost;  I believe he did mutter perhaps two words before leaving). He had sketched the key feature of an article by Ethan L. Fisher and Tristan H. Lambert entitled Leaving Group Potential of a Substituted Cyclopentadienyl Anion Toward Oxidative Addition (DOI: 10.1021/ol901598n). This triggered the following question in my mind: could the aromatic cyclopentadienyl anion act as the X group in the pentacoordinate carbon example above? The essential property of group X is that it must be big!  Well, cyclopentadienyl can be made big! It would also achieve the purpose of forming a penta-coordinate carbon with  five  C…C bonds.

So in it goes for a B3LYP/6-311+G(2df) calculation. Surely, the life of a computational chemist is an easy one; all one  has to do is wait a few hours (or, with a large basis set, days) for an answer. The result is shown below.

The SN2 reaction captured with cyclopentadienyl anion

The SN2 reaction captured with cyclopentadienyl anion

The key vibrational mode (which you can see animated if you click on the image above) has a wavenumber of 194 cm-1 (B3LYP/6-311+G(2df); other basis sets show similar values). It corresponds to the SN2 mode,  and is what we normally think of as the  transition or reaction normal mode for this reaction. But  in this case, it is not an imaginary mode, but a real mode!  The SN2 has been (virtually) captured for a penta-coordinate carbon with five C…C interactions. How does it compare with the astatine system noted in 10.1002/anie.200902125? Well, unfortunately, the umbrella-mode for that system  is only reported as a force constant without mass weighting, so it cannot be compared to the mass-weighted value we have here. The calculation is digitally archived (e.g. as 10042/to-2407 or 10042/to-2415) so you can analyze it for yourself!

An obvious question to ask is what the nature of the  axial bonds for X=cyclopentadienyl is. Is the central carbon hypercoordinate, or hypervalent, or both? But this blog is quite long enough already, and so this will all be discussed in part 2, to follow shortly.

Oh, one final comment. The issue of hypervalency and hypercoordination of carbon has previously been discussed largely in conventional scientific publications (for which DOIs are provided above). The forum moved to Salt Lake  City in the  USA, where some of the results were presented orally at the ACS spring conference in 2009.  Now that it  has been formally published, it has been taken up by Bachrach in his blog, where some of the discussion has continued. So where should I have presented the present result?  In the primary scientific literature? Or perhaps another ACS meeting? Well, here it is in another blog (I have been variously told I am either brave or very foolish for doing so!). And as I write this, of course it is not peer reviewed (but there is nothing to stop people from commenting on this of course, as has happened in Bachrach’s blog). Will it “count” here – in other words, does it (yet) have any scientific respectability? Should  blogs report new scientific results, or merely be reserved for commenting on such results which have been reported in the “proper scientific manner”? Will indeed this result appear in the future in the scientific literature under different authorship, but with no accreditation for this blog? If I do choose to “write it up properly” (assuming the journals now let me), can I cite this blog in the way one can cite the ACS conferences? I do not suppose many people know what the answers are to all these questions. Perhaps the appearance of this post might provide some?

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Posted in Hypervalency, Interesting chemistry | 3 Comments »

Spotting the unexpected: Anomeric effects

Friday, September 18th, 2009

Chemistry can be very focussed nowadays. This especially applies to target-driven synthesis, where the objective is to make a specified molecule, in perhaps as an original manner as possible. A welcome, but not always essential aspect of such syntheses is the discovery of new chemistry. In this blog, I will suggest that the focus on the target can mean that interesting chemistry can get over-looked (or if observed, not fully exploited in subsequent publications). Taking a synthesis-oriented publication at (almost) random entitled Synthesis of 1-Oxadecalins from Anisole Promoted by Tungsten (DOI: 10.1021/ja803605m) which appeared in 2008, the following molecule appears as one of the (many) intermediates.

A cyano-substituted cis decalin

A cyano-substituted cis decalin. Click for 3D

This molecule has an X-ray structure reported, as a means of confirming the stereochemistry at the various centres, and particularly at the carbons bearing a cyano group. Labelled as compound  22 in the publication, there is no discussion or follow-up on the resulting conformation of this compound, which in fact adopts one with both cyano groups axial (there are three other possibilities of course,  in which the cyano groups can be both equatorial, or one axial and the other equatorial). A B3LYP/6-31G(d,p) calculation of these conformations confirms that the di-axial isomer is indeed the most stable (see for example DOI: 10042/to-2402 for a digital repository entry for the calculation).

An inspection of the  molecular orbitals for the di-axial isomer reveals that the HOMO involves interaction of the alkene π-MO with the  C…CN bond (top) and the HOMO-1 involves interaction of the oxygen lone pair with the  C…CN bond (bottom). This sort of interaction is a classical anomeric effect!

HOMO.

HOMO with alkene-cyano anomeric interaction. Click for 3D

HOMO-1 showing anomeric interaction

HOMO-1 with O-CN anomeric interaction. Click for 3D

So what is unusual about it? Well, anomeric effects are normally described in text books and lecture courses as involving predominantly oxygen (and nitrogen) as an electron pair donor, and C…O (and C…N and C…F) σ-bonds as the acceptors. The stereoelectronic alignment of course has to be anti-periplanar, and this orientation will control how the anomeric effect operates. What you may not find in the text books is a C…CN bond as the electron acceptor! But if  e.g. C…F  can be one, why not  C…CN (the cyano group is often described as a pseudo-halogen).  If you inspect the  3D model above, you can see that the  C…CN bond associated with the adjacent oxygen is perfectly set up for anti-periplanar alignment with one of the oxygen lone pairs (an arrangement not possible if the  CN group had been equatorial).  The C…CN bond length (1.49 Å) is indeed about  0.02Å longer than one would normally expect of such a bond.

Inspection of the  HOMO shows an almost identical interaction between the C…CN bond and the alkene, implying that here it is the electrons from an alkene that are the donor. This combination, of an alkene as donor and a C…CN group as an acceptor has  (to my knowledge) never been suggested as an anomeric effect pair. It is not as strong as before (C…CN 1.47Å) and perhaps in this case, it adopts the axial position because the alternative equatorial conformation is disfavoured for other reasons.

But, and this is the point of this blog, the structure of compound 22 in the synthesis project above has some interesting aspects, which perhaps can lead to new insights and even new chemistry.  One can but wonder how many reported compounds have properties which are perhaps more interesting than their authors realize, and how much new chemistry is lurking in the literature which has not  (yet) been noticed. With more than 50,000,000 compounds now reported in Chemical Abstracts, there is surely lots out there to discover. However, will it be humans who will increasingly do so in the future, or automatons scouring the Semantic Web? But here we digress to a new topic!

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Posted in Chemical IT, Interesting chemistry | 7 Comments »

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