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Zwitterions vs allenes

25 June 2009 Part II updated 26 July

No long ago this blog reported on an allene vs zwitterion debate featuring Bertrand & group vs Christl & Engels (here). The fundamental question is if cylic allenes can exist despite built-up of strain energy and if so whether the central carbon atom in the allene can be zerovalent with proper substituents. The Bertrand-yes team have now come up with an even smaller cyclic allene than the one they created to start the debate (Melaimi et al. DOI).

Starting from spiro compound 1 , triethyloxonium tetrafluoroborate adds an ethyl cation in 2, the ethoxy groups are replaced by piperidine in 3 and finally the proton is removed by LDA to cyclobutane allene 4. The reaction product with (RhClcod)2 , 5 can be isolated. The allene is found to be a strong donor ligand. Reaction with tetrafluoroboric acid gives the dication 6 which supports evidence for the two lone pairs on the central carbon atom. These two findings do not support the alternative zwitterion 7 that could perhaps be favored by Christl & Engels.

Update (July 26): Hanninen et al. (DOI) find by computation that when an allene is bent the central carbon atom becomes a carbene with two pi electrons delocalized on the adjacent carbon atoms. No longer an allene then!


24 June 2009 - News

In the field of organopalladium chemistry there is some debate about the possible existence of unconventional Pd(II)-Pd(IV) cycles in palladium catalyzed reactions in addition to familiar Pd(0)-Pd(II) cycles (see earlier blog on this topic here). The debate is not always obvious: all too often Pd(IV) is presented as nothing unusual like announcing Martians can ride bicycles without explaining first that Martians have finally been found. Likewise the palladium 0-II camp happily ignores anything to do with II-IV or so it seems.
New work by Powers & Ritter (DOI) does not exactly settle the debate but introduces a new palladium species , Pd(III) in certain C-H activation reactions.

In this reaction benzo(h)quinoline 1 is first reacted with palladium acetate resulting in Pd insertion into the C-H bond and simultaneous Pd coordination to the quinoline nitrogen atom. In the dimer 2 the palladium atoms are connected with two acetate bridging ligands. Addition of an oxidizing reagent such as chlorine or dichloroiodobenzene has the surprising effect of forming 3 with a Pd(III)-Pd(III) chemical bond by oxidative addition. No evidence was found for a Pd(IV) species such as 6.

By heating the dimer the chlorinated benzoquinoline 4 is formed in a concerted 1,1-reductive elimination. An equal amount of an as yet unknown mixture of Pd(II) compounds (5) is also formed which by adding silver acetate and more of 1, reforms the dimer 3. The palladium dimer also works in catalytic amounts.


22 June 2009 improbable molecules

Diberyllium or Be2 is is not supposed to exist yet pursued by scientists for over 70 years with over 100 published papers. Recently Merrit et al. (DOI) have recorded new experimental evidence for the molecule but prefer to call it the beryllium dimer.

A simple MO diagram explains why Be2 must be indefinitely unstable. When the two beryllium 2s orbitals interact they split in two energy levels - one bonding (lower energy) and one antibonding (higher energy) - and when the four electrons of both Beryllium atoms are divided over these two new molecular orbitals both levels get fully occupied and there is no net energy gain and therefore no bond. Many inprobable diatomic molecules spend their lives in obscurity. For some time in Wikipedia dilithium was called dilithium (real) because the actual dilithium page was devoted to dilithium: the fictional Star Trek chemical element.

The physics and experimental setup as always in this type of research is fuzzy, the Meritt work is no exception. Creating a beryllium gas in the first place is difficult due to the high melting point of the metal, the ease of oxidation and the toxicity of beryllium oxides. It is created by pulsed laser vaporation - must be something like pulsed laser deposition but without the deposition - and cooled by so-called pulsed supersonic expansion of the helium carrier gas into a vacuum. Two more lasers (one called the pump the other one the dump) are then pointed at this gas and resonance fluorescence decay from excited beryllium dimers is somehow measured at right angles of the laser beam.

After a lot of data processing the end result is a Morse potential graph describing the dimer as it snugly sits in an energy well with the two beryllium atoms separated by 2.5 angstrom, hence a true chemical bond. The precise shape of this graph of course defies all theory and is attributed to various stages of orbital hybridization and will no doubt attract the attention of theoretical chemists for years to come.

Chemical hydrogen storage latest

16 June 2009 - recent literature

Just in case you have been hiding under a rock for the past decade: hydrogen storage, an integral part of the hydrogen economy is hot!. One particular branch of hydrogen storage that attracts the attention of chemists (and research funds) is chemical storage and it seems no element in the periodic table is left behind when it comes to ingenious solutions. Here is a pick just from the recent literature.

First up is gallium. All elements in the boron group are able to react with small molecules such as hydrogen and ammonia and gallium is no exception as in the aryl Ga(I) reaction depicted below (Zhu et al. 2009 DOI)

Tetrahydroborates are reducing agents but also potential hydrogen donors with lithium borohydride containing up to 20% hydrogen by weight. This compound reversibly decomposes to LiH and B. Problem is that the reaction is endothermic and temperatures in excess of 400 °C are required to release the hydrogen. So destabilizers are added for example in a system recently explored containing LiBH4, CaH2 and additive V2O5 (Ubikunle et al. DOI) . The authors are quick to remark that trying out all these chemical in different formulations can "be quite time consuming" but at least the reaction CaH2 + 6 LiBH4 -> 6LiH + CaB6 + 10H2 was the result of prior computer modelling.

A new solid-state synthesis for LiBH4 (wet-chemistry procedures exists) is also reported recently using lithium hydride and diborane at 120 °C (Friedrichs et al. DOI). This blog however struggles to understand the need to source the diborane from a reaction of zinc chloride with ahum.. said lithium borohydride, according to 2LiBH4 + ZnCl2 -> Zn(BH4)2 + 2LiH (by milling) followed by heating Zn(BH4)2 to gaseous Zn + B2H6 + H2. Going round in circles.

lanthanum, praseodymium, neodymium, magnesium, nickel and aluminum join forces to bring you the alloy La0.55Pr0.10Nd0.12Mg0.23Ni3.4Al0.1 with again, surprising hydrogen storage capabilities (Huizhong et al. DOI). This kind of research must be tedious to the extreme: the number of formulations with just these 6 elements is almost infinite and on top of that the alloys formed are multiphasic. Computer modelling is useless in predicting any atomic packing - surely one of those unsolved problems in chemistry - let alone predicting additional hydrogen storage capacity.

Carbonic materials can also be adapted for hydrogen storage. In a recent report, nitrogen enriched graphite is synthesized by mixing cyanuric chloride and melamine with pyridine in DMF at room temperature followed by curing at 120 °C (Yang et al. 2009 DOI). The experimental hydrogen capacity is 0.34% at 100 bar and 298 K and not exactly meeting the standard for practical implementation of 6.5% by weight.

The hydrogen storage capacity of nanotubes can be improved by creating defects for example by decorating them with metal nanoparticles. The process responsible is called hydrogen spillover :the metal splits diatomic hydrogen into monoatomic hydrogen which then enters the nanotube. A recent report reduces silver nitrate with hydrizine in a nanotube suspension (Rather et al. DOI) resulting in metal coated nanatubes with 0.86% H2 capacity (still modest).

Metal-organic frameworks are porous composite materials ideally suited for hydrogen storage and a lot of research is invested into this particular field. Covalent organic frameworks (COF's) are less common and the trick is to find a rigid organic molecule that forms channels in their crystal structure just as in a zeolite. In one report, the Cambridge Structural Database was mined (or the CSD "desert was sieved" according to the authors) to produce a biphenyl compound that did fit the bill and the hydrogen capacity was found to be 0.80% at 10 bar (Msayib et al. DOI)

Chemistry on the Web

June 1 2009 - finding information - updated June 5

News on the search engine front. First up is the brand new search engine from the Wolfram Mathematica people called Wolfram Alpha and widely recognized as the nerdiest of all search engines (question: meaning of life? answer 42!). A simple query for ethanol does not yield a long list of websites that have something to do with ethanol but all relevant data on ethanol such as boiling point, formula , 3D structure , safety data and a complete phase diagram. Entering C4H8 returns all 4 isomers, it knows how to handle a cup of sugar or 100 grams of sodium hydroxide. On the other hand dodecahedrane is is not recognized as a molecule but only as the geometrical shape. Listed in the literature inventory are the CRC handbook and the Aldrich catalogue. Not to be outdone, Google has announced a similar service called Google Public Data and started of Google Squared in a rush job. Typing in organic reaction produces an odd table with material pilfered from Wikipedia.

In the mean while Microsoft's answer to Google Bing has the distinctive advantage that the search results are not that cluttered with restricted-access pages (especially those from scientific publishers) but still many exist. Other than that, it appears to be yet another search engine.

Chemical data aggregator Chemspider is now part of the Royal Society of Chemistry according to this press release which makes it the British counterpart of CAS maintained by the American Chemical Society.

CAS and Wikipedia announced a collaboration last month culminating in This Website has information of over 7000 common chemicals stored in CAS and a link to the relevant page in Wikipedia. The CAS contribution to this project is rather disappointing and limited to CAS registry numbers and synonyms. CAS is sitting on a huge amount of (expensive!) data, not just data on chemicals but also data on chemical reactions and could have been more generous in sharing for free. What about a ranking of all known solvents? or how about breaking up all known chemical compounds in the type of bond formed?. The Wolfram guys for sure would have been more inventive.

The buzzy month of May also saw the introduction of another common chemistry initiative at, a brainchild of thechemblog. This wiki aims to become the online depository for basic chemistry technique such as packing a column, distilling a compound or properly quenching a reaction (howto's Wikipedia is staying away from), no doubt with an enthusiastic following of those people involved in the manufacture of illicit drugs.

As stated in an earlier blog here there is no shortage of initiatives collecting and reorganizing Internet content or initiatives inviting people to generate content. The bottleneck appears to be finding these people who are willing to do the actual work and generate original content. A lot of so-called content generation is more like the information regurgitated and forced into machines from the 1989 Ministry song this blog takes its name from.