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Oxyluciferin revisited

31 January 2014 - Bugs

oxyluciferin revisited  The firefly problem has already been solved in 2009 here but why is oxylucerifin so unstable? Supposedly it is impossible to have it synthesised. Maltsev et al. have been doing some reinvestigation on the synthesis of the compound from 2-cyano-6-hydroxybenzothiazole and ethyl 2-mercaptoacetate in alkaline methanol / water and have identified the culprit (DOI). With an insufficient amount of base present, the reaction product oxyluciferin is present both as the enol and keto form and both products can dimerise in a Mannich reaction. This dimer was extensively analysed via LC-HRMS and crystallography. A revised synthetic protocol for the synthesis of oxyluciferin now demands the right amount of base and low temperatures. Column chromatography is possible provided small amount of acetic acid is added to the eluent.


24 January 2014 - Nano

phosphorene.PNGNew in the exclusive family of single-layered two-dimensional materials that includes graphene molybdenum disulfide and silicene: phosphorene! as reported by Han Liu et al. here (not peer-reviewed so absorb with caution). Not exactly monolayer, the researchers call their invention 'few-layer phosphorene'. The raw material is black phosphorus, first synthesised in 1914 with a well-known two-dimensional structure very much like graphite. On average three phosporene layers were peeled from this material (scotch-tape!, again!) into a regular silicon layer.

A field-effect transistor based on a fleck of this new material is reported to have an on/off ratio of ten thousand which is the ratio of current passing through from source to drain when switching between two arbitrary voltages at the gate.

Update 28 January: Borophene just around the corner!

The organic-inorganic flow battery

18 January 2014 - Physical organic chemistry

the organic flow battery.PNGFlow batteries are nothing new and metal-free inorganic flow batteries are nothing new either (see for example the polysulfide bromide battery) but the set is not complete with an metal-free organic variation as well. The new flow battery described here works with two flows that meet separated by carbon paper. In the charging mode one flow 9,10-anthraquinone-2,7-disulphonic acid (AQDS) (a quinone) in sulfuric acid is reduced to the corresponding AQDSH2 diol and in the other flow hydrobromic acid is oxidized to bromine. The carbon paper is permeable for proton-exchange. The researchers report a cycle (charging / discharging) efficiency of 99%. They also mention the following advantages: sulfonated anthraquinones are already used in wood pulp processing and the crude reaction product of oleum and anthracene could do the trick. The voltage of the flow cell can be enhanced by adding hydroxyl groups. Hydroxylated derivatives are known biomolecules and a quinone solution could be sourced from natural resources. The researchers kindly suggest rhubarb.

Himmel, Krossing and Schnepf on dative bonds

11 January 2014 - Coordination chemistry

A dative bond takes place between an atom with an available lone pair and an atom that is an electron acceptor. A good example is the adduct of ammonia and borane or ammonia borane with the dative bond depicted as H3N->BH3 with an arrow indicating that nitrogen is donating both electrons to create the chemical bond. The classic Lewis structure H3N+-B-H3 would have a positive change on nitrogen even though nitrogen is more electronegative than boron and creates confusion. Dative bonds are considered weak, are longer than a regular bond, charge transfer is small and in the case the bond is severed the mode is heterolytic and not homolytic. Application of the dative bond is troublesome. The problems starts with amine oxides that are for some unknown reason are also often depicted with a dative N-O bond.

In a recent essay Himmel, Krossing and Schnepf (HK&S) see more issues with the dative bond. They see an increased popularity of them but without justification. They examined some recent invocations and assign most of them to the scrapheap. The so-called carbones, a class of carbon(0) compounds of the type L->C<-L (example bis(triphenylphosphoranylidene)methane) as advocated by Frenkel are generally depicted with two dative bonds. According to HK&S however a class Lewis structure is more in agreement with the calculated high partial charge on carbon. Same case with the PPN cation, depicted as PPh3->N+<-PPh3. The positive charge on nitrogen is an eyesore given that its partial charge is -1.55.

In a similar vein a N3+ cation with three dative ligands also has been reported. Quote of the day: "Is there any intellectual profit in describing a negatively polarized nitrogen atom through the use of arrows as cationic N3+?"