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The Mystery of the Missing Methane

30 January 2011 - Deepwater Horizon aftermath

klik hier voor de afbeelding op ware grootteWhen a group of US based scientists boarded the vessel Pisces and headed for the Deepwater Horizon disaster site in the Gulf of Mexico on a chemical fact finding mission they fully expected to find large quantities of dissolved methane. The spill after all, had emitted a total of 12,5 billion moles of the gas in addition to the 4.4 million barrels of oil. The concentration of methane in the air had been constantly monitored since the spill started and in one estimation only 0.01% of the gas had as yet surfaced. So the bulk of it had to be still in the water. In a 500 km wide stretch water was sampled on 207 locations up to a depth of 1200 meter (DOI). The researchers were in for a surprise.

Whereas the presence of oil residue was evident from fluorescence measurements, gas chromatography did not signal any methane. On the other hand CTD probing combined with a Winkler dissolved oxygen test did reveal a large oxygen deficit. In one estimate 25 billion moles of O2 was respirated within a 120 day period nicely reflecting the oxygen/methane 2:1 oxidation ratio. The culprits were also found: a DNA survey revealed the presence of host of methane-eating bacteria such as the methylococcaceaeand the methylophaga or at least their DNA remnants. Mystery solved!

The 1,1-Carboboration reaction

21 January 2011 - Nice to have

carboboration Chen 2010  What: 1,1-carboboration, cleavage of a carbon-boron bond by terminal alkyne
Variation of: hydroboration
Reverse of: Fritsch-Buttenberg-Wiechell reaction
Most recent incantation: Chen et al. 2011 => DOI
Specifics: the carboboration of 5-phenyl-1-pentyne is followed by photochemical cis/trans isomerization and then followed by palladium catalyzed coupling reaction with iodobenzene

Desiraju on hydrogen bonds

15 January 2011 - Chemical bonding

the hydrogen bond desiraju 2011  A hydrogen bond can depicted as an X-Y...H-Z interaction involving 0.5 to 40 kcal/moles of energy with the strongest hydrogen bond stronger than weakest covalent bond and the weakest H-bond in the range of a van der Waals bond. In an Angewandte essay Gautam R. Desiraju elaborates on the nature of the hydrogen bond and a proper definition with unusual clarity. (DOI). For those of you without an Angewandte subscription or with without patience to read all 8 pages, here is a brief capture. To start with just a few quotes:
On definitions: The history of chemistry is strewn with names that were once hotly contested and disputed by various protagonists and why do chemists fight over names so much, good question.
On trivial names: a term is acceptable if the largest numbers of chemists are in a maximum degree of agreement about what it means. A trivial name is the victory of such a consensus
On chemical bonds: the word bond has an almost religious connotation for chemists (...) every chemist has his or her own idea as to what constitutes a bond
On the origin of life : did life on earth become water-based because the hydrogen bond was the only interaction of choice to facilitate life?
So what is the problem with these hydrogen bonds. Strong hydrogen bonds or hydrogen bridges found in O-H--O-R configurations pose no problem. Problems arise with weaker bonds, not always possible or difficult to detect it experimentally More disagreement: in the original Pauling definition and later IUPAC definition Y and Z are both electronegative as in R-O-H...O-R (electropositive hydrogen partners with two electronegative partners) while in an scenario with C-H...O=C-R the carbon atom is electronegative and the oxygen atom electronegative. So not a hydrogen bond then?
An elite team of IUPAC chemists of which Desiraju was part of have now decided on the future of the hydrogen bond. In a new definition the hydrogen bond is an attractive interaction between a hydrogen atom from a molecule or a molecular fragment X-H in which X is more electronegative than H, and an atom or a group of atoms in the same or a different molecule, in which there is evidence of bond formation. So far so good. The definition goes on with the evidence for hydrogen-bond formation may be experimental or theoretical, or ideally, a combination of both. Here Desiraju stresses that theory and experiment have equal status which may come as a surprise to those who believe in the ancient scientific principle that theories are validated by experiment. The new definition also stipulates that the actual bridge is formed by Y-H but if Desiraju has had his way the bridge would be formed by all 4 atoms in X-Y-H-Z.
The X to Y distance no longer needs to be smaller than the sum of the van der Waals radii of X and Y: the precision of X-ray analysis does not allow it.
Here is one more quote, this time on IUPAC meetings: the letters X, Y, and Z were selected after much discussion


14 January 2011 - Host-guest chemistry

Pillararenes  Pillararenes are macrocycles composed of arene units linked in a para-fashion. In this way they resemble the cucurbiturils and calixarenes that play an important part in host-guest chemistry.

Groups involved in this type of research are that of Cao/Meier (DOI) with pillar-6-arenes and pillar-5-quinones, that of Feihe Huang with pillar-5-arene copolymers (DOI), pillar-5-arenes with isobutyl substituents (DOI) and rotaxane-like supramolecular polymers (DOI) and that of Ogoshi/Nakamoto with pillar-5-arenes with EtO and MeO side groups (DOI) , with ionic liquids as guest (DOI), with pillar-5-arenes as rotaxane components (DOI), with alkyl substituted pillar-5-arenes (DOI), with molecular dynamics (DOI) and with a viologen salt as quest (DOI).

The last group mentioned is sitting on gold because they created their pillararene simply by adding together 1,4-dimethoxybenzene and formaldehyde (dichloroethane, boron trifluoride etherate, rt) when this sort of reaction is supposed to yield just linear oligomers. In a most recent publication the group reported for this reaction an unusual 71% yield (DOI). In their original 2008 publication the yield was just 22% but it was discovered that less is more in formaldehyde (not 10 equivalents but just three) and that the optimum reaction time is not 30 minutes but just three. Deprotection of the methoxy groups (tribromoborane) gives the water soluble decahydroxylpillarene. X-ray analysis reveals flipping of two of the arene units for this compound.

Click chemistry corrupted?

08 January 2011 - Applied chemistry

Click chemistry is a concept introduced by K. Barry Sharpless in 2001 and describes chemistry tailored to generate substances fast and reliable by joining small repeating units together in the same way as nature does. Its poster boy is the azide alkyne cycloaddition.

In a recent essay in Angewandte Chemie (DOI) Barner-Kowollik/Du Prez/Espeel/Hawker/Junkers/Schlaad/van Camp warn that the original definition formulated by Sharpless has become corrupted. They identify at least 20 reaction types now labeled as a click reaction that do not meet the original specifications. Emphasizing the impact of click chemistry on polymer science they reiterate the main points: a reaction product should be isolated by nonchromatographic methods, such as crystallization or distillation, the reaction should give very high yields, quickly proceed to completion, with reagents readily available and reaction products stable. A reaction may be efficient but not a click reaction when the criterion of equimolarity is not met. Most reactions listed as click fail the wide in scope requirement. The term click should be handled with more caution otherwise the authors state it may become over time a synonym for - successful - and thus largely irrelevant and meaningless. So noted!

Moerdijk burns

05 January 2011 - Hot news (updated 28-1)

The Dutch media have declared a national emergency as in the city of Moerdijk chemical company Chemie-Pack is ablaze. This company processes and packages chemical products and for some reason it caught fire: an impressive thick black plume of smoke is accompanied by Hollywood-style explosions. The smoke has a North-Westerly direction and one tweet joked Iceland is being payed back in full for their volcanic adventure last year. Nobody died so we can relax and wonder how the event turns up in the media. There are a lot of uncertainties, for starters no one knows what kind of chemicals were actually on the site. Possibly a common safety-management error: all relevant documentation concerning the chemicals is stored on-site and no one bothered to keep copies on an off-site server for backup. The media mention 400,000 kilogram of carcinogenic chemicals, the amount makes sense (about 20 trucks worth) but the carcinogenicity hardly matters as it is burned away anyway. Some media also mention 23,000 liter storage drums containing chemicals which seems large but other media report more reasonable 2300 liter ones. The chemicals cannot be blamed for the black smoke, that is courtesy of the packaging part of the company. Sulfuric acid is mentioned and also its flammability which it is not.

Another issue is how to get fire out? Even the army and airport fire control specialists are called in but the fire now rages on for 10 hours already having consumed one neighbor in ship parts and threatening another more ominous one ,a chemical waste recycling facility. The firemen use water to contain the fire and this is odd for two reasons: if a main component is sulfuric acid Wikipedia asserts that adding water to sulfuric acid can lead to exothermic overheating and explosions. Also the addition of water to overheated metal scrap (the remnants of the plant) may result in the formation of hydrogen gas (see water gas). This controversial topic was first raised in the aftermath of the Enschede fireworks disaster. Would explain the gas explosions.

Update 06-01:
11 hours into the fire the firemen abandoned water and opted for a foam blanket. That strategy worked out. See the pics@nrc. According to the Volkskrant a spokes person for the Moerdijk city council said the fire brigade did have a list of all chemicals located on the site after all but that it was 80 pages long (...). This blog agrees: you cannot really expect people to read that many pages.

Next update 06-01:. A chemical brew has now entered the environment as evidenced from unusual colored surface water in the vicinity of the disaster site. But is it toxic? In NOS News a reporter is certain we will never know what kind of toxic chemicals have spilled into the environment , it would be like looking for a needle in the haystack. An odd statement that he probably just made up. In the current affairs program Uitgesproken EO that started right after NOS News, a reporter took a surface water sample, rushed it to a local laboratory, filmed a gas chromatograph in action and then interviewed an actual chemist-in-a-white-lab-coat who reported the presence of a whole range of unpleasant volatile organic compounds. See NOS News? Really not that difficult to find news instead of making it up!

Update 07-01: It is NOS News again. Today they report that water used to put the fire out is contaminated with VOCs such as toluene and xylene. This water has collected in the ditches surrounding the industrial estate (by design) and has to be disposed of. Here NOS News fumbles again when they state that the water has to be purified by removing the poisonous compounds (two errors there). In another scoop they report that the chemical inventory list mentioned earlier is actually declared a state-secret by the public prosecution office. So now you cannot read it and if you can it is too much to read.

Update 07-01: The Volkskrant interviewed employees who say a fire started by a spark during the unloading a shipment of volatile chemicals. This is a common problem when handling chemicals. Even in a laboratory setting when you want to transfer the content of a 10 liter metal drum containing ether you have to ground the drum otherwise you risk a spark and an combustion.

Update 07-01: NOS again. We now have a list of chemicals found in the local surface water here and here is the top 3: tetrachloroethylene 96 mg/L, (dry-cleaning liquid), total xylenes (130 mg/L, ) and toluene 81 mg/L

Update 09-11: We've got him: the chemical inventory list! Until last week the fire department used to get an updated version of this list (52 pages) every day (NOS report). Tetrachloroethylene (see above) is on the list with 155 100 Kg drums but not sulfuric acid. Unfortunately most often the description is just a tradename. Lipaton (24000 Kg) is a kind of latex dispersion, Empimim (24,000 Kg) is sodium lauryl ether sulfate , Nekal BX (11,000 Kg) is sodium butylnaphthalenesulfonate if we have to believe one of many Chinese websites but what is Infineum R372 IBC (25,000 L)? or HFA 360 IBC with 10,000 L?. At least anyone can understand 25,000 L of toluene. The list is helpful with an elaboration on dangerous reactions with , for example sodium hydroxide will react dangerously react with acids. Also listed are fire extinguishing aids (foam, powder, carbon dioxide, sand or water mist (blanket)), flashpoint for each chemical and the combustion products (carbon, nitrogen oxides, chlorine and bromine).

Update 12-01. More chemical analysis provided by the RIVM here (NOS News). Detected in air samples: tetra, VOCS and large concentrations acetone. Detected in grass samples: dioxines at 7 ng TEQ / kg.
The report tries to be helpful in calculating the amount of dioxines digested per Kg human body weight when eating 200 grams of polluted vegetables (Moerdijk is Brussels sprout country) per day but makes an error. The correct amount is calculated as (88% dry weight, 60 Kg person) : (7 x 0.2 x (100/88)) = 25 pg/Kg which is 12 to 25 times the legal norm. The report for some reason multiplies the 0.2 factor twice and their conclusion is therefore more favorable.
One more surprise: at a distance of 3 kilometers from the burn site levels of lead have been detected at 1600 times the background level (879 mg/Kg) way over any safety limit. To keep spirits up the report suggests washing the crops: rainfall will cause a reduction on grass and this will also happen with vegetables for human consumption. Lead by the way is not listed on Chemie-Pack's chemical inventory list mentioned earlier.

Update 28-01. And now it is aluminum!. NOS News (again) asked environmental consultancy agency BK to perform additional sampling (link) and they found 54,000 mg Al per kilo ground sample! Just to confirm: the NOS news article (with research editor Hugo van der Parre) specifies 54,000 mg and not 54,001 or 53,999 mg of the stuff found near the location of the disaster site. Aluminum oxide was on the chemical inventory list so that makes sense and 10 gram is the safety limit. But the aforementioned RIVM has already announced that the whole area is safe from toxins, so who is right? A RIVM spokes person kindly replied the aluminum in that concentration was found at a depth of 30 to 50 cm and could not possibly have originated from Chemie-Pack. The consultancy agency BK in their rebuttal advises to do more consultancy (...). Their first report is a whopping 114 pages and very thorough. For example it offers photographs taken on all research locations. One of them is featuring some of the innocent victims: