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How to sample a shaking tube

Dear Reader,

I enjoy solvent extraction, it is enjoyable and allows me to probe the very fabric of matter with a simple experiment which measures a system at equilibrium. While there are some things which solvent extraction can not do such as prove the existence (or non existence) of God there are lots of things it can do.

Now I am aware of a man who has attempted to use quantum mechanics to prove that Christianity is right this is a true story and not a joke, but we will leave that matter for another day and get back to solvent extraction.

Now lets consider the things which solvent extraction can do, we can develop new industrial processes using shaking tube experiments. In these experiments we can measure key details about the proposed process. We can work out the conditions which would be required to extract, purify and back extract metals from a liquid.

We can use it to measure binding constants in either phase, we do that by making measurements of a system with different concentrations of the binding agent.

We can also use solvent extraction to determine activity coefficents, for this we need a well understood system and some patience.

We can separate metals from each other in a small scale for an anayltical purpose, here we can clean up a sample before either using ICPMS, a radioactivity measurement or some other determination.

We can test the purity of some organic molecules using a solvent extraction experiment.

We can measure the Delta H and the Delta S of an extraction reaction using solvent extraction at different temperatures.

Sounds like great fun and excitement, but to do it we have to be able to cleanly take samples of the two layers. The top layer is easy as all you need to do is stick the tip of a pipette in it and suck some out. The lower layer is a bit harder.

Like many things there is more than one way to do it, one method is to remove the whole of the upper layer and then take the sample. This is not easy to do, it is hard to avoid leaving a little of the upper layer in the vial. So in fact we will always have to use some care and skill to sample the lower layer.

Now to help spread the love, I have taken some photos with my student (Cen Peng) to show how to do it. Start by taking the lid off the shaking vial with great care to avoid shaking it all up again into an emulsion. Now in this photo you can see me holding the opened vial with my right hand as a 200 microlitre pipette tip is about to go into the liquid. At this stage press your thumb down to the first stop of the pipette to push out much of the air.

get ready to stick it in.png

Next lower the pipette into the lower phase, make sure you have the point of the tip in the lower layer. Try not to press it against the bottom of the vial as you can seal it up. Now press a little harder on the button with your thumb to squeeze out a couple of air bubbles. Do this to remove any droplets of the upper phase from the tip of the pipette.

Squeeze out an air bubble.png

Now slowly relax your thumb and allow the pipette button to rise slowly, this will suck up some liquid into the tip. I have done this with blue liquid to make sure that you can see it more clearly. My advice at the end is to take your thumb off the button and count to five.

I have sampled the lower blue layer.png

Now with care raise the pipette out of the lower liquid.

Carefully raise the pipettee.png

Now raise it further

Final step now relax.png

Now pull it all the way out of the vial, I like to wipe the outside of the tip with a bit of clean paper tissue to remove any liquid from the upper layer. Now I tend to then pipette it out into a preweighed plastic vial. I then weigh the vial after the pipetteing to check the volume of liquid that I have dispensed. You need to know the density of the lower layer to do this, unless you also weigh out the starting aqueous layer as well.


Extinction Rebellion

Dear Reader,

It has come to my attention that a group of protesters have caused a great deal of disruption in central London. These protesters are concerned about climatic change and air pollution. The problem I see with these people is that they seem so blinkered by their devotion to their cause that they fail to see that they may well be sabotaging their own campaign.

Now before we get going, I hold a view that we should exercise care with the environment on earth. To be blunt with you, if we foul it up then we can not go to the shops and buy a replacement one !

But if while campaigning for people to change their ways someone was to disrupt the lives of others and cause them to suffer then it is likely that the message will be lost. I find it interesting that Gail Bradbrook suggested that people take the day off work and join their protest and have fun.

The problem is that many people need to go to work to earn a living, if you block up the transport system of a city then you will not have a group of people who want to (or can) drop what ever is in their life and join some party protest.

Some years ago there was a group called “Reclaim the Streets” who did things like close down Camden Highstreet. They disrupted the movement of traffic, the problem I see with this is that they treated the journeys of others as being irrelevant. While they might be rather happy about the idea of stopping for the day and having a joyous festival in the middle of the street. The problem was that not everyone else wanted or could do.

Now a street festival like the Notting Hill festival might cause disruption for a whole weekend, some people might love or while others would hate it. But at least it is an event which is well publicised in advance. Some people might book the weekend to enable them to attend while those who did not wish to attend were free to take measures to reduce its impact on themselves.

The protests of Reclaim the Streets however occurred with no warning to the public at large. Now imagine that you are a small / medium business and you are trying to earn a living delivering bricks for the construction of homes. Suddenly instead of being able to deliver 3 tons of bricks to Mr Jones at 101 Some street and 4 tons to Miss Smith at 42 Elsewhere road you are stuck in traffic due to this protest. Imagine that you have five building workers who are ment to arrive on tuesday morning, it is monday afternoon and the bricks they will be using are now stuck in traffic as a result of the protest.

Imagine that you are the manager of a hospital, you need 100 litres of liquid oxygen a day. You have a tank which holds 300 litres. It is friday afternoon, the tank has 100 litres in it. You are expecting the liquid oxygen truck, but it is stuck in traffic as a result of the protest. Instead of being able to go home to your family you now need to start phoning around to find an alternative supply of medical grade oxygen.

You are a driver with 200 kilos of hot food which is intended for old people and the disabled. You are a “meals on wheels” truck driver who needs to meet four drivers of cars and vans who will then dart around with the food to deliver it to the local old people and the infirm, You are supposed to park behind the library and then transfer the food to the others. You are all stuck in traffic. I do not think I need to continue with examples of people who need to get from A to B.

By the way I did a academic literature search on Gail Bradbrook, I have found seven papers on what I would consider to be biological chemistry. It all appeared to me to be crystallography.

The address on the oldest paper was Manchester. Five papers from Manchester and two from Grenoble (France). Her h index is only 5. I have looked and I can not find her thesis at the British library thesis service, for a person who got their PhD about the same time as me not every thesis is on line. I am estimating that she got her PhD in about 1997 based on when she started to publish.

I find it rather shocking that a person with a background in a chemical science would be willing to ingest ibogaine. Ibogaine is an indole containing drug which can cause hallucinations and a range of rather disagreeable side effects. She also took Ayahuasca. Now this is not some sort of Daily Mail smear, I am sure that the Mail readers might sit there with their G&Ts looking in a disapproving manner at people who “do drugs”.. But Gale has gone on the record and explained how her drug use has changed her life.

I note that she commented that “When I got home I ended a marriage and separated my family. It was a huge decision, but it was the right thing to do and I am a stronger and happier person now. ” I see it in a different way, maybe the drug use altered her and as a result her family broke up. Now I might be an incurable romantic but I have always held the view that the breakdown of relationships and the fragmentation of a family is a sad event.

Now lets look at the chemistry of the drugs, in case Gail is watching I will have to be careful to get everything right. Now Gail has experience of crystallography so it is rather fitting that one of my favorite methods is X-ray diffraction for getting the strucutre of a small molecule. Now ibogaine is a drug whose strcutre was published by M.Soriano-GarciaActa Crystallographica,Section C: Crystal Structure Communications, 1992482055, DOI: 10.1107/S0108270192002786.

This structure has two independent molecules in the asymmetric unit. It is clear in the following diagram that the left hand side of the molecule is an indole.


The molecule has a resemblance to serotonin this is shown below.


I have redrawn the ibogaine using just lines to show the chemical bonds plus the non carbon / non hydrogen atoms.


Now here is the other drug, one of the problems with the drug abuse sector is that unlike the pharma sector there is often a lack of standardization and quality controls. There is the problem that people are sometimes being supplied with one drug which is being offered as something else. Sometimes this is due to a mistake while sometimes the drug dealer will chose to replace one drug with another in an attempt to make more money. With the herbal brews made in south america which are known as ayahuasca, different people making it will use different plants. As a result it is the case that different suppliers of ayahuasca regardless if they are drug dealers or shamans may make brews with different concentrations of the drugs and sometimes different drugs. To my mind this looks like a perfect recipe for an overdose, a person who has done it before might think that they know their limit. But hey presto they drink the brew and suddenly discover they have taken too much !

The brews tend to contain DMT, this is another indole drug together with harmala alkaloids which act like MAOI drugs. Without the MAOI like harmala alkaloids the DMT would not be nearly as active in humans when swallowed. The harmala alkaloids themselves might cause chaos if you were to take them as they will cause the concentrations of serotonin in the brain to climb up a lot. Depending on the diet of the person this effect could be larger or smaller, but it is still a big bad idea to take a brew of unknown drugs in unknown concentrations.

The 1-Methyl-7-methoxy-β-carboline and similar substances in the brew act as the MAOI drug, the crystallography of this molecule (one of the drugs) was reported in a paper V.Ferretti, P.Gilli, P.A.BoreaActa Crystallographica,Section B: Structural Science200460481, DOI: 10.1107/S0108768104013564. Here is the molecule in its glory.

MAOI like drug






Dear Reader,

It has come to my attention that the EU will soon be banning a fungicide named chlorothalonil. This is a rather small molecule which has one benzene ring in it, two nitrile groups and four chlorine atoms. The molecular structure of this substance was reported by D. Britton (Cryst.Struct.Commun. , 1981, 10, 1501). Here is a picture of the molecule.


Some of the chemistry and biology of this pesticide is discussed in a paper from the EFSA. This is a paper with a lot of authors.

Maria Arena, Domenica Auteri, Stefania Barmaz, Giulia Bellisai, Alba Brancato, Daniela Brocca, Laszlo Bura, Harry Byers, Arianna Chiusolo, Daniele Court Marques, Federica Crivellente, Chloe De Lentdecker, Mark Egsmose, Zoltan Erdos, Gabriella Fait, Lucien Ferreira, Marina Goumenou, Luna Greco, Alessio Ippolito, Frederique Istace, Samira Jarrah, Dimitra Kardassi, Renata Leuschner, Christopher Lythgo, Jose Oriol Magrans, Paula Medina, Ileana Miron, Tunde Molnar, Alexandre Nougadere, Laura Padovani, Juan Manuel Parra Morte, Ragnor Pedersen, Hermine Reich, Angela Sacchi, Miguel Santos, Rositsa Serafimova, Rachel Sharp, Alois Stanek, Franz Streissl, Juergen Sturma, Csaba Szentes, Jose Tarazona, Andrea Terron, Anne Theobald, Benedicte Vagenende, Alessia Verani and Laura Villamar-Bouza, EFSA Journal, 2018, 16(1), 5126.

While the impurity hexachlorobenzene which is found in the commercial product was characterized by .N.Strel’tsova and  Yu.T.Struchkov (Zh.Strukt.Khim.(Russ.)(J.Struct.Chem.) , 1961, 2, 312). This should not be confused with lindane which is sometimes known as hexachlorobenzene. Lindane is an isomer of 1,2,3,4,5,6-hexachlorocyclohexane. Here is a picture of hexachlorobenzene.


Like the pesticide it is a simple flat molecule which is a hexagon of carbon atoms within a hexagon of chlorine atoms.

The commercial product also contains small amounts of deachlorobiphenyl, as it is a PCB it is something which automatically grabbs my attention. This was characterized by B.F.Pedersen (Acta Crystallogr.,Sect.B:Struct.Crystallogr.Cryst.Chem., 1975, 31, 2931). This is a bit different, due to steric effects the two benzene rings are not in the same plane. Here are two views of it. First we have the side view.

side view of decachlorobiphenyl

Now here is the end view which is almost along the axis formed by the C-C single bond which links the two benzene rings together.

end view of decachlorobiphenyl

In the European food safety authority report, two metabolites (biological breakdown products) code named R613636 (2,3,4,6-tetrachloro-5-cyanobenzamide) and R182281 (2,4,5-trichloro-6-hydroxybenzene-1,3-dicarbonitrile) were listed as being of concern. We hope that we can discuss this molecule and chemistry soon.

Uranium at the Grand Canyon II

Dear Reader,

The story continues, now I am not going to pretend that uranium ore is harmless but at the same time we should not exaggerate how bad it is. One of the problems is that there is a shortage of information on the subject of what was present in the museum building, and also I have no idea of the shape, size and other properties of the museum.

Now I hold the view that the main threat posed by uranium ore in a bucket is the release of radon from the ore. I would like to point out that uranium is not a very toxic substance. Uranium if it is inhaled by a human will be able to dissolve, form a substance that can be excreted with ease via the urine.

So I think that if a person had inhaled some uranium radioactivity then in terms of damage done per Bq inhaled it is less than what something which forms a much less soluble oxide (such as plutonium) would be able to do.

I imagine that the uranium ore was being stored dry, while dry solids tend to form more dust than wet solids in some ways this may have reduced the radiological risk posed by the uranium. The main risk of uranium ore is from the radon which is generated by the radium in the ore.

What will happen is that the uranium (238U) will decay according to the following decay chain.

238U → 234Th → 234Pa → 234U → 230Th → 226Ra → 222Rn → 218Po → 214Pb → 214Bi → 214Po → 210Pb → 210Bi → 210Po → 206Pb

I have chosen to ignore the small amount of 235U as this decays by a pathway which goes via a very short lived radon (219Rn) which due to its very short half life is unable to escape as a gas from the rocks and then deliver an alpha dose to the lungs of the people. In the following diagram I am showing the decay chain of the minor isotope of uranium, I have chosen to ignore any branch which is less than 1 % of the decay chain. The diagonal arrows are alpha decays while the vertical arrows are beta decays.

u235 chain

When a radium containing mineral sample is stored dry the emission of radon from the solid is less than when it is stored wet. A good example of this can be seen in the paper by A. Sakoda, Y. Ishimori, K.Hanamotoa, T. Kataokaa, A. Kawabea and K. Yamaoka (Radiation Measurements, Volume 45, Issue 2, February 2010, Pages 204-210). In this paper the effect of changing the size of the particles was not very clear.

What has to happen for radon to be released from a mineral grain is for the radon atom to be close to the surface of the grain or in the air space between two grains. The radium starts off in the solid grains, when it undergoes an alpha decay the recoil from the emission of the alpha particle will make the atom jump backwards. This recoil can help to liberate the radon atom from the solid.

If the recoil does not bring the radon to the top layers of the grain (a) then it will be trapped so long inside the grain that it will decay. If it recoils into the air gap (b) and the air gap is nice and large then it will slow down in the air gap and find itself floating about in the air gap. However if the air gap is very thin and the recoiling atom strikes the surface of another grain then it can hop between grains. It is possible if it strikes the other grain with sufficient energy that it will bury itself (c) in the other grain where it will decay harmlessly without being able to fly off into the air.

radon recoils

When the ore is wet the gaps between the grains are filled with water, this will reduce the distance the recoils taking path c can take. This can prevent the radon atoms hitting the other grain as they fly along path c. This is because the recoiling nuclei will lose more energy per unit distance of travel when they are flying through water instead of air. The radon can then transfer from the water into the air with ease.

I imagine that the ore was in the form of large lumps, this is a good thing. The reason is that the radon is being generated at an equal rate throughout the whole of the volume of the ore. After being generated it has to diffuse out of the lumps before it can enter the air. The radon has a half life of about 3 days.

To escape from the rock lump it must first be free from the grains and in the air spaces. It then has to diffuse out through the cracks and large pores in the lump to the surface of the rock. One method of reducing the emission of radon from the rock lump would be to paint the outer surface of the rock. But I doubt if they will do that in the museum as it would spoil the appearance of the rock lumps. Another method is to put the rock lumps in a sealed container, if the sealed container delays the escape of the radon by a few weeks then it will make a large difference as the radon will decay inside the container rather than in the air of the room.

If the ore had been crushed to a fine solid then the distance that the radon must migrate is smaller than if the ore is left in large lumps.

Now the next thing which needs to happen for the radon to deliver a dose to people is it has to get into the lungs and stay there. Now if you inhale radon gas then if it is 222Rn from the decay of natural uranium then it is unlikely to decay inside your lungs. You are more likely to exhale the radon before it has had a chance to decay. Even if the radon is adsorbed into your blood in your lungs it still has a good chance of being rereleased again from your body.

The bigger problem is if the radon decays in the air to form a radon daughter such as 218Po, this short-lived polonium can absorb onto dust and smoke particles. These are much more able to lodge in the lungs than the radon gas. One method of greatly reducing the alpha dose to lungs due to radon is to wear a dust mask. This will stop the dust and smoke particles from getting to the lungs. It is well known that uranium miners who are smokers are more susceptible to the induction of lung cancer by radon than non smoking miners. This is thought to be due to the smoke effect.

I am of the view that as smoking is banned in US goverment buildings, as long as the building is clean and free of smoke the radon is less dangerous than it would be in a smoky place. The escape of radon from the building as a result of ventillation will lower the lung dose caused by the radon. I am unable to make a dose estimate due to the fact that I am not privy to the full facts of the case. For my british readers who are able to read between the lines the meaning of the phrase “I am not privy to the full facts of the case” will be very clear. For those of my readers who do not understand british understatement, this means I am missing so many important details about he situation in the museum that it is clearly impossible to make a meaningful dose estimate or prediction of what will happen next.

But at least I can explain some of the things which are important in this case.

I have seen that the US goverment will be investigating what was going on in the museum, this will include dose reconstruction. Rather than jumping to any conclusions I think it will be better to wait for the report from the experts which should appear in about 90 day.+åps0

Uranium at the museum

Dear Reader

It has come to my attention that in the USA that some buckets of uranium ore were found in a museum site at the Grand Canyon.

Now it is claimed that where the buckets were that the dose rate was 13.9 milliREM per hour, this in european units translates into 139 microSv per hour. I find it interesting that at 5 feet from the buckets the dose rate was zero. A common error is to use a radiation meter which is senstive to beta particles to estimate the gamma dose rate without protecting the detector from the beta particles. This will cause the meter to over read.

Depending on the conditions and the meter in question the over estimate can be small or it can be large.

The problem with a bucket of uranium ore is that the self adsorption of gamma rays can be very large. The late John Pecket told me a funny story about this sort of thing. He had a kilo of plutonium in a glove box as the dioxide. This was in a bottle of dry powder, he pulled a small amount out and dissolved it in acid.

When he changed the geometry and spread it out by dissolving it the dose rate in the glove box went up.

As a result of the self adsorption problem it is hard to make an estimate of the dose rate. It will take me a lot of effort to calculate the dose rate in a room which has thick tiles of uranium dioxide on the walls. This will be a lot more effort than if the room had been painted with a uniform coating of something with a much greater radioactivity put unit volume.

I will have a go at making an estimate for a 5 gallon (25 litre) bucket. If we assume that bucket has a diammeter of 300 mm, it will be 350 mm high and it is a perfect cylinder then we can calculate some things.

If we consider the radiation dose at 1 meter from the end of the cylinder of uranium along the axis we can reduce the problem to a series of disks. Lets for example treat the bucket as a stack of 350 disks. We can consider first the top layer. If we assume that it is pure uranium dioxide which has reached a radioactive equilibrium with its daughters.

The volume of a 1 mm thick slice of the cylinder will be 70.7 cubic cm, as the relative density of uranium dioxide is 11, this means that in the 1 mm slide we will have 777.5 grams of uranium dioxide.

This is 2.88 moles of uranium atoms, this is 1.734E+24 atoms, we will have 8.53 MBq of activity of each nuclide in the decay chain in this slice. So the dose rate due to the top slice will be 1.29 microSv hr-1 at one meter from this slice. If we had no self adsorption then the dose rate at one meter from the cylinder would be about 450 microSv per hour which would be a jolly high dose rate. This is a dose rate which would under almost any circumstances cause me to back away from the source quickly. Well it is not the worst I have heard of, I have heard of a radioactivity worker who on arrival at a possible accident scene in Israel who encountered a radiation field of 500 mSv per hour, he very quickly retreated away from it. If I was to spend one minute in such a place then I would get a 8.33 mSv dose which is almost half my yearly limit as a nuclear worker in Sweden.

I think that when you encounter an unexpected radiation field of 500 mSv per hour the correct procedure is to turn and run (This could be a live saving act), if possible run around a corner in the hope that you can put some concrete between you and the source. So run around the corner and quickly check your dose rate meter before hissing some colourful language, getting to a place of safety, handing in your dosemeter for emergency rapid evaluation, going for a blood test (biological dosemetry), handing over any sugar cubes in your pockets to your radiation protection officer (For ESR dosemetry) and filling in an accident report. The swearing is optional but I will not have a problem with you if you let out some technicolour rant of dirty words which will turn the air blue.

I think that it is very hard to come up with a situation in which you could have a radiation field of 500 mSv per hour (500 mGy per hour). I estimate that you would need to have a point source of 36.5 curies of cobalt-60 at one meter. This is a very large source. Some radiographic sources might be in this range.

But as a result of self adsorption it will be much lower in our case of the uranium cylinder. If we use the NIST data for uranium, as I did and treat the uranium as a series of point sources along the axis of the cylinder. Then I got a value of 9.06 microSv per hour, this will work out at 0.9 milliREM per hour.

While the dose rate of 9 microSv per hour is higher than an area that the general public can legally have access to in Europe (2.5 microSv hr-1) it is not a dose rate which is superhigh. If we assume that a child goes to the museum each weekend and spends 1 hour 1 meter from the uranium bucket then they will get a dose of 453 microSv. This is half of what a member of the public (children are never allowed to be radiation workers so they will always be “members of the general public”).

So I do not think it is likely that any visitor has had a gamma ray dose which is anything to worry about.



I daniel blake

Dear Reader,

I recently viewed the film “I daniel blake”, I have to admit that this is a rather shocking film. It is in some ways a bit like “Threads” which was a science fiction about nuclear warfare. While on a few occasions a scenario like threads came rather close to occurring, thankfully threads remained science fiction rather than science fact.

Sadly while Daniel Blake is likely to not be a real man, the events shown in the film are based on fact. While it is perfectly reasonable that these events have occurred, it is not reasonable that these events should have been allowed to occur in real life.

I have to warn you that like Threads the film is a gloomy film which I think is equally sad. While watching threads I was hoping to be able to dismiss it as exaggeration but in that case as a radiation worker I could not find a major fault in it with which to dismiss it. On the other hand “On the Beach” is riddled with nonsense, but we can save that for another day.

In the film “I Daniel Blake” we see a hardworking man who is forced to down tools because of a serious health issue. Despite the fact that several doctors declare him unfit for work he is told by DWP (Department for Work and Pensions) that he is fit for work.

We also see a woman being forced into prostitution by poverty, this is also clearly not the sort of thing which should be happening in society.

Now while some people might want to ignore or mock this film, I think it is a rather unpleasant but important wake up call for society. I have heard that the UK government are exceptionally displeased about the film, sadly sometimes the news that people need to hear is not the news that they want to hear !

I hold the view that a safety net should exist for those who have fallen on hard times, despite what some people might say, think, or think that they know this safety net is not a comfortable hammock. I also find it interesting that in society a large series of hue and crys have existed against the benefits cheat while adverts suggesting that people should try to turn in tax cheats are much more rare. It is noteworthy that a typical tax cheat costs society more than one of the rare benefits cheats.


Dear Reader,

Today I got the VNA which I purchased recently out of the box, and set up the software. This VNA is intended for use in my chemistry lab where it will be used to help unlock the very secrets of the ionic liquids and the deep eutectic solvents. When there are some results I will share with you the results.

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