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Palomares and the H-bombs

Dear Reader,

Now some doomsayers may have tried to tell you that once radioactivity appears in soil that you should give up all hope, also on the otherhand some false prophets of insincere reassurance will just tell you to stop worrying and that “everything will be OK”. My advice is not to trust either of these two false friends.

The story of the air crash which involved four H-bombs has popped up again, the BBC report that the local people in Spain are fifty years after the air crash unhappy about what has been done.

The BBC report suggests that the local farmers have a problem getting a good price for their produce at market. I would like to point something out.

The plutonium in the H-bombs would have been in the form of the metal, during the accident this would have been burnt into plutonium dioxide. Now the thing to note about plutonium dioxide is that it is very hard to dissolve in acid, also it is not mobile in soil. Any plutonium which was in a water soluble form is likely to have bonded to the soil minerals thus making it impossible for plants to absorb it via their roots.

M.I. Sheppard and D.H. Thibault, Health Physics, 1990, 59, 471 to 482 gives the binding constants for most metals to the four common soil types. It lists for plutonium the following Kd values.

Sand, 150 L/kg

Loam, 1200 L/kg

Clay, 5100 L/kg

Organic, 1900 L/kg

This means in a bucket containing a mixture of clay type soil and water that the plutonium content of the soil (Bq per kilo) will be 5100 times higher than the plutonium content of the water (Bq per litre).

Hence when 1000 Bq of plutonium is added to a litre of water mixed with a kilo of clay type soil, then the soil will absorb 999.8 Bq of plutonium while 0.2 Bq of plutonium will stay in the water. This calculation is for a static batchwise experiment but it will help experts in the field make predictions about the mobility of plutonium solutions in soil.

Another good bit of news is the fact any plutonium dioxide in the dust will not be well absorbed if it is swallowed (dust on the surface of the food), so orally the plutonium dioxide is not a great threat to life and limb. If you were to swallow a well sintered particle of plutonium dioxide it will pass unchanged through your digestive system.

However plutonium dioxide in the lungs is very dangerous to a persons health, I think that a key thing to do in Spain is to keep the plutonium in the most contaminated soils from entering the air as a dust. I think that the ban on building, farming or walking in the contaminated area is a good idea. But I think that it might be a good idea to pour concrete or asphalt onto the worst hot spots to try to fix the soil to keep it from becoming mobile again.

One of the problems with plutonium is that the colloidal particles of clay can make the plutonium mobile, while the plutonium does not move freely through the soil in aqueous solution the colloidal particles can move through the cracks in the soil. Thus sealing the soil would help to stop the plutonium from reaching the surface again in the form of dust.


Cesium maps for Japanese farmland

Dear Reader,

The Japanese government have issued maps of cesium contamination on farmland in the areas near to the Fukushima reactor accident. The main map of that area of Japan is here. Based on a google translate examination of the text with the map the soil has been taken from paddy fields at up to 15 cm depth while for upland soils it is the top 30 cm of soil. If any of my readers can read Japanese then I would be very grateful if they could give me a translation of the text from the Japanese Agriculture, Forestry and Fisheries Research Information Technology Center.

The bad news is that the cesium level in some areas is high, but the good news is that there are things which normal farmers can do which will lower the transfer of cesium to the food crops. I think that farms are going to need to learn a few new skills to allow them to farm in a safe and healthy way using their contaminated land.

Peachs, cesium, fruit and fukuashima

Dear Reader,

I have read with interest the blog of a lady called Dr Susan Burton who teaches English at a Japanese University. She is quite reasonable to be concerned about the levels of radioactivity in her diet. In her blog she questioned the wisdom of selling fruit from the Fukuashima area in the supermarket, right now I can not say if they are safe or not to eat. This question is one which can be better answered by the radiation protection authority in Japan.

Susan lamented that the cesium has a half life which is greater than a decade, she was worried that the cesium would spoil her enjoyment of Japan for a very long time. This comment about cesium and peaches prompted me to check the literature on radioactivity and fruit.

Back in 2001 a person in Italy published a review paper on the transfer of radioactivity from soil to fruit (F. Carini, Journal of Environmental Radioactivity, 2001, volume 52, pages 237 to 279). I went through this review and I found some data for peach trees.

One of the most important things to know about farming in a radioactive area is the transfer factor. The transfer factor is a measure of how easy it is for radioactivity to get from the soil into the part of the plant which you eat. It is defined as the ratio of the radioactivity (Bq kg-1) of the food to the radioactivity level of the soil (Bq kg-1). It is important to bear in mind that the transfer factor depends on the species of the plant, the soil type and the element.

Element Soil type Transfer factor
Cs Not recorded 0.0131
Cs Sandy loam 0.009
Sr Not recorded 0.0218
Sr Sandy loam 0.07
Pu Not recorded 0.000163
Am Not recorded 0.000436
I Not recorded 0.0109
Ru Not recorded 0.00109
Ce Not recorded 0.000436
Cm Not recorded 0.000436

As the main radioisotopes released by the accident were noble gases, iodines and cesiums it should be clear from the table above that in future years the humble peach tree will have a filtering effect. While most people do not like eating mud, if you were to eat mud then you would get a greater intake of cesium than if you ate the same mass of fruit from a tree grown on the radioactive soil.

I predict that in future years that the radioactivity level in the fruit will be dictated by the absorption of radioactivity by the roots of the tree and the transport of the radioisotopes through the tree into the fruit. But this year due to the direct deposition of radioactivity onto the leaves of the plant we need to consider a different route.

Sadly I could not find any results for peach trees but for bean plants I could find some results. In an experiment a leaf of a bean plant was soaked in a solution of a radioisotope to simulate radioactive rain. Then the plant was grown further before the radioactivity levels in different parts of it was measured. It was found that most of the radioactivity absorbed remained in the leaves.

Only 13 % of the cesium, 0.06 % of the strontium, 0.2 % of the americium and 0.002 % of the plutonium was found in the bean pods.(P. Henner, C. Colle and M. Morello, Journal of Environmental Radioactivity, 2005, volume 83, pages 213 to 229) This suggests that while cesium might be mobile inside plants the other elements are not very mobile inside the plants. While this effect may protect the consumer from plutonium, strontium and americium (which have not been released from Fukuashima in large amounts) due to the fact that the cesium is mobile it is possible that fruit grown this year on trees may be contaminated by cesium which was absorbed directly into leaves and then transferred through the plant into the fruit. So this year great care is needed to check the contamination level of the fruit, in future years it is likely that the cesium contamination level in the fruit could be much lower than this years contamination level.

Now one of the wicked lies which some parts of society like to either spread about deliberately, imply or assume is that humans are powerless in the face of the evil radioactive atoms. This idea is clearly wrong in several ways.

  1. Atoms and radiation knows no morality, no matter how good or evil you are atoms / radiation will treat you the same way.
  2. Humans can take action to alter their exposure to radiation and radioactivity.

For example by changing farming methods the level of cesium in the crop can be lowered. I saw one paper (W.L. Robison, P.H. Brown, E.L. Stone, T.F. Hamilton, C.L. Conrado and S. Kehl, Journal of Environmental Radioactivity, 2009, volume 100, pages 76 to 83) which explained that by using potassium fertiliser on coconut trees which were growing on Bikini island (Where the Americans used to test H-bombs) that the cesium level in the edible parts of the coconuts can be greatly lowered.

My advice to any Japanese farmers who might be reading this blog is to do the following.

  1. Find out what sort of soil your farm has.
    1. Clay soil tends to bind cesium more than sandy soil
  2. Find out from a cesium map how contaminated your farm is likely to be
  3. Ask the farmer’s union, TEPCO and the state radiation protection authority for advice on how to lower the contamination level of your crops. I would suggest that you ask about the following
    1. Deep ploughing to prevent the transfer of cesium via grass to livestock
    2. Prussian blue to decontaminate livestock
    3. Potassium fertilizers to prevent plants taking up cesium
    4. Changing to a different crop which is less able to take up contamination. Oilseed rape might be a good plant. The oil pressed from the seeds is normally has very little contamination in it even if the rest of the plant is contaminated. Also onions may be a good crop to plant. Below is some data from 1989 in Finland ( A. Paasikallio, A. Rantavaara and J. Sippola, The Science of the Total Environment, 1994, volume 155, pages 109-124) which shows that some crops are better able to avoid taking up cesium from the soil.

Transfer factors for different crops in three different soil types


Well dearest reader,

While I have been blogging about nuclear matters recently I have something more mundane to tell you about.

I have just planted my potatoes, I run an “organic” vegetable patch, so far I have never had to use any pesticides or man made fertilizer on my vegetable patch. This morning before the middle of the day and the intense heat I planted a total of 25 seed potatoes. I sincerely hope that I will get a good yield of potatoes from my patch.

While I am not chemophobic I hold the view that if I can keep my plants healthy without using insecticides or other pesticides then I will be happy and glad to have saved myself the time, expense and trouble of having to spray the plants.

We also will be growing peas and turnips this year as well, I hope to also get plenty of fruit from the trees and the bushes in my garden.

Peas and nitrogen II

OK some of you might ask what peas have to do with catalysis, the peas do not have anything special in them but in their roots, they have bacteria, which have very special enzymes, which are able to break the super strong nitrogen nitrogen bond found in a nitrogen molecule. When humans want to break the N N triple bond they need to use harsh conditions but the bacteria in the roots of the peas can do it at 20 oC and 1 atmosphere.


I looked at the literature and I found that it is thought that the active site of the enzyme contains iron and molybdenum bonded together with sulphur groups. I then saw a paper on ruthenium chemistry, some of you might ask, “what has ruthenium got to do with it?”. Good question, in organometallic chemistry and homogenous catalysis it is often the case that the second and third row transition metals can do the same chemistry as the first row metal. But the rate of reaction is often lower, and the strength of metal carbon bond is often greater for the more heavy elements. For example nickel carbon bonds are often too weak to be useful, platinum carbon bonds are often too strong to be useful while palladium carbon bonds have just the right strength. For example, palladium cross coupling chemistry (Heck etc) has become a very important tool in modern organic chemistry.


The way in which the enzyme converts nitrogen gas into ammonium ions is not clear. Many hours of effort have been expended by some very bright people but the answer is not clear yet. One of the methods, which can be used to find out about a chemical process, is to try to grow crystals of the reagents. If you are lucky, you might be able to observe the structure of a key intermediate, there is a grave danger with this method. It is possible to trust the crystal structure too much. The great problem is that most processes occur in solution state, while crystallography is done on the solid state. In addition, it is possible to have different forms of a compound both in the solid state and in the solution state.


Before we will look at some nitrogen fixation, we should look for a moment at some examples of how crystallography can trap the unwary. The most simple example I can think of is [RuHCl(CO)(PPh3)3], it has two different forms one is pink and the other is yellow. I was once warned by a teaching lab technician that if you run a teaching lab using it then make sure you give all the students samples from the same batch. The students do not like having a different coloured starting material to their classmates.


Before the arch critics of crystallography rejoice, I would like to point out several things.

  1. Few solution state methods (if any) have the same ability to measure bond lengths, angles and atomic positions with the same accuracy as crystallography.
  2. Plenty of molecules are known which can have several forms in solution.
  3. Homogenous systems do exist where a minor constituent in a mixture has almost all the catalytic activity.
  • For example in cobalt based hydroformylation much of the catalyst can be in an inactive resting state [HCo(CO)4] while [HCo(CO)3] is the real catalyst.

      4. There is a way out of the problem.

The way out of the problem is to find a spectroscopic method, which can be used, on both a solid-state sample and on a solution state sample. If the properties of the two forms of a substance are wildly different then it is likely that the structure of the two forms are different. Good methods include infra-red (ideal for metal carbonyl complexes), UV/vis (good for d-block metal complexes) and EXAFS (good for many things but expensive).

Back to nitrogen fixation, I saw a ruthenium dinitrogen complex. While the crystal structure alone does not prove that nitrogen binds this way to the iron in an enzyme, it shows that it is possible for nitrogen to bind to metals in this way. If we consider the nitrogen molecule with VSEPR then it should have two lone pairs on a pair of sp type atoms. One complex (I hope to show you a picture soon) has the nitrogen molecule bridging between two ruthenium atoms. Each ruthenium has a phosphine and a diamino-dithiol ligand attached.

This ruthenium complex will make a good example for the 18 valence electron rule, I will get onto that soon.

Peas and nitrogen

I have been growing peas recently in my garden.

Pea patch

When I started to grow my own veg my wife got a planting scheme which starts off with potatoes (mechanical breaking up of the soil) and then in the second year you plant peas to put the goodness back into the soil. I then recalled that the roots of peas have bacteria which convert the nitrogen of the air into ammonia.

I hope to tell you more about this soon.

How to off the bugs, or maybe how not to off the bugs !

OK for a while (100s of years) people have been looking for methods of killing off insects which trouble them. The methods used for insect control over the years have included some rather novel ones.   

One I like is “mosquito finito”, it is my 2000 volt electric insect whacker (it leaves no chemical residue in my house). I have found that it works very well on flying pests. But for protecting a farm field we can not use it as I doubt if you can afford to pay a mob of people to rush about whacking each troublesome insect. I also suspect that “mosquito finito” would not work on large insects such as locusts. I can think of a way to modify “mosquito finito” into a weapon which would blast even the most hardy insects but I think in the interests of public safety I will not share this idea with you.   

A more interesting one was reported in “Chemistry in the Marketplace” by Ben Selinger, many years ago he wrote that Pliny sent a young lady to dance in an insect infested orchard to entice caterpillars from the trees. Later on some horrible inorganic poisons such as lead arsenate (PbHAsO4) were introduced, quite rightly these horrible toxins were identified quickly as targets for replacement.   

Below is the unit cell of PbHAsO4, I have left out the hydrogens because they are disordered. Disorder is when in different unit cells the atoms are either different or are arranged in different ways. For example cobalt and nickel have the same crystal structure, and an alloy has the two different elements randomly arranged in the solid. In the solid unit cells are arranged like bricks, next to each other and on top of each other to create the solid.   

Unit cell of PbHAsO4


It is interesting that DDT was brought into service as a non-toxic replacement for the lead and arsenic. I hold a view that sadly it is often the case that todays wonder substance will turn out in twenty years to become public enemy number one. Maybe it might become public enemy number two if some other ‘worthy substance’ beats it to the number one slot. Just so you know what DDT looks like here is a picture of a molecule of a close relative (methoxychlor). The difference between methoxychlor and DDT is that methoxychlor has methoxy (CH3O) groups rather than chlorine atoms on the benzene (six membered rings). These methoxy groups make methoxychlor degrade more quickly than DDT. Before you ask methoxychlor has been banned in both the EU and the USA.   

Here is a picture of methoxychlor, I have used the crystal structure of the compound to create a picture of the molecule. There are some things to note about this molecule. Firstly look at the arrangement of the green chlorine atoms on the carbon at the back. Note that these atoms are placed in sites (staggered arrangement) such that they are as far as possible from the atoms or groups on the next carbon. This is due to something called a steric effect. I will cover steric effects another day on the blog for those who do not know about them yet.   

A molecule of methoxychlor (1,1-di-(4-methoxyphenyl)-2,2,2-trichloroethane)


The above diagram was drawn to allow you to see where the atoms and bonds are, in the following diagram the shape of the molecule as seen by another molecule is shown. In the next diagram the radius of the atoms have been set to about their real size so you can see how the shape of the molecule looks to another molecule.   

Picture of methoxychlor using van der waals sizes for the atoms


When DDT and the other chlorine containing insecticides were brought out they were viewed as wonder substances which would make the world a better place. They were viewed as being cheap, easy to use and non toxic to humans and other higher life forms. While chemicals such as DDT are low in acute (short term) human toxicity when compared with the lead and arsenic, they are clearly not harmless. The problem which the chemical industry did not know about was that the chronic (long term) effects of some of the chlorine containing insecticides on humans are very bad. Some of the organochlorine containing insecticides have been linked to cancer. For example the classic breakdown product of DDT (DDE) has been linked to cancer in humans. A recent paper on this link was written by Mark P. Purdue et. al. (Environmental Health Perspectives, 2009, volume 117, issue 10, pages 1514-1519). Also some of the long lived organochlorine insecticides have been found to harm other higher life forms, a classic example is the shell thickness of bird eggs. It is known that DDE causes the shells of bird eggs to become too thin, this then leads to a reproductive failure (eggs break and chicks die). A recent paper which discusses this matter was published by Eric Mellnk et. al. in Environmental Pollution, 2009, volume 157, pages 2184 to 2188.   

Now the saddest part, I know that many women hold the view that breast is best. This is not a bad idea, I know that in many ways that breast milk is a safer and better way to feed a baby in the third world. One classic 1980s nuclear warfare textbook indicates that a woman with a baby should breast feed her baby under the conditions of nuclear warfare. I would say that while breast feeding is normally a good and healthy way to feed a baby it is not perfect. I can think off the top of my head of three health problems. The HIV positive woman who has a HIV negative baby (solution use formula milk), the woman who has just had a thyroid test using radioactive iodine (I-131) (Solution is to bottle feed the baby on formula milk for a few days while the woman uses a breast pump so that she continues to make milk) and the last and saddest one is organochlorine compounds in milk. In many places in the world organochlorine insecticides have been detected in human breast milk, the fact that these substances can get into the breast milk which a woman feeds to her baby is a good reason for society to regulate the use of long lived organic pollutants.  S.M. Waliszewski et. al. in the Bulletin of Environmental Contamination and Toxicology, 1996, volume 57, pages 22-28 showed (yet again) that DDT and lindane could be detected in Mexican human milk. If the use of DDT is reduced or stopped then the concentration in human milk will go down. I suspect that for most woman their DDT level in their milk is not at a dangerous level, but if you are a woman who has a fear of passing on DDT to your baby then I would suggest that you discuss it with your doctor. A wise precaution would be for a pregnant or breast feeding woman to avoid using DDT and to avoid areas where it is being sprayed.   

In recent times a movement towards using short lived biocides has occurred. The reasoning is that the biocide only needs to be present in the environment for a short time, and that it will decay away into harmless substances quickly rather than lurking about to assail plants and animals. The advantages of these short lived are that they do not linger in the environment and harm non targeted lifeforms long after they were needed but the disadvantage is that they may need to be applied more often than longer lasting biocides.   

For example for keeping the weeds under control in a substation a long lasting herbicide such as sodium chlorate might be a better choice than paraquat. Paraquat becomes inactive as soon as it touches soil while sodium chlorate remains active in soil for years. On the other hand a non chemical method of pest control can be used, I once saw a substation in the Czech Republic where a flock of sheep were used to keep the grass short in one part of the compound.   

One thing in favour of the sheep is that sodium chlorate and paraquat are being banned for environmental and safety reasons but it is very unlikely that sheep will be outlawed. Before we get any further I think it is important to make one thing clear the nastiness or niceness of a compound is not related to if a substance is natural or artificial.   

Cocaine, ricin, alfatoxin, lead and radon are natural. Each is perfectly horrible. In case you wonder what an alfatoxin is, it is a nasty carcinogen which causes liver cancer and is formed by a mold which grows on nuts. This is why it is important for every batch of nuts imported into the UK to be checked for mold and/or the toxin. The structure of the alfatoxin is shown below.    

Alfatoxin, now you get to look at the monster !


 Salbutamol is artificial and is one of the nicest chemicals you can think of. It is a drug which helps to keep many people’s lungs working normally.   

Salbutamol (Nitrogen is shown in blue)


 One of the more nasty natural insecticides is nicotine, it is a pyridine and pyrrolidine compound which has the pyrrolidine ring bonded at the 2 position to the pyridine at the 3 position. In heterocycles it is normal to start counting atoms at the heteroatom.   



Nicotine is a nasty poison which can be absorbed through the skin, I think that nicotine is just as dangerous as some of the worst of the organophosphorus insecticides which are in current use. The LD50 of nicotine is about 50 mg per kilo in rats. (http://www.inchem.org/documents/pims/chemical/nicotine.htm)   

Tetraethyl pyrophosphate (TEPP) is a nasty insecticide (http://www.osha.gov/SLTC/healthguidelines/tepp/recognition.html) which I think is almost as bad as sarin. It is a very poisoning chemical and the LD50 in rats is about 1 mg per kilo. Thankfully TEPP has largely been withdrawn from use in favour of other chemicals. Currently parathion is banned in many parts of the world, or is strongly restricted in many places. With the dire toxicity of parathion I hold the view that these restrictions and bans are a good thing.   

For example parathion has an oral LD50 of about 3 to 6 mg per kilo in many animals, while the less toxic malathion has a LD50 of about 1600 mg per kilo in mammals. When I was a teenager, malathion was supplied to the general public for dealing with nasty insects. So nicotine is more toxic than some of the organophosphorus poisons which used to be sold to the general public.   

Table of LD50 values

Substance Animal LD50
Sarin Rabbit 0.247 mg kg-1
TEPP Rat 1 mg kg-1
Parathion circa 4 mg kg-1
Nicotine Rat 50 mg kg-1
Malathion 1600 mg kg-1

A much nicer class of insecticides are the pyrethrins of which pyrethrin I is a classic example, it is extracted from Chrysanthemum cinerariaefolium which is a nice flower. This flower is grown in africa, the extracted pyrethrins are used to control insects. One use is dog shampoo, one of the weaknesses of pyrethrin I is the fact that it is not light stable.   

The pyrethrins from the flowers tend to be oils so I can not show you a crystal structure of them. But I can show you a salt of the carboxylic acid. The carboxylic acid (chrysanthemic acid) can be formed as an ethyl ester by the action of ethyl diazoacetate on a 1,3-diene. This in the past has been an undergraduate experiment at some university chemistry departments. The carboxylic acid ester is formed as a mixture of cis an trans forms, each of these forms has two stereoisomers so a total of four isomers are known of the carboxylic acid. A recent paper was published (Goffredo Rosini et. al., Green Chemistry, 2007, volume 9, pages 441 to 448) in which a simple method of separating the isomers was described. From the data in this paper here is a picture of the carboxylic acid on the right with the resolving (separation agent) on the left.   

A chrysanthemic acid salt


Even while the pyrethrins are safer than most insecticides they should still be treated with a great deal of respect. They are esters which are sensitive to light, I have not been able to find LD50 values for pyrethrin and I suspect that these values would be high. A high LD50 value means that something is not very toxic. The LD50 value is the dose required to kill haf the population. I am sure you can all imagine how in humans the LD50 for ethanol is likely to be very high, while the LD50 for sodium cyanide is likely to be much lower.    

The measurement of LD50 values is very controversial, maybe another day I might discuss this issue with you. But please understand that my mention of the LD50 values is not an attack on or endorsement of animal testing. One day you might get my view on the matter. One weakness of animal testing is that for some substances such as dioxin the LD50 value differs greatly from one species to another.    

One of the insecticides which is only weakly toxic to mammals which is still very toxic to insects is azadirachtin, this is a very oxygen rich and complex molecule. Now you may have noticed that we have been going from some simple insecticides such as DDT to the more complex ones such as chrysanthemic acid esters. Now we are going to go to a super complex molecule. This is one which is found in neem oil and is responsible for most of the antiinsect activity of the oil. It has a misleading name, normally the letters “aza” in chemistry mean “contains nitrogen” in this case the molecule has the aza prefix but contains no nitrogen. I would like to now present to you azadirachtin.   

Azadirachtin could be the test of tests for any chemist to make it, it has so many different functional groups in it. It has alcohols, ethers, esters, an acetal and an epoxide group. Here is a picture of what the molecule looks like as a flat drawing on paper, I sincerely hope I have not made an error with it.   

Azadirachtin as a flat drawing on paper


Now here is a picture of the real shape of the molecule, this is from the crystal structure. This is what we sometimes call a cluster of spiders.   

Azadirachtin ball and stick view


Now here is the space filling version of the same picture.   

Azadirachtin space filling version

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