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Poisoned car door

Dear Reader,

Reports are coming in suggesting that poison smeared on a car door might be responsible for the serious injuries suffered by the Skripals. It is interesting that the labour leader is calling for a more open discussion of the evidence associated with the poisoning.

I also find it interesting that the inventor of the Novichok agents is making a statement on the likely long term effects of the substance on the general public. Looking at his statement I see a problem which can exist, all of the nerve agents work by altering a key enzyme in the nervous system.

I reason that the reason why these substances can cause serious injury is that they greatly reduce the amount of the active enzyme in the body at one moment. One could regard this effect as being due to the nerve agents simply lowering the concentration of this enzyme.

While there are some differences in the rates of both reactivation and further inhibition by the different nerve agents in terms of their mechanism the classic nerve agents are all the same in terms of how they cause the acute effect. What happens is that the nerve agents normally bind to an OH group in the enzyme (on a serine residue). For many of the chemical warefare agents they tend to then lose an alkoxy group thus making it harder for the enzyme to become reactivated as shown below.

sarin binding to enzyme

However it is known that a delayed condition known as organophosphate-induced delayed polyneuropathy exists. According to Milan Jokanović and Melita Kosanović the OPIDP normally appears within 10 to 20 days of a one off exposure. So I suspect that unless the Novichok agents have some special ability to bind to some important biomolecules which are very rare in a human when compared with acetylcholinesterase and the other things which the “normal organophosphates” bind to that if the general public manage to stay healthy for a month after the event then they should remain healthy. That is assuming that something else does not go wrong with them.

It is interesting that a lot of phosphorus compounds are used as enzyme inhibitors, for example the herbicide “roundup” is N-(phosphonomethyl)glycine which is the chemical of choice for many people who want to keep their drive free of weeds.


Milan Jokanović and Melita Kosanović, Environmental Toxicology and Pharmacology, 2010, 29, 195-201.


The Novichok agents

Dear Reader,

Things have become more complex in more ways than one, it has been claimed in the UK that the nerve agent attack involved a so-called novichok agent. I also posted this post to the wrong blog last night.

Now I can not claim to know where these novichok agents came from, who did it or even if a novichok agent was used. I would rather not get sucked into a debate about who did it, I am mainly going to consider the chemistry.

However I can consider some of the chemistry, according to the internet the novichok agents were invented in the Soviet Union in an attempt to make chemical warfare agents even worse than sarin and VX. On Wikipedia it is claimed that methyl-(1-(diethylamino)ethylidene)phosphoramidofluoridate and 1-chloropropan-2-yl (E)-(((chlorofluoromethylene)amino)oxy)phosphonofluoridate are examples of novichok agents.

1-chloropropan-2-yl (E)-(((chlorofluoromethylene)amino)oxy)phosphonofluoridate

Part of the problem is that very little if anything has been written in the academic literature about novichok agents, well at least under that name. I did a search of the web of science and I did not find any mention of any paper with that word in the topic or title on the subject of chemical warfare. On the other hand I found almost 800 papers which have the word “sarin” in the title.

I also looked for methyl (E)-(1-(diethylamino)ethylidene)phosphoramidofluoridate in the organic chemistry literature using one common database, and I could not find any mention of this substance. Looking at it as a organophosphorus chemist I can see that it has the correct groups attached to a phosphorus atom to act as an acetylcholinesterase inhibitor. I also see an electron releasing group which would reduce the partial positive charge on the phosphorus atom when it is compared with sarin. This reduction in partial positive charge would reduce the rate at which the substance will react with water. This change would be likely to make the substance more able to persist in the environment.

However when you look for 1-chloropropan-2-yl (E)-(((chlorofluoromethylene)amino)oxy)phosphonofluoridate you can find plenty written on the subject in the Soviet chemical literature back in the 1960s and 1970s. By reacting dichlorofluoro(nitroso)methane with a phosphorus(III) compound a reaction similar to the Arbuzov reaction occurs which forms the product. Here is my best effort for the mechanism by which the compound is formed.


I hold the view that while the Soviets are thought to have developed the novichok compounds it would not be very hard for a competent (and well protected) phosphorus chemist to make a moderate amount of one of these rather exotic substances. So unlike polonium-210 (which is only produced) in very few nuclear reactors it is impossible to argue based on the identity of the nerve agent where it came from.

One of the problems in life is that sometimes bad people will choose tools or methods which are not normally used by people from their country in an attempt to confuse any investigator. For example the NKVD used German pistols to murder Polish officers at Katyn. This offers some degree of plausible deniability. Thus I think some other evidence other than the identity of the nerve agent is required before anyone can blame anyone for the horrible event which has just occured.

Mrs May and the nerve agent

Dear Reader,

It has come to my attention that Mrs May the prime minister of the UK has made a public statement in which she suggested that it was likely that Russia was in some way responsible for the poisoning of people in the UK.

The problem is that based on the information which has been released into the public domain it is not possible to prove that a “military grade” nerve agent was used. Even with the benefit of a PhD and some further experience of organophosphorus chemistry I have to confess that I do not know what a “military grade nerve agent” is.

I note that the cult in Japan which used sarin was not part of the military, thus it is a civilian organisation. I still hold the view that the sarin released by the cult was equally harmful as sarin which was made by (or for) the military.

While I wrote yesterday about nerve agents which have traditionally been viewed as military weapons only, I am aware that there are some substances which have very similar effects on humans and animals which have uses in civilian life. It is also interesting that “Chemistry in the Market Place” (I am not totally sure if it is that book or another one from the same era) made the claim in the 1980s that the Germans experimented with sarin in a vineyard. The Germans found that it exterminated all the insects in the vine yard but every accident which workers had was fatal.

If it is true this attempt at using sarin as a agricultural pesticide does slightly change the “military only” status of sarin a little further.

I would advise people to keep an open mind regarding what the poison was and where it came from. I hold the view that Russia does not have a monopoly on making the vile abomination known as “nerve gas”, the problem is that people in other places know how to do it and in some cases have gone and done it.

I do not know who was responsible for releasing the structure of VX to the general public, years ago when I was in Aberdeen (Scotland) I randomly chanced on the article by Dr Yang and I recall asking myself the question of “was it a good idea to tell the scientific community what the structure of VX is ?”.

One of the problems we have in our current age is the management of information, I have encountered people who have got it wrong equally from both extremes. There are some people who think it is proper and right that no information on some topics should be released into the public domain. Some years ago I read with interest an article in Chemistry World on the subject of “fracking” which wrote about “chemicals” being injected into fracking wells to stimulate the production of gas. The problem in my mind is that some substances either injected or recovered from a oil or gas well are quite harmless while others are harmful to humans, animals, plants, bacteria or other life forms. The failure to discuss openly the question of “what is going into and out of the well” does inhibit a honest and reasonable debate about “fracking”.

Equally wrong is the “pirate party” / wikileaks types who think that they have a right or even duty to release all and any information into the public domain without considering the results of releasing the information. These people seem to hold the view that “everone should know everything about everone” and that no restrictions or controls should exist on intellectual property. Commonly the pirate party people think that they should be able to get music for free and watch feature films for free, but their views are harmful to many sectors.

The problem is that some information does have misuse potential, how about.

  1. How many armed guards will the king of Sweden have with him on Tuesday afternoon and where will be spending the afternoon.
  2. How many 999 calls can be handled at once in London at any one time.
  3. What make / model of safe is used at a hospital pharmacy to store a large amount of diamorphine (heroin)
  4. What is the location of a shelter for battered women who are fleeing from a violent partner or ex-partner.
  5. How much gold is stored in a jewelry workshop over the weekend.

Now I suspect that the vast majority of my readers are decent people who if they chanced upon one of these bits of information would not misuse it. Some of them might even be so publicly spirited to report the security leak

In the interests of public safety I will not be telling you how to do it or answering some other questions. You are free to ask me questions via a comment on this blog, but keep in mind that I will refuse to answer some questions on this topic.

Nerve agent in Salisbury

Dear Reader,

It has come to my attention that a “nerve gas” attack has occured in england, a man named Sergei Skripal and his daughter Yulia were stricken with the poison as was a police officer who remains in hospital. We have to ask ourselves “what has happened”, many of my readers might be wanting to know “what is nerve agent”.

Now at this point I think it is important to keep an open mind and stay calm. There is some good news and some bad news regarding nerve agent. There are two main classes of nerve agent, they are the G agents and the V agents.

The G agents such as sarin have quite low boiling points and have a P-F bond (except for GA tabun which uses a cyanide group as a leaving group), these substances are likely to react with water quickly. I would expect a short environmental half life for these compounds. Here is a picture of the classic G agent (sarin GB). Like all phosphorus based acetylcholinesterase inhibitors it has a phosphorus (V) atom bearing a leaving group and two lipophilic groups. After the loss of the flourine atom when the sarin binds to the enzyme the isopropyl group tends to be lost thus making it harder for the enzyme to be reactivated. Somon (GD) is even more age in this way making it even harder to treat.


There are some drugs which will reverse the binding of sarin to the enzyme such as PAM, but a lot of the treatment for nerve agent poisoning is simply management of the symptoms.

The V agents are slower to react with water and tend to have higher boiling points, these lack the P-F bond. Here is a picture of VX showing the molecule.


According to Yu-Chu Yang (Accounts of Chemical Research, 1999, 32, 102-115) when VX reacts with a nucleophile it can either lose the sulfur group or the ethoxy group as a leaving group. Looking at VX as the molecule has larger alkyl groups than sarin and as it does not have such as potent leaving group it is clear to me why it reacts more slowly with water.

The good news is that if it was a G agent then it would be likely that the poison will have become inactivated by now, the G agents can be spread as either vapor (gas) or as droplets. When I consider the attack in Japan, there the cult were delivering it as vapor. They broke open plastic bags contaning it on the subway spilling the liquid out onto the floor. This will not create many aerosol droplets but it will release the vapor into the air.

While it is possible to get poisoned through skin contact with either liquid sarin or the vapour sarin and the other G agents in my view are mainly a threat by inhalation.

The V agents can be dispersed as aerosol droplets, in this form they could be inhaled but I am aware that they can be adsorbed through skin. As they react more slowly with water they are a greater threat when we consider the skin adsorption problem.

The bad news is that we do not know how the poison was delivered to the two people, as a police officer who responded to the incident was taken ill I suspect that either the police officer entered a location where aerosol (either VX or a G agent), vapour (G agent) or unfixed contamination (most likely VX) was present. Alternatively it might be some other toxin which was used.

The idea of fixed and unfixed contamination is a concept from the radioactivity sector. An object or surface which is contaminated with radioactivity but does not release radioactivty with ease is far less of an contamination threat than an object which can release its contamination.

Now the good news, some of you will be aware of something known as the LNT model in radiation protection. This model is based on the assumption that the ability of radiation to induce cancer does not depend on the dose rate (rate of exposure). It also is based on the assumption that the likelyhood of developing cancer is proportional to the dose.

In fumigation and chemical warfare there is something known as “Haber’s Law” or “Haber’s rule” that states the likelyhood of causing death or another health effect depends merely on the mathmatical product of the exposure time and the concentration.

For example according to this rule a 10 minute exposure to 100 ppm of substance X in air is equally harmful as a 1 minute exposure to 1000 ppm (0.1 % v/v) of substance X.

I hold the view that with nerve agent that Haber’s rule does not apply at low exposure levels. Equally with hydrogen cyanide it does not apply. With both nerve agent and cyanide even without medical help the human body has an ability to repair some of the damage that these substances cause. As a result a prolonged exposure to the substance at a very low level will not have the same ability to cause harm as a short exposure to a high level of the substance.

More on organic peroxides

Dear Reader,

Regarding the organic peroxides at the Arkema site in Texas, I took the time and looked up the safety datasheet (SDS) of one of their products. I choose an organic peroxide product (Luperox 331M80) which a 80 % solution of a peroxide which is suitable for plastics processing.

Now after the tales of explosion in the popular media I checked the SDS for any signs of explosive behaviour, I did not see any warnings about detonation of the 1,1-di-(tert-butylperoxy) cyclohexane which is the peroxide in this product.

I also note that the product is a very long way away from being an oxygen balanced explosive. If we consider the chemistry of a detonation. It is normally assumed that an explosive such as TNT is converted to a mass of atoms, these atoms then combine to form a series of products.

The formula of the C14H28O4 if we decompose this into atoms then we would have a great deal of carbon and hydrogen which requires an oxidant to burn. If we apply the Kistiakowsky–Wilson rules then we would expect 4CO + 14H2 + 10C as the products. I suspect that the reaction would form a lot of soot and maybe some hydrocarbons. To me this does not look like a compound which has much promise as an explosive.

The formula weight of the compound is 260.374 grams per mole, I have worked out the oxygen balance of it to be -234 %, this is very far away from the values for typical explosives such as ammonium nitrate (+20 %) TNT (-74 %), nitroglycerine (+3 %) and TATB (-56 %). I suspect that such an extreme lack of oxygen together with a lack of nitrogen would lower the heat of explosion to the point at which detonation would be impossible to at least very difficult.

What the substance could do would be to generate heat in an exothermic reaction and thus burst open a container. If we consider a substance which can decompose in a reaction which has an activation energy EA. Then the rate of reaction will be given by the equation (Arrhenius).

k = A exp (- EA/RT)

Thus as A, R and Estay the same, when T changes the rate constant will change.

If we take data from Sigma-Aldrich for the rate of decompstion of di-tert-butyl peroxide and we calculate that Eis 141124 joules per mole. While A is 5.623 x 1013 s-1.

If we consider the energy release when one mole of di-tert-butyl peroxide decomposes to 2,5-dimethyl-2,5-hexanediol then by using the difference in the heats of combustion we can work out the heat (enthalpy) of the reaction. I have worked out that the energy release when one mole of the peroxide decomposes will be 30080 joules.

If the heat capacity of both compounds is assumed to be 310 J mol-1K-1 we can work out what will happen if a infinite drum of di-tert-butyl peroxide is left at 60 oC. The drum would sit nicely doing very little for days on end, and then suddenly it will bite back in a rather nasty way. The temperature will suddenly spike. What happens is that the self heating in the drum will suddenly make it heat up to the point at which it will boil violently.

selfheating of ditertbutyl peroxide

What I did was to compute the rate of the reaction at 60 degrees C, from this I worked out the heat generated by the mixture. I also worked out the amount of the peroxide which had been consumed. I assumed that the reaction rate would be constant for 30 seconds. I worked out the temperature and the peroxide concentration at the end of each 30 second time period and then used these values to start another calculation. After doing this many times I had the data for the graph.

If doubt if I have got the exactly right time between leaving the drum and the fiery exotherm, an error in the activation energy or another parameter will change the answer. What will be needed would be for someone to go and do DSC on the peroxide. compound. It is also important to note that sometimes an impurity can increase the rate of the decomposition. For example amines can increase the rate at which some peroxides decompose.

In a DSC machine a sample is heated in a small furnace in which the amount of heat energy required to increase the temperature of sample. The sample is compared with a blank (empty sample holder). In this way it is possible with a very small sample to determine if self heating can occur.

Crosby in Texas and the organic peroxides

Dear Reader,

It has come to my attention that in Texas at a place called Crosby there has been an incident at the Arkema plant. What has happened is that as a result of the extreme weather that the plant has lost electrical power. This is the non nuclear version of what we in nuclear chemistry call a “Station Blackout”. During a station blackout a plant will have lost both the ability to generate electric power for itself, the ability to import electric power from elsewhere and also if things go very badly it will run out of battery power.

What has been reported is that after the electric power failed the refrigeration failed and containers of organic peroxides started to warm up. Some organic peroxides are rather stable while some others tend to decompose quite quickly. The degradation of the organic peroxides will release chemical energy as heat. This will then speed up the rate of the chemical reaction which in turn warms them up more.

What then can happen is that under some conditions that the reaction can go into a thermal runaway which results in it over heating. In general the larger the volume of a container and the less inert solvent which is present then the greater the likelihood and effects of a thermal runaway will be. This is one good reason for storing such substances in small containers.

Now one of the effects which has been reported in the press is that explosions have occurred, I want to ask the question of is it a true explosion or was it just a loud noise of a container bursting in a fire. The problem is that both can appear to be the same. But it is important to keep in mind that the explosion effects of a true detonation tend to be far greater than just a container bursting.

I am currently handicapped by the fact that I do not know exactly what products are overheating in Texas, but I am looking into things. I hope to be able to give more information soon.


Dear Reader,

We have had a lot to think about recent regarding polyurethane, so I think it is a good idea if we discuss the chemistry which is the basis of polyurethanes. The key chemicals for making polyurethanes are the isocyanates.

Now for those of you who have never encountered the isocyanates, I can tell you that they are rather reactive electrophiles which are often strong irritants. It is normal to make then from phosgene (carbonyl chloride) and a primary amine. They are similar to both carbon dioxide and the protein synthesis reagent (DCC, N,N’-Dicyclohexylcarbodiimide). All three have a sp carbon in an allene like system.

Using extended Huckel theory we can predict that carbon dioxide will have a charge of + 0.6 on the carbon, while diphenylcarbodiimide will have a charge of + 0.37 on the central sp carbon while the phenyl isocyanate will have a charge of + 0.46 on the central sp carbon. Here is a picture of phenyl isocyanate.

phenyl isocyanate space

Nucleophiles such as water, alcohol and amines will attack this carbon to form addition products. Here is a picture of phenyl isocyanate in which I have calculated the charges on the atoms, these are projected as colours onto the solvent accessable surface of the molecule. The more red they are then the more positive they are and the more blue then the more negative they are.

phenyl isocyanate charges

What you should be able to see is that the carbon in the isocyanate group is the most positive part of the molecule. I have a line drawing for you which will explain what happens when the molecule reacts with an alcohol, which is below.

urethane formation

In this way the isocyanate group can react with an alcohol group to form a bond between the alcohol molecule and the isocyanate molecule. The synthesis of polyurethane normally uses a diisocyanate and a long molecule which has two alcohol groups at the different ends of it. This will allow the creation of bigger and bigger molecules (polymerization) which transforms the small molecules into a very large molecule (a macromolecule).

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