How to deal with moelcular orbitials in polyatomic molecules

Recently a student asked me about how to deal with the problem of making molecular orbitials in a polyatomic molecule. For example we can consider carbonyl sulfide (S=C=O). This has a sulfur, a carbon and an oxygen.

The first step of the problem is to count up the number of valence electrons which the atoms have. For it is best to have a periodic table to hand.

We should now make a Lewis strucutre for the molecule, we need to decide what the central atom will be in the molecule. I am sure that C=S=O will be a far higher energy than O=C=S and anyway if we look up the strucutre of carbonyl sulfide we will find that the carbon is at the centre of the molecule. We can make a first attempt at the Lewis strucutre where we have only sigma bonds and lone pairs.

This is wrong as it has twenty (20) electrons in the outer valence shells of the atoms. We only have 16 electrons in the valence shells of the atoms. So we need to make a new attempt. In the new attempt we will have fewer electrons. I am showing the inner shells which are part of the inner noble gas cores. But for speed and ease you should leave them out.

In the new strucutre I assume that we will have a higher bond order between the carbon and the outer two atoms in the molecule.

This is now right, each atom has eight electrons in the outer valence shell, the total number of valence electrons in our molecule now add up to 16 which is the sum of the number of valence electrons in the molecule.

Many years ago when I was an undergraduate people like Henry Rzepa and Derek Woollins taught me to always consider the sigma bonding first. The sigma bonds have a higher bond dissociation energy than the pi bonds. Also for the VSEPR we only consider lone pairs and sigma bonds. We should now consider the arrangement of bonds around the carbon.

We have a sum of two sigma bonds and lone pairs on the carbon. To maximize the angle between the two groups on a sphere we need a sulfur carbon oxygen angle of 180 degrees (pi radians). This will dictate that the moelcule is linear.

When we make hybrid atomic orbitials from the original atomic orbitials there is the rule that if we start with x orbitals we must end up with x orbitials. We need to have the atomic orbitials on the carbon needed to make two sigma bonds, we also know that we need to have two pi bonds to the carbon.

We have three choices with the hybird orbitial formation.

s + p + p + p makes 4 x sp3 orbitals

s + p + p makes 3 x sp2 orbitials with one p orbitial left over

s + p makes 2 x sp orbitials with two p orbitials left over.

Lets go through the options

The first one we can rule out as it would require us to have two lone pairs on the carbon and we need more electrons than are possible for the neutral molecule. We would have to have a molecule with a charge of -4. This is not reasonable. Lets leave it alone now.

The second one we need to have a lone pair on the carbon. This will force us in the VSEPR step to have a angular shape to our molecule. As real life evidence indicates that the carbonyl sulfide molecule is linear we can discount this idea. There are triatomics which are angular such as sulfur dioxide and the nitrogen dioxide radical but O=C=S is linear.

So we are left with the last option that the O=C=S molecule is linear. So at least we can decide that the central atom is sp hybridized.

The shapes of the orbitials

There are multiple levels, my coworker Christian Ekberg has the saying “There are many levels in hell”. There is no divinity or theology department at Chalmers and right now I do not have easy access to a theology prof so we will not discuss the nature of hell. But what CHE means is that there are multiple levels of understanding.

In MO theory we can go very deep but there is a level which I think is suitable for first year classes such as KTK112 at Chalmers. In this article I will restrict myself to the basic understanding. If you are a genius of MO theory and want to discuss with me the deeper part of MO theory then please feel free to contact me privately, there is a possibility that we might be able to have a shared joyous experience but I wish to bring peace and clarity to the troubled minds of first year students.

Now we need to consider the shapes of the orbitials. We can agree that there are pi systems which are involved with the carbon and also sigma bonds. We should consider the sigma bonds first.

Now lets take a step back and consider a more simple example, lets consider hydrogen cyanide for a moment. We have in hydrogen cyanide sigma bonds which exist between the hydrogen and the carbon along with a bond which exists between the carbon and the nitrogen. We can make up our mind that the carbon and the nitrogen are both sp hybridized. There are two ways of looking at the problem, we have the KTK112 view of the situation as having a pair of sp orbitials on the carbon which are pointing in opposite directions and they form both bonding and antibonding orbitials with the two atoms at the ends of the molecule. Here is a MO diagram for the sigma bonds and the lone pair in HCN.

Now we go back to the O=C=S example. We can make a MO diagram for the sigma bonding only. It will look like this. We should consider the molecule as having two independent sets of sigma orbitials for the two different bonds. Here is the MO diagram for the sigma orbitials only.

Now we have the shapes of the molecular orbitials. If we want to understand what the shapes of the sigma orbitials look like at the KTK112 level our best chance is to look at the orbitials calculated for F2. The sigma bonding orbitial between two atoms of the same electronegativity will look like this.

The sigma star (sigma antibonding) orbitial will look like this

Now we should consider the pi bonding in our molecule. For the O=C=S molecule we will have pi bonds. Our central carbon will be sp hybridized so it will have two p orbitials which are normally at 90 degrees to each other. If we concentrate on the bonding between two atoms then we will have a pi system which looks like this. Firstly here is the pi bonding orbitial between two atoms.

And now is the antibonding pi orbitial associated with the two atoms.

For the KTK112 level of understanding I would tell you to consider O=C=S as a molecule which has two pi systems, these will be at 90 degrees to each other. If we were to look at the molecule along the axis of the bonds then if we could see the pi clouds then we would see this for one of the pi clouds.

While for the other we would see this

I will write more later on the more advanced view of the bonding in the molecule.

Ammonium nitrate explosion

Dear Reader,

I have been asked to explain the dire event which occurred this week in Beirut, what happened was that thousands of tons of ammonium nitrate stored in a dockside warehouse exploded after a fire broke out.

My view of the event is that we are facing the problem of the DDT (deflagration detonation transition).

This is an important thing to understand in energetic materials, it is possible for a single substance or composition to react in both a deflagration and a detonation.

In a deflagration a reaction front moves through a mass of material by means of heating, as one part of the mass reacts it heats the next part of the mass. This propagates the reaction in a much slower way than a true detonation which is propagated by a supersonic shockwave which passes through the mass.

It is important to also note that for many explosives if they are burning under pressure that the higher the pressure the faster, they react. It is important to keep in mind that if a container contains a mass of an explosive then if the explosive is ignited with heat then the pressure caused by the gases generated by the reaction as they exit through a small hole will generate pressure. This increase in pressure can make the reaction rate at the surface of the explosive increase.

It is possible to reach a tipping point at which rate of reaction becomes so fast and the pressure so large that the remaining bulk of the explosive starts to be initiated by a shock wave which outpaces the thermal propagation of the reaction. At this point the reaction has undergone the DDT.

The far greater rate of gas production and heat release will now make the physical effects of the reaction far more devastating.

I am aware of a firearms accident which destroyed an elephant gun, I never saw the gun and I do not know the person who had it. It might be an old wives tale but the chemistry / physics of it is plausible. What happened was there was a person who was hunting dangerous large animals with some scary monster high powered rifle. What happened was it was a bolt action rifle which had a magazine.

With some bolt action designs, which includes some WW I rifles, it is possible to pull back the bolt and then add more cartridges to the magazine while the magazine is inserted into the rifle. The story was that the hunter kept on shooting and then topping up by adding more from the top.

What happened was that each time the gun was fired the almighty recoil slammed the bullet a little further back into the brass case than it should have been.

Eventually the misguided hunter went and fired the cartridge which was at the bottom of the magazine.

The firing pin falls on the primer which then ignites the propellant, the propellant in a shotgun shell, rifle cartridge, pistol cartridge or even a giant artillery gun is supposed to deflagrate giving the projectile a prolonged shove as it races faster and faster along the barrel.

But when the propellant was inside too small a volume (pushing the bullet too far back into the case lowers the free space inside the case) the rate of burning became too high. This speeded up the burn rate which then caused the pressure in the case to build up to some level which the gun was never intended to cope with.

The gun then broke apart, I have no idea what happened to the person holding it. Some firearms accidents where guns break apart in use can prove fatal. I have seen some horror photos of guns which have failed in use due to things like mistakes in ammunition production. I have seen photos of revolvers where the block of metal which holds the cartridges has split apart the photos, I have seen of rifles which have failed are scarier. My reasoning is that when firing a revolver, you have it at arm’s length away from your head and torso, with some luck the rain of metal fragments will fly sideways away from you.

With a rifle you are likely to have the breach close to your chin thus putting your tender bits rather closer to the event.

But back to the ammonium nitrate explosion, we have considered how a defective (or abused) cartridge can blow up a gun. There is another way in which a normally placid substance can change from a friendly pussycat into a raging tiger with a dire attitude problem.

If I was to place a small amount of an energetic material on a smooth concrete floor and then ignite the pile, then it will burn smoothly in open air. There will be lots of sparks, smoke and maybe a flash.

But if we make the pile bigger and bigger then the outside of the pile will burn creating gas pressure which compresses the core of the heap. If we were to make the heap sufficiently large, then we could have a DDT which would then result in a gentle fire suddenly transforming into a mighty explosion.

I think that during the early stages of the event in Beirut that a fire started in the warehouse, I have seen reports that welding was being done on the building during repairs. This is one of the big errors which I see in this case.

I hold the view that hot work should as welding should not be done in a building packed with either a flammable or explosive substance. If I had been in charge of the site I would have insisted that the workers either empty the building and then do the hot work OR find a method of repairing the building which does not require hot work to be done.

For example, when making a roof it is possible to get tarred sheets which are sealed by means of heating them with a gas torch and there is also another type of sheets which do not require this heating. I would argue that the latter type is a safer type to work with near flammable or explosive materials.

I have seen reports that the welding was being done to plug a hole in the building, one option I see would be to use welding to build a new section of wall. But do the welding somewhere else on the site and then move the new section to the building and then bolt it onto the building thus fixing the hole. While it is possible to make some sparks when ferrous metal touches either stones or other ferrous metal, I think that bolting two bits of metal together is safer than using welding equipment.

A well-designed explosives / petrol / flammables store should be free of ignition sources, this includes making sure that the electrical fittings in the building are not going to ignite things. I would want to include some means of lighting inside the store which is sealed or otherwise guarded to prevent an explosion. One common trick I have seen on solvent stores is to put the light switch on the outside of the building, the idea is that if the switch is going to make sparks then it is better to put it outside the building rather than inside it.

Another step I would have wanted to take would be to limit the amount of ammonium nitrate in the building. Ammonium nitrate is classified as 1.5, this is a rather special class of explosives. The normal classes are 1.1, 1.2, 1.3 and 1.4.

Class
1.1	Mass detonation possible	Bulk storage / transport of TNT
1.2	Projectile hazard	Typical hand grenades
1.3	Fire hazard, minor blast / projectile hazard	Firework rockets
1.4	Minimal hazard	A box of garden fireworks
1.5	Mass detonation possible but very insensitive	Ammonium nitrate
1.6	Very insensitive, mass detonation impossible

 

This means that while it is possible to create a detonation with ammonium nitrate it is normally very difficult to do so. The IRA used to use ammonium nitrate mixed with fuel oil (ANFO) for large bombs. To make such a bomb explode the ANFO must be subject to an almighty shock, I would rather not discuss the topic of how to build a bomb out of ANFO. Do not bother me by asking me, the only answer you will get is “No comment” or some swearing if you are very unlucky.

But once a mass of a secondary explosive such as TNT or ammonium nitrate has been provoked into detonation it is possible for the shock wave of the detonation to trigger other masses of explosives. There is a munitions ship which sank in the Thames estuary (SS Richard Montgomery) which is packed with explosives, it is feared that if one bomb inside this wreck was to detonate it could cause other bombs to detonate as well this could result in a large explosion which could cause a lot of damage.

One method of mitigating against a vast explosion is to split the explosive store into different areas, if the heaps of the ammonium nitrate were sufficiently spread out that the detonation of one could not trigger another then the worst case event would be made smaller. As blast obeys an inverse square law if the ammonium nitrate had been stored in four equal amounts then the distance at which a given effect occurs would be halved, this would greatly reduce the number of square miles over which the horrible off site consequences would be experienced.

There is the problem that if a series of warehouses in different parts of the city / country were built which each contained a quarter of the total stockpile that it would increase the security cost of keeping the material away from malefactors. It could be argued that the security cost will be proportional to the perimeter of the explosives storage area.

We also have the also the problem that if the explosive was more spread around the city that if the malefactors were to trigger detonations as an act of terror then they might stand to cause more damage. As blast effects obey an inverse square law with the distance from the explosion but the energy delivered to a surface by an explosion is proportional to the amount of explosive.

The surface area of a sphere is given by the equation

If we assume that the explosion occurs on the surface of a flat earth then if energy deposited on the surface of a hemisphere between ground level and 100 meters up into the air matters then we can consider the fraction of the blast energy which is lost into space / the air.

If we have a perfect sphere with radius r, then the circumference at latitude (q) is given by the following equation.

The surface area of the part of a sphere which is north of a given latitude is given by

The blast effect of an explosion can be predicted using the following equation where k is a constant, q is the yield and r is the distance from the explosion.

Now if we rearrange the formula we can get the distance r if we keep b and k constant and alter q.

If we assume that a blast which is at value b or higher will destroy buildings or kill people then if this value of b is set at 1, then when k = 1 then when q is 1000 then r will be 31.62 km and at the edge of the zone of destruction 0.0003162 of the energy of the explosion will be in the 0 to 100 m high range then the blast will deliver 3.16 units of energy into this important strip around the hemisphere.

If we reduce the yield (q) to 250 then r will become 15.81 km and then the explosion will deliver 0.006324 of its energy into the important strip, thus 1.58 units of energy are used to cause damage at this distance. Thus we can see how the quarter scale explosion is twice as able to use its energy to cause damage.

With much smaller explosions this effect is not very important, but at the upper end of the explosion yields it does become more important. I think that normally we need to consider this loss of energy into space normally only for nuclear bombs and large rocks which crash into the earth from space. With nuclear bombs and the rocks from space often the explosion occurs in the air (air burst) rather on the surface of the earth. For an air burst at a very high height such as starfish prime test or the test of the air genie (John  in operation Plumbbob) the fraction of the energy which is lost into space is very high as the event occurs far above the earth’s surface.

With a curved earth this effect is even greater but the maths is a bit more complex. This also explains why MRV / MIRV systems have been deployed on ICBMs. I would rather not write “use” as use suggests something does something useful, I think that blowing up cities is never a “useful act”. The idea of MRV technology is to launch a single ICBM which then releases several nuclear bombs which then land at different points. The reasoning is that if the area being attacked is defended by an antiballistic missile system then the defensive system will be more likely to be overwhelmed by the number of objects approaching and also if all the warheads get through then it will cause more damage for a given total explosive yield than a single warhead would.

A solution which avoids creating the giant ANFO version of a MRV attack on the city is to put all the ANFO at a single site but in multiple piles. Each pile should be separated from the other piles by a mound of earth or some other suitable object which will prevent blast and projectiles from one pile exploding triggering another pile. In this way a compact and safer explosives store can be built.

Another issue I see on the news is that there are reports that fireworks were being stored in the same building as the ammonium nitrate. I checked the international rules on explosives, bulk ammonium nitrate is in compatibility group D while fireworks are in group G. Group D can be defined as

“Secondary detonating article containing a secondary detonating explosive substance without means of initiation and without a propelling charge”

While group G is

“Pyrotechnic substance, or article containing a pyrotechnic substance, or article”

The UN rules state that classes D and G can be stored / transported together but this is “at the discretion of the national competent authority”. I understand this as meaning “you can do it BUT you first need to argue a good case to the national explosives safety authority and get them to give you permission”.

I do not think that putting nylon bags of fireworks which customs have seized in the same building as a bulk storage of ammonium nitrate is wise. My worry is that the fireworks are easy to ignite, the fireworks could ignite and then the fire could spread to the ammonium nitrate. Also if the fireworks are in class 1.3 or worse still in 1.2 then they could hinder firefighting efforts thus making it harder to control a fire which is endangering the ammonium nitrate store.

My gut feeling is that illegal fireworks should be kept in a separate area of the site well away from the ammonium nitrate. I also hold the view that as soon as any court case which revolves around the fireworks is over then they should be disposed of. There are various options which work for the safe disposal of fireworks. While it might seem primitive burning them inside cages is a far better method of dealing with them than the dire method used by Donaldson Enterprises in Hawaii (2011 accident).

What happened in Hawaii was that fireworks were seized by the customs authority after someone attempted to import display fireworks (1.3) claiming that they were in the lower hazard class (1.4). The problem was that the fireworks could not be sold on the open market and thus they needed to be disposed of. The task was given to a company who then did the work in a very dangerous way. I think that the system of work changed fireworks which were in class 1.3 into material which was in a higher hazard class. The accident site also had various ignition sources in it which should have been absent.

Trump Tantrum

Dear Reader,

I have become aware that Donald Trump (not the most level headed of men) has thrown a tantrum during a meeting with members of the press. Now I am sure that many of the readers of this blog will have spotted some time ago that Donald is not “of sound mind and sober habit“. By the way I can not claim to have coined this wonderful phrase, it is a phrase from the UK law on firearms and explosives.

Section 25 of the 1968 Firearms Act states

“It is an offence for a person to sell or transfer any firearm or ammunition to, or to repair, prove or test any firearm or ammunition for, another person whom he knows or has reasonable cause for believing to be drunk or of unsound mind.“

While for real poetic text see Section 30 which relates to revoking a firearms certificate. This is the legal basis in the UK for taking guns away from someone who is licensed but has either gone mad, turned into a drunk, is no longer physically able to comply with the terms of the license, appears to have turned bad or has some other new (or previously undetected which has now come to light) character flaw. This reads

“The certificate may be revoked if the chief officer of police has reason to believe—

(a)that the holder is of intemperate habits or unsound mind or is otherwise unfitted to be entrusted with a firearm; or

(b)that the holder can no longer be permitted to have the firearm or ammunition to which the certificate relates in his possession without danger to the public safety or to the peace.“

I would apply the same test when considering the question of is a person a fit person to have a license for explosives, a license for explosives can cover a range of things. It includes firework factorys, firework dealers, coal mine operators and a range of other things which might not at first to the public look like explosives work. It is interesting that more explosives tend to be used for peaceful tasks such as mining than are used in acts of war.

In the case of both Donald Trump and Boris Johnson I would feel quite reasonable in writing both men fall within the subset of people who are of intemperate habits or unsound mind or are otherwise unfitted to be entrusted with a country.

One of my objections to both men is the fact they are either recklessly or deliberately communicating false facts to the outside world and that it appears that both men have a conflict of interests. But OK now on with the chemistry, now one of the possible drugs for the treatment of the new virus is a antimalarial drug which dates back to the 1940s. It is chloroquine. This is a drug which is being considered and trialed for the treatment of the virus but it is not clear that the drug is effective. It is also a drug which can have some serious side effects, so I do not think we can argue a case that people should take chloroquine on the off chance that it protects against the new virus.

If the medical trials produce evidence that it is effective, then it might be possible to make an evidence based choice to start to use the drug for the treatment of the virus. But if we consider the chemistry of the compound. It has amine groups and a benzopyridine (Quinoline) system in it. Here is a 2D drawing of the freebase form of the molecule.

Now we have three nitrogen atoms, we need to consider which of the nitrogen atoms will have the greatest amount of electron density. I first used molecular mechanics to work out what shape the floppy group attached to the nitrogen which is bonded to the ring will have. The nitrogen bonded to the ring has one hydrogen atom attached and a rigid group (the quinoline) attached and also a flexible group made up of carbons bonded with single bonds to each other.

The calculated structure of the drug

According to the extended Huckel calculations done by Chem 3D, the nitrogens have the following partial charges on them. The most right nitrogen which has three carbons attached has a charge of -0.138, the nitrogen bearing two carbons and a hydrogen atom has a charge of +0.247 and the last nitrogen (the quinoline nitrogen) has a charge of -0.379. we need to ask why the nitrogens have such different charges on them.

The best thing for us to do is to consider the resonance in the aromatic ring, there are four resonance forms in which we only have two charges and the left hand aromatic ring is left aromatic. Thus these are the likely to be be to lowest four resonance forms in terms of energy. Here they are.

The four lowest energy resonance forms of the aromatic system

We should understand that all the resonance forms exist at the same time, and that reality is a combination of all the possible resonance forms. The combination is not one where each form has an equal contribution, instead those resonance forms with lower energies will make a greater contribution than those with higher energies. Because of the bottom left one we should understand quickly how electron density is withdrawn from one of the amine groups is then transferred to the “pyridine” nitrogen.

We can draw some more resonance forms which have higher energies, it is interesting to note that the nitrogen in the ring will increase the positive charge character on the atom bearing the chlorine atom. This is due to withdrawal of electron density by resonance. Here are these slightly higher energy resonance forms. It is also important to keep in mind that the resonance effects also withdraw electron density from the chlorine atom.

The medium energy resonance forms of the drug’s aromatic ring system.

The charge predicted by the computational software on the chlorine atom was 0.036 while the carbon atom bearing it is predicted to have a charge of 0.166. If we compare this with chlorobenzene which are shown below. Then it appears that the computational software did not predict that the nitrogen in the aromatic ring would increase the positive charge of the chlorine or the carbon bearing it.

The charges on the non hydrogen atoms of chlorobenzene

But back to the drug, when we look at the crystallography of the drug then we find that it is dominated by salts. There is one form which has the spacegroup P21/c which is listed at GEXXAI which is a bis dihydrogen phosphate. There is also another form with a spacegroup of P21/c (HOJLOI) and another one which is P21/a (CLQUON). These three different structures have the following cells.

Name	A	b	c	a	b	γ	V	Z
	Å	Å	Å	Degrees	Degrees	Degrees	Å3
GEXXAI	9.835	16.865	15.786	90	105.75	90	2520.118	4
CLQUON	15.741	16.865	9.815	90	105.58	90	2509.868	4
HOJLOI	12.544	9.484	20.700	90	93.97	90	2456.766	4

I do think that the cell for GEXXAI does look very similar to CLQUON,

HOJLOI is reported in a paper A Solid-State Dehydration Process Associated with a Significant Change in the Topology of Dihydrogen Phosphate Chains, Established from Powder X-ray Diffraction, by David Albesa-Jové, Zhigang Pan,Kenneth D. M. Harris and  Hidehiro Uekusa in Cryst.Growth Des. , 2008, volume 8, page 3641. This paper is the paper with work done using powder diffraction methods.

The other two are of more interest CLQUON is from a 1970 paper by H.S.Preston and J.M.Stewart, J. Chem. Soc. D., 1970, page 1142. This is a strucutre which has been redetermined by some other workers (G.Macetti, L.Loconte, S.Rizzato, C.Gatti, L.Lo Presti, Cryst.Growth Des. 2016). I will have to ask a crystallographer the difference between P21/a and P21/c. I do not want to stick my neck out and write something which I later discover is wrong.

One of the books which was instrumental in my development as a radioactivity worker was “Lessons Learnt from Accidents in Industrial Radiography“, it is a book all about radiological safety mainly considering what can go wrong with sealed source work and also how it should be done correctly. One of the bits of advice in the book which is aimed at the radiographic worker is on page 39. Here it crisply states in the 11th commandment to radiographers that they should refuse work which they are either not trained or equipped for.

In todays world where everyone wants their 15 minutes of fame on the internet, it is still important that before we comment on a matter we should equip ourselves with some knowledge of the thing and try to come up with a reasoned view of the matter rather than a knee jerk reaction.

The some of the other commandments to the radiographer are good general life lessons, but we will leave that for another day.

What risks should we take with the new virus

Dear Reader,

I feel rather shocked at the new virus, now I think we should all sit down and have an adult conversation about risk and reward.

When I was a PhD I have the privilege to be a member of the Loughborough and District Amateur Radio Society. One of the men in the club was a high voltage electrical enginner (expert in protection and switchgear) who had spent much of his life building and servicing high voltage systems. He told me a story from his youth about risk and reward.

In world war two he was a test pilot, it was his job to fly bombers after their wiring had been modified around England. He told me that the chance of encountering a German fighter was low and if he had a problem with the aircraft he could have landed at plenty of airfields. He was likely to have been given this relatively safe duty as he was an electrical engineer. He told me that one night after a day of safe flying he was having a drink when a bunch of men who have just got back from bombing Germany find him. They accused him of being a cowardly engineering BLEEPER and other bad things. They then tell him should join then on the next combat mission.

While drunk he agreed to it, and the next day when sober he did not wiggle out of it. He boarded a plane as a passenger and then was taken on a round trip to south east Germany. He told me that it was a horrible experience which filled him with terror as a series of people were doing their best to kill or seriously harm him. He got off the plane when it landed a wiser man. He told me from that point on he viewed risk in a different way, he made an effort to never take a risk unless it was outweighed by the reward.

For example one of his favorite methods of finding corona discharges in substations was to visit at night to look for the tell tale glow. But he had a well planned method. In the day he would arrange for a chair to be delivered to a safe location in the substation. He would wait for dark, order it to be deenergized, he would go to his chair. Sit down and then order the power to be switched back on. He would then survey the site from the comfort and safety of his chair. After this he would order the power to be disconnected again before leaving the substation. To my mind this is a adult and sensible method of working. He plans the work to reduce the risk to himself.

What we can learn from this man is that we should not take large risks in our lives when the reward is small or non existent. We should not do dangerous things out of machismo, neither should we risk our well-being (or that of others) for an easy life.

Now with the virus it is impossible to eliminate the risk to our wellbeing, but we can take steps to reduce the risk to ourselves. One step we can take is to try to avoid touching our faces in public places. As one of my coworkers commented “the whole world has become like a radioactivity area”. When you are in a contaminated area I would strongly advise you not to rub your face. At Chalmers we have a system of work which I call “clean hand, dirty hand”. The idea is that for many tasks I keep one hand clean while the other hand is gloved, the gloved hand is in the fumehood. The idea is the gloved hand reaches into the hood and moves contaminated objects around. The glove never leaves the hood, I would not want to pick up a contaminated object in a gloved hand before pulling the hand out of the hood and then touching “my face, my notebook, my biro, the handle of a pipette, a door handle, the handset of a phone, the fridge door etc etc”.

Another thing we can do is to avoid entering situations where we put ourselves at risk of infection, think before we travel.

The problem I see is that some governments are not willing to take action to reduce the spread of the virus. While it will be impossible to totally prevent the spread of the virus there are things which can be done to slow the spread. In the FT it was explained that the UK approach is based trying to obtain “herd immunity” by allowing the virus to spread more in society. This has been reported elsewhere. It has been pointed out that depending on herd immunity when it is a disease which causes about 2 % of those to be infected to die and causes serious health effects in about 20 % is not a good public health policy.

One of the problems is that the new virus spreads with greater ease that SARS. I am considering trying to model the spread of the new virus using some of the equations used for nuclear criticaility calculations. It might seem an odd choice but in some ways the operation of an atomic bomb (like those dropped on Japan) is similar to a vast outbreak of a nasty disease. Both in terms of the effect on human health and also in terms of some of the maths.

The Spectroscope

Dear Reader,

I was recently at Nuclear Chemistry when Anders brought a collection of scientific toys along, Anders operates a on line store which sells a range of different things. All of his toys are things which have a strong science theme in them.

When I got home, my wife (Paula) looked at what I had and she was of the view that I looked happy with the range of things which I had brought home.

One of the items I had got was a visible spectrometer which contains a grating, a slit and a lens. After an hour or so of folding and gluing with UHU solvent glue I was ready to go with my spectrometer.

Anders had suggested that I should point the thing at an energy saving compact fluorescent light bulb. When I did so I was rewarded with a lovely spectrum with a series of lines.

I took the photograph using a mobile phone camera, my normal camera was unsuitable as the lens of my camera is far wider than the eyepiece of the spectrometer. All this for less than 100 SEK !

I also got some photochromic beads, and some mechanical toys.

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.

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.

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.

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

Now raise it further

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 meant 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-Garcia, Acta Crystallographica,Section C: Crystal Structure Communications, 1992, 48, 2055, 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.Borea, Acta Crystallographica,Section B: Structural Science, 2004, 60, 481, DOI: 10.1107/S0108768104013564. Here is the molecule in its glory.

 

 

 

 

Chlorothalonil

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.

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.

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.

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.

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.