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Electrochemistry calculations (redox potentials and cells)

Dear Reader,

I was recently teaching some electrochemistry to some students, now before we get going it is important to note that the conventions on writing electrode potentials changed years ago. So if thou gets one’s ye olde text book out or ye olde almanack of chemie be ready for some possible problems.

For example in the 1950s paper on plutonium redox chemistry by Sherman W. Rabideau and  Joe F. Lemon, Journal of the American Chemical Society, 1951, 73, 2895-2899 the redox couple for Pu(IV)/Pu(III) is listed as being -0.953 volts vs the standard hydrogen electrode. Now in modern text books it is listed as about + 0.95 volts. This modern use is an example of the “European” convention while the example I gave as an example of the “American” convention. I would say that both are equally valid but if you want to do a redox calculation be careful that you do not mix unwittingly mix data from both conventions up.

I have not seen the american convention being used much in modern text books, but please be aware that it does exist.

OK Health warning over lets get on with some chemistry. Now as a brain teaser (or brain expanded) I asked my students to consider the question of will a solution of iron(II) tend to reduce a solution of plutonium(IV) to plutonium(III) thus forming iron(III) in the process.

Now the redox couple of iron(II) / iron (III) is +0.77 volts (European convention). So we can calculate the cell voltage for our cell under “standard” conditions (1 mole per litre of everything, at 25 ºC and 1 bar).

We can combine the following two half equations

Fe2+ → Fe3+ + e

e + Pu4+ → Pu3+

To give us

Fe2++ Pu4+ → Fe3+ + Pu3+

The emf of the cell will be under standard conditions equal to 0.18 volts, but which thing will be reduced and what will be oxidized. The plutonium couple is higher (more positive) than the iron one in our European type text. So the plutonium will tend to oxidize the iron to form plutonium(III).

We get the emf of the cell from the difference between the two redox couples. All redox couples are expressed relative to hydrogen gas / hydrogen ions in 1 M acid. This choice of standard is simply a convention. Like the Greenwich meridian we need some arbitrary point to call zero. Hydrogen is a good choice as it features in so many reactions.

From the value of the emf of our cell we can get the ΔG of the reaction, to do this we use the following equation.

ΔG = -nFE

n is the number of electrons which are transferred in the cell reaction (1) and F is Faraday’s constant (charge on a mole of electrons) which is equal to 96485 C. Using this we can get a value for the Gibbs free energy of the reaction. Keep in mind that a cell with a positive emf is a cell which is able to do work, thus ΔG for the reaction in the cell must be negative.

This works out as -17367.3 joules per mole.

We can now get the equilibrium constant for this reaction, when a cell has a emf of zero then it has reached equilibrium. Now we need to use a different equation.

ΔG = ΔGº + RT Ln Q

In our case

Q = aPu3+ aFe3+ / aPu4+ aFe2+

Now in the ideal world (nice place I wish I lived there) the activity coefficient is equal to one, the closest we get to an ideal world is a dilute solution. So for nice and dilute solutions we can write

Q = [Pu3+] [Fe3+] / [Pu4+] [Fe2+]

If ΔG = 0 (zero) then

ΔGº = -RT ln ([Pu3+] [Fe3+] / [Pu4+] [Fe2+])

Rearrange to

-ΔGº / RT = ln ([Pu3+] [Fe3+] / [Pu4+] [Fe2+])

exp (-ΔGº / RT) = ([Pu3+] [Fe3+] / [Pu4+] [Fe2+])

Now do the maths

exp (7) = ([Pu3+] [Fe3+] / [Pu4+] [Fe2+]) = k

Now k = 1107

we can rewrite the equations to give us

ΔGº = -RT ln k

Now it should be clear to my readers that a solution of iron(II) will reduce tetravalent plutonium into trivalent plutonium. You might be interested to read that the classic method of adjusting the oxidation state of plutonium from +4 to +3 in the PUREX process is to use ferrous sulfamate.

Facebook and young earth

Dear Reader,

I have little urge or time for the social media site known as facebook, but occasionally I will visit it. I was reminded that I had posted years ago on this blog about the “young earth” theroys and radioactive decay. Now for your information the “young earth” hypothesis is that the conventional wisdom that the earth is many millions of years old is wrong and that the earth is much younger.

One site which is putting forwards the “young earth” theroy can be seen here, this site appears to be written by someone who holds a religous faith who also holds the view that the age of the earth is an important issue. They are expressing a creationist view that they hold. They have a series of principles which they call “the principles of scientific creationism“. I am not going to reproduce them in full but here is a sample of them. I have included their their views in italics with my comments in plain text.

  • The physical universe of space, time, matter, and energy has not always existed, but was supernaturally created by a transcendent personal Creator who alone has existed from eternity.

This is something which science can not address, the question of did the universe start as a result of a big bang (or some other process) which was set in motion by God is not something which science is able to address and typically science is not attempting to prove the existence (or absence / nonexistence) of God.

  • The phenomenon of biological life did not develop by natural processes from inanimate systems but was specially and supernaturally created by the Creator.

The problem with the bible is that it gives no details about the manner in which God created the living things on this earth. Even if we assume that God did create the sea, fishes, trees, animals and humans the bible in Genesis 1 does not give any indication of how this was done by God. The hypothesis that a all powerful and all knowing God created a universe and then set in motion a series of events which God knew would result in the first humans evolving from something like plants which live in ponds is not in my view incompatibly with either the bible or Darwin’s work.

  • Each of the major kinds of plants and animals was created functionally complete from the beginning and did not evolve from some other kind of organism. Changes in basic kinds since their first creation are limited to “horizontal” changes (variations) within the kinds, or “downward” changes (e.g., harmful mutations, extinctions).

As I said already the bible (at least in Genesis 1) does not comment on mechanism by which the different creatures and plants were created.

  • The first human beings did not evolve from an animal ancestry, but were specially created in fully human form from the start. Furthermore, the “spiritual” nature of man (self-image, moral consciousness, abstract reasoning, language, will, religious nature, etc.) is itself a supernaturally created entity distinct from mere biological life.

As I said already the bible (at least in Genesis 1) does not comment on mechanism by which the different creatures and plants were created. While it might not be a pleasant prospect that humans evolved from monkeys or some other animals. I can not see a reason why the fact that I have much of my DNA in common with monkeys, cats and dogs makes me any less a man.

I will concentrate on a question which I know something about, this is the question of can we trust radioactive decay clocks to allow us to date objects such as rocks. In this page one of the young earth people (Brian Thomas) points out that the decay rate of Si-32 and Rn-222 have been shown to not be constant. I want to look at the evidence, one paper which they cited was “Possible effect of solar tides on radon signals” by G. Steinitz, O. Piatibratova and P. Kotlarsky, Journal of Environmental Radioactivity, 2011, 102, 749-765. In this paper the authors claim that they see evidence of a change in the rate of the radioactive decay rate of radon. Now if we assume that they are right it is important to note that another later paper suggests that with Cs-137 it is impossible to see any change of the rate of decay (half life) as a function of time while for Ba-133 it is possible to see a change in the rate.

Now an important difference between Ba-133 and Cs-137 is that barium-133 decays by electron capture to Cs-133 while Cs-137 decays by electron emission (beta minus) to form Ba-137. The later paper (“Concerning the time dependence of the decay rate of 137Cs“, J.H. Jenkins, E. Fischbach, D. Javorsek II, R.H. Lee and P.A. Sturrock, Applied Radiation and Isotopes, 2013, 74, 50-55) quite wisely comments that the claimed effect can not be observed for all radionuclides. To me this later paper about Ba-133 and Cs-137 does make a major hole in Brian’s argument. He was claiming that radioactive decay rates in general are not fixed, in the paper by Jenkins et. al. evidence is shown and an argument is made that an effect can be seen with some radioisotopes (radionuclides) but not with all of them.

I hope to get back to this issue soon with something more on it.

Sound mind and sober habit ?

Dear Reader,

It has come to my attention that in the USA a man started shooting at people in the baggage reclaim area of an airport. What he did was to transport a gun by checking it in as hold luggage, he then reclaimed it. Went off to the toilet (bathroom in US english) and loaded it before embarking on his murderous rampage.

You will be interested to know that the law enforcement authorities in the USA have arrested this man, he is alive and apparently unharmed. Now this event raised some deeply disturbing issues.

According to the Daily Mail and adn the man who is suspected of having done it had some mental health problems and also had been charged with “fourth-degree assault and damage of property in January 2016, stemming from a domestic violence incident.” While the Guardian did not report that he had been in trouble for domestic violence.

As a person who was for some time a named person on a Swedish explosives license (for scientific work on fireworks) I have a view of the matter which might be slightly different to that of the general public. If a person is to be issued in the UK with either a firearms or explosives license then they must show both a genuine need to have the license and that they are a fit to hold the license for the objects or materials listed in the license.

When I went through the application process I am sure that the official at MSB applied a similar two part assessment of me and the project. The official wanted to know why I wanted the license to do the work (this relates to need) and also about me and the facility where the work was to be done (fitness). At one point I asked if I needed to prove I was (in UK terminology) a person of “sound mind and sober habit“, I was told that “it was not needed”. I suspect that MSB would have looked at me without me doing anything to make the judgement regarding the “sound mind and sober habit” question.

I think that the event at the airport is a reminder that the US should set up a licensing system, right now I think that they should concentrate on the “fitness” issue rather than the “need” issue. I know that many people in the US do not like the idea of the state knowing about their guns, I think that I have thought of a way of dealing with that problem.

I reason that if a valid gun license is needed to transport a gun by air, use a public (or private commerical) shooting range or a series of other acts then a person could apply for a license to allow themselves to do these things. If on the otherhand they do not want to transport it by courier or air or pay for access to a range then they might not have to be required to take out a license. My reasoning is that if they want to keep their gun on their own land and use it there then it might be reasonable to exempt them from the license requirement. Now lets look at some of the things which have been reported.

If a man has been acting strangely and had claimed to the FBI that he has been subject to mind control, then surely it would be reasonable to ask the question of “if he of sound mind ?“. One of the symptoms of schizophrenia is delusions, now the vast majority of people with schizophrenia are quite harmless. They tend to be more of a threat to themselves than others as a result of the way they behave. But it would be prudent for society to prevent a person who is delusional from having access to a firearm until they have obtained medical clearance to show that they are not a danger to themselves or others.

A man who has been charged with a violent crime such as domestic abuse clearly needs to be checked regarding the “sober habit” part of the question. While my biggest concern about a person who has a record of domestic abuse is that they might use a firearm or explosives to attack their partner or ex-partner. I would say in general that a domestic abuser is not a person who I would regard as being of “sound mind and sober habit“.

It is clear to me that regardless of how the NRA and the gun lobby feel about it that the US needs some form of licensing to own, keep or possess guns. Maybe this event would have been prevented if the airline had been required to see that the man held license(s) which would have permitted him to have the gun both in the place where he checked in the gun and where he was flying to.

I hold a view that it is reasonable for a person who has been charged with or arrested for some crimes to have any firearms which they own / possess taken off them by the police. However with many things abuses of the law must be prevented. I hold the view that for a law to be obeyed, some degree of respect for the law must exist. By abusing a law this law (and laws in general) will no longer be respected.

One safeguard I see is that if guns (or any other legally held article) is taken away by the police then it should remain the property (in law) of the person it was taken from. If either the police / public prosecutor drop the matter or a court orders the matter closed (in favor of the person) then the police should have to take responsibility for the prompt return of the property in the same state as it was when they took it away.

For example if the police seize a car from an innocent man then they should return the car as soon as the legal basis which they might have had at first no longer exists. I also hold the view that the keeper of the car should be paid the hire cost or a replacement car to compensate him / her for the loss of the use of the car. Also rather than being able to charge a storage fee for the car the police should have to provide the person with a partial refund for any road tax or insurance which had been purchased on the car. Also if the car is damaged, rusts or otherwise degrades while the police have it then they should have to take responsibility for getting the car repaired.

Also if the police were to take a so called dangerous dog from a person and the dog has been ordered to be returned to the person then the police should while they have the dog be required to look after the dog’s welfare (provide it with walks, feed it, keep it clean etc) while they have the dog. They should also be required to return the dog. If it is a dog which must be muzzled in public then to return the dog without a muzzle or reasonable warning to the owner in a public place then the owner should not be regarded as being guilty of having an unmuzzeled dog in a public place. Instead it would be reasonable to regard the police as being responsible for this crime.

It would be reasonable for me to hold the view that bashing holes in other people’s houses with rocks is a crime (vandalism). To set in motion an event which causes unlawful damage to the property of another person where you do not come into contact with the other person’s property, such as rolling stones down the hill towards the otherperson’s house should still be regarded as vandalism. In the same way if you perform an action which causes an act which is normally regarded as unlawful to be performed by another person against their will then you should face the penalty for the crime rather than the person compelled by your actions.

An interesting problem exists when the police lose, dispose of or damage an item which is not commercially available. For example if they seize artwork (how about Vincent VanGogh’s Sunflowers) from a person wrongly (but while they have the sincere belief that they are acting lawfully) and then rip the painting while transporting it, then this would be a difficult thing to replace or compensate a person for. I think we would need a whole room of law Profs to work out the right answer.

Another problem is that some items might be legal to own / possess but only if they were transferred to a person before a particular date. For this I have a simple solution, if the US police for example were to confiscate wrongly a M16 or antique Thompson sub-machine gun which was legally held by a person and then dispose of it wrongly. Then I reason the best way for the law to deal with the problem is for the goverment to transfer an identical item to the person and then that item is treated in law as if it was the original one. Thus the goverment would have to transfer a restricted item to a person to reverse an involuntary and wrongful transfer of a restricted item from the person to the state. The alternative is for the state to have to pay far in excess of the resale value of the item to the owner.

I suspect that the gun issue in the US is not going to be an easy matter to fix, but something needs to be done to iron out the problems.

Reckless use of pesticides

Dear Reader,

It has come to my attention that a person in the USA caused the deaths of four members of his family when he attempted to use a restricted pesticide to kill bugs at his home in Texas. What this man did was to use a product which is not intended to be sold to or used by the general public. In the UK the use of this chemical is strongly limited to professional users who have to undergo special training before they use it.

It was aluminium phosphide, this is one of the more dangerous pesticides which is in current use. It is a solid which on contact with water (or acids) will generate phosphine gas. The take home message is if you face a pest control job which you can not solve using over the counter products sold to the general public then unless you have the special training (and equipment) required to use a professional use only product then leave work with such a product to a professional (and I hope competent) pest control worker.

You might wounder what aluminium phosphide is, it is AlP, it is a solid with the same crystal strucutre as zinc sulfide (zincblende). Here the aluminium and phosphrous atoms have tetrahedral coordination environments. This is a compound with a cubic cell (a = 5.451 Å). The fractional coordinates of the atoms are

Al 0, 0, 0

Al ½ ½ 0

Al ½ 0 ½

Al 0 ½ ½

P ¼ ¼ ¼

P ¾ ¾ ¼

P ¼ ¾ ¾

P ¾ ¼ ¾

We can make a xyz file for a single unit cell.

18
XYZ file : Unit cell AlP
Al 0 0 0
Al 5,451 0 0
Al 0 5,451 0
Al 5,451 5,451 0
Al 0 0 5,451
Al 5,451 0 5,451
Al 0 5,451 5,451
Al 5,451 5,451 5,451
Al 2,7255 2,7255 0
Al 2,7255 2,7255 5,451
Al 2,7255 0 2,7255
Al 2,7255 5,451 2,7255
Al 0 2,7255 2,7255
Al 5,451 2,7255 2,7255
P 1,36275 1,36275 1,36275
P 4,08825 4,08825 1,36275
P 1,36275 4,08825 4,08825
P 4,08825 1,36275 4,08825

Here are three views of the unit cell for you to look at

alpview1

alpview2

alpview3

It should be clear that the empirical formula of the compound is AlP. We have eight aluminiums at the corners of the cell, each is shared equally between eight cells, we also have six aluminiums on the faces. Each of these six aluminiums is shared between two cells. This gives us a total of four aluminiums.

We have four phosphorus atoms (in a fetching orange) which are totally inside the unit cell. Thus we have a 1:1 ratio of aluminium to phosphorus atoms.

 

Gamma spectroscopy under different conditions

Dear Reader,

While working on the project for SSM I had to make some measurements by means of gamma spectroscopy using a high purity germanium detector, note that it is not a high purity geranium detector. Being a main group chemist I do occasionally allow myself a joke. One such joke among main group chemists regards the fact that germanium sounds a little like a flowering plant which is popular in the UK.

What happens in a high purity germanium detector is that gamma photons enter a crystal of germanium which has a high voltage (2 to 3 kV) applied to it. When the photon deposits energy in the crystal this produces charge carriers (free electrons and holes). As a result of the event charge flows through the crystal, the electronics measures the amount of charge, and from that it is possible to work out the amount of energy which was deposited in the crystal during the event.

This sounds all very simple and easy but in real life it is not easy, for example some energy can enter the crystal in the form of the photon and some of this energy can then escape from the crystal as a result of Compton scattering or pair production.

Also the photons from the radioactive decay event must be able to enter the detector, also they have a finite probability of being able to interact with the crystal. The issue of penetration and overpenetration add a new layer of complexity, it causes the sensitivity of the detector to change greatly as a function of the energy of the photons.

Also the radioactivity can generate secondary radiations, for example beta particles which strike high Z (atomic number) materials can generate characteristic X-rays and braking radiation (Bremsstrahlung). During my efforts to make some measurements I created what I think is a good set of spectra which show off some of these effects.

My first problem was that I wanted to verify that I had iodine-131, I choose to put some methyl iodide which contained a lot of radioactivity into the detector. I knew that putting the vial into the detector would overload the detector, so I used a trick to cut down the gamma flux. I put the sample inside a lead pot. Or lead pig, this greatly reduces the photon flux near the vial. I knew that the activity calibration already made for that detector with a different geometry would not work, but all I wanted to do was to verify the identity of the radionuclide.

In some ways I got a better answer than the one which I would have had if I had used an unsheilded vial with less activity in it, I was more able to observe the higher energy gamma photons from the radionuclide. This was because the lower energy photons from the radioactivity were strongly attenuated by the lead pot.Here are the gamma spectra for iodine-131 recorded under different conditions.

Firstly here is the gamma spectrum for the radioactive iodine in a LSC vial.

i131lsclinear

i131lsclog

I have shown both a view of the graph with a log and a linear scale on the y axis. Now here are the graphs for the radioactive iodine inside a lead pot.

i131piglinear

i131piglog

What you should be able to see is that the high energy end of the spectrum is now more important, the moderate energy gamma line for I-131 at about 300 keV is much weaker, as a result the higher energy gamma lines are now more important in the spectrum.

It is also interesting that when we look at the low energy end of the spectrum that the lead pot changes things greatly.

i131lowenergy

What we have here are some x-ray peaks and a low energy gamma line. It is important to understand that the beta decay of the iodine forms a xenon atom in an excited state. The capture of an electron by the xenon atom can result in the generation of photons. In this case it is k line photons. The radioactive iodine also emits gamma rays with about 80 keV energy. Please keep in mind that the energy calibration of the spectrometer is a bit off, it tends to over report the energy of the events.

The lead pot was responsible for the generation of some lead K x-rays. What I suspect happened was that the gamma rays from the radioactive iodine with 300 or more keV interacted with the pot and generated plenty of fast moving electrons. This would have been by both the photoelectron and the Compton effects. Those electrons which were generated close to the surface of the lead pot were able to excite lead atoms, these lead atoms then emitted x-rays, here you can see the K alpha and K beta lead x-ray photons. The lead pot was able to screen out the 80 keV photons from the radioactive iodine so the X-ray generation must have occurred on or near the outer surface of the lead pot. One interesting experiment would be to put a pure high energy beta emitter such as strontium-90 inside a range of lead pots and then count these with the HPGe gamma spectrometer.

If I was to have covered the outside of the lead pot with a layer of copper then these lead x-rays would have been attenuated. One option for getting the best shielding out of a lead (or DU) object is to cover the object with copper, then aluminium and then finally plastic. The idea is that the secondary radiations from the lead (fast electrons and X-rays) will be captured in the copper. The copper being a lighter element is less able to generate x-rays from the electrons and it will also offer some attenuation of the lead x-rays. The lower energy x-rays generated in the copper will then be attenuated by the aluminium. Finally the very low energy x-rays generated in the aluminium will be captured in the plastic.

It is interesting that the lead shielding for the gamma spectrometers are lined with copper sheet to try to reduce the formation of secondary radiations by the action of cosmic rays (and other background radiation) and the radiation from the sample in the spectrometer on the lead shielding. It is also interesting to note that photographic film is more sensitive to high energy gamma rays if it is placed in contact with a thin lead sheet.

During the Fukushima event some people claimed that workers at the site were issued with lead sheets to make their dosimeters less sensitive, under some conditions by wrapping a dosimeter in lead sheet it would be possible to make it over report a dose of gamma rays. A lot will depend on the energy of the gamma rays, while a thin lead sheet will make a dosimeter under-report things like x-rays from a dental radiography set (70 kV tube) it will make the dosimeter over report the dose from a high energy gamma emitter such as cobalt-60. The old fashioned film badges which we used to use back in 2000 for gamma dose measurement of people had a series of metal filters designed to allow the badge to make better measurements of gamma photons with different energies.

Note that before you put anything into a gamma spectrometer it is important to wrap it in a plastic bag. If you have ever been a responsible dog owner you will know how to pick up dog poo (or other objects) using a plastic bag in such a way that you never touch the dirty side of the plastic bag. Put your hand into the bag, pick up the object and then turn the bag inside out and tie it shut. I did this with the lead pot containing the radioactive iodine and then just to be sure I bagged it a second time. I reason that no harm can come from using a second bag, and just in case something went wrong during the first bagging the second bag added while the singly bagged object was on a clean bench would reduce the potential for the transfer of radioactive contamination yet further.

My second problem was that I wanted to get a quench curve for liquid scintillation counting with large chemical amounts of methyl iodide present, any of my readers who are organic chemists will know how methyl iodide is a toxic and very volatile liquid which is difficult to pipette out. While my one of favorite pipettes (200 microlitre) is unable to measure out 20 or 50 microlitre volumes of methyl iodide a 10 microlitre pipette can dispense 5 microlitres it as the diameter of the tip is much smaller. But for 10, 20 and 50 microlitres I used a gas tight syringe designed for gas chromatography work.

Rather than trusting my pipetteing with this volatile liquid, I choose to use the gamma spectrometer to check my volumes. By making a measurement of the number of counts per second I was able to make an independent measurement of the radioactivity in the LSC vials. I will save the results of this for another day.

Homopathic medicine

Dear Reader,

Some years ago I read an article about a woman who choose to use homopathic medicine instead of “normal medicine” to treat her breast cancer. Sadly she died a horrible death, I think it was worse care than that given to Adolf Hilter’s mother (Klara). Klara also died of breast cancer, but she had a conventional doctor (Eduard Bloch) who did his best to treat her cancer and ease her symptoms. While sadly her cancer was too advanced when she contacted her doctor, she did have surgical treatment which could have saved her (if she had been treated at a more early stage). Sadly she had a secondary tumor which then killed her.

The thing which shocks me is that a pair of doctors about 100 years ago did a better job for Mrs Hilter than the alternative healers did for the woman in that sorry tale.

One of the drugs used to treat Klara was iodoform, this is triiodomethane. If a person was to just trust the wikipedia entry on Klara Hilter then it is not clear what the intent of the doctor was when he used this compound on Klara. However one science blog explains how iodoform has been used in medicine for wound dressings. Unfortunately for both Klara Hilter and the modern woman whose breast cancer was mismanaged the tumor grew so large that it broke the skin.

I have to say that I would expect less from Eduard Bloch and his coworkers about 100 years ago than I would of a modern doctor, imagine.

No decent X-ray equipment

No Ir-192 for brachytherapy

No Co-60 or Cs-137 for decent teletherapy sets

No modern drugs

So I would say that Mrs Hilter’s doctor was doing a much better job for Klara than the modern homopathic doctors. I hold the view that homopathic doctors are not real doctors, homopathic medicine is something which claims a mechanism which is not supported by science. It is interesting that young Adolf was very pleased with the efforts of his mother’s doctor, it has been reported that he had a great liking for Eduard Bloch even while Hilter knew that Eduard was jewish. Sadly the fact that a Jewish doctor had tended his mother in her final illness did not make the older Hitler understand that the antijewish policies of the nazi state were deeply wrong. It is important to understand that Hitler and the nazi state did not just harm jews, they hated (and harmed) gipsys (roma), slavs, homosexuals, freemasons, Jehovah’s witnesses and a range of other people who did not see the world the world the same way as themselves. Sadly I am unable to understand the reasons why Adolf Hitler did the things he did, as the choices made in this vile man’s mind can not be explained with chemistry we will not discuss them in my blog. Now back to chemistry.

Iodoform is a simple molecule which has been used for dressing wounds, one of the concerns with a case like Klara’s one of the concerns was infection. Now you might wounder what iodoform is, it is a simple molecule with the formula CHIwhich has C3 symmetry. The molecule is tetrahedral in shape, if it is turned on the same axis as the CH bond then it can be turned three times by 120 degrees to get something with exactly the same atomic coordinates.

F.Bertolotti, N.Curetti, P.Benna and G.Gervasio recently reported the solid state structure of iodoform in J. Mol. Strucutrue, 2013, 1041, page 106. they were not the first people to do strucutral crystallography on iodoform. The first report was in the 1950s by T.L.Khotsyanova, A.I.Kitaigorodskij and Yu.T.Struchkov, Zh.Fiz.Khim.(Russ.)(Russ.J.Phys.Chem) , 1953, 27, 647. I have looked and the two groups got very similar results.

The unit cell dimensions for the original determination were

a = 6.830, b = 8.830 and c = 7.530 Å

alpha = 90, beta = 90 and gamma = 120 degrees

The more modern determination has the following cell dimensions

a = 6.555, b = 6.555 and c = 6.985 Å

alpha = 90, beta = 90 and gamma = 120 degrees

This makes the cell very much noncubic, one side has a different length and also one of the angles is clearly not 90 degrees. This makes it a hexagonal cell, the space group is P63. Here is one view of a unit cell.

iodoformcell

Iodoform cell showing the two molecules in the cell.

iodoformcell2

Second view of the cell showing clearly that it is a hexagonal cell

If we look at the bond angles in the iodoform molecule angle I1 C I1b is 114.85 degrees, the angle I1a C I1b is 114.85 and the last angle I1a C I1 is 114.85 degrees. This means that the molecule is distorted away from a perfect tetrahedron by repulsion between the large iodine atoms. The H C I angle is 103.35 degrees. Here is a ball and stick view of a single iodoform molecule from the side.

sideviewballandstickiodoform

Side view of iodoform, ball and stick view

Here is the view from the same angle now using a spcae filling model

sideviewspacefillingiodoform

Side view using space filling model

Now if we take a view from the top along the axis of the CH bond we should be able to see that the molecule has a C3 axis.

topviewspacefillingiodoform

Lastly the C-H distance in iodoform is 1.136 Å while the C-I distance is 2.118 Å. Iodoform is not normally made by the reaction of methane, methyl iodide or methylene diiodide (diiodomethane) with iodine. Instead it is normally made by the reaction of a methyl ketone such as acetone with iodine under alkaline conditions. We might be able to go through the mechanism of this reaction another day.

For those of you might want some light relief about homopathic medicine, I suggest that you look at this film. Which is a black comedy about how homopathic doctors would treat a car crash victim. It is even better than seeing internet Hilter getting mad about the parody films.

Trinitite II

Dear Reader,

I have reexamined the gamma spectrum from the trinitite, and I have some news for my loyal readers. What I did was to look at someone else’s gamma spectrum of trinitite and then try to match peaks.

Here is the spectrum

trinitite9

Gamma spectrum of trinitite

What we can now see are two peaks (51.7 and 129.3 keV) which are due to the gamma emissions from plutonium-239. Also we can see a set of three lines due to uranium L lines X-rays.

We might ask why are we seeing uranium x-rays coming from a sample which contains so little uranium. One explanation which I think is very reasonable is that the alpha decay of the plutonium-239 forms uranium-235 which is formed in an electronically excited state. The uranium-235 then undergoes a rearrangement of the electrons to form the X-rays. This has been observed by others during XRF studies on plutonium metal.

This is further evidence that the sample contains the radionuclides which should be expected from the trinitiy test. So now I have managed to prove that the sample contains plutonium.

As the sample also contains americium-241 I think it would be reasonable to next make an attempt to find the lines for neptunium X-rays. These could be a further sign that the sample contains americium. I can not think of any other alpha emitters which will be present in large / moderate or even less than tiny amounts in the trinitite.

I will have to think further about the sample.

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