Thermodynamics

Dear Reader,

As my friend and fellow teacher is away in Germany I had to teach thermodynamics to the first years. I have to admit that I do not love all aspects of classical thermodynamics which is a bit of a misnomer it should be thermostatics as it deals mainly with static states.

One of the things I do not love about thermodynamics is that classical thermodynamics tells us nothing about how fast or the mechanism by which we go from A to B. All it tells us is the difference between A and B. The more modern thermodynamics which is based on the molecular motion can tell us more but I think that I will leave that some either some other day or some other person to write about.

As an incurable organic / inorganic chemist I love mechanism, mechanism explains to us how things happen. From that we can know what can and what can not happen.

One of the questions which I had to teach was the idea that we take an ideal gas and consider the heat capacity both under constant volume and constant pressure conditions.

For a monoatomic gas such as helium the heat capacities are

Cv = R 3/2 (constant volume)

Cp = R 5/2 (constant pressure)

If we were to assume that we have 2 grams of helium in a box which has a fixed volume of 1 litre then the box will have a pressure. The temperature of our box is 273 K. The formula mass (FW) of helium is 4 g mol^-1

We can calculate this with PV = nRT

If we assume that R is equal to 8.3 J K^-1 mol^-1 then we can calculate P

n = M / FW = 0.5 moles

P = nRT / V = 0.5 mol x 8.3 J K^-1 mol^-1 x 273 K / 1 x 10^-3 m³ = 1132950 Pa

OK so we have a start pressure of 1132950 Pa, or for those of us who do not like so many points before the decimal point we have about 1133 kPa or circa 1.133 MPa. This is about 10 bar.

Now if we heat the box up to 100 ^oC (373 K) then the energy of the helium will increase.

As Cv = ΔU / ΔT

We can rearrange our equation to give us

Cv ΔT = ΔU = 8.3 x 3/2 x 100 K = 1245 J mol^-1

As we have half a mole then we have to put in 622.5 J of energy if the volume is going to stay the same. The pressure will increase we can predict it with the following equation.

P₂ / P₁ = T₂ / T₁

My calculations give us a value of 1547950 Pa for the final value.

Now lets do it again with constant pressure

As Cp = ΔH / ΔT = 5/2 R

If the pressure stays the same then the amount of energy required will be higher at 1037.5 J.

We might for a moment ask why is the energy higher for the fixed pressure case than it is for the fixed volume.

When the gas is heated up at a fixed pressure then it has to expand to continue to satisfy the equation PV = nRT

We can calculate the volume increase

V₂/V₁ = T₂/T₁

So the box has to increase by 366.3 ml to a volume of 1.3663 litres or 1.3663 x 10^-3 m³

Now E = P ΔV

For fun lets do the dimensional analysis

Joules = N m^-2 x m³ = N m

Now E = P ΔV = 1132950 Pa x 0.3663 x 10^-3 m³ = 415 J

Now 622.5 J + 415 J = 1037.5 J

I am hoping that you can see that the difference between the two energies which need to be added to the gas to increase the temperature. I hope to add some diagrams shortly.

Muons and Fukushima

Dear Reader,

One of the great problems right now is working out where the fuel in the damaged cores and the ponds is, and in what condition the fuel is in. We can take for granted that the fuel which was in units 1, 2 and 3 has been damaged by overheating. But the state of the fuel in the ponds was a bit more of a mystery to us.

After clearing the rubbish out of the pond at unit three it has been possible to inspect the pond, the pond is frankly in a bit of a mess. But the fuel seems to have escaped serious damage. Photographs have been taken of the fuel racks in the pond and it does not look like there has been been any dire melting or explosions in the pond.

I have seen that some samples have been taken from the pond at unit four to allow them to be examined (these were samples of unused fuel which were being stored in the pond at the time of the accident). The work so far suggests that the fuel in the pond is in good condition. This suggests strongly that no nuclear explosion occurred in the pond.

The other great question is the state of the reactors. I saw something interesting recently, it is a sensing system based on cosmic rays (muons). This looks to me like a good method for finding the fuel inside the damaged reactors without having to get up close and personal with the stricken reactors.

Another thing which needs to be done is for society to recover from the accident, I have seen some advice from the IAEA on the subject of remediation of the contaminated land (outside the nuclear reactor park). This document might be of interest to some of my readers. It includes a discussion of the cleaning of different types of areas which include farmland. As I predicted it does include the question of deep ploughing the land.

Palomares and the H-bombs

Dear Reader,

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

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

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

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

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

Sand, 150 L/kg

Loam, 1200 L/kg

Clay, 5100 L/kg

Organic, 1900 L/kg

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

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

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

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

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

The top of Bloom’s ladder

Dear Reader,

The other day I was looking at a web site devoted to PVC, it is written by some people who are strongly opposed to Greenpeace’s opinion on chlorine chemicals. Greenpeace is strongly opposed to the use of organic chlorine compounds (including PVC) while the chlorophiles say that PVC is great and good for the environment.

One of Greenpeaces’s claims that adding chlorine compounds like PVC to incinerators will lead to the formation of dioxin, and that PVC under the conditions in a landfill forms vinyl chloride. While I do not have an infinite amount of time I will have to choose to only deal with the second point.

However there is a little bit of a problem which was pointed out by the chlorophiles, they claim that bacteria in the landfills are forming the vinyl chloride from waste which is not related to PVC.

I took a look in the literature T.E. Mattes et. al. in FEMS Microbiology Reviews, 2010, 34, pages 445-475 writes at length about how bacteria can degrade polychloroethylenes (tetrachloroethylene, trichloroethylene and dichloroethylene) into vinyl chloride (chloroethylene) and then ethylene. Now while in hindsight things always look very clear and simple, I choose not to fall into the trap of assuming that Greenpeace had a crystal ball which allowed them to see the future. While some elements in the Green movement want industry to have a crystal ball to allow them to see every future effect of their activities (regardless of how unexpected these effects might be) I think it is unreasonable to expect either the “Greens” or the “Chemical Industry” to have these crystal balls.

If any of my readers know where I can get one from them please drop me a line as I think I would find it very useful in both my professional life and in my private life. I am not holding my breath waiting as I do not think such crystal balls exist !

But I then looked further back into the past, when I looked in the academic literature for “Biodegradation” and “Chloroethenes” I found back in 1995 a paper by J. Gerritse et. al. in Applied Microbiology and Biotechnology,  1995, 43 (5), pages 920-928. In this paper it reported that under anoxic conditions that “PCE was converted mainly into cis-1,2-dichloroethene, small amounts of TCE and chloroethene, and chloride”.

It is interesting to note that J. Gerritse has published more on this subject since the paper in 1995, (for example J. Gerritse et. al. Archives of MicroBiology, 1996, 165, pages 132-140) in which the abstract reports

“A strictly anaerobic bacterium, strain PCE1, was isolated from a tetrachloroethene-dechlorinating enrichment culture. Cells of the bacterium were motile curved rods, with approximately four lateral flagella. They possessed a gram-positive type of cell wall and contained cytochrome c. Optimum growth occurred at pH 7.2-7.8 and 34-38 degrees C. The organism grew with L-lactate, pyruvate, butyrate, formate, succinate, or ethanol as electron donors, using either tetrachloroethene, 2-chlorophenol, 2,4,6-trichlorophenol, 3-chloro-4-hydroxy-phenylacetate, sulfite, thiosulfate, or fumarate as electron accepters. Strain PCE1 also grew fermentatively with pyruvate as the sole substrate. L-Lactate and pyruvate were oxidized to acetate. Tetrachloroethene was reductively dechlorinated to trichloroethene and small amounts (< 5%) of cis-1,2-dichloroethene and trans-1,2-dichloroethene. Chlorinated phenolic compounds were dechlorinated specifically at the ol-tho-position. On the basis of 16S rRNA sequence analysis, the organism was identified as a species within the genus Desulfitobacterium, which until now only contained the chlorophenol-dechlorinating bacterium, Desulfitobacterium dehalogenans.”

Looking at the reference list for the 1995 paper I quickly found papers published around about 1990 on how bacteria reduce the more chlorinated ethylenes into less chlorine rich ethylenes. The reduction of these chlorine rich solvents (which have nothing to do with PVC) is a more reasonable source of vinyl chloride in landfill gas. PVC does not degrade into vinyl chloride, when it is heated it forms hydrochloric acid and a black tar which is rich in benzene, styrene, napthalene and soot. While the thermal degradation products of PVC are not nice, they are clearly not the same as vinyl chloride.

Now I would like to point out that chemicals like perchloroethylene (PCE, perc or tetrachloroethylene) and trichloroethylene (TCE or trike) should never have been added to a land fill but I think to blame one industry for the deeds of another is not fair. Blaming one industry for the misdeeds of another is as unreasonable as a policeman arresting a person at random so that he has someone to blame for a crime !

I think that Greenpeace should have devoted more time to reading the literature on vinyl chloride and landfills, as they have a team of full time people who incloude some people who have a background in science then I do not think it would be too hard for them to have found the papers on bacteria and vinyl chloride. I would also suggest to them that they take care to avoid the pitfalls of “groupthink” and other forms of tunnel vision which can lead to some very poor choices.

In British chemistry we have an ironic joke about people who dash into the lab becuase they do not want to spend time reading boring books becuase they want to do exciting chemistry, the joke is

“Why waste a week in the library when you can waste a month in the lab”

I would suggest to Greenpeace that they should adopt an altered version of this joke,

“Why waste a week in the library when you can expose yourself to ridicule, lose credibility and look silly while making an ill advised protest or pressrelease”

While the environment does need a friend, right now the claims which Greenpeace has made about the evils of PVC being added to landfills have caused them to lose credibility in my eyes. Now some of you might ask what is Bloom’s ladder and what is at the top of it. Bloom’s ladder is a series of levels of learning, at the top is the ability to compare and judge the worthyness of one source compared with another. Looking at a single item on the chlorophiles site, it does appear that they are more trustworthy than Greenpeace. This is becuase the science which the chlorophiles site is based on is better.

Now I imagine that I may have enraged some of my readers (If I have enraged you then sorry but people do not come to my blog to be pandered to) but I suggest that anyone who is enraged by my disection of a small part of Greenpeaces antiPVC campaign should go through the chlorophiles website with great care. If they can find any science which they doubt there, then please contact me and I will make a literature search before showing the world the results. I look forward to seeing what my readers think of the debate between Greenpeace and the chlorophiles.

BNCT a great way to cure cancer

Dear Reader,

Recently I looked into the core of a nuclear reactor for the first time in my life, the closest I had been before then was looking through the door in the inner shielding at the top cap of a defunct reactor which had been shut down decades ago.

I was standing in the operating position above the water pool of a 250 kW reactor which is used for research, training and for treating cancer; the reactor was not running while I was visiting. Apparently in that location the dose rate is about 400 microsievert per hour when the reactor is running, while this dose rate is no where near the level which would cause an injury or death. As the 1970s LD₅₀ dose for radiation was about 3.5 grays, it would take 8750 hours there to reach this dose. The 365 days required to get this dose would mean that the self repair mechanisms in my body would reduce the baneful effect on my body. I do not think that it would make me fall down dead, but within a week or so I would be hitting my yearly limit, so that I would not want to linger in that spot while the reactor is running.

It was an interesting view looking down through a 6 meter pool of water at the core of the reactor; this reactor is a type which is not designed to make electric power. Instead it is designed to make neutrons for radioisotope production, for training and for the treatment of cancer. Almost twenty years ago the reactor was modified to allow it to be used as a neutron source for the treatment of cancer by the boron capture method.

Now I know that some elements in society are very antinuclear but I would ask even the most antinuclear people to stop, read this and think for a while. Frankly I would like it if you shared my point of view but even if you do not come away from reading this with my point of view I accept that people are free to choose what they like to believe.

Now if you have the misfortune to get cancer then one of the treatment methods is radiation, now the problem is that it is best to give the cancer cells one heck of a going over with one almighty dose of radiation while only giving the healthy tissue a very small dose. This is the ideal but sadly with many radiation treatments it is not quite possible to do this.

The most common method seems to be either X-rays or gamma rays delivered from a source outside the patient. The problem with these treatments is that the beam of radiation damages all tissue that it passes through. One solution to try to spare the healthy tissue is to aim beams of radiation into the person from different angles so that the paths of all the different directions converge on the spot where the nasty tumour is. This is not a perfect way of doing things, no matter how good the radiation expert is they will damage some healthy tissue.

The next step up in controlled and localised dose is to implant a source into the person; it is possible to implant a small but intensely radioactive source right at the spot where the cancer is. This can be used to treat a range of different cancers which include cancer of the cervix, breast and prostate. As radiation obeys an inverse square law this treatment is often very good at sparing the healthy tissues.

If you double the distance from the source you make the dose four times lower, while if you triple the distance from the source then the dose is nine times smaller. I hope that you can now see that the effect should be very well localised in one part of the body. With the right choice of photon and beta particle energy you can make the dose even shorter ranged thus allowing you to wipe the smile off the cancer’s ugly face, send it away with its tail between its legs while leaving the vast majority of the person undamaged.

Sounds great doesn’t it! But there is a fly in the ointment. Today for some applications some of the greens are yelling that we need to stop using nuclear reactors. The problem is that for the generation of the radioactive sources often the only thing which will do the job is a nuclear reactor which has been optimised for a high neutron flux. To do this you need to make the core nice and compact and run the reactor with a highly enriched fuel. Here is one of the best arguments for keeping radioisotope production reactors, while they might not fit in with some people’s idea of what is green they do provide an affordable and reliable supply of lifesaving diagnostic and curative medical products.

Now some people might be yelling at the screen that we should ditch the old fashioned radioactive sources for medical use and use modern particle accelerators like LINACs. I would like to point out that the treatment systems based on radioactive sources are simpler and there is much less to go wrong. Using no more than a sheet of graph paper it is possible to predict the strength of a radioactive source on day X, while accelerators are more complex. I am aware of radiotherapy accidents in both Poland and the USA where accelerators have failed to behave as expected. Both cases caused some ugly overexposures of people.

Also to deliver the radiation just where it is needed to some where like the cervix or the prostrate it is not possible to do it with a typical medical accelerator. The way that the LINACs typically work is by whipping up electrons to very high speeds and then slamming them into a metal target. The change in velocity (deceleration) of the electrons cause them to emit very high energy gamma rays. An alternative second method is to use a gadget called a betatron. Both the betatron and the LINAC are suitable as replacements for the cobalt-60 based teletheraphy units which used radioactive sources to make beams of gamma rays, but they are not able to replace the treatments based on radioactive sources which are placed right in the tumours.

Now while brachytherapy is all very well, there is something even better. One of the problems with cancer is the oxygen effect. If tissue is nice and well oxygenated then low LET radiation like gamma and X-rays are good at causing harm. But when the tissue is poorly oxygenated then it has much less effect. While the surface layers of a tumour are often well oxygenated, the core of a tumour is often poorly oxygenated. What can happen is that when a tumour is given a dose of radiation the inner less oxygenated cells survive and then continue to grow thus making the tumour reappear.

But a high LET radiation such as alpha particles still works even if the oxygen content of the tissue is low. If boron is subjected to neutron bombardment then it forms alpha particles which are able to then do immense damage to the cancer while leaving the healthy tissue alone. The reason that this works is that the person is given a dose of a boron containing drug which mainly absorbs into the cancer cells. The drug used in Finland for this treatment is L-para-Boronophenylalanine, this is an amino acid bearing a B(OH)₂ group.

The boron-10 reacts with the neutrons to form alpha particles and lithium-7.

¹⁰B + n → ⁴He + ⁵Li

The helium and lithium-7 ions then damage the cancer cells, as the boron concentration in the healthy cells are low the healthy tissue gets a far lower dose. Here is a picture of the boron compound which is used for the treatment.

A molecule of the amino acid which bears the B(OH)2 group required for the BNCT

Now some of those of you reading this blog might not be the greatest enthusiasts of the nuclear sector, but I would like to caution the “antinuclear brigade” against throwing the baby out with the bath water.

While I am well aware that it is possible to make bombs using some nuclear technology, I would like to point out that Patrick Moore pointed out that the fact that car bombs made with ANFO (Ammonium Nitrate Fuel Oil) are bad. Frankly I have to say I strongly agree that ANFO based car bombs are perfectly horrible.

But he wrote that the fact that you can make a nasty large bomb out of a car, some ammonium nitrate fertilizer and some diesel fuel is not a good reason to ban any of these three items.

I would like to also point out that the nuclear equipment in the form of a radiotherapy reactor is not in a form which is suitable for use as a weapon, I think that the only weapon I had access to at the reactor site were some lead bricks in the radiochemical lab and the bright yellow extra long tongs. I think I can get some weapons which are more suitable for mindless violence from a typical garden centre !

I have to explain something to you, it is possible to use many objects as weapons but the fact that it is possible to employ or adapt an object into a weapon is never a valid reason for banning an object. I will give you an example, in Mr Archer’s prison diary it explains how one person once took a toilet brush, they cut off the bristles and then sharpened it into a sword. The fact that someone managed to adapt a toilet brush into a sword should not be used as an excuse to ban the things !

Another of the hard unit cells

Dear Reader,

After my success with the sodium nitrate I will now present tripotassium hexacyanoferrate(III) which is an example of a monoclinic cell. Again we have to start with drawing a box to make our cell. The lengths of the cell are 7.047, 10.400  and 8.384 Å. Two of the angles (alpha and gamma) are 90 degrees while the beta angle is 107.29 degrees.

This will give us a box which is more complex than an orthorhombic box.

We start by adding iron atoms, the fractional coordinates of the iron atoms are 0 0 0 and 0 0.5 0.5 which means we have two iron atoms in the unit cell.

We next have to add the potassiums at the following fraction coordinates 0.000 0.000 0.500, 0.000 0.500 0.000, 0.5025 0.7700 0.6252, 0.5025 0.7300 0.1252, 0.4975 0.2700 0.8748 and 0.4975 0.2300 0.3748.

We should now understand that we will have six potassium atoms to go with our two irons.

Next we add the cyanide carbons

These are at the following fractional coordinates

0,1875	0,9480	0,2102
0,1887	0,945	0,886
0,8795	0,8317	0,9712
0,8795	0,6683	0,4712
0,8113	0,445	0,614
0,8125	0,448	0,2898
0,8125	0,0520	0,7898
0,8113	0,0550	0,1140
0,1205	0,1683	0,0288
0,1205	0,3317	0,5288
0,1887	0,5550	0,3860
0,1875	0,5520	0,7102

We should understand that they are all fully inside the cell so we have 12 cyanide carbons.

Next we do the cyanide nitrogens

0,8004	0,7335	0,9515
0,2974	0,9120	0,8160
0,2962	0,9180	0,3361
0,8004	0,7665	0,4515
0,7026	0,4120	0,6840
0,7038	0,4180	0,1639
0,1996	0,2665	0,0485
0,7026	0,0880	0,1840
0,7038	0,0820	0,6639
0,1996	0,2335	0,5485
0,2974	0,5880	0,3160
0,2962	0,5820	0,8361

Now lets have a look at what we have done, from the side we can see how one of the angles (beta) is a long way from ninety degrees.

Side view of unit cell

Now we will have a look from a different angle.

The front view of the cell

Here are the x,y,z coordinates of the atoms on a conventional 90 degree and 90 degree set of x y and z axis. I have marked on bold the iron atoms which are at the corners of the cell.

46
XYZ file   for : K3Fe(CN)6
K	0.28089	-3.45899	-5.16955
K	-5.00083	0.38661	-3.78117
K	5.38365	0.38134	-3.21339
K	0.10193	4.22694	-1.82501
K	-2.32040	-2.87755	-1.40161
K	2.82526	-0.96562	-0.24795
K	-2.82526	0.96562	0.24795
K	2.32040	2.87755	1.40161
K	-0.10193	-4.22694	1.82501
K	-5.38365	-0.38134	3.21339
K	5.00083	-0.38661	3.78117
K	-0.28089	3.45899	5.16955
Fe	-4.91135	-3.45635	-5.45344
Fe	5.47313	-3.46163	-4.88566
Fe	0.19141	0.38398	-3.49728
Fe	-5.09031	4.22958	-2.10890
Fe	5.29417	4.22430	-1.54112
Fe	-5.29417	-4.22430	1.54112
Fe	5.09031	-4.22958	2.10890
Fe	-0.19141	-0.38398	3.49728
Fe	-5.47313	3.46163	4.88566
Fe	4.91136	3.45635	5.45344
C	4.80935	-2.73005	-3.21574
C	0.69724	-1.37587	-2.85930
C	-1.59727	0.07097	-2.84632
C	0.66992	1.11497	-1.76490
C	-3.38358	3.91480	-1.26682
C	4.72002	2.46500	-0.96219
C	-4.72002	-2.46500	0.96219
C	3.38358	-3.91480	1.26682
C	-0.66992	-1.11497	1.76490
C	1.59728	-0.07097	2.84632
C	-0.69724	1.37587	2.85930
C	-4.80935	2.73005	3.21574
N	0.98970	-2.42716	-2.50303
N	4.41252	-2.27534	-2.24005
N	-2.64379	-0.14067	-2.41469
N	-2.39058	3.70212	-0.72368
N	4.38940	1.41403	-0.63999
N	0.95847	1.56933	-0.75174
N	-4.38940	-1.41403	0.63999
N	2.39058	-3.70212	0.72368
N	-0.95846	-1.56933	0.75174
N	-4.41252	2.27534	2.24005
N	2.64379	0.14067	2.41469
N	-0.98969	2.42716	2.50303

If you want a free program (free to academic users only) then I would suggest ORTEP which I have provided a link for on the right hand side of this blog.

The harder unit cells (NaNO3)

Dear Reader,

A short time ago I chickened (lost my courage) out of the harder unit cells, then it started to rain which stops me doing my project in the garden. I have come back into the house and I am now sitting in front of the PC again.

We will be attempting to deal with a rhombohohdral cell, we will use the suggested example of sodium nitrate from that book which I mentioned recently. This cell has three equal lengths for the sides which are 6.3108 Å long. The angles alpha, beta and gamma are all 47.267 degrees.

N. Elliott, Annales Academiae Scientiarum Fennicae, Series A6: Physica, 1962, 94, 1 to 34 publishes the crystal strcutre. I will use this person’s data to make our cell.

The first part is to draw the box for the cell, this is not so easy as the angles in the cell are not 90 degrees. After you have been able to draw the cell we should start to add the atoms.

The sodiums are easy as we have them at fractional coordinates of 0 0 0 and 0.5 0.5 0.5, those of you who have been paying attention should quickly understand that we have two sodium atoms in each unit cell.

We have nitrogens at two fractional coordinates 0.25 0.25 0.25 and 0.75 0.75 0.75. This means we have two nitrogen atoms in our unit cell.

Finally we have oxygens at six sites, here are the fractional coordinates for these oxygen atoms.

0,0067	0,4933	0,2500
0,2500	0,0067	0,4933
0,4933	0,2500	0,0067
0,9933	0,5067	0,7500
0,7500	0,9933	0,5067
0,5067	0,7500	0,9933

Here is one view of what is inside the cell

A view of a unit cell of sodium nitrate

Sadly one of the sodiums blocks the view of a nitrate anion, so here is a second view.

Second view of the sodium nitrate

Finally here is a table of the cartesian coordinates of the atoms, this will allow some of my readers at home to recreate the unit cell. The sodium at 0 0 0 is the sodium at the centre of the cell. This will help you recreate a cell for yourselves.

17
XYZ	file	for	:
Na	6.90253	2.83847	-3.83540
Na	0.66278	2.74622	-2.89430
Na	2.88070	-1.75338	-2.23276
Na	-3.35906	-1.84563	-1.29166
Na	0.00000	0.00000	0.00000
Na	3.35906	1.84563	1.29166
Na	-2.88070	1.75338	2.23276
Na	-0.66278	-2.74622	2.89430
Na	-6.90253	-2.83847	3.83540
N	3.45126	1.41924	-1.91770
N	-3.45126	-1.41924	1.91770
O	3.33488	0.54360	-2.77519
O	2.91164	2.51399	-2.07865
O	4.10727	1.20012	-0.89926
O	-4.10727	-1.20012	0.89926
O	-2.91164	-2.51399	2.07865
O	-3.33488	-0.54360	2.77519

The liebig condensor

Dear Reader,

I was filming a chemistry experiment recently to produce some teaching materials. This made me think about the liebig condenser, this is a classic item of chemical equipment. A great question is which way around to connect the water hoses.

If we were to attach the in hose at the top and the out at the bottom then with low flow rates it is likely that much of the surface which should be cooling the vapours will not be cooled with water. If we add the water at the bottom then more of the vapour cooling surface will be wetted with the water.

What I going to do is to set up a liebig condenser in the near future with the water connected in the wrong direction, I will then photograph the system and then restore the connections to the right way around and then take another photograph. I will have to wait until I get back to my lab before I can take these photographs.

Toad juice

Dear Reader,

I was informed by one of my PhD students that a place in Sweden is sponsoring toads, the idea is that you pay a fee to support a toad. As a result the nuclear chemistry and industrial materials recycling sections of the department of chemical and biological engineering are considering if they should have a whip round and then sponsor a toad.

Now before we get going toads have had a bit of a raw deal, they get a bad press which they frankly do not deserve (at least not always). For example they get blamed for giving people warts, and toxic mushrooms are called “toadstools” (why can they not have sofas or armchairs ?) and why are driving test examiners compared with toads ? You might argue that this web page is biased against toads and is an example of hate speech against toads.

But I would say that the cane toad is a nasty little so and so who needs to be put in his/her place, maybe the other toads should take the cane toad behind the potting shed and reeducate it a little.

It is important to note that all the toads have toxin which protect them, one of the toxins which the common european toad has is a cardiotoxic steroid. This is an interesting molecule called bufotalin which has been isolated from a range of different toads. One paper (A.Kalman, V.Fulop, G.Argay, B.Ribar, D.Lazar, D.Zivanov-Stakic, D.Vladimirov, Acta Cryst., 1988, C44, 1634-1638) used the Chinese toad Ch’an Su as a source of the toxin. The molecule is a steroid which has an additional six membered ring group attached. The additional group is an aromatic ring which is in disguise. Here is a molecule of bufotalin.

Bufotalin a toxin from a toad

I will write more about the “toad toxin” later

Carbon tetrachloride

Dear Reader,

I saw a chemistry world blog article about carbon tetrachloride so now I feel compelled to write to you about an organic solvent from yesteryear, it is carbon tetrachloride or more correctly tetrachloromethane. This is the substance which sent Margo Jones to the other side when her carpet was dry cleaned with it, it also almost sent a friend of mine to the same place years ago. An old chemist who I know used to mouth pipette everything, one day he mouth pipetted solutions of things in carbon tetrachloride (I think he was measuring distribution ratios) and he told that hours later he started to vomit. He told me that he continued to puke for about three days and he suspects that he had a lucky escape (He recovered and then went onto have a productive life).

Top tip of the day : Never mouth pipette anything !

The thing which interests me most about carbon tetrachloride is the free radical chemistry of this molecule. I strongly suspect that the trichloromethyl radical is a very stable radical which contributes to some of the chemistry of carbon tet. I know many years ago both the Soviets and the Americans built PUREX plants using carbon tetrachloride as the diluent. The nice thing about carbon tet is it gives a very good quality uranium and plutonium product, also it is easy to purify the process solvent to recover pure carbon tet, it is non flammable and the phase separation is easy. But it had a horrible sting in its tail, when you irradiate carbon tetrachloride you form chloride anions. I suspect that the solvated electrons are captured by the LUMO of the carbon tetrachloride and then it splits up to form anionic chloride ions and trichloromethyl radicals. The chloride impurity in the PUREX plants quickly formed aqua regia with the nitric acid used in the PUREX process. The resulting corrosion soon caused both plants to be shut down.

I will get onto the free radical chemistry which occurs in flames later, but an interesting bit of free radical chemistry using carbon tetrachloride is used in the production of cypermethrin. This is a insect killing agent which I have bought at Ica and used to kill creepy crawlies in my house. A key step in the production of cypermethrin is the formation of the cyclopropane ring. The synthesis starts with a pericyclic reaction (Claisen rearrangement) which uses an allylic alcohol and triethyl orthoacetate to form γ,δ unsaturated ester. This ester it then reacted with carbon tetrachloride in a free radical reaction. Treatment with two bases then forms the cyclopropane ring which makes up a key part of the carboxylic acid part of the insect killing agent.