Update on your new best friend

Dear Reader,

Slightly more than one year ago I wrote about the new best friend of the Japanese people. Rather than a person who will go out and go for a karaoke session with you, drink beer with you or go for a walk in the park with you this new friend is one who can clean up your drinking water and keep your fruit and veg safe. Also this friend can help keep the milk healthy. Now you might ask what sort of super nice person can do all these things, or what sort of imp or kappa is able to do all these things.

The identity of this new friend is a bit more humble sounding, it is the clay in the soil. I have seen a recent paper by Naofumi Kozai, Toshihiko Ohnuki, Makoto Arisaka, Masayuki Watanabe, Fuminori Sakamoto, Shinya Yamasaki and Mingyu Jiang (Journal of Nuclear Science and Technology, 2012, 49(5), pages 473 to 478) in which the cesium behaviour in the soil is reported.

In this paper the soil was examined with X-ray diffraction. This found smectite, mica, hornblende, kaolinite, quartz, orthoclose, cistobalite, feldspar, stishovite, gibbsite, sodalite, olivine and sorosilicate minerals in the soils.

The smectite clay is rather similar to the illite clay which I showed a picture of recently. The two clays are related, I have seen a thesis which explains how the smectite clay transforms into illite clay. For your information the thesis is here. The difference between these two layered clays is in the anionic bread layers between the potassium jam. The smectite and the illite have slightly different layers.

A smectite clay, the oxygens are in orange red, the potassium ions in blue, the aluminium/silicon atoms are in sea green. Note that layers of potassium ions which look like slices of bread.

I think that both the smectite and illite are formed from mica, so I would say that the more mica in the rocks which formed the soil the better when you are considering cesium in soil. The mica is very similar to the two clays, again it is a layered solid.

Many of us know mica, it is a mineral which can be made into thin sheets. We will soon see why it is possible to split mica into thin sheets. It is easy to separate the mica by peeling apart the layers.

Here is a view of a mica (Muscovite) which was studied some time ago. (O.V. Sidorenko, B.B. Zvyagin and S.V. Soboleva, Kristallografiya, 1975, 20, 543-549). Should should see again that the solid is layered, the potassiums (blue) have anionic layers of alumo-magnesium silicate between them. I have shown all the non oxygen atoms in the layers as green.

Mica showing the layers of potassium ions between the anionic layers

The important thing about the mica is that the aluminium atoms are randomly mixed with magnesium and silicon atoms in the two layers. The authors of the paper I am working from expressed the view that one of the types of layers (the middle layer in the trilayer anionic layer) has 20 % magnesium and 80 % aluminium. While the two outer layers of the anionic trilayer have 28.4 % aluminium and 71.6 % silicon. The mica also contains some hydroxyl anions which I have been unable to locate in that solid. I have made a new drawing of the mica which shows the mixed aluminium/silicon and aluminium/magnesium layers in different colours to show you how the solid fits together.

Diagram of mica. The potassium ions are in blue. The mixed aluminium/magnesium sites are in grey. The mixed aluminium/silicon sites are in green. The oxygens are in a rather fetching shade of orange.

It is important to note that the green aluminium/silicon sites have a tetrahedral arrangement of oxygen atoms around the central atoms while the grey mixed magnesium/aluminium sites have a distorted octahedral arrangement of oxygens around the central atoms.

The hornblende clay is a very different mineral, I have looked at the crystal structure and it looks in some ways like a SBA-15 or MCM-41 to me. It has tube like holes which pass in one direction through the clay. These tubes are then filled with sodium and potassium cations. As the clay is so different, I suspect that it may behave differently to the layered clays which I showed you.

The mica based minerals can change the spacing between the anionic layers to suit a new cation which has a larger diameter than the potassium. In this way the larger cesium ions can be held in the solid. But in the case of the hornblende, I do not think it will be so easy to add a larger cation. I think that the holes will get plugged up and blocked by the larger cations.

Here is a view of several unit cells of the hornblende clay, the solid is a little disordered. It has a mixture of sodium (yellow) and potassium (blue) cations in the solid. Also note that it has grey calcium ions in the alumosilicate layers. The aluminiums are purple, the silicons are sea green and the iron atoms in the clay are orange. The oxygen is in a rather fetching orange/red as before.

A view of hornblende clay showing the holes in which the potassium/sodium ions go.

I will try and give you an update soon on the clay and the cesium.

Plastic fantastic

Dear Reader,

In recent times I have shown how a lad can have fun with the unit cells of inorganic solids, but now it is time to move onto something with carbon in it. I choose to look at the solid state structure of a polymer which is a high temperature engineering polymer.

LIMMUP in the crystallographic database is Poly((4,4′-diphenylene)pyromellitimide) which was described by Y. Obata, K. Okuyama, S. Kurihara, Y. Kitano and T. Jinda in Macromolecules, 1995, 28, 1547. This is a solid which is an endless chain of atoms covalently linked to the next. Here is a picture of the unit cell.

Unit cell of the polymer

While here is a picture of five of the polymer chains.

Polymer chains

While looking for examples of the polymer chains I noticed something else, this brings me onto another subject. I hold the view that one of the first steps to maturity is the point at which a person truly accepts that things which they are not interested in, involved in or have experience in can be truly worthwhile and valid. I have to add the warning that there is some work out there which is not worthwhile and is frankly close to worthless, but I do not want to point the finger by naming names well at least not today.

I have spent much of my life working on trying to get molecules to selectively recognise metals; I used to share an office with a man (Zhixue Zhu) who worked for Howard Colquhoun on a project where he was trying to get molecules to recognise short parts of polymer chains. While it might not have been quite the sort of thing that I have done in life, I still hold the view that the work is good work which is worthwhile.

Here what Dr Zhu did was to use a pair of pyrene groups to recognise part of a short chain model of kapton (poly(4,4′-oxydiphenylene-pyromellitimide)); his tweezers recognized the pyromellitimide part of the chain. Here is a picture of the solid which he published in Chemical Communications, 2004 page 2650 together with H.M. Colquhoun, C.J. Cardin and Yu Gan.

Dr Zhu's mini tongs which grip the polymer chain

I suspect that Christine Cardin found this solid interesting as her group have done a lot of work in the past on how things like acridines bond onto DNA through pi-pi effects.