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Peas and nitrogen II

OK some of you might ask what peas have to do with catalysis, the peas do not have anything special in them but in their roots, they have bacteria, which have very special enzymes, which are able to break the super strong nitrogen nitrogen bond found in a nitrogen molecule. When humans want to break the N N triple bond they need to use harsh conditions but the bacteria in the roots of the peas can do it at 20 oC and 1 atmosphere.

 

I looked at the literature and I found that it is thought that the active site of the enzyme contains iron and molybdenum bonded together with sulphur groups. I then saw a paper on ruthenium chemistry, some of you might ask, “what has ruthenium got to do with it?”. Good question, in organometallic chemistry and homogenous catalysis it is often the case that the second and third row transition metals can do the same chemistry as the first row metal. But the rate of reaction is often lower, and the strength of metal carbon bond is often greater for the more heavy elements. For example nickel carbon bonds are often too weak to be useful, platinum carbon bonds are often too strong to be useful while palladium carbon bonds have just the right strength. For example, palladium cross coupling chemistry (Heck etc) has become a very important tool in modern organic chemistry.

 

The way in which the enzyme converts nitrogen gas into ammonium ions is not clear. Many hours of effort have been expended by some very bright people but the answer is not clear yet. One of the methods, which can be used to find out about a chemical process, is to try to grow crystals of the reagents. If you are lucky, you might be able to observe the structure of a key intermediate, there is a grave danger with this method. It is possible to trust the crystal structure too much. The great problem is that most processes occur in solution state, while crystallography is done on the solid state. In addition, it is possible to have different forms of a compound both in the solid state and in the solution state.

 

Before we will look at some nitrogen fixation, we should look for a moment at some examples of how crystallography can trap the unwary. The most simple example I can think of is [RuHCl(CO)(PPh3)3], it has two different forms one is pink and the other is yellow. I was once warned by a teaching lab technician that if you run a teaching lab using it then make sure you give all the students samples from the same batch. The students do not like having a different coloured starting material to their classmates.

 

Before the arch critics of crystallography rejoice, I would like to point out several things.

  1. Few solution state methods (if any) have the same ability to measure bond lengths, angles and atomic positions with the same accuracy as crystallography.
  2. Plenty of molecules are known which can have several forms in solution.
  3. Homogenous systems do exist where a minor constituent in a mixture has almost all the catalytic activity.
  • For example in cobalt based hydroformylation much of the catalyst can be in an inactive resting state [HCo(CO)4] while [HCo(CO)3] is the real catalyst.

      4. There is a way out of the problem.

The way out of the problem is to find a spectroscopic method, which can be used, on both a solid-state sample and on a solution state sample. If the properties of the two forms of a substance are wildly different then it is likely that the structure of the two forms are different. Good methods include infra-red (ideal for metal carbonyl complexes), UV/vis (good for d-block metal complexes) and EXAFS (good for many things but expensive).

Back to nitrogen fixation, I saw a ruthenium dinitrogen complex. While the crystal structure alone does not prove that nitrogen binds this way to the iron in an enzyme, it shows that it is possible for nitrogen to bind to metals in this way. If we consider the nitrogen molecule with VSEPR then it should have two lone pairs on a pair of sp type atoms. One complex (I hope to show you a picture soon) has the nitrogen molecule bridging between two ruthenium atoms. Each ruthenium has a phosphine and a diamino-dithiol ligand attached.

This ruthenium complex will make a good example for the 18 valence electron rule, I will get onto that soon.

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