Iron atoms

The first crystal structure to be detennined that had an adjustable position parameter was that of pyrite, FeS2 In this structure the iron atoms are at the comers and the face centres, but the sulphur atoms are further away than in zincblende along a different tln-eefold synnnetry axis for each of the four iron atoms, which makes the unit cell primitive. 

Figure B3.3.12. Sulphur atoms in liquid iron at the Earth s core conditions, simnlated by first-principle Car-Parrinello molecular dynamics, (a) Initial conditions, showing a mannally-prepared initial cluster of snlphur atoms, (b) A short tune later, indicating spontaneous dispersal of the snlphur atoms, which mingle with the surroundmg iron atoms. Thanks are dne to D Alfe and M J Gillan for this figure. For fiirtlier details see [210. 211].

Figure C3.2.5. Strongest tunnelling patliways between surface histidines and tire iron atom in cytochrome c. Steps in patliways are denoted by solid lines (covalent bonds), dashed lines (hydrogen bonds), and tlirough-space contacts (dotted lines). Electron transfer distance to His 72 is 5 A shorter tlian in His 66, yet tire two rates are approximately...

Ironilll) chloride is a black, essentially covalent solid, in which each iron atom is surrounded octahedrally by six chlorine atoms. It is prepared by direct combination of iron with chlorine or by dehydration of the hydrated chloride, by one of the methods given on p.343). 

Ferrocene Figure 2-47) provides a prime ex.ample of multi-haptic bonds, i.e, a situation where the electrons that coordinate the cyclopentadienyl rings with the iron atom arc contained in molecular orbitals delocalised over the iron atom and the 10 carbon atoms of the cyclopentadienyl rings [82. ... 

Representation of such a system by a connection tabic having bonds between the iron atom and the five carbon atoms of either one of the two cyclopentadienyl rings is totally inadequate. A few other examples of structures that can no longer be adequately described by a standard connection table are given in the Section 2.G.2. 

Ferrocene (Figure 2-61a) has already been mentioned as a prime example of multi-haptic bonds, i.c, the electrons tlrat coordinate tire cyclopcntadicnyl rings with the iron atom are contained in a molecular orbital delocalized over all 11 atom centers [811, for w hich representation by a connection table having bonds between the iron atom and the five carbon atoms of cither cyclopcntadicnyl ring is totally inadequate. 

There are 26 electrons in the Iron atom but each has little mass. The electrons are spread out around the nucleus, occupying most of the space but very little of the mass. 

The nucleus of an iron atom contains 26 protons and 30 neutrons, which occupy very little space but make up most of the mass of the atom... 

An electron carries one unit of negative electrical charge (Figure 46.2). Its mass is about 1/2000 that of a proton or neutron. Therefore, very little of the mass of an atom is made from the masses of the electrons it contains, and generally the total mass of the electrons is ignored. For example, an atom of iron has a mass of 56 atomic units (au also called Daltons), of which only about 0.02% is due to the 26 electrons. Thus an iron atom (Fe ) is considered to have the same mass as a doubly charged cation of iron (Fe " ), even though there is a small mass difference. 

The unit positive charge on the proton balances the unit negative charge on the electron. In neutral atoms, the number of electrons is exactly equal to the number of protons. In an iron atom (Fe ), there are 26 electrons and just 26 protons. A cation is formed by removing electrons not by adding protons. An ion has one electron less than the neutral atom M . Similarly, an anion M" is formed by adding an electron and not by subtracting a proton from M°. 

Figure 8.39 shows some results of EXAFS following absorption by iron atoms in proteins with three prototype iron-sulphur active sites. In the example in Figure 8.39(a) application of a 0.9-3.5 A filter window before Fourier retransformation shows a single wave resulting... 

Diffusion of Carbon. When carbon atoms are deposited on the surface of the austenite, these atoms locate in the interstices between the iron atoms. As a result of natural vibrations the carbon atoms rapidly move from one site to another, statistically moving away from the surface. Carbon atoms continue to be deposited on the surface, so that a carbon gradient builds up, as shown schematically in Figure 5. When the carbon content of the surface attains the equihbrium value, this value is maintained at the surface if the kinetics of the gas reactions are sufficient to produce carbon atoms at least as fast as the atoms diffuse away from the surface into the interior of the sample. 

The deterrnination of the stmcture of Fe (00) 2 proved to be a difficult problem. An early report on the crystal stmcture claimed the molecule was a monoclinic prism and estabHshed the molecular formula (22). In a later report stmcture (8) was shown to be a triangular array of iron atoms with two bridging and 10 terminal CO molecules. This accepted stmcture was initially deduced from an x-ray crystal stmcture of the Fe2(CO)22H analogue (23). 

The important thing about the oxide film is that it acts as a barrier which keeps the oxygen and iron atoms apart and cuts down the rate at which these atoms react to form more iron oxide. Aluminium, and most other materials, form oxide barrier layers in just the same sort of way - but the oxide layer on aluminium is a much more effective barrier than the oxide film on iron is. 

Iron atoms pass into solution in the water as Fe leaving behind two electrons each (the anodic reaction). These are conducted through the metal to a place where the oxygen reduction reaction can take place to consume the electrons (the cathodic reaction). This reaction generates OH ions which then combine with the Fe ions to form a hydrated iron oxide Fe(OH)2 (really FeO, H2O) but instead of forming on the surface where it might give some protection, it often forms as a precipitate in the water itself. The reaction can be summarised by... 

The most conspicuous use of iron in biological systems is in our blood, where the erythrocytes are filled with the oxygen-binding protein hemoglobin. The red color of blood is due to the iron atom bound to the heme group in hemoglobin. Similar heme-bound iron atoms are present in a number of proteins involved in electron-transfer reactions, notably cytochromes. A chemically more sophisticated use of iron is found in an enzyme, ribo nucleotide reductase, that catalyzes the conversion of ribonucleotides to deoxyribonucleotides, an important step in the synthesis of the building blocks of DNA. 

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

FIGURE 15.29 The arrangement of snbnnits in horse methemoglobin, the first hemoglobin whose strnctnre was determined by X-ray diffraction. The iron atoms on metHb are in the oxidized, ferric (Fe ) state. (Irving Gets)... 

In deoxyhemoglobin, histidine F8 is liganded to the heme iron ion, but steric constraints force the Fe His-N bond to be tilted about 8° from the perpendicular to the plane of the heme. Steric repulsion between histidine F8 and the nitrogen atoms of the porphyrin ring system, combined with electrostatic repulsions between the electrons of Fe and the porphyrin 77-electrons, forces the iron atom to lie out of the porphyrin plane by about 0.06 nm. Changes in... 

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