Porphyrins molecules, structures

The first chosen example refers to the control of surface-supported supramolec-ular assembly by judicious distribution of substituents in porphyrin molecules (Yokoyama et al, 2001). Substituted porphyrin molecules OMBD-deposited on a Au( 111) surface form monomers, trimers, tetramers or extended wire-like structures... 

Assuming a smooth spherical structure of the micellar surface [73] with a uniform density distribution, the average distances of the micellar carbon and the ironcenter of the porphyrin complex were evaluated [67] and the disposition of porphyrin molecule in the micelle was determined (Fig. 15). The propionic acid side chains in the heme molecule have been proposed [67] to be directed... 

In free heme molecules (heme not bound to protein), reaction of oxygen at one of the two open coordination bonds of iron (perpendicular to the plane of the porphyrin molecule, above and below) can result in irreversible conversion of Fe2+ to Fes+. In heme-containing proteins, this reaction is prevented by sequestering of the heme deep within the protein structure where access to the two open coordination bonds is restricted. One of these two coordination bonds is occupied by a side-chain nitrogen of a His residue. The... 

Fig. 1. Suggested structure of a metal-free porphyrin molecule...

A simple approach to understanding the factors which control the "conductivity of proteins towards electron tunneling is to develop "small molecule model systems to mimic intramolecular electron transfer in the protein systems. Appropriate models obviously require that the donor and acceptor be held at fixed distances and orientations which correspond to those in the protein-protein complexes. Models of this type have recently been obtained and investigated [103,104]. In these models the protein matrix is replaced by a simple synthetic spacer which separates two porphyrin molecules. By changing the chemical structure of the spacer, a series of molecules with different reaction distances and geometries has been synthesized. Typical examples of such molecules are presented in Fig. 21. 

FIGURE 7.26. (a) Molecular structure of compounds 42—45 (b) TEM images of a bundle of nanorods formed by compound 43 (Upper), and closer view of the bundle (Lower), (c) Pictorial representation of the nanorods formed by self-assembly of salt 43 in water, (d) Nanotubules formed by compound 45 observed at different scales. The measures of the two focused tubules are 35 x 530 and 50 x 470 nm. (e) Most stable dimeric structures of 45. Note that Upper is 6 kcal/mol per molecule more stable than Lower. (Upper) Interlayered structure (see text). (Lower) Porphyrin stacked structure. Notice that the porphyrin stacked structure is 2 kcal/mol per molecule more stable than the interlayered structure. 

Fig. 10.2. Catalytic cycle of P450 including the peroxide shunt pathway. RH is substrate, and ROH is product. The porphyrin molecule is represented as a parallelogram. The overall charge on the structures is shown to the left of each bracket. Intermediates 1, 2, 7, and 8 are neutral. Refer to text for a full description.

Figure 2. Structures of chlorin and porphyrin molecules found in plant and animal matter. Several different chlorophylls have the same basic ring structure but different peripheral substituents.

Peroxidase catalysis is an oxidation of a donor to an oxidized donor by the action of hydrogen peroxide, liberating two water molecules. Horseradish peroxidase (HRP) is a single-chain /3-type hemoprotein that catalyzes the decomposition of hydrogen peroxide at the expense of aromatic proton donors. HRP is a Fe-containing porphyrin-type structure and is well-... 

Resins and asphaltenes are also of interest as a result of the fact that most of the heteroatoms reside in these fractions [7,16], Beaton and Bertolacini [5] report that about equal amounts of V and Ni reside in the resins as in the asphaltenes, while sulphur is concentrated in resins. The chemical associations between the heteroatoms and organic molecules are far from certain, although general descriptions in terms of porphyrin like structures have been advanced [5]. Sulphur appears to be easily accessible and thiophenic sulphur has been identified [8]. Vanadium is more accessible than nickel. 

Fig. 3 - Some typical porphyrinic molecules a) Ni star-porphyrazine, with four fused thiolene groups (4PZ), b) basic porphyrazine structure with peripherally fused-benzo rings (PC) and c) dithiolene groups (PZ).

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