Boxes, porphyrins

Hwang, I.-W. Kamada, T. Ahn, T. K. Ko, D. M. Nakamura, T. Tsuda, A. Osuka, A. Kim, D. Porphyrin boxes constructed by homochiral self-sorting assembly Optical separation, exciton coupling, and efficient excitation energy migration. J. Am. Chem. Soc. 2004,126, 16187-16198. 

In 2005, Rowan, Nolte, and coworkers described an efficient and templated synthesis of porphyrin boxes using DCC and reversible metathesis reaction [54]. Cyclic tetramers were successfully prepared in good yields (62%) from an olefin-functionalized zinc porphyrin in the presence of first generation Grubb s catalyst and upon addition of a tetrapyridyl porphyrin (TPyP) serving as a template. While a mixture of linear and cyclic oligomers was obtained in the absence of template, addition of TPyP resulted in a reorganization of the DCL to favor the formation of the desired tetrameric box (Fig. 7a). 

Figure 5.20 a) The porphyrin Tr-system produces a thickness o/ 0.35 nm of the porphyrin box , of which the length and width measures only twice as much. Electron-rich pyrrole rings tends to combine with the electron-poor porphyrin cavity, b) Porphyrin forms polymer stacks, whereas c) octaethylporphyrin only dimerizes. 

The photophysics of a three-dimensional zinc(II) porphyrin box, (PyZZ)4, was followed by resonance Raman spectroscopy - giving evidence for perturbation of the ring planarity.256 DFT calculations have been reported for the vibrational wavenumbers of Zn(2-N02 TPP).257 The IR spectra of two isomers (50, vCN 1640 cm-1) and (51, vCN 1610, 1587 cm-1) were both seen in solution (in C2D2C14)258... 

Fujita and coworkers have also reported the encapsulation of multimeric porphyrin assemblies in the box-shaped cavities of ternary Pd6 coordination cages. Two types of cofacial porphine dimers A and B could be stabilized (133). In the smaller [Pd6(L14)2(L15)6]12+ cage 29, whose diameter is 10.4 A (Fig. 21), two porphyrin molecules can be stackedo directly on top of each other with an interplane distance of 3.4 A. In the larger cage 30, an additional molecule of L14 is intercalated between the two porphyrin bases. All complexes were found to be water-soluble in contrast to other 7i-stacked porphyrin dimers. The encapsulation... 

Ubiquinone is readily reduced to ubiquinol, a process requiring two protons and two electrons similarly, ubiquinol is readily oxidized back to ubiquinone. This redox process is important in oxidative phosphorylation, in that it links hydrogen transfer to electron transfer. The cytochromes are haem-containing proteins (see Box 11.4). As we have seen, haem is an iron-porphyrin complex. Alternate oxidation-reduction of the iron between Fe + (reduced form) and Fe + (oxidized form) in the various cytochromes is responsible for the latter part of the electron transport chain. The individual cytochromes vary structurally, and their classification... 

The simplest covalently linked systems consist of porphyrin linked to electron acceptor or donor moiety with appropriate redox properties as outlined in Figure 1. Most of these studies have employed free base, zinc and magnesium tetrapyrroles because the first excited singlet state is relatively long-lived (typically 1-10 ns), so that electron transfer can compete with other decay pathways. Additionally, these pigments have relatively high fluorescence quantum yields. These tetrapyrroles are typically linked to electron acceptors such as quinones, perylenes , fullerenes , acetylenic fragments (14, 15) and aromatic spacers and other tetrapyrroles (e.g. boxes and arrays). 

The search for RNAs with new catalytic functions has been aided by the development of a method that rapidly searches pools of random polymers of RNA and extracts those with particular activities SELEX is nothing less than accelerated evolution in a test tube (Box 26-3). It has been used to generate RNA molecules that bind to amino acids, organic dyes, nucleotides, cyano-cobalamin, and other molecules. Researchers have isolated ribozymes that catalyze ester and amide bond formation, Sn2 reactions, metallation of (addition of metal ions to) porphyrins, and carbon-carbon bond formation. The evolution of enzymatic cofactors with nucleotide handles that facilitate their binding to ribozymes might have further expanded the repertoire of chemical processes available to primitive metabolic systems. 

The general properties of siderophores have been described extensively (2), and up-to-date lists of the individual compounds, their sources from aerobic and facultative aerobic species, and their properties have been published (3,4, 5). (Porphyrin Products, P. O. Box 31, Logan, UT 84321, sell a limited number of siderophores.) The earlier literature on iron assimilation by microbes, including enteric species, may be found elsewhere (6,7). For information on the chemical constitution and physiological role of the outer membrane of enteric bacteria, the reader is referred to Nakae and Nikaido (8). 

Fig. 3. Nature of free radical associated with compound I in peroxidases/catalases. Structure of first intermediate, following peroxide addition to ferric peroxidases and catalases. Boxes denote porphyrin ring. The amino-acid free radicals are depicted as protonated (tryptophan) and deprotonated (tyrosine), although this is yet to be conclusively determined.

The free base 5,10,15,20-tetraphenyl-21 A/,23//-porphine (H2tpp) may be prepared from pyrrole and benzaldehyde4 or purchased from Strem Chemicals, P.O. Box 108, Newbury Port, MA 01950 or Aldrich Chemical Co., 940 St. Paul Ave., Milwaukee, WI 53233. The material should be chlorin free, which can be effected either by dry column chromatography using alumina and chloroform or by oxidation of the chlorin to porphyrin using 2,3-dichloro-5,6-dicyano-... 

Fig. 7 (a) Selection-amplification of porphyrin tetrameric boxes using olefin metathesis, (b) Structure of dynamers formed via reversible Diels-Alder reaction, (c) Generation of a DCL of (R) and (S) nitroaldols from five differently substituted benzaldehydes... 

The bis-porphyrin supramolecular box 26 has also been assembled using a molecular recognition process involving hydrogen bonding between pendant-arm... 

Figure 2. Cofacial macrocycles associated via electrostatic interactions to give (a) dimers, (b) trim-ers and (c) higher aggregates. Typical cationic groups are pyridinium or trimethylanilinium typical anionic groups are sulfonate or carboxylate. Boxes represent porphyrin, phthalocyanine or por-phyrazine M = 2H, Zn, Cu, MnCl, etc.

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