Biological model compounds

There is quite a large body of literature on films of biological substances and related model compounds, much of it made possible by the sophisticated microscopic techniques discussed in Section IV-3E. There is considerable interest in biomembranes and how they can be modeled by lipid monolayers [35]. In this section we briefly discuss lipid monolayers, lipolytic enzyme reactions, and model systems for studies of biological recognition. The related subjects of membranes and vesicles are covered in the following section. 

The problem of molecular recognition has attracted biologically oriented chemists since Emil Fischer s lock-and-key theory l0). Within the last two decades, many model compounds have been developed micelle-forming detergents11, modified cyclodextrins 12), many kinds of crown-type compounds13) including podands, coronands, cryptands, and spherands. Very extensive studies using these compounds have, however, not been made from a point of view of whether or not shape similarity affects the discrimination. 

For quantitative work, it is necessary to estimate the concentration of 5-amino-l-(P-D-ribofuranosyl)imidazole in aqueous solution. It seems that the only available method is the Bratton-Marshall assay, which was originally developed for the estimation of arylamines in biological fluids. The principle of the method is the spectrometric estimation of a salmon-pink colored dyestuff obtained by diazotation in situ, followed by coupling with /V-( 1 -naphthyl)ethyl-enediamine.65 The only remaining problem then is to know the molar extinction of this dye because pure samples of AIRs are not available. A value of 16800 at 520 nM was obtained for the dyes prepared from a model compound, 5-amino-l-cyclohexylimidazole-4-carboxylic acid (54), which is crystalline. A comparable molar extinction can be expected for the dye prepared from imidazole 55, if the carboxyl group does not exert too much influence on the chromophore. Actually, its influence is perceptible even with the naked eye, the dyestuff prepared from 53 having a somewhat different, wine-red color, with max>520 nM. The molar extinction for 55 is 17400 at 500 nM. When the decarboxylation of 54 was conducted under mild acidic conditions (pH 4.8, 50°C, 1 hour), estimation of 5-aminoimidazole 55 by the Bratton-Marshall method led to the conclusion that the reaction was almost quantitative.66 Similar conditions for the final decarboxylation were adopted in the preparation of samples of AIRs labeled with stable isotopes.58... 

Suggest syntheses for TMs (9) and (10) needed as intermediates TM (9) in the synthesis of brominated hydroxy benzoic acids and TM (10) in the synthesis of model compounds for studying biological mechanisms of ester hydrolysis,... 

Exanrple Ester ( 2) was needed as a model compound to study mechanisms of biological ester hydrolysis. It is clearly made from acid (33) which could be made from aldehyde (34) by a Wittig reaction. We discussed the synthesis of (3b) on page 21. 

The spectra we have so far discussed were recorded using CDC13> the best allround solvent for organic molecules. However, many molecules, especially biomolecules, are only soluble in water biological systems often remain stable only in aqueous solution. Thus NMR measurements in water are extremely important our model compound is also water-soluble, so that we can use it to demonstrate some important experiments. 

If the solute concentration is very low, this signal can become very strong investigations on biological systems are often carried out in 1 1 mixtures of H20 and D20, and spectrum (c) shows that if we do this for our model compound we see no signal from the dissolved molecules ... 

Neese, F. 2003. Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds EPR and Mossbauer properties. Current Opinion in Chemical Biology 7 125-135. 

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