Abiotic systems

FIGURE 3.3.2 Hypothesized mechanism of formation of lycopene oxidation products in an abiotic system. The compound numbers correspond to those cited in Britton, G. et ah, Carotenoids HandbookP... 

Carotenoid oxidation products, as carotenoids, may exert protective or detrimental effects on human health. Efforts must be made to try to identify them in vivo where they may appear in lower quantities than carotenoids. Studies of abiotic systems can provide great support for their identification and the comprehension of their stability and reactivity. 

Liquid water is an essential component of most terrestrial chemical processes, including those of living organisms. The cooperativity of H-bonding in water clusters is therefore of primary importance for understanding the structure and dynamics of pure water, as well as a vast spectrum of aqueous solvation phenomena in biotic and abiotic systems. In the present section we examine cooperativity effects for a... 

There have been many attempts to mimic some features of photosynthesis with abiotic systems for purposes of artificial solar energy conversion. Ideally a fuel, e.g., H2, is formed through a photosynthetic process. Photolysis of water is a highly endergonic process ... 

Ehrlich et al. (submitted) measured Cu isotopic fractionation between aqueous Cu(II) and covellite between 2 and 40°C (Fig. 10). The temperature-dependent isotope fraction is fairly large 3%o) and hints at a redox control of Cu isotopic variability in abiotic systems. Marechal and Sheppard (2002) conducted experiments at 30 and 50°C between malachite and a chloride solution for Cu isotope fractionation and between smithsonite and a nitrate solution for Zn. They found that, in this temperature range, Cu in malachite is 0.2 to 0.4%o lighter than in the chloride solution. Replacing the chloride by nitrate ion reduces fractionation which indicates that the coordination of the Cu ion dictates isotopic fractionation. In contrast, Zn isotope fractionation between smithsonite and fluid is extremely small (<0.1%o). 

The results obtained for these abiotic systems support the conclusion that 1/ and the branching equations are effective In modelling sterlc effects on Intermoleou lar complex formation and the Interaction of moleoul es with surfaces. We conclude that the use of these methods to i present sterlc effects occurring In steps 1 and 2 of the bloactlvlty model Is Justifiable. 

This hydrogen-bond-driven large-scale structural organization has parallels in abiotic systems as well. For example, 1 1 mixtures of ra -l,2-diaminocyclohexane and C2 symmetric 1,2-diols self-assemble into well-defined supramolecular structures which have been characterized by X-ray diffraction analysis. The structures, some of which are stable to sublimation, are helical, the handedness of the helices being determined by the handedness of the 1,2-diamine [222]. 

The soil is a dynamic biotic and abiotic system. Pesticides deposited in or on the soil have varying capacities to be adsorbed to clay minerals and organic matter. Such adsorption reduces both the movement and the biological activity of the pesticide. In addition to soil adsorption, several other factors are known to influence the behavior and fate of pesticides after the chemicals are in contact with soil. 

It appears pointless to discuss the validity of these findings today, but it is noteworthy that the procedure was in essence similar to what today is called bioimprinting [20,21], a technique whereby a protein or other biopolymer is used as the matrix for molecular imprinting instead of an abiotic polymer. Moreover, the apparent success in preparing antibodies in vitro led Pauling to initiate an investigation of the application of the selective theory in an abiotic system, as is evident from the following recollection ... 

A brief discussion of some aspects of alcohol dehydrogenase will be used to illustrate the potential for catalysis. This system is chosen for illustration because it has been studied so extensively. Lessons drawn can be applied in a broader context. The 1,4-dihydropyridine (2a) is the reductant and this affords a nico-tinium ion (1) on transfer of hydride, as illustrated in equation (1). This process is mimicked in many abiotic systems by derivatives of (2 R = alkyl or benzyl), by Hantzsch esters (7), which are synthetically readily accessible, and 1,4-dihydro derivatives (8) of pyridine-3,5-dicarboxylic acid. A typical abiotic reaction is the reduction of the activated carbonyl group of an alkyl phenylglyoxylate (9), activated by a stoichiometric amount of the powerful electrophile Mg(CI04)2, by, for example, (2b equation 8). After acrimonious debate the consensus seems to be that such reactions involve a one-step mechanism (i.e. equation 5), unless the reaction partner strongly demands a radical intermediate, as in the reduction of iron(II) to iron(III). 

Hard electrophiles like Mg(C104)2 are used to activate abiotic systems. In the enzyme liver alcohol dehydrogenase (LAD) a considerably different catalytic apparatus is present a zinc ion coordinated to two cysteines and a histidine serves as a coordinating site for the carbonyl compound/alcoholate, as illustrated in equation (10). This zinc ion has amphoteric properties consistent with the capacity to activate the reaction in both directions without being consumed, in other words to act as a catalyst. Synthetic models of this catalytically active zinc have been shown to possess some catalytic activity in analogy to the enzyme (see Section L3.3.5.1iii). 

This mechanism of oxidative attack has two facets, namely the regeneration of ferric ions by the organism and the chemical interaction of ferric ions with the sulfide mineral. Singer and Stumm (1970) have shown that the rate of oxidation of ferrous iron by oxygen in abiotic systems is a function of pH. At pH values greater than 4.5, the kinetic relationship is described by eqn. (13) ... 

Biotic and Abiotic Systems, in Effects of Petroleum on Arctic and Subarctic Marine Environments and Organisms, Nature and Fate of Petroleum Malins, D. C., Ed. Academic New York, 1977 Vol. I, pp. 1-89. 

Finally, whereas most laboratory experiments have been conducted in largely abiotic environments, the action of bacteria may control reaction rates in nature (e.g., Chapelle, 1993). In the production of acid drainage (see Chapter 23), for example, bacteria such as Thiobacillus ferrooxidans control the rate at which pyrite (FeS2) oxidizes (Taylor et al., 1984 Okereke and Stevens 1991). Laboratory observations of how quickly pyrite oxidizes in abiotic systems (e.g., Williamson and Rimstidt, 1994, and references therein), therefore, might poorly reflect the oxidation rate in the field. 

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