Acids and Bases in Nature

Acids and bases are found throughout nature. In fact, acids and bases are used as a defense mechanism by insects and can produce beautiful limestone cave formations. If not monitored carefully, however, acids and bases in the environment can cause a lot of harm. 

Other ant species also use formic acid as a weapon. In fact, this acid is fairly common in ants. It got its name from the Latin word formica, which means ant. Some ants, such as the red ant, inject formic acid into their victims just as bees do. Ants, bees, and wasps actually all belong to the same biological order, Hymenoptera. Animals in this order have an ovipositor (a special organ for depositing eggs in hard to reach places). In some ants, bees, and wasps, this ovipositor has evolved into a stinger that is used to inject venom instead of eggs. 

Other ants, like the carpenter ant, are incapable of stinging, but that does not stop them from biting and then squirting formic acid into the wound. In this case, because the venom is not injected, a baking soda paste can quickly neutralize the venom and ease the pain. Fire ants, however, have toxic alkaloid venom. Regardless of whether the ant that bites or stings you has acidic or alkaline venom, however, one thing remains the same—it hurts  

Other living things besides animals also use acid to sting. The stinging nettle bush has sharp, hollow hairs that contain various chemicals, including formic acid, that irritate the skin of any animal that is unfortunate enough to rub up against it. 

The reaction between acids and bases is also responsible for some of the most spectacular, breathtaking cavern formations on Earth. As rainwater falls through the air, it encounters carbon dioxide (C02) gas. As it moves through the ground, the rainwater comes into contact with even more carbon dioxide from decaying plants and animals. Eventually, some portion of the rainwater reacts with the carbon dioxide it comes into contact with to form a weak carbonic acid  

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Table 5.10 Weak Acids and Bases in Natural Waters. ...

Table 3.1 Concentrations of weak acids and bases in natural waters...

Values of p/f =-log at 25°C for some important dissolved acids and bases in natural waters are given in Table 5.1. In the table Fe " and AP" have been written as aquocomplexes, to show the role of water in their acid-base behavior. The convention is generally not to write the waters of hydration. Notice that the species HSO4, H2PO4, Fe0H(H20), HCO3, HPO, and H SiOi can act either as acids or as bases. Thus they are called ampholytes or amphiprotic. 

The nature of the association between cement-forming cation and anion is important. As we shall see from theoretical considerations of the nature of acids and bases in section 2.3, these bonds are not completely ionic in character. Also while cement-forming cations are predominantly a-... 

The subject of acids and bases is very extensive. The discussion in this book is restricted to the definitions of acids and bases in aqueous solutions and their applications to the nature of ions in aqueous solutions and their stabilities. The two main definitions are those accredited to... 

In the same year Jacob Berzelius introduced the concept of catalysis, which he developed as a result of studies of the effects of acids and bases in promoting the hydrolysis of starch and of the effects of metals on the decomposition of hydrogen peroxide. Berzelius proposed the term catalyst from the Greek "katalysis," meaning "dissolution." Although he had been concerned primarily with inorganic catalysts, Berzelius recognized that a natural catalyst,... 

Acids and bases are two of the most common types of substances in the laboratory and the everyday world. We need to know how to recognize them, what their characteristic reactions are, and why they are such important chemicals. We shall see that keeping the concentrations of acids and bases in plant and animal cells within certain limits is necessary for the survival of individual organisms, and controlling the acidity of rain, of natural waters such as lakes and rivers, and of municipal water supplies is necessary to sustain human societies. 

Researchers have devised numerous extraction and fractionation schemes to deal with the heterogeneous nature of humic substances. Traditionally, the operational definition of humic substances as used by the International Humic Substances Society (Hayes et al., 1989) is based on the solubility in a series of acids and bases. In this scheme, humic substances are classified into three chemical groupings (1) fulvic acid, soluble in both alkali and acid solutions, has the lowest molecular weight and is generally considered the most susceptible to microbial degradation (2) humic acid, soluble in alkali but not in acid, is intermediate in molecular weight and decomposability and (3) humin, insoluble in both alkali and acid solutions, is the most... 

It is important to notice that water appears in these equations as both a proton acceptor and a proton donor. This is an example of the amphoteric (sometimes termed the amphiprotic) nature of water. Although the ionisation of acids and bases in water is best described using the equations above, it is convenient to disregard the water when deriving useful expressions and relationships. 

The classical theory of catalysis supposed that the hydrogen and hydroxyl ions were the only effective catalysts in solutions of acids and bases. In a few instances early attempts were made to remedy some of the discrepancies encountered by attributing some catalytic power to undissociated acid molecules, but these attempts were mostly based on incorrect values for degrees of dissociation, and they did not take into account the possibility of primary or secondary salt effects. However, later work has shown definitely that species other than hydrogen and hydroxyl ions often can exert a catalytic effect, and the development of these ideas was closely linked with a closer understanding of the nature of the hydrogen ion in solution, and with the clarification of acid-base definitions (cf. Bell, 11). 

This chapter collates data from various sources so that the roles the metal ions play in the enzymic manipulation of phosphate derivatives might be assessed. The use of model systems has allowed an estimation of the degree of activation (rate enhancement) expected for particular modes of metal ion-phosphate derivative interaction. In the enzymic systems, some of the roles proposed from the model systems seem to be especially relevant and it is no coincidence that the multiple metal ions required for high activity in the models are reflected in the clusters of metal ions in the reaction centers of some enzymes apparent when high-resolution structural analyses have been carried out. Clearly, charge neutralization, polarization, intramolecular nucleophiles, and effects on the leaving groups are all pertinent aspects for the metal ion s role in the natural systems. They are certainly important in the model systems. Moreover, much, but not all, of the rate enhancement in the metalloenzymes can be accounted for by these effects. Also, the role of intramolecular acids and bases in the enzyme systems is probably important. Certainly, the structures imply intimate... 

It is possible that the acidic or basic nature of components Cl and C2 were not manifested by lowering the pH from 6 to 4. For example, this would occur for an acidic component with a pK. of 2 or lower or for a basic component with a pA, of 8 or higher. Figure 5-10a shows theoretical curves of retention factor vs pH for these acidic and basic compounds. This could also occur for acidic compounds with a very high pA"., and bases with a very low pA". Figure 5-1 Ob shows these theoretical curves. The retention factors for these theoretical acids and bases in Fig,. 5-10a and b are very similar in the pH range 4-6. It can be seen in Fig. 5-9 that, when the pH was lowered from 6 to 4. this did not provide any specific information on the nature of the compounds. 

Since interaction with the solvent causes such complications, especially for alkyl substitution near the acid-base site, it is natural to ask whether any information can be obtained about the relative strengths of acids and bases in the gas phase. Measurements of thermal equilibria are not possible because of the very low equilibrium concentrations of ionic species, but many ions of interest can be generated by electron bombard-... 

The above description of acids and bases, in which H (aq) and OH (aq) ions are viewed as responsible for acidic and basic properties, respectively, and different acidic (or electrolytic) strengths are attributed to varying degrees of ionic dissociation, was developed by the Swedish chemist S. Arrhenius between 1880 and 1890. While very useful, this theory has some problems. The first problem has to do with the nature of the positive-charge carrier in aqueous solutions the second problem is that some substances can act as bases, even though they do not release OH (aq) ions. We will now consider both of these problems. 

Lewis proposed his stiU broader and more useful definition of acids and bases in the late 1920s and early 1930s. Classifying acids as electron-pair acceptors and bases as electron-pair donors, he thereby liberated acid—base theory entirely from its former dependence on the presence of hydrogen. The advantage of the Lewis definition is that a larger number of reactions can be classified as acid-base than under either the Arrhenius or Bronsted-Lowry definitions. The classic example used to demonstrate the more general nature of the Lewis definition is the gas-phase reaction between boron trifluoride and ammonia, as represented in Equation (4.1) ... 

Nature s aldolases use combinations of acids and bases in their active sites to accomplish direct asymmetric aldolization of unmodified carbonyl compounds. Aldolases are distinguished by their enolization mode - Class I aldolases use the Lewis base catalysis of a primary amino group and Class II aldolases use the Lewis acid catalysis of a Zinc(II) cofactor. To accomplish enolization under essentially neutral, aqueous conditions, these enzymes decrease the pKa of the carbonyl donor (typically a ketone) by converting it into a cationic species, either an iminium ion (5) or an oxonium ion (8). A relatively weak Bronsted base co-catalyst then generates the nucleophilic species, an enamine- (6) or a zinc enolate (9), via deprotonation (Scheme 4.2). 

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