2.1 Addition and Elimination Reactions

An addition reaction is an organic reaction where two or more molecules combine to form a product (the adduct) (March, 1992; Morrison et al., 1992). Addition reactions are limited to chemical compounds that have multiple bonds, such as molecules with carbon-carbon double bonds (alkenes, > CC <), or with triple bonds (alkynes, CC). Molecules containing carbon-heteroatom double bonds such as the carbonyl group (> CO) groups, or the imine group (CN) groups, can also participate in addition since they also have double bond character. An addition reaction is the reverse of an elimination reaction, such as the hydration of an alkene to an alcohol which is reversed by dehydration:

$\begin{array}{l}{\mathrm{C}\mathrm{H}}_2={\mathrm{C}\mathrm{H}}_2+{\mathrm{H}}_2\mathrm{O}\to {\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}\\ {\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}\to {\mathrm{C}\mathrm{H}}_2={\mathrm{C}\mathrm{H}}_2+{\mathrm{H}}_2\mathrm{O}\end{array}$

The main driver behind addition reactions to alkene is that alkenes contain the unsaturated > CC < functional group which characteristically undergoes addition reactions which is the conversion of the weaker π bond into two new, stronger σ bonds. In addition to addition reactions being typical of the unsaturated hydrocarbon derivatives (alkenes and alkynes) and aldehydes and ketones, which have a carbon-to-oxygen double bond, an addition reaction may be visualized as a process by which the double or triple bonds are fully or partially broken in order to accommodate additional atoms or groups of atoms in the molecule. Addition reactions to alkenes and alkynes are sometimes called saturation reactions because the reaction causes the carbon atoms to become saturated with the maximum number of attached groups.

In addition, reactions to aldehydes and ketones, the sequence of events is reversed insofar as the initial step is addition of the negatively charged component of the reagent to the carbon atom, followed by addition of the positively charged component to the oxygen atom.

2.2 Substitution Reactions

A substitution reaction (sometime referred to as a single displacement reaction or single replacement reaction) is a reaction in which a functional group in an organic chemical is replaced by another functional group (March, 1992; Morrison et al., 1992). Substitution reactions are of prime importance in environmental organic chemistry because of the simplicity of the reaction which is accompanied by a substantial change in the chemical and physical properties of the product vis-à-vis compared to the chemical and physical properties of the starting chemical. Substitution reactions in organic chemistry are classified either as (1) nucleophilic substitution or (2) electrophilic substitution depending upon the reagent involved.

A nucleophile is a chemical species (an ion or a molecule) which is strongly attracted to a region of positive charge in something else. Nucleophiles are either fully negative ions or have a strongly (δ⁻) charge somewhere on a molecule. Common nucleophiles are hydroxide ions (OH⁻), cyanide ions (CN⁻), water (H₂O), and ammonia (NH₃). An example of a simple nucleophilic substitution reaction is the halogenation of an alkane such as when methane (CH₄) is reacted with chlorine (Cl₂) to form methyl chloride and hydrogen chloride:

${\mathrm{C}\mathrm{H}}_4+{\mathrm{C}\mathrm{l}}_2\to {\mathrm{C}\mathrm{H}}_3\mathrm{C}\mathrm{l}+\mathrm{H}\mathrm{C}\mathrm{l}$

Thus, a nucleophilic substitution reaction (which is common in organic chemistry) is a reaction in which an electron-rich nucleophile selectively bonds with or attacks the positive or partially positive charge of an atom or a group of atoms to replace the leaving electrophile:

$\left(\mathrm{Nucleophile}\right)+\mathrm{R}-\left(\mathrm{leaving}\mathrm{group}\right)\to \mathrm{R}-\left(\mathrm{Nucleophile}\right)+\left(\mathrm{leaving}\mathrm{group}\right)$

On the other hand, electrophilic substitution involves electrophiles and an example is electrophilic aromatic substitution. In this type of substitution, the benzene ring (which has a π-electron cloud above and below the plane of the ring of carbon atoms) is attacked by an electrophile (shown as E⁺). The π-electron cloud is disturbed and a carbocation resonating structure results after which a proton (H⁺) is ejected from the intermediate and a new aromatic compound is formed:

${\mathrm{C}}_6{\mathrm{H}}_6+{\mathrm{E}}^{+}\to {\mathrm{C}}_6{\mathrm{H}}_5\mathrm{E}+{\mathrm{H}}^{+}$

A relevant reaction in the environment (because of the ever-presence of water in many ecosystems) is the hydrolysis reaction in which an organic chemical compound is decomposed by reaction with water—also the hydrolysis reaction should not be confused with the hydrogenolysis reaction which is a reaction of hydrogen as practiced widely in the petroleum industry to produce liquid fuels (Speight, 2014, 2016). Hydrolysis is an example of a larger class of reactions referred to as nucleophilic displacement reactions in which a nucleophile (an electron-rich species containing an unshared pair of electrons) attacks an electrophilic atom (an electron-deficient reaction center). Hydrolytic processes encompass several types of reaction mechanisms that can be defined by the type of reaction center (i.e., the atom bearing the leaving group, X) where hydrolysis occurs. The reaction mechanisms encountered most often are direct and indirect nucleophilic substitution and nucleophilic addition-elimination.

This type of reaction can be used to predict the persistency of a chemical in the environment, the chemical's physical-chemical properties and its reactivity in the environment need to be known or at least estimated (Rahm et al., 2005). The chemicals that can undergo elimination reactions are rapidly transformed, as are perhalogenated chemicals that can undergo substitution reactions. These chemicals are not likely to persist in the environment, while those that do not show any observable reactivity under similar hydrolytic conditions are likely to be POPs (Chapter 1), the fate of which are intimately linked to the cycling or organic chemicals in the environment (deBruyn and Gobas, 2004).

Typically, the hydrolysis reaction is a chemical transformation in which an organic molecule, RX, reacts with water, resulting in the formation of a new covalent bond with the hydroxy function (OH) and cleavage of the covalent bond with halogen function (e.g., Cl) (the leaving group) in the original molecule. The net reaction is the displacement of the halogen group (X) by the hydroxyl group (OH) (Table 7.4). In fact, for many types of organic contaminants, hydrolysis may be the dominant pathway for their transformation in aquatic ecosystems. Hydrolytic processes are not limited to the bodies of water such as rivers, streams, lakes, and oceans usually associated with the term aquatic ecosystems. Hydrolysis of organic chemicals can also occur in groundwater systems and the aqueous environment in solids and sediments.

In the aqueous hydrolysis reaction, the reacting water molecules are split into hydrogen (H⁺) and hydroxide (OH⁻) ions, which react with and break up (or “lyse”) the other reacting compound. The term hydrolysis is also applied to the electrolysis of water (i.e., breaking up of water molecules by an electric current) to produce hydrogen and oxygen. The hydrolysis reaction is distinct from a hydration reaction, in which water molecules attach to molecules of the other reacting compound without breaking up the latter compound, such as:

${\mathrm{C}\mathrm{H}}_2={\mathrm{C}\mathrm{H}}_2+{\mathrm{H}}_2\mathrm{O}\to {\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}$

The hydrolysis reaction mainly occurs between an ion and water molecules and often changes the pH (acidity or alkalinity) of a solution. In chemistry, there are three main types of hydrolysis: (1) salt hydrolysis, (2) acid hydrolysis, and (3) base hydrolysis.

In water, salts will dissociate to form ions (either completely or incompletely depending on the respective solubility constant, K_sp. For example:

${\mathrm{N}\mathrm{H}}_4\mathrm{B}\mathrm{r}\left(\mathrm{s}\right)\to {{\mathrm{N}\mathrm{H}}_4}^{+}\left(\mathrm{a}\mathrm{q}\right)+{\mathrm{B}\mathrm{r}}^{-}\left(\mathrm{a}\mathrm{q}\right)$

In this equation, the salt (ammonium bromide, NH4Br) is dissolved in water upon which the salt dissociates into ammonium ions (NH₄⁺) and bromide ions (Br⁻).

In the hydrolysis reaction, water can act as an acid or a base: (1) if that water acts as an acid, the water molecule would donate a proton (H⁺), also written as a hydronium ion (H₃O⁺) or (2) if the water acts as a base, the water molecule would accept a proton (H⁺). An acid hydrolysis reaction is very much the same as an acid-dissociation reaction.

${\mathrm{C}\mathrm{H}}_3\mathrm{COOH}+{\mathrm{H}}_2\mathrm{O}\rightleftharpoons {\mathrm{H}}_3{\mathrm{O}}^{+}+{\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{O}\mathrm{O}}^{-}$

In the above reaction, the proton H⁺ from CH₃COOH (acetic acid) is donated to water, producing the hydronium ion (H₃O⁺) and an acetate ion (CH₃COO⁻). The bonds between proton and the acetate ion are dissociated by the addition of water molecules. A reaction with acetic acid (CH₃COOH) a weak acid, is similar to an acid-dissociation reaction, and water forms a conjugate base and a hydronium ion. When a weak acid is hydrolyzed, a hydronium ion is produced.

A base hydrolysis reaction will resemble the reaction for base dissociation. A common weak base that dissociates in water is ammonia:

${\mathrm{N}\mathrm{H}}_3+{\mathrm{H}}_2\mathrm{O}\rightleftharpoons {{\mathrm{N}\mathrm{H}}_4}^{+}+{\mathrm{O}\mathrm{H}}^{-}$

In the hydrolysis of ammonia, the ammonia molecule accepts a proton from the water (i.e., water acts as an acid), producing a hydroxide anion (OH⁻). Similar to a basic dissociation reaction, ammonia forms ammonium and a hydroxide from the addition of a water molecule.

Generally, in organic chemistry, hydrolysis can be considered the reverse (or opposite) of condensation, a reaction in which two molecular fragments are joined for each water molecule produced. Since hydrolysis may be a reversible reaction, condensation, and hydrolysis can take place at the same time, with the position of equilibrium determining the amount of each product, such as the hydrolysis of an ester to an acid and an alcohol:

${\mathrm{R}}^1{\mathrm{C}\mathrm{O}}_2{\mathrm{R}}^2+{\mathrm{H}}_2\mathrm{O}\rightleftharpoons {\mathrm{R}}^1{\mathrm{C}\mathrm{O}}_2\mathrm{H}+{\mathrm{R}}^2\mathrm{O}\mathrm{H}$

Thus, hydrolysis reactions involving organic compounds may be illustrated by the reaction of water with an ester of a carboxylic acid; all such esters have the general formula R¹COOR², in which R¹ and R² are combining groups (e.g., if R¹ and R² are both methyl groups, CH₃, the ester is methyl acetate). The hydrolysis involves several steps, of which the slowest is the formation of a covalent bond between the oxygen atom of the water molecule and the carbon atom of the ester. In succeeding steps, which are very rapid, the carbon-oxygen bond of the ester breaks and hydrogen ions become detached from the original water molecule and attached to the nascent alcohol molecule. The whole reaction is represented by the equation:

$\underset{\mathrm{Ester}}{{\mathrm{R}}^1{\mathrm{COOR}}^2}+{\mathrm{H}}_2\mathrm{O}\to \underset{\mathrm{acid}}{{\mathrm{R}}^1\mathrm{COOH}}+\underset{\mathrm{alcohol}}{{\mathrm{R}}^2\mathrm{O}\mathrm{H}}$

Thus, the products of hydrolysis depend very much upon that substrate that is to be hydrolyzed (Table 7.4).

More pertinent to the present text, the hydrolysis of a pesticide is basically a reaction with a water molecule involving specific catalysis by proton or hydroxide, and sometimes inorganic ions such as phosphate ion, present in the aquatic environment that play a role in general acid-base catalysis (Katagi, 2002). However, the hydrolytic profiles depend on the chemical structure and functional group(s) in the pesticide molecule, which are not always consistent within a chemical class of pesticides (Stoytcheva, 2011). For example, pesticides that are composed of organophosphorus derivatives are primarily susceptible to alkaline hydrolysis with less acidic catalysis, but some of phosphorodithioate derivatives are found to be acid labile. Various instrumental techniques have been applied to chemical identification of degraded products, leading to clarification of the reaction mechanisms involved. Moreover, pesticides are usually applied as a suitable formulation, and thus the effects of surfactants and other formulation reagents on hydrolysis should be examined in more detail. To assess the fate and impact of pesticides and their degraded products in real aquatic environments, these concerns should be further examined using the various analytical techniques together with simulation models.

When substituted benzene compounds undergo electrophilic substitution reactions it is necessary to compare the relative reactivity of the compound compared with benzene itself. Experiments have shown that substituents on a benzene ring can influence reactivity in a profound manner. For example, a hydroxy substituent (−OH) or methoxy (− OCH³) substituent increases the rate of electrophilic substitution about 10,000-fold, as illustrated by the case of anisole in the virtual demonstration (above). In contrast, a nitro substituent decreases the reactivity of the ring substantially. This activation or deactivation of the benzene ring toward electrophilic substitution may be correlated with the electron donating or electron withdrawing influence of the substituents, as measured by molecular dipole moments. Electron donating substituents activate the benzene ring toward electrophilic attack, and electron withdrawing substituents deactivate the benzene ring and render it less reactive to electrophilic attack.

The influence a substituent exerts on the reactivity of a benzene ring may be explained by the interaction of two effects: (1) an inductive effect and (2) a conjugative effect. The inductive effect arises because most elements other than metals and carbon have a significantly greater electronegativity than hydrogen. Consequently, substituents in which nitrogen, oxygen, and halogen atoms form sigma-bonds to the aromatic ring exert an inductive electron withdrawal, which deactivates the ring (left-hand diagram below). The second effect (the conjugative effect) is the result of a conjugation of a substituent function with the aromatic ring which facilitates electron pair donation or withdrawal, to or from the benzene ring, in a manner different from the inductive shift. If the atom bonded to the ring has one or more nonbonding valence shell electron pairs, as do nitrogen, oxygen, and the halogens, electrons may flow into the aromatic ring by π conjugation (resonance), as in the middle diagram. Finally, polar double and triple bonds conjugated with the benzene ring may withdraw electrons, as in the right-hand diagram. The charge distribution in the benzene ring is greatest at sites ortho and para to the substituent. In the case of the nitrogen and oxygen activating groups displayed in the top row of the previous diagram, electron donation by resonance dominates the inductive effect and these compounds show exceptional reactivity in electrophilic substitution reactions. Although halogen atoms have nonbonding valence electron pairs that participate in p-π conjugation, their strong inductive effect predominates, and compounds such as chlorobenzene are less reactive than benzene.

2.3 Redox Reactions

Redox reactions (reduction-oxidation reactions) are reactions in which one species is reduced and another is oxidized. Therefore, the oxidation state of the species involved must change. The word reduction originally referred to the loss in weight upon heating a metallic ore such as a metal oxide to extract the metal—the ore was reduced to the metal. However, the meaning of reduction has become generalized to include all processes involving gain of electrons. The term hydrogenation could be used instead of reduction, since hydrogen is the reducing agent in a large number of reactions, especially in organic chemistry and biochemistry. But, unlike oxidation, hydrogenation has maintained its specific connection to reactions that add hydrogen to another substance such as the hydrogenation processes used in a petroleum refinery (Speight, 2014, 2016). On the other hand, the word oxidation originally implied reaction with oxygen to form an oxide but the word has been expanded to encompass oxygen-like substances that accomplished parallel chemical reactions and ultimately, the meaning was generalized to include all processes involving loss of electrons. For example, the production of iron from the iron oxide ore:

${\mathrm{F}\mathrm{e}}_2{\mathrm{O}}_3+3\mathrm{C}\mathrm{O}\to 2\mathrm{F}\mathrm{e}+3{\mathrm{C}\mathrm{O}}_2$

Similarly, in the context of organic chemistry, there is the oxidation of ethyl alcohol (CH₃CH₂OH) where it is oxidized to acetaldehyde (CH₃CHO) and the reverse reaction in which acetaldehyde is reduced to ethyl alcohol:

${\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}\to {\mathrm{C}\mathrm{H}}_3\mathrm{C}\mathrm{H}\mathrm{O}+{\mathrm{H}}_2\to {\mathrm{C}\mathrm{H}}_3{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}$

This equation can be subdivided as follows into oxidation by loss of hydrogen and reduction by gain of hydrogen. Thus:

The two species that exchange electrons in a redox reaction are given special names. The ion or molecule that accepts electrons is the oxidizing agent which, by accepting electrons causes the oxidation of another species. Conversely, the species that donates electrons is the reducing agent which; when the reaction occurs, reduces the other species. Thus, the species that is oxidized is the reducing agent and the species that is reduced is the oxidizing agent. To complicate matters even further, the oxidizing and reducing agents can be the same element or compound, as is the case when disproportionation of the reactive species occurs. For example:

$2A\to \left(A+n\right)+\left(A-n\right)$

In this equation, n is the number of electrons transferred. Disproportionation reactions do not need to commence with a neutral molecule and can involve more than two species with differing oxidation states.

Redox reactions are important for a number of applications, including energy storage devices (batteries), photographic processing, and energy production and utilization in living systems including humans. For example, a reduction reaction is a reaction in which an atom gains an electron and therefore decreases (or reduces) its oxidation number. The result is that the positive character of the species is reduced. On the other hand, an oxidation reaction is a reaction in which an atom loses an electron and therefore increases its oxidation number. The result is that the positive character of the species is increased.

Although oxidation reactions are commonly associated with the formation of oxides from oxygen molecules, these are only specific examples of a more general concept of reactions involving electron transfer. Redox reactions are a matched set, that is, there cannot be an oxidation reaction without a reduction reaction happening simultaneously. The oxidation reaction and the reduction reaction always occur together to form a whole reaction. Although oxidation and reduction properly refer to a change in the oxidation state, the actual transfer of electrons may never occur. The oxidation state of an atom is the fictitious charge that an atom would have if all bonds between atoms of different elements were 100% ionic. Thus, oxidation is best defined as an increase in oxidation state, and reduction as a decrease in oxidation state. In practice, the transfer of electrons will always cause a change in oxidation state, but there are many reactions that are classed as redox reactions even though no electron transfer occurs (such as those involving covalent bonds). There are simple redox processes, such as the oxidation of carbon to carbon dioxide (CO₂) or the reduction of carbon by hydrogen to methane (CH₄).

${\mathrm{C}\mathrm{H}}_4+2{\mathrm{O}}_2\to {\mathrm{C}\mathrm{O}}_2+2{\mathrm{H}}_2\mathrm{O}$

The key to identifying oxidation-reduction reactions is recognizing when a chemical reaction leads to a change in the oxidation number of one or more atoms.

2.4 Rearrangement Reactions

Organic reactions typically yield products that are in accordance with the generally accepted mechanism of the reactions. However, in some instances, organic reactions do not give exclusively and solely the anticipated products but may lead to other product that arise from unexpected and mechanistically different reaction path. These unexpected products are often referred to as rearranged products and, while such a product may not be the expected product it may be the major product of the reaction. Thus, the reaction has involved a rearrangement of the expected product to an unexpected product—a rearrangement reaction has occurred. More than likely, this may have resulted from a plausible rearrangement occurring during the mechanistic course of the reaction to fulfill the principle of the minimum energy state of the whole system, that is, of the transition state which assumed another configuration to maintain a minimum energy balance to the system. In many cases, the rearrangement affords products of an isomerization, coupled with some stereochemical changes. An energetic requirement is also observed in order for a rearrangement to take place; that is, the rearrangement usually involves an evolution of energy (typically in the form of heat, i.e., the reaction is overall an exothermic reaction) to be able to yield a more stable compound (Moulay, 2002).

Thus, a rearrangement reaction falls into a class of organic reactions where the carbon skeleton of an organic molecule is rearranged to form a structural isomer of the original molecule that assumes the minimal energy content of the product—i.e., the most stable product is formed (March, 1992; Morrison et al., 1992; Moulay, 2002). As a result of the reaction, a substituent group typically moves from one atom to another atom in the same molecule to yield an isomer of the original reactant:

In the above equation, there has been movement of the substituents group (represented by R) from carbon atom number 1 to carbon atom number 2.

Thus, a rearrangement reaction is a reaction in which an atom or a group (or in some cases a bond) is caused to move or migrate to another part of the molecule. The atom, having been initially located at one site in a reactant molecule ultimately becomes located at a different site in the product molecule. A rearrangement reaction may involve several steps, but the defining feature is that the atom or a group or the bond shifts from one site of attachment to another. The simplest (perhaps, the most common) types of rearrangement reactions are intramolecular rearrangements insofar as the reactions occur in one reactant molecule and the product of the reaction is a structural isomer of the reactant. In summary, molecular rearrangement reactions occur in many organic reactions and the rearranged product usually results from the thermodynamic stability aspect of the compound or the reaction (Moulay, 2002).

2.5 Hydrolysis Reactions

Many organic compounds can be altered by a direct reaction of the chemical with water (hydrolysis) in which a chemical bond is cleaved and two new bonds are formed, each one having either the hydrogen component (H) or the hydroxyl component (OH) of the water molecule. Typically, the hydroxyl replaces another chemical group on the organic molecule and hydrolysis reactions are usually catalyzed by hydrogen ions or hydroxyl ions. This produces the strong dependence on the acidity or alkalinity (pH) of the solution often observed but, in some cases, hydrolysis can occur in a neutral (pH 7) environment. Adsorption on to a mineral sediment (such as a clay sediment that has strong adsorptive powers) generally reduces the rates of hydrolysis for acid- or base-catalyzed reactions. Neutral reactions appear to be unaffected by adsorption although there is always the possibility that the mineral sediment can cause catalyzed chemical transformation reactions.

The rate of a hydrolysis reaction is typically rate expressed in terms of the acid-catalyzed, neutral-catalyzed, and base-catalyzed hydrolysis rate constants. Furthermore, the hydrolysis of organic compounds is influenced by the composition of the solvent (Lyman et al., 1982) and the rate constants may be much higher in water than in organic solvents. In fact, the introduction of a complex mixture of chemicals into a water body can be expected to produce a significant shift in acidity or alkalinity of the medium and, therefore, it would not be surprising to anticipate that hydrolysis would be affected in complex mixtures.

2.6 Photolysis Reactions

Photolysis is a chemical process by which chemical bonds are broken as the result of transfer of light energy (direct photolysis) or radiant energy (indirect photolysis) to these bonds. The rate of photolysis depends upon numerous chemical and environmental factors including the light adsorption properties and reactivity of the chemical, and the intensity of solar radiation (Lyman et al., 1982). In the process, the photochemical mechanism of photolysis is divided into three stages: (1) the adsorption of light which excites electrons in the molecule, (2) the primary photochemical processes which transform or de-excite the excited molecule, and (3) the secondary (“dark”) thermal reactions which transform the intermediates produced in the previous step (step 2).

In addition, before photolysis can occur, the photochemically excited state must be deactivated, such as a radiative process (fluorescence) in which energy (usually in the form of light) is emitted during the transition to ground electronic state and some residual vibrational excitation is rapidly lost via collision processes. Quenching of a photochemical process occurs when the excitation energy in the target organic molecule is transferred to some other chemical species in solution. This process results in net deactivation of the organic substance of concern via energy transfer. Energy can be transferred to any chemical species with a lower triplet energy. A very important and effective quencher (acceptor) is molecular and other chemicals in a complex mixture could act as acceptors and thereby reduce the photolytic degradation rate of a given compound to below that expected.

Indirect photolysis or sensitized photolysis occurs when the light energy captured (absorbed) by one molecule is transferred to the organic molecule of concern. The donor species (the sensitizer) undergoes no net reaction in the process but has an essentially catalytic effect. Moreover, the probability of a sensitized molecule donating its energy to an acceptor molecule is proportional to the concentration of both chemical species. Thus, complex mixtures may, in some cases, produce enhancement of photolysis rates of individual constituents through sensitized reactions.

4.1 Adsorption

Adsorption is the physical accumulation of material (usually a gas or liquid) on the surface of a solid adsorbent and is a surface phenomenon (Calvet, 1989). Typically, adsorption processes remove solutes from liquids based on their mass transfer from liquids to porous solids. Ion exchange is the exchange of dissolved ions for ions on solid media. The process can be used to remove water hardness and toxic metals during wastewater treatment. Disinfection is the removal or inactivation of pathogenic organisms in wastewater prior to discharge to the receiving body of water.

The adsorption process creates a film of the adsorbate on the surface of the adsorbent and the process differs from the absorption process in which a fluid (the absorbate) is dissolved by a liquid or permeates into a solid (the absorbent), respectively. Thus, adsorption is a surface-based process while absorption involves the whole volume of the material. The term sorption encompasses both processes, while desorption is the reverse of sorption. In the environment, organic compounds will collect on the surfaces of particles, such as soil or suspended sediment. Most of these particles are covered with a layer of organic material; thus, the adsorption results from the attraction of two organic materials for one another.

In an industrial setting, adsorption processes are used to remove certain components from a mobile phase (i.e., a gas phase or a liquid phase) or to separate mixtures. The applications of adsorption can be production-related or abatement-related and may include the removal of water from natural gas or the removal of organic constituents from flue gas, such as is often witnessed in refinery processes and/or in natural gas processing operations and/or coal gas processing operations (Mokhatab et al., 2006; Speight, 2007, 2014, 2016). The most preferential adsorbents are characterized by a wide distribution of a large number of varying-sized pores and, accordingly, activated carbon, zeolites, silica gel, and aluminum oxide are the most commercially important adsorbent. This enable adsorbent to accommodate types and sizes of the various molecular species that occur in gas or liquid streams. Zeolites (molecular sieves) have a very narrow distribution of micropores and preferentially adsorb polar or polarizable materials (e.g., water or carbon dioxide). By contrast, activated carbon has a hydrophobic character and is especially suitable for the removal of organic substances.

In nature, it is different—a variety of potential natural adsorbents exits in the soil—adsorption occurs in many natural, physical, biological, and chemical systems (especially in the environment) where organic molecules can adsorb on to minerals (such as clay) or on to charred wood that remains after a forest fire. In fact, clay minerals are particularly good adsorbents and have a high adsorption capacity for organic chemicals that have been released into the environment.

Clay minerals are typically ultrafine-grained [normally considered to be less than 2 μm (< 2 μm, < 2 × 10^− 6 m) in size on standard particle size classifications]. In the present context, clay minerals, which can be classified into various chemical groups, such as the silicate clay mineral groups (Table 7.6) are an important part of many soils thus rendering the soil capable of having a high adsorption capacity for organic chemicals. Generally, no two clay minerals are the same and the adsorption capacity will vary accordingly.

Adsorption of an organic chemical on to a solid adsorbent is measured by a partition coefficient, which is the ratio of the concentration of the organic chemical on the solid to the concentration of the chemical in the fluid (usually water) surrounding the solid:

$K_{\mathrm{d}}=C_{\mathrm{solid}}/C_{\mathrm{water}}$

The concentration on the solid has units of mol/kg, and the concentration in the water is mol/L and, thus, the adsorption coefficient (K_d) has units of L/kg. Assuming a solid density of 1 kg/L, these units are often ignored. The adsorption coefficient will often depend on how much of the total mass of the particle is organic material. Thus, the adsorption coefficient can be corrected by the fraction of organic material (f_om) in the particles:

$K_{\mathrm{o}\mathrm{m}}=K_{\mathrm{d}}/f_{\mathrm{o}\mathrm{m}}$

Adsorbed molecules are those that are resistant to washing with the same solvent medium in the case of adsorption from solutions. The washing conditions can thus modify the measurement results, particularly when the interaction energy is low. The exact nature of the bonding depends on the details of the chemical species involved, but the adsorption process is generally classified as physisorption (which is characteristic of weak van der Waals forces) or chemisorption (which is characteristic of covalent bonding). It may also occur due to electrostatic attraction.

4.2 Absorption

Absorption is another phenomenon that can be a beneficial or adverse influence of the environment and involves the uptake of one substance into the inner structure of another; most typically a gas into a liquid solvent. Furthermore, absorption is a physical or chemical phenomenon or a process in which atoms, molecules, or ions enter some bulk phase—gas, liquid, or solid material. This is a different process from adsorption, since molecules undergoing absorption are taken up by the volume, not by the surface (as in the case for adsorption). A more general term is sorption, which covers absorption and adsorption—the former (absorption) is a condition in which something takes in another substance. In many processes important in technology, the chemical absorption is used in place of the physical process. It is possible to extract from one liquid phase to another a solute without a chemical reaction. The process of absorption means that a substance captures and transforms energy and distributes the material it captures throughout whole absorbent whereas an adsorbent only distributes it on the surface.

In industry, absorption is a unit operation not only for chemical production but also for environmental protection in the abatement of gaseous emissions (where it may be known as washing or scrubbing), such as course in gas processing operations (Mokhatab et al., 2006; Speight, 2007, 2014, 2016). The interaction of absorbed materials with the solvent can be physical or chemical in nature. In physical absorption, the gas molecules are physically changed (polarized) but remain chemically unchanged. The concentration of dissolved gases in the absorbing solvent increases in relation to the partial pressure of the gases.

In chemical absorption (sometimes referred to in the shortened word form as chemisorption), the absorbed material is generally converted to a product different to the starting material. Thus, chemical absorption or reactive absorption involves a chemical reaction between the absorbent (the absorbing substance) and the absorbate (the absorbed substance) and may be combined with the physical absorption phenomenon. This type of absorption depends upon the stoichiometry of the reaction and the concentration of the potential reactants.

Reactions and conversions between gaseous and liquid phases are much slower than those between one-phase mixtures, and so relatively large reaction volumes are required in gas absorption installations. Absorption equipment generally consists of a column with internals for heat and material exchange in which the feed gas is brought into counter-current contact with the regenerated absorbent (Mokhatab et al., 2006). The equipment internals (which may be absorption plates, randomly poured packing, or structured packing) direct the liquid and gas streams into close contact and also serve to maintain the contact area between the two phases.

Physical absorption or nonreactive absorption is made between two phases of matter: a liquid absorbs a gas, or a solid absorbs a liquid. When a liquid solvent absorbs a gas mixture or part of it, a mass of gas moves into the liquid. For example, water may absorb oxygen from the air. This mass transfer takes place at the interface between the liquid and the gas, at a rate depending on both the gas and the liquid. This type of absorption depends on the solubility of gases, the pressure and the temperature. The rate and amount of absorption also depend on the surface area of the interface and its duration in time. For example, when the water is finely divided and mixed with air, as may happen in a waterfall or a strong ocean surf, the water absorbs more oxygen. When a solid absorbs a liquid mixture or part of it, a mass of liquid moves into the solid. This mass transfer takes place at the interface between the solid and the liquid, at a rate depending on both the solid and the liquid. Absorption is essentially molecules attaching themselves to a substance and will not be attracted from other molecules.

On the other hand, chemical absorption or reactive absorption is a chemical reaction between the absorbed and the absorbing substances. Sometimes it combines with physical absorption. This type of absorption depends upon the stoichiometry of the reaction and the concentration of its reactants.

5.1 Chemical Reactions

Biodegradation of hydrocarbons can occur under both aerobic (oxic) and anaerobic (anoxic) conditions (Zengler et al., 1999), albeit by the action of different consortia of organisms. In the subsurface, biodegradation of chemicals occurs primarily under anoxic conditions, mediated by sulfate-reducing bacteria (e.g., Holba et al., 1996) or other anaerobes using a variety of other electron acceptors as the oxidant. Thus, two classes of biodegradation reactions are: (1) aerobic biodegradation and (2) anaerobic biodegradation.

Aerobic biodegradation involves the use of molecular oxygen (O₂), where oxygen (the “terminal electron acceptor”) receives electrons transferred from an organic contaminant:

$\mathrm{Organic}\mathrm{substrate}+{\mathrm{O}}_2\to \mathrm{biomass}+{\mathrm{C}\mathrm{O}}_2+{\mathrm{H}}_2\mathrm{O}+\mathrm{other}\mathrm{inorganic}\mathrm{products}$

For example, hydrocarbons are major components of crude oil and of refined products such as naphtha, kerosene, gas oil, and lubricating oils. These compounds may enter the environment as a result of accident and bioremediation has been attempted in the aquatic and the terrestrial environments (Speight and Arjoon, 2012). They may enter groundwater in which anaerobic degradation is significant and bacterial degradation under aerobic conditions is initiated by either of two reactions: (1) terminal hydroxylation followed by successive dehydrogenation. The resulting carboxylates are further degraded by oxidation to yield ultimately acetate from even-membered alkanes or propionate from odd-membered alkanes or (2) subterminal hydroxylation followed by oxidation to ketones.

Terminal oxidation of alkane derivatives:

$\underset{\mathrm{alkane}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_3}\to \underset{\mathrm{alcohol}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2\mathrm{O}\mathrm{H}}\to \underset{\mathrm{aldehyde}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2\mathrm{C}\mathrm{H}\mathrm{O}}$

Subterminal oxidation of alkane derivatives:

$\underset{\mathrm{alkane}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_3}\to \underset{\mathrm{alcohol}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2\mathrm{C}\mathrm{H}\left(\mathrm{O}\mathrm{H}\right){\mathrm{C}\mathrm{H}}_3}\to \underset{\mathrm{ketone}}{{\mathrm{R}\mathrm{C}\mathrm{H}}_2{\mathrm{C}\mathrm{H}}_2{\mathrm{COCH}}_3}$

Further reaction will produce a wider range of oxygenated products and, in the case of long-chain alkane derivatives, hydroxylation may occur at both ends of the chain (Neilson and Allard, 2008).

Thus, the organic substrate is oxidized (addition of oxygen), and the oxygen is reduced (addition of electrons and hydrogen) to water (H₂O). In this case, the organic substrate serves as the source of energy (electrons) and the source of cell carbon used to build microbial cells (biomass). Some microorganisms (chemo-autotrophic aerobes or litho-trophic aerobes) oxidize reduced inorganic compounds (NH₃, Fe^2 +, or H₂S) to gain energy and fix carbon dioxide to build cell carbon:

${\mathrm{N}\mathrm{H}}_3\left(\mathrm{or}{\mathrm{F}\mathrm{e}}^{2+}\mathrm{or}{\mathrm{H}}_2\mathrm{S}\right)+{\mathrm{C}\mathrm{O}}_2+{\mathrm{H}}_2+{\mathrm{O}}_2\to \mathrm{biomass}+{\mathrm{NO}}_3\left(\mathrm{or}\mathrm{F}\mathrm{e}\mathrm{or}{\mathrm{SO}}_4\right)+{\mathrm{H}}_2\mathrm{O}$

At some contaminated sites, as a result of consumption of oxygen by aerobic microorganisms and slow recharge of oxygen, the environment becomes anaerobic (lacking oxygen), and mineralization, transformation, and cometabolism depend upon microbial utilization of electron acceptors other than oxygen (anaerobic biodegradation). Nitrate (NO₃), iron (Fe^3 +), manganese (Mn^4 +), sulfate (SO₄), and carbon dioxide (CO₂) can act as electron acceptors if the organisms present have the appropriate enzymes (Sims, 1990).

Anaerobic biodegradation is the microbial degradation of organic substances in the absence of free oxygen. While oxygen serves as the electron acceptor in aerobic biodegradation processes forming water as the final product, degradation processes in anaerobic systems depend on alternative acceptors such as sulfate, nitrate, or carbonate yielding, in the end, hydrogen sulfide, molecular nitrogen, and/or ammonia and methane (CH₄), respectively.

In the absence of oxygen, some microorganisms obtain energy from fermentation and anaerobic oxidation of organic carbon. Many anaerobes use nitrate, sulfate, and salts of iron (III) as practical alternates to oxygen acceptor. The anaerobic reduction process of nitrates, sulfates, and salts of iron is an example:

$\begin{array}{l}2{{\mathrm{NO}}_3}^{-}+10{\mathrm{e}}^{-}+12{\mathrm{H}}^{+}\to {\mathrm{N}}_2+6{\mathrm{H}}_2\mathrm{O}\\ {{\mathrm{SO}}_4}^{2-}+8{\mathrm{e}}^{-}+10{\mathrm{H}}^{+}\to {\mathrm{H}}_2\mathrm{S}+4{\mathrm{H}}_2\mathrm{O}\\ \mathrm{F}\mathrm{e}{\left(\mathrm{O}\mathrm{H}\right)}_3+{\mathrm{e}}^{-}+3{\mathrm{H}}^{+}\to {\mathrm{F}\mathrm{e}}^{2+}+3{\mathrm{H}}_2\mathrm{O}\end{array}$

Anaerobic biodegradation is a multistep process performed by different bacterial groups. It involves hydrolysis of polymeric substances like proteins or carbohydrates to monomers and the subsequent decomposition to soluble acids, alcohols, molecular hydrogen, and carbon dioxide. Depending on the prevailing environmental conditions, the final steps of ultimate anaerobic biodegradation are performed by denitrifying, sulfate-reducing or methanogenic bacteria.

In contrast to the strictly anaerobic sulfate-reducing and methanogenic bacteria, the nitrate-reducing microorganisms as well as many other decomposing bacteria are mostly facultative anaerobic insofar as these microorganisms are able to grow and to degrade organic substances (under aerobic as well as anaerobic conditions). Thus, aerobic and anaerobic environments represent the two extremes of a continuous spectrum of environmental habitats which are populated by a wide variety of microorganisms with specific biodegradation abilities.

Anaerobic conditions occur where vigorous decomposition of organic matter and restricted aeration result in the depletion of oxygen. Anoxic conditions may represent an intermediate stage where oxygen supply is limited, still allowing a slow (aerobic) degradation of organic compounds. In a digester the various bacteria also have different requirements to the surrounding environment. For example, acidogenic bacteria need pH values from 4 to 6, whilst methanogenic bacteria from 7 to 7.5. In batch tests the dynamic equilibrium is often interrupted because of an enrichment of acidogenic bacteria as a consequence of lacking substrate in- and outflow.

The inherent biodegradability of these individual components is a reflection of their chemical structure, but is also strongly influenced by the physical state and toxicity of the compounds. As an example, while the n-alkane derivatives (Chapter 2) are the most biodegradable hydrocarbon derivatives, the C₅–C₁₀ homologs have been shown to exhibit the occasional inhibitory action to the majority of hydrocarbon degrading microbes (Speight and Arjoon, 2012). As solvents, these homologs tend to disrupt lipid membrane structures of microorganisms. Similarly, alkanes in the C₂₀–C₄₀ range are hydrophobic solids at physiological temperatures. Apparently, it is this physical state that strongly influences their biodegradation (Bartha and Atlas, 1977).

Primary attack on intact hydrocarbons requires the action of oxygenase organisms and, therefore, requires the presence of free oxygen. In the case of alkanes, mono-oxygenase attack results in the production of alcohol. Most microorganisms attack alkanes terminally whereas some perform subterminal oxidation. The alcohol product is oxidized finally into an aldehyde. Extensive methyl branching interferes with the beta-oxidation process and necessitates terminal attack or other bypass mechanisms. Therefore, n-alkanes are degraded more readily than iso-alkanes.

Cycloalkanes are transformed by an oxidase system to a corresponding cyclic alcohol, which is dehydrated to ketone after which a mono-oxygenase system forms a lactose-type ring, which is subsequently opened by a lactone hydrolase. These two oxygenase systems usually never occur in the same organisms and hence, the frustrated attempts to isolate pure cultures that grow on cycloalkanes (Bartha, 1986b). However, synergistic actions of microbial communities are capable of dealing with degradation of various cycloalkanes quite effectively.

As in the case of alkanes, the monocyclic compounds, cyclopentane (C₅H₁₀), cyclohexane (C₆H₁₂), and cycloheptane (C₇H₁₄) have a strong solvent effect on lipid membranes, and are toxic to the majority of hydrocarbon degrading microorganisms. Highly condensed cycloalkane compounds resist biodegradation due to their relatively complex structure and physical state (Bartha, 1986a).

Condensed polycyclic aromatics are degraded, one ring at a time, by a similar mechanism, but biodegradability tends to decline with the increasing number of rings and degree of condensation. Aromatics with more than four condensed rings are generally not suitable as substrates for microbial growth, though, they may undergo metabolic transformations. The biodegradation process also declines with the increasing number of alkyl substituents on the aromatic nucleus. In fact, some iso-alkanes are apparently spared as long as n-alkanes are available as substrates, while some condensed aromatics are metabolized only in the presence of more easily utilizable hydrocarbons, a process referred to as cometabolism (Wackett 1996).

Finally, a word on the issue of adhesion as it affects biodegradation and, hence, bioremediation. Adhesion to hydrophobic surfaces is a common strategy used by microorganisms to overcome limited bioavailability of hydrocarbons. Intuitively, it may be assumed that adherence of cells to a hydrocarbon would correlate with the ability to utilize it as a growth substrate and conversely that cells able to utilize hydrocarbons would be expected to be able to adhere to them. However, species like Staphylococcus aureus and Serratia marcescens, which are unable to grow on hydrocarbons, adhere to them (Rosenberg et al., 1980). Thus, adherence to hydrocarbons does not necessarily predict utilization (Abbasnezhad et al., 2011).

Biodegradation of poorly water-soluble liquid hydrocarbons is often limited by low availability of the substrate to microbes. Adhesion of microorganisms to a hydrocarbon-water interface can enhance this availability, whereas detaching cells from the interface can reduce the rate of biodegradation. The capability of microbes to adhere to the interface is not limited to hydrocarbon degraders, nor is it the only mechanism to enable rapid uptake of hydrocarbons, but it represents a common strategy. The general indications are that microbial adhesion can benefit growth on and biodegradation of very poorly water-soluble hydrocarbons such as n-alkanes and large polycyclic aromatic hydrocarbons dissolved in a nonaqueous phase. Adhesion is particularly important when the hydrocarbons are not emulsified thereby giving limited interfacial area between the two liquid phases.

When mixed communities are involved in biodegradation, the ability of cells to adhere to the interface can enable selective growth and enhance bioremediation with time. The critical challenge in understanding the relationship between growth rate and biodegradation rate for adherent bacteria is to accurately measure and observe the population residing at the interface of the hydrocarbon phase.

5.2 Kinetics

The kinetics for modeling the bioremediation of contaminated soils can be extremely complicated. This is largely due to the fact that the primary function of microbial metabolism is not for the remediation of environmental contaminants. Instead the primary metabolic function, whether bacterial or fungal in nature, is to grow and sustain more of the microorganism. Therefore, the formulation of a kinetic model must start with the active biomass and factors, such as supplemental nutrients, oxygen source, that are necessary for subsequent biomass growth (Cutright, 1995; Rončević et al., 2005; Pala et al., 2006).

Studies of the kinetics of the bioremediation process proceed in two directions: (1) the first is concerned with the factors influencing the amount of transformed compounds with time and (2) the other approach seeks the types of curves describing the transformation and determines which of them fits the degradation of the given compounds by the microbiologic culture in the laboratory microcosm and sometimes, in the field. However, studies of biodegradation kinetics in the natural environment are often empiric, reflecting only a basic level of knowledge about the microbiologic population and its activity in a given environment (Maletić et al., 2009).

One such example of the empirical approach is the simple (perhaps over-simplified) model:

$dC/dt=k{C}^n$

C is the concentration of the substrate, t is time, k is the degradation rate constant of the compound, and n is a fitting parameter (most often taken to be unity) (Hamaker 1972; Wethasinghe et al. 2006). Using this model, the curve of substrate removal can be fitted by varying n and k until a satisfactory outcome is obtained. It is evident from this equation that the rate is proportional to the exponent of substrate concentration. First order kinetics are the most often used equation for representation of the degradation kinetics (Heitkamp et al. 1987; Heitkamp and Cerniglia 1987; Venosa et al. 1996; Seabra et al. 1999; Holder et al. 1999; Winningham et al. 1999; Namkoonga et al. 2002; Grossi et al. 2002; Hohener et al. 2003; Collina et al. 2005; Rončević et al. 2005; Pala et al. 2006).

However, researchers involved in kinetic studies do not always report whether the model they used was based on theory or experience and whether the constants in the equation have a physical meaning or if they just serve as fitting parameters (Rončević et al., 2005).

5.3 Effect of Salt

Salt is a common cocontaminant that can adversely affect the bioremediation potential at sites such as flare pits and drilling sites (upstream sites) contaminated with saline produced formation water, or at natural oil and crude oil processing facilities contaminated by refinery wastes containing potassium chloride (KCl) and sodium chloride (NaCl) salts (Pollard et al., 1994). Because of increasing emphasis and interest in the viability of intrinsic bioremediation as a remedial alternative, the impact of salt on these processes is of interest.

The effect of salinity on microbial cells varies from disrupted tertiary protein structures and denatured enzymes to cell dehydration (Pollard et al., 1994), with different species having different sensitivities to salt (Tibbett et al., 2011). A range of organic pollutants, including hydrocarbons, has been shown to be mineralized by marine or salt-adapted terrestrial microorganisms that are able to grow in the presence of salt (Margesin and Schinner, 2001; Oren et al., 1992; Nicholson and Fathepure, 2004). In naturally saline soils, it has been shown that bioremediation of diesel fuel is possible at salinities up to 17.5% (w/v) (Riis et al., 2003; Kleinsteuber et al. (2006).

However, an inverse relationship between salinity and the biodegradation of hydrocarbons by halophilic enrichment cultures from the Great Salt Lake (Utah) has been observed (Ward and Brock, 1978). These cultures were unable to metabolize hydrocarbons at salt concentrations above 20% (w/v) in this hyper-saline environment. An inhibitory effect of salinity at concentrations above 2.4% (w/v) sodium chloride was found to be greater for the biodegradation of aromatic and polar fractions than for saturated hydrocarbons incubated with marine sediment (Mille et al., 1991). This represents exsitu hydrocarbon degradation by salt-adapted terrestrial microorganisms.

Furthermore, the effects of salt as a cocontaminant on hydrocarbon degradation in naturally nonsaline systems has been described (De Carvalho and daFonseca, 2005). The results showed that in the degradation of C₅–C₁₆ hydrocarbons at 28°C (82°F) in the presence of 1.0%, 2.0%, or 2.5% (w/v) NaCl by the isolate Rhodococcus erythropolis DCL14 the lag phase of the cultures increased and growth rates decreased with increasing concentrations of sodium chloride. In a similar study (Rhykerd et al., 1995), soils were fertilized with inorganic nitrogen and phosphorus, and amended with sodium chloride at 0.4%, 1.2%, or 2% (w/w). After 80 days at 25°C (77°F), the highest salt concentration had inhibited hydrocarbon mineralization.

However, investigation of the combinations of factors limiting biodegradation of hydrocarbon contamination at upstream natural and crude oil production facilities have received relatively little attention. A laboratory solid-phase bioremediation study reported that high salinity levels reduced the degradation rate of flare pit hydrocarbons (Amatya et al., 2002), and more recently it has been observed that addition of sodium chloride to a contaminated soil decreased hexadecane mineralization rates in the initial stages of bioremediation and increased lag times, but that the final extent of mineralization was comparable over a narrow range of salinity from 0% to 0.4% (w/w) (Børresen and Rike, 2007). However, before embarking on anaerobic microcosm tests, field evidence of indicators of anaerobic biodegradation including changes in terminal electron acceptors, presence of metabolites, and isotopic analysis would be a reasonable way to initiate the investigation (Ulrich et al., 2009).

6.1 Chemistry in the Atmosphere

Organic chemicals can be emitted directly into the atmosphere or formed by chemical conversion or through chemical reactions of precursors species. In these reactions, highly toxic organic chemicals can be converted into less toxic products but the result of the reactions can also be products having a higher toxicity than the starting chemicals. In order to understand these reactions, it is also necessary to understand the chemical composition of the natural atmosphere, the way gases, liquids, and solids in the atmosphere interact with each other and with the earth's surface and associated biota, and how human activities may be changing the chemical and physical characteristics of the atmosphere.

There are a number of critical environmental issues associated with a changing atmosphere, including photochemical smog, global climate change, toxic air pollutants, acidic deposition, and stratospheric ozone depletion (Gouin et al., 2013). A great deal of research and development activity aimed at understanding and hopefully solving some of these problems is underway. Much of the anthropogenic (human) impact on the atmosphere is associated with our increasing use of fossil fuels as an energy source—for things such as heating, transportation, and electric power production. Photochemical smog/tropospheric ozone is a serious environmental problem associated with burning fossil fuels. In fact, the combustion of fossil fuels (which are in fact, organic chemicals) is one of the most common sequences of chemistry that causes pollution in the atmosphere. This phenomenon may not be classed as direct pollution (in the sense of organic chemistry) but is certainly an indirect form of pollution (again, in the sense of organic chemistry). The result is the formation and deposition of acid rain.

Acid rain is formed when sulfur dioxide and nitrogen oxides react with water vapor and other chemicals in the presence of sunlight to form various acidic compounds in the air. The principle source of acid rain-causing pollutants, sulfur dioxide and nitrogen oxides, are from fossil fuel combustion and from the combustion of fossil fuel-derived fuels:

$\begin{array}{l}2{\left[\mathrm{C}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{O}}_2\to 2\mathrm{C}\mathrm{O}\\ \begin{array}{l}{\left[\mathrm{C}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{O}}_2\to {\mathrm{C}\mathrm{O}}_2\hfill \\ 2{\left[\mathrm{N}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{O}}_2\to 2\mathrm{NO}\hfill \\ {\left[\mathrm{N}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{O}}_2\to {\mathrm{NO}}_2\hfill \\ {\left[\mathrm{S}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{O}}_2\to {\mathrm{SO}}_2\hfill \\ 2{\mathrm{SO}}_2+{\mathrm{O}}_2\to 2{\mathrm{SO}}_3\hfill \end{array}\end{array}$

Hydrogen sulfide and ammonia are produced from processing sulfur-containing and nitrogen containing feedstocks:

$\begin{array}{l}{\left[\mathrm{S}\right]}_{\mathrm{fossil}\mathrm{fuel}}+{\mathrm{H}}_2\to {\mathrm{H}}_2\mathrm{S}+\mathrm{hydrocarbons}\hfill \\ 2{\left[\mathrm{N}\right]}_{\mathrm{fossil}\mathrm{fuel}}+3{\mathrm{H}}_2\to 2{\mathrm{N}\mathrm{H}}_3+\mathrm{hydrocarbons}\hfill \end{array}$

$\begin{array}{l}{\mathrm{SO}}_2+{\mathrm{H}}_2\mathrm{O}\to {\mathrm{H}}_2{\mathrm{SO}}_3\left(\mathrm{sulfurous}\mathrm{acid}\right)\hfill \\ {\mathrm{SO}}_3+{\mathrm{H}}_2\mathrm{O}\to {\mathrm{H}}_2{\mathrm{SO}}_4\left(\mathrm{sulfuric}\mathrm{acid}\right)\hfill \\ \mathrm{NO}+{\mathrm{H}}_2\mathrm{O}\to {\mathrm{H}\mathrm{N}\mathrm{O}}_2\left(\mathrm{nitrous}\mathrm{acid}\right)\hfill \\ 3{\mathrm{NO}}_2+2{\mathrm{H}}_2\mathrm{O}\to {\mathrm{H}\mathrm{N}\mathrm{O}}_3\left(\mathrm{nitric}\mathrm{acid}\right)\hfill \end{array}$

Two of the pollutants that are emitted are hydrocarbons (e.g., unburned fuel) and nitric oxide (NO). When these pollutants build up to sufficiently high levels, a chain reaction occurs from their interaction with sunlight in which the NO is converted to nitrogen dioxide (NO₂)—a brown gas and at sufficiently high levels can contribute to urban haze. However, a more serious problem is that nitrogen dioxide (NO₂) can absorb sunlight and break apart to produce oxygen atoms that combine with the oxygen in the air to produce ozone (O₃), a powerful oxidizing agent, and a toxic gas.

In addition, as a result of a variety of human activities (e.g., agriculture, transportation, industrial processes) a large number of different toxic organic chemical pollutants are emitted into the atmosphere. Among the chemicals that may pose a human health risk are pesticides, polychlorobiphenyl derivatives (PCBs), polycyclic aromatic hydrocarbon derivatives (PAHs), dioxin derivatives, and volatile organic compounds (e.g., benzene, carbon tetrachloride).

Many of the more environmentally persistent compounds (such as the PCBs) have been measured in various floral and faunal species.

6.2 Chemistry in the Aquasphere

Water pollution has become a widespread phenomenon and has been known for centuries, particularly the pollution of rivers and groundwater (Samin and Janssen, 2012). By way of example, in ancient time up to the early part of the 20th century, many cities deposited waste into the nearby river or even into the ocean. It is only very recently (because of serious concerns for the condition of the environment) that an understanding of the behavior and fate of chemicals, which are discharged to the aquatic environment as a result of these activities, is essential to the control of water pollution. In rivers the basic physical movement of pollutant molecules is the result of advection, but superimposed upon this are the effects of dispersion and mixing with tributaries and other discharges. Some of the chemicals discharged are relatively inert, so their concentration changes only due to advection, dispersion, and mixing. However, many substances are not conservative in their behavior and undergo changes due to chemical or biochemical processes, such as oxidation.

In addition, there are many indications that the organic chemicals materials in the aquasphere (also called, when referring to the sea, the marine aquasphere) are subject to intense chemical transformations and physical recycling processes imply that a total organic-carbon approach is not sufficient to resolve the numerous processes occurring. The transport of anthropogenically produced or distributed organic compounds such as petroleum hydrocarbons and halogenated hydrocarbons, including the PCBs the DDT family, and the Freon derivatives and the chemistry of these organic chemicals in water is not fully understood.

The effects of an organic chemical released into the marine environment (or any part of the aquasphere) depends on several factors such as (1) the toxicity of the chemical, (2) the quantity of the chemical, (3) the resulting concentration of the chemical in the water column, (4) the length of time that floral and faunal organisms are exposed to that concentration, and (5) the level of tolerance of the organisms, which varies greatly among different species and during the life cycle of the organism. Even if the concentration of the chemical is below what would be considered as the lethal concentration, a sublethal concentration of an organic chemical can still lead to a long-term impact within the aqueous marine environment. For example, chemically induced stress can reduce the overall ability of an organism to reproduce, grow, feed or otherwise function normally within a few generations. In addition, the characteristics of some organic chemicals can result in an accumulation of the chemical within an organism (bio-accumulation) and the organism may be particularly vulnerable to this problem. Furthermore, subsequent bio-magnification may also occur if the organic chemical (or a toxic product produced by one or more transformation reactions) can be passed on, following the food chain up to higher flora or fauna.

In terms of the marine environment and a spill of crude oil, complex processes of crude oil transformation start developing almost as soon as the oil contacts the water although the progress, duration, and result of the transformations depend on the properties and composition of the oil itself, parameters of the actual oil spill, and environmental conditions. The major operative processes are (1) physical transport, (2) dissolution, (3) emulsification, (4) oxidation, (5) sedimentation, (6) microbial degradation, (7) aggregation, and (8) self-purification.

In terms of physical transport, the distribution of oil spilled on the sea surface occurs under the influence of gravitation forces and is controlled by the viscosity of the crude oil as well as the surface tension oil and water. In addition, during the first several days after the spill, a part of is lost through evaporation of oil (into the gaseous phase) and any water-soluble constituents disappear into the sea. The portion of the crude oil that remains is the more viscous fraction. Further changes take place under the combined impact of meteorological and hydrological factors and depend mainly on the power and direction of wind, waves, and currents. A considerable part of oil disperses in the water as fine droplets that can be transported over large distances away from the place of the spill.

Crude oil is not particularly soluble in water although some constituents may be water-soluble to a certain degree, especially low-molecular-weight aliphatic and aromatic hydrocarbons. Polar compounds formed as a result of oxidation of some oil fractions in the marine environment also dissolve in seawater. Compared to evaporation process, the dissolution of cured oil constituents in water is a slow process. However, the emulsification of crude oil constituents in the marine environment does occur but depends predominantly on the presence of functional groups in the oil, which can increase with time due to oxidation. Emulsions usually appear when heavy oil is spilled into the ocean because of the higher proportion of polar constituents compared to conventional (lighter) crude oil (Speight, 2014). The rate of emulsification process can be decreased by use of emulsifiers—surface-active chemicals with strong hydrophilic properties used to eliminate oil spills—which help to stabilize oil emulsions and promote dispersing oil to form microscopic (invisible) droplets that accelerates the decomposition of the crude oil constituents in the water.

Oxidation is a complex process that ultimately results in the destruction of the crude oil constituents. The final products of oxidation (such as hydroperoxide derivatives, phenol derivatives, carboxylic acid derivatives, ketone derivatives, and aldehyde derivatives) usually have increased water solubility. This can result in the apparent disappearance of the crude oil from the surface of the water. What is actually happening is the incorporation of functional groups into the oil constituents which results in a change in density with an increase in the ability of the constituents to become miscible (or emulsify) and sink to various depths of the ocean as these changes intensify. These chemical changes also result in an increase in the viscosity of the crude oil which promotes the formation of solid oil aggregates. The reactions of photo-oxidation, photolysis in particular, also initiate transformation of the more complex (polar) constituents in the crude oil (Speight, 2014).

As these processes occur, some of the crude oil constituents are adsorbed on any suspended material and deposited on the ocean floor (sedimentation), the rate of which is dependent upon the ocean depth—in deeper areas remote from the shore, sedimentation of oil (except for the heavy fractions) is a slow process. Simultaneously, the process of biosedimentation occurs—in this process, plankton and other organisms absorb the emulsified oil—and the crude oil constituents are sent to the bottom of the ocean as sediment with the metabolites of the plankton and other organisms. However, this situation radically changes when the suspended oil reaches the sea bottom—the decomposition rate of the oil on the ocean bottom abruptly ceases—especially under the prevailing anaerobic conditions—and any crude oil constituents accumulated inside the sediments can be preserved for many months and even years. These products can be swept to the edge of the ocean (the beach) by turbulent condition at some later time.

The fate of most of the constituents of crude oil in the marine environment is ultimately defined by their transformation and degradation due to microbial degradation. The degree and rates of biodegradation depend, first of all, upon the structure of the crude oil constituents—alkanes biodegrade faster than aromatic constituents and naphthenic constituents and, with increasing complexity of molecular structure as well as with increasing molecular weight—the rate of microbial decomposition usually decreases. Besides, this rate depends on the physical state of the oil, including the degree of its dispersion as well as environmental factors such as temperature, availability of oxygen, and the abundance of oil-degrading microorganisms.

Aggregation occurs when crude oil forms lumps or tar balls which are produced from crude oil after the evaporation and dissolution of its relatively low-boiling fractions, emulsification of oil residuals, and chemical and microbial transformation. The chemical composition of oil aggregates is changeable but typically includes asphaltene constituents (up to 50%) and other high-molecular-weight constituents of the oil (Speight, 2014). These tar balls have an uneven shape and vary from 1 mm to 10 cm in size (sometimes reaching up to 50 cm) and complete their life cycle by slowly degrading in the water column, on the shore (if they are washed there by currents), or on the sea bottom (if they lose their floating ability).

Self-purification is a result of the processes previously described above in which crude oil in the marine environment rapidly loses its original properties and disintegrates into various fractions. These fractions have different chemical composition and structure and exist in different migrational forms and they undergo chemical transformations that slow after reaching thermodynamic equilibrium with the environmental parameters. Eventually, the original and intermediate compounds disappear, and carbon dioxide and water form. This form of self-purification inevitably happens in water ecosystems if the toxic load does not exceed acceptable limits.

As an example of chemical transformation that can occur in a water system, the chemistry of methyl iodide (which is thermodynamically unstable in seawater) is known and its chemical fate is kinetically controlled. The equations showing the fate of methyl iodide are as follows (Gacosian and Lee, 1981):

$\begin{array}{l}{\mathrm{C}\mathrm{H}}_3\mathrm{I}+\mathrm{C}{1}^{-}={\mathrm{C}\mathrm{H}}_3\mathrm{C}1+\mathrm{I}\\ \begin{array}{l}{\mathrm{C}\mathrm{H}}_{3}1+{\mathrm{B}\mathrm{r}}^{-}={\mathrm{C}\mathrm{H}}_3\mathrm{B}\mathrm{r}+{\mathrm{I}}^{-}\hfill \\ {\mathrm{C}\mathrm{H}}_3\mathrm{B}\mathrm{r}+{\mathrm{C}\mathrm{l}}^{-}={\mathrm{C}\mathrm{H}}_3\mathrm{C}\mathrm{l}+{\mathrm{B}\mathrm{r}}^{-}\hfill \\ {\mathrm{C}\mathrm{H}}_3\mathrm{X}+{\mathrm{H}}_2\mathrm{O}={\mathrm{C}\mathrm{H}}_3\mathrm{O}\mathrm{H}+{\mathrm{X}}^{-}\hfill \end{array}\end{array}$

In this equation, X = C1⁻, Br⁻, I⁻.

Chloride ion was theoretically predicted to be the most kinetically reactive species, with water second, and other anions of lesser importance. This suggested that methyl iodide in seawater would react predominantly via a nucleophilic substitution reaction with chloride ion to yield methyl chloride. Methyl iodide and the methyl chloride produced by would also react with water, although more slowly, to yield methanol and halide ions. According to these experiments, substantial amounts of methyl chloride should be formed in seawater. Methyl chloride has a long half-life for decomposition by known reactions in seawater. Hence, its presence could be a useful label for some surface-derived water masses. Methyl chloride is in fact found in the atmosphere, where compared to methyl iodide, it is less stable to photo-degradation reactions.

Steroids are a class of biogenic compounds which may serve as an indicator of certain processes transforming organic matter in seawater and sediments. The steroid hydrocarbon structure forms a relatively stable nucleus which may incorporate functional groups such as alcohols (sterol derivatives and stanol derivatives), ketone derivatives (stanone derivatives), and olefin linkages (sterene derivatives) either in the four ring system or on the side chain originating at C-17.

The hydrocarbon framework of the steroid system (ring lettering and atom numbering are shown).

These compounds are produced by a wide variety of marine and terrestrial organisms and often have specific species sources. Diagenetic alteration of steroids by geochemical and biochemical processes can lead to the accumulation of transformed products in seawater and sediments.

Within the group of chlorinated compounds, chlorinated ethylene derivatives are the most often detected groundwater pollutants. Tetrachloroethylene (PCE) is the only chlorinated ethylene derivative that resists aerobic biodegradation. TCE, all three isomers of dichloroethylene (CCl₂CH₂ and the cis/trans isomers of CHClCHCl), and vinyl chloride (CH₂CHCl) are mineralized in aerobic cometabolic processes by methanotropic or phenol-oxidizing bacteria. Oxygenase derivatives with broad substrate spectra are responsible for the cometabolic oxidation. Vinyl chloride is furthermore utilized by certain bacteria as carbon and electron source for growth. All chlorinated ethylene derivatives are reductively dechlorinated under anaerobic conditions with possibly ethylene or ethane as harmless end-products.

PCE (CCl₂CCl₂) is dechlorinated to trichloroethylene (CCl₂CHCl) in a cometabolic process by methanogens, sulfate reducers, homoacetogen derivatives and others. Furthermore, PCE and TCE serve in several bacteria as terminal electron acceptors in a respiration process. The majority of these isolates dechlorinate PCE and TCE to cis-l,2-dichloroethene although they have been isolated from systems where complete dechlorination to ethene occurred.

The natural organic subsurface products coal and crude oil have been and are still used to cover the tremendous energy demand of industrialized countries and to produce almost innumerable synthetic organic chemicals. Due to leakage of underground storage tanks and pipelines, due to spills at production wells, refineries and distribution terminals, and due to improper disposal and accidents during transport, organic compounds have become subsurface contaminants that threaten important drinking water resources. One strategy to remediate such polluted subsurface environments is with the help of the degradative capacity of bacteria.

6.3 Chemistry in the Terrestrial Biosphere

The terrestrial biosphere is predominantly the soil that is on the surface of the earth and which can house many different types of organic chemicals. A prime exposure pathway, either directly or indirectly, for soil-borne organic chemical contaminants is via transport in the pore-water solution though the structured and chemically reactive medium of our soils. Soils are also home to plant roots and a myriad of floral and faunal species. In predicting pollutant transport, it is important to distinguish between whether the fate is in the soil itself, or in the receiving water (Clothier et al., 2010).

The monocyclic aromatic compounds benzene, toluene, ethylbenzene, and the xylene isomers and the PAHs belong to the most often encountered subsurface contaminants and they are the most threatening compounds within the hydrocarbons. Aerobic bacteria able to degrade aromatic hydrocarbons are widespread. However, several reasons make the application of an aerobic treatment in the subsurface difficult. The limited availability of oxygen due to its low solubility restricts not only the respiration process, but also the degradation itself. Oxygen is needed by aerobic bacteria to activate and cleave the aromatic ring by the action of oxygenase derivatives. In contrast to the oxidative attack of the ring during aerobic degradation, aromatic compounds are reductively activated under anaerobic conditions.

Nitroaromatic compounds are widespread in the environment and are mainly of anthropogenic origin. One of the most problematic is 2,4,6-trinitrotoluene, a munition compound that is found wherever munition is produced, loaded, handled, or packed. Aerobic bacteria can use nitroaromatic compounds as growth substrates and derive carbon, nitrogen, and energy from their degradation.