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1.4: Organic Chemistry

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    Learning Objectives

    • Explain carbon-based compounds like hydrocarbons, alkanes, alkenes, alkynes, alcohols, aldehydes, ketones, carboxylic acid
    • Describe molecular structure
    • Describe organic matter
    • Describe methane, trihalomethanes, acetic acid, haloacetic acid

    Organic compounds contain carbon. All organic compounds are covalently bonded molecules, and most organic compounds are large molecules. All other chemicals are considered inorganic compounds. These compounds include water, salts, and many acids and bases. Organic and inorganic compounds are equally essential for life.

    Organic materials are derived from plant fibers and animal tissues, which are produce by synthesis reactions that produce materials like rubber, plastics, and other compounds; and fermentation reactions that produce alcohols, acids, antibodies, and other compounds.

    Inorganic compounds, in contrast to organic compounds, are combustible, high in molecular weight, and sparingly soluble in water and a source of food for animal consumers and microbial decomposers.

    Molecules unique to living systems are carbohydrates, lipids, proteins, and nucleic acids. Each of these molecules contains carbon and they are referred to as organic compounds. Organic compounds are distinguished by the fact that they contain carbon, and inorganic compounds are defined as compounds that lack carbon. However, carbon dioxide and carbon monoxide are carbon-containing compounds but are considered inorganic compounds.

    Organic molecules are large molecules; however, only small, reactive parts of their structure interact with other compounds. These areas are referred to as active sites and are functional groups, such as acid groups, amines, and others.

    Carbon is a special atom. No other small atom is so electroneutral. The consequence of its electroneutrality is that carbon does not lose or gain electrons. It shares them. With four valence shell electrons, carbon forms four covalent bonds with other elements, as well as with other carbon atoms. As a result, carbon helps to form long, chainlike molecules, ring structures, and other structures that are uniquely suited for specific roles in living systems.

    Many biologic molecules are polymers like carbohydrates and proteins. Polymers are chainlike molecules made of many similar or repeating units, monomers, which are joined together by dehydration synthesis. During dehydration syntheses, a hydrogen atom is removed from one monomer and a hydroxyl group is removed from another monomer. The resultant products are joined together with a covalent bond, and in the process, a water molecule is released. The removal of a water molecule at the bond site occurs each time a monomer is added to the growing polymer chain.


    In organic chemistry, any chemical compound that consists of the elements of carbon and hydrogen is a hydrocarbon. Carbon and hydrogen atoms share an electron pair forming covalent bonds in hydrocarbons. One of the special properties of carbon is its ability to form double and triple bonds.

    Saturated hydrocarbons contain only the elements of carbon and hydrogen with single bonds between carbon atoms. Methane is the simplest hydrocarbon, and it is a gas produced in the anaerobic decomposition of organic compounds.

    When hydrocarbon molecules include one or more double or triple bonds between some of the carbon atoms it is not possible for as many hydrogen atoms to be included in the molecule as when the bonds are single bonds. The term used to describe the presence of one or more double or triple bonds in a molecule of an organic compound is unsaturated. If the organic compound contains all single bonds, it is called saturated.

    Alkanes, Alkenes, and Alkynes

    Hydrocarbons are classified as unsaturated or saturated. Alkanes are a group of saturated hydrocarbons meaning that the hydrocarbon contains only single-bonded carbon atoms represented as:

    C-C-C-C (\(\ce{C_nH_{2n+2}}\))

    Alkenes are a group of unsaturated hydrocarbons meaning that the hydrocarbon contains double carbon-carbon bonds represented as:

    C=C=C (\(\ce{C_nH_{2n}}\))

    Alkynes are hydrocarbons that include triple carbon-carbon bonds (\(\ce{C_nH_{2n-2}}\)).

    A bromine solution is used to test for unsaturation of hydrocarbon molecules. Bromine solution is orange in color. When an alkene is added to a bromine solution, the orange color disappears resulting in a colorless solution. Bromine reacts with alkenes forming a new colorless compound. This test is useful in distinguishing alkenes from alkanes because alkanes do not react with bromine solution.

    Unsaturated hydrocarbons, like olefins, are distinguished from paraffins by the presence of multiple bonds between some carbon atoms. The multiple bonds between carbon atoms displace hydrogen atoms, creating molecules containing fewer hydrogen atoms.

    Vegetable shortenings available as solid fats are produced from oils through the process of hydrogenation which adds hydrogen atoms through the addition of hydrogen gas under controlled conditions. Reducing the number of unsaturated bonds increases the melting point, converting an oil to a solid fat.

    Chemical Structure

    The parent compound of aromatic hydrocarbons is benzene. It is a 6-carbon ring with double bonds between alternate atoms. Benzene is used in the manufacture of a variety of commercial products including insecticides, plastics, solvents, explosives, and dyes.


    Alcohols are formed from hydrocarbons by replacing one or more hydrogen atoms by hydroxyl groups (-OH). Methanol is manufactured synthetically by a catalytic process form carbon monoxide and hydrogen. It is used extensively in manufacturing organic compounds, like solvents, fuel additives, and formaldehyde. Ethyl alcohol for beverage purposes is produced through the fermentation of a variety of natural organic materials, like corn, wheat, rice, and potatoes. Industrial ethanol is produced from fermentation of waste solutions containing sugars, like blackstrap molasses and residues resulting from the purification of cane sugar. Propanol has two isomers, the more common is isopropyl alcohol, which is widely used by industry and sold as a medicinal rubbing alcohol. The three primary alcohols have boiling points less than 100oC, and they are miscible with water.

    • Methanol or methyl alcohol (CH3OH)
    • Ethanol or ethyl alcohol (CH3CH2OH)
    • Isopropyl alcohol or 2-Propano (CH3CH3CHOH)

    Miscible liquids are homogenous when mixed together.

    The derivative of benzene containing one hydroxyl group, known as phenol, has a molecular formula of C6H5OH. The formula and –ol in the name indicate the characteristics of an alcohol; however, phenol, known as carbolic acid, ionizes in water yielding hydrogen ions, and exhibits features of an acid. It occurs as natural component of wastes from coal, gas, petroleum, and a variety of industrial wastes where phenol is used as a raw material. Phenol is a strong toxin that makes the waste materials particularly difficult to treat in biological systems. Phenols impart undesirable tastes to water at low concentrations.

    Aldehydes and Ketones

    Aldehydes and ketones are compounds containing a carbonyl group. Formaldehyde is used to produce plastics and resins. Acetone (dimethyl ketone) is a good solvent of fats and is a common cleaning agent for laboratory glassware.

    • Formaldehyde (CH2OH)
    • Acetone (CH3CHCOH)

    Carboxylic Acids

    Organic acids contain the carboxyl group, -COOH. Carboxylic acid is the highest state of oxidation that an organic radical can achieve. Further oxidation results in the formation of carbon dioxide and water. Acids through 9-carbons are liquids, and those acids with more carbons are greasy solids, fatty acids. Organic acids are weak and ionize poorly.

    Formic, acetic, and propionic acids have sharp penetrating odors, and butyric and valeric acids have extremely disagreeable odors associated with rancid fats and oils. Anaerobic decomposition of long chain fatty acids result in the production of 2 and 3-carbon acids, which are converted to methane and carbon dioxide gas in decomposition reactions.

    • Formic acid (HCOOH)
    • Acetic acid (CH3COOH)
    • Propionic acid (CH3CH2COOH)
    • Butyric acid (CH3CH2CH2COOH)
    • Valeric acid (C4H9COOH)
    • Caproic acid (C5H11COOH)

    Basic compounds react with acids to produce salts. NaOH, sodium hydroxide, reacts with acetic acid to produce sodium acetate. Soaps are slats of long chain fatty acids. Other derivatives of carboxylic acids include esters, such as ethyl acetate and amides.

    • Methylamine (CH3NH2)

    Organic Matter

    Biodegradable organic matter in water is classified into three categories: fats, carbohydrates, and proteins. Carbohydrates consist of sugar units containing the elements of carbon, hydrogen, and oxygen. A single sugar is known as a monosaccharide. Disaccharides are composed of two monosaccharide units. Sucrose, table sugar, is glucose plus fructose. The most prevalent sugar in milk is lactose, consisting of glucose plus galactose. Polysaccharides, long chains of sugar units, are divided into two groups: readily degradable starches, like potatoes, rice, corn, and other edible plants; and cellulose which is found in wood, cotton, paper, and similar plant tissues. Cellulose compounds degrade biologically at a slower rate than starches.

    Proteins are long strings of amino acids containing carbon, hydrogen, oxygen, nitrogen, and phosphorus. They form an essential part of living tissue and constitute a diet necessary for higher life forms.

    Fats refer to a variety of biochemical substances that have the property of being soluble to varying degrees in organic solvents, like ether, ethanol, acetone, and hexane, while being sparingly soluble in water. Because of their limited solubility, degradation by microorganisms is very slow. A simple fat is a triglyceride composed of a glycerol unit with short or long chain fatty acids attached.

    The majority of carbohydrates, fats, and proteins in nature are in the form of large molecules that cannot penetrate the cell membrane of microorganisms. Bacteria, in order to metabolize high-molecular weight substances, must be capable of breaking down the large molecules into diffusible fractions for assimilation into the cell. The first step in bacterial decomposition of organic compounds is hydrolysis of carbohydrates into soluble sugars, proteins into amino acids, and fats into short fatty acids. Aerobic biodegradation results in the formation of carbon dioxide and water. Anaerobic digestion, decomposition in the absence of oxygen, results in the formation of organic acids, alcohols, and other liquid intermediates as well as gaseous entities of carbon dioxide, methane, and hydrogen sulfide.

    Several organic compounds, like cellulose, long chain saturated hydrocarbons, and complex compounds, although available as a bacterial substrate, are considered non-biodegradable because of the time and environmental limitations of biological treatment systems. Petroleum derivatives, detergents, pesticides, and synthetic organic compounds are also resistant to biodegradation, and some of these compounds are toxic and inhibit the activity of microorganisms in biological processes.

    Some waste odors are inorganic compounds, like hydrogen sulfide gas; however many odors are caused by volatile organic compounds, such as mercaptans and butyric acid. Industries may produce a variety of medicinal odors in the processing of raw materials. Surface water supplies plagued with blooms of blue-green algae have fishy or pigpen odors. The cause of odors can be anaerobic decomposition, industrial chemicals, or growths of obnoxious microorganisms.

    Methane and Trihalomethane

    Chlorine is used to inhibit or destroy harmful organisms. This method of disinfection alters cell chemistry causing microorganisms to die. Chlorine is the most widely used disinfectant chemical. Chlorine is relatively inexpensive and leaves residual chlorine that can be measured. An increased interest in disinfection other than chlorine has developed because of the carcinogenic compounds that chlorine may form, trihalomethanes, THMs.

    The exact mechanism of chlorine disinfection action is not fully understood. It is felt that chlorine exerts a direct action against bacterial cell, destroying them. Another theory is that the toxic character of chlorine inactivates the enzymes, which enable living microorganisms to use their food supply. As a result, the organisms die. However, the exact mechanism of chlorine disinfection is less important than its demonstrated effects as a disinfectant.

    When chlorine is added to water, several chemical reactions take place. Some of the reactions involve the molecules of the water, and some reactions involve organic and inorganic substances suspended in the water.

    Chlorine combines with organic and inorganic materials to form chlorine compounds. If chlorine is added continuously, eventually all of the materials in the water that will react with chlorine are used and the chlorine reactions stop. At this point, the chlorine demand is satisfied.

    The chemical reactions between chlorine and organic and inorganic substances produce chlorine compounds. Some chlorine compounds have disinfecting properties, and some compounds do not. Chlorine also reacts with the water and produces substances with disinfecting properties. The total of all of the compounds with disinfection properties plus any remaining free, uncombined, chlorine is known as the chlorine residual. The presence of this measurable chlorine residual indicates that all possible chemical reactions with chlorine have taken place and that a sufficient available residual of chlorine is available to kill microorganisms present in the water.

    When organic materials are present in water being disinfected with chlorine, the chemical reactions that take place can produce suspected carcinogenic compounds, THMs. The formation of these compounds can be prevented by limiting the amount of chlorination and by removing the organic materials before chlorination of the water.

    Methane is an organic compound that is produced in the decomposition of organic matter. Methane is considered to be a volatile organic compound. This compound will react with chlorine to produce a compound that is considered to be carcinogenic.


    Methane is a colorless, odorless, flammable gas, and it is the primary constituent of marsh gas and the firedamp of coal mines. It is obtained commercially from natural gas, and it is the first member of the alkane series of hydrocarbons. The formation of methane can occur through organic matter decomposition or through organic synthesis which involve microorganisms, methanogenesis. The synthesis involves anaerobic and aerobic processes. Naturally occurring methane is produced by microbial methanogenesis. This multistep process is used by microorganisms as an energy source. The net reaction is:

    • CO2 + 8H+ → CH4 + 2 H2O

    The final step in the process is catalyzed by the enzyme coenzyme-B sulfoethylthiotransfersase. Methanogenesis is a form of anaerobic respiration used by organisms that occupy landfills, ruminants, and the guts of termites.


    Trihalomethanes are harmful by-products arising from a process of water disinfection with chlorine. Trihalomethanes are formed when organic materials react with chlorine to form chlorinated by-products. Trihalomethanes are chemical compounds where 3 of the 4-hydrogen atoms of methane are replaced by halogen atoms. Trihalomethanes (THMs) are used in industry as solvents or refrigerants. THMs are environmental pollutants, and many of them are considered carcinogenic. Trihalomethanes with all the same halogen atoms are called haloform, and they are considered to be volatile organics. Some examples of trihalomethanes are:

    • Chloroform
    • Bromodichloromethane
    • Bromoform
    • Carbon tetrachloride
    • Tetrachloroethlene

    Trihalomethanes are formed as a by-product when chlorine is used to disinfect drinking water. They represent a group of chemicals referred to as disinfection by-products. They result from the reaction of chlorine or bromine with organic matter present in the water being treated. THMs have been associated through epidemiological studies with adverse health effects. Governmental agencies have set limits on the amount permissible in drinking water. The EPA limits the total concentration of the four chief constituents, chloroform, bromoform, bromodichloromethane, and dibromochloromethane, referred to as total TTHMs to 80 parts per billion in drinking water.

    In drinking water, THM levels tend to increase with pH, temperature, contact time with chlorine, and the level of the organic precursors. The precursors, organic material, reacts with chlorine to form THMs. One method that is used to decrease THMs is to eliminate or reduce chlorination before the filters and to reduce precursors. Since more precursors are present before filtration, the treatment process is directed toward reducing or eliminating the time chlorine is in contact with the water. If some oxidation before filtration is required, an alternative disinfectant like potassium permanganate or peroxide should be considered. This strategy is not an option if pre-chlorination is necessary to achieve the required CT, contact time, values.

    The EPA has advocated that the best available technology for THM control at treatment facilities is to remove precursors through enhanced coagulation. Enhanced coagulation refers to a process of optimizing the filtration process to maximize removal of precursors. Removal is improved by decreasing pH levels to 4 or 5, increasing the feed rate of coagulants, and using ferric coagulants in place of alum.

    Acetic Acid and Haloacetic Acid

    Haloacetic acids are carboxylic acids where a halogen atom takes the place of hydrogen atoms in acetic acid. In monohaloacetic acid, a single halogen replaces a hydrogen atom. Chloroacetic acid has the structural formula of CH2ClCO2H. In this manner, two chlorine atoms are present in dichloroacaetic acid where two hydrogen atoms are replaced with chlorine atoms. Dichloroacetic acid has a structural formula of CHCl2CO2H.

    Haloacetic acids (HAA) are a common undesirable by-product of drinking water chlorination. Exposure to such disinfection by-products in drinking water, at high levels has been associated with undesirable health outcomes through epidemiological studies. The five most common HAAs in water are:

    • Monochloroacetic acid (CLCH2COOH)
    • Dichloroacetic acid (Cl2CHCOOH)
    • Trichloroacetic acid (Cl3CCOOH)
    • Monobromoacetic acid (BrCH2COOH)
    • Dibromoacetic acid (Br2CHCOOH)

    Collectively, these chemicals are called HAA5.

    HAAs can be formed by chlorination, ozonation, or chloramination of water with the formation of HAAs promoted by slightly acidic water, high organic matter content, and elevated temperature. Chlorine from the water disinfection process reacts with organic matter and small amounts of bromide present in the water to produce various HAAs.

    Review Questions

    1. What is an organic compound?
    2. (2) List some types of organic compounds.
    3. Define an inorganic compound.

    Chapter Quiz

    1. ___________ are covalently bonded molecules, and most are large molecules.
      1. Inorganic compounds
      2. Hydrocarbons
      3. Aldehydes
      4. Organic compounds
    2. ___________ are harmful by-products arising from a process of water disinfection with chlorine. They are formed when organic materials react with chlorine to form chlorinated by-products.
      1. Ketones
      2. Trihalomethanes
      3. Organic compounds
      4. Alkehydes
    1. The EPA limits the total concentration of the four constituents, chloroform, bromoform, bromodichloromethane, and dibromochloromethane to ___________ in drinking water.
      1. 80 ppb
      2. 100 ppb
      3. 20 ppb
      4. 120 ppb
    2. ___________ can be formed by chlorination, ozonation, or chloramination of water. They are promoted in slightly acidic water, high organic matter content, and elevated temperature. These compounds are precursors to Trihalomethanes.
      1. Haloacetic acids
      2. Organic compounds
      3. Inorganic compounds
      4. Carboxylic acids
    1. ___________ is(are) a colorless, odorless, flammable gas, and it is the primary constituent of marsh gas and the firedamp of coal mines.
      1. Bromides
      2. Chlorates
      3. Methane
      4. Chloroform
    2. ___________ is the highest state of oxidation that an organic radical can achieve. Further oxidation results in the formation of carbon dioxide and water.
      1. Haloacetic acids
      2. Organic compounds
      3. Inorganic compounds
      4. Carboxylic acids
    3. Biodegradable organic matter in water is classified into three categories ___________.
      1. THMs, HAA5s, carboxylic acids
      2. Fats, carbohydrates, and proteins
      3. Alkanes, alkenes, alkynes
      4. Chloroform, bromodichloromethane, bromoform
    4. The parent compound of aromatic hydrocarbons is ___________.
      1. Benzene
      2. Alcohol
      3. Chloroform
      4. Acetic acid
    5. Hydrocarbons are classified as unsaturated or saturated. ___________ are a group of saturated hydrocarbons meaning that the hydrocarbon contains only single-bonded carbon atoms.
      1. Alkanes
      2. Alkenes
      3. Alkynes
      4. Acetic acids
    6. ___________ are derived from plant fibers and animal tissues, which are produce by synthesis reactions that produce materials like rubber, plastics, and other compounds; and fermentation reactions that produce alcohols, acids, antibodies, and other compounds.
      1. Inorganic materials
      2. Biologic acids
      3. Hydrocarbons
      4. Organic materials

    1.4: Organic Chemistry is shared under a not declared license and was authored, remixed, and/or curated by John Rowe.

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