Nitrogen Compounds

Type of physical science: Chemistry

Field of study: Chemical compounds

The chemistry of nitrogen and its compounds is dominated by their properties as bases.

Nitrogen compounds are important because they are fundamental to life. For example, amino acids and other nitrogenous bases are nitrogen compounds that constitute the basic building blocks of proteins and the nucleic acids.

Overview

Atomic nitrogen consists of a nucleus comprising seven protons and seven neutrons, surrounded by seven electrons. Five of these electrons make up the valence, or outermost, shell of electrons and are the ones that determine the chemical characteristics and reactivity of nitrogen.

According to the octet rule, it is expected that nitrogen tends to accept three electrons from a suitable metallic donor and obtain an octet of electrons in its valence shell during formation of an ionic compound. Such a configuration of a filled shell is known to be energetically stable, and it is this stability that provides the driving force for the process. The complete shell can also result from sharing electrons with nonmetals to form covalent compounds. In this type of process, it is found that nitrogen forms three covalent bonds by sharing three of its electrons with three electrons of a nonmetal. This effectively provides nitrogen with the three additional electrons required for a completely filled valence shell of eight electrons. One pair of these is not involved in bonding and therefore is said to be "nonbonded," or is referred to as a "lone pair."

It is a consequence of these driving forces that, in its naturally occurring state, the element nitrogen exists as a diatomic, gaseous molecule. In this molecule, each nitrogen atom shares three electrons with the other, resulting in a triple bond between the two atoms and providing each atom with a completely filled valence shell.

In those compounds in which nitrogen has three bonds, the nitrogen atom can form another bond by donation of its lone pair of electrons to the fourth bond. A species that donates electrons is called a Lewis base, while the one that accepts electrons is termed a Lewis acid.

Because nitrogen can form bonds to hydrogen ions in this manner, it is also a hydrogen-ion acceptor or Bronsted-Lowry base. The chemistry of nitrogen compounds is characterized by their base properties.

When nitrogen donates electrons to form a fourth bond, the product is usually a soluble ionic compound, called an ammonium salt. This chemistry is exemplified by the protonation of ammonia, where nitrogen bonds to a hydrogen ion to form the ammonium ion.

Carbon-containing nitrogen compounds behave similarly. Thus, alkyl amines (in which the nitrogen is bonded to carbons that are not an integral part of an aromatic system), aromatic amines (in which the nitrogen is bonded to carbons that are part of an aromatic system), and heterocyclic nitrogen compounds (in which the nitrogen is part of a ring system, which may be aromatic) all function as Lewis bases and can be protonated.

The Lewis base behavior of nitrogen compounds is not restricted to protonation by Bronsted-Lowry acids (hydrogen ion donors). Bonding to Lewis acids is another process that dominates the chemistry of nitrogen compounds. Thus, ammonia forms complex ions with copper or silver ion, and amines bond to uncharged Lewis acids, such as boron trifluoride.

The porphyrin ring system is a cyclic tetrapyrrole that is present in the cytochromes, hemoglobin, and chlorophyll. The nitrogen atoms in each pyrrole are firmly complexed, as Lewis bases to Lewis acids, to iron ions (in the cytochromes and hemoglobin), and to magnesium ions (in chlorophyll).

The Lewis basicity of nitrogen compounds is strong enough that they attack weak Lewis acid sites in other molecules. Such sites may be present in a carbon compound because of a polar bond, which effectively attracts electrons away from carbon, generating a partial positive charge on the carbon. Attack by nitrogen on this Lewis acid site results in bonding to carbon by displacing a "good leaving group" from the carbon compound. For example, pyridine will displace halide from an alkyl halide to give an alkyl pyridinium compound.

A third feature of the chemistry of nitrogen compounds is also related to the lone pair of electrons of nitrogen, as well as to the electronegativity of nitrogen. Electronegativity refers to the extent of attraction of an atom for the electrons in its bonds. Only fluorine and oxygen have greater electronegativities, and chlorine is about the same as nitrogen. These factors favor the participation of nitrogen in a special kind of bonding known as hydrogen bonding.

When hydrogen is bonded to a very electronegative atom such as fluorine, oxygen, or nitrogen, these attract electron density to themselves at the expense of the hydrogen. Therefore, the hydrogen has partial positive charge and can form so-called hydrogen bonds with another electronegative atom (fluorine, oxygen, or nitrogen) bearing partial negative charge, in another molecule or within the same molecule. Although a single hydrogen bond is relatively weak compared to a covalent or ionic bond, hydrogen bonds exert a tremendous effect on those systems in which they are present because generally there will be many such hydrogen bonds present.

Hydrogen bonds play a central role in the structure of proteins and nucleic acids.

Proteins consist of amino acids, which are bonded in long chains to one another by peptide linkages. These are formed by attack of the nitrogen (acting as a Lewis base) of one amino acid on the carboxyl group (Lewis acid) of another. One of the structural features of proteins is the adoption of a helical conformation by the long chains of amino acids. This conformation is preferred because of the extensive degree of hydrogen bonding that occurs between hydrogens bonded to electronegative nitrogen and oxygens bonded to carbons in peptide linkages further along the chain.

The two major classes of nitrogen-containing compounds present in the nucleic acids are the purines and pyrimidines. Purines contain four nitrogens in two rings, which are fused together. Pyrimidines contain two nitrogens in a single ring. There are five nitrogenous bases that are most commonly encountered in nucleic acids, each falling into one of these classes of compounds. The purines are adenine (A) and guanine (G); the pyrimidines are cytosine (C), uracil (U), and thymine (T). The presence of nitrogenous bases and their participation in hydrogen bonding impart the structural characteristics required by nucleic acids for their functions in cellular metabolism, growth, and reproduction.

Finally, it is worth noting that volatile nitrogen compounds have unpleasant odors, which may be pungent (as in ammonia) or fishlike (as with various amines). Putrescine and cadaverine are nitrogen-containing compounds that are the stench-producers of decaying flesh.

Putrescine consists of four carbons with a nitrogen atom at each end of the chain; cadaverine is similar, but contains five carbons. They arise from the decomposition of proteins.

Applications

Many industrial applications exist that utilize the properties of nitrogen compounds.

Hexamethylenediamine is a compound containing six carbons with one nitrogen at each end of the chain and is used in the manufacture of nylon. The reaction takes place with another organic compound in which each end of the molecule has a carboxylic acid group. After the reaction, a long-chain polymer is obtained in which the linkages are of the peptide type, called amides. The hydrogen bonding interactions also exist to some extent in nylon, conferring strength to the polymer. Kevlar, another polymer containing amide linkages, is one of the toughest materials known and is used for bullet-proofing and armor-plating.

In addition, nitrogen is one of the major constituents of all the compounds that make up living matter, the other constituents being carbon, oxygen, and hydrogen. The main source of biological nitrogen is the air, because few mineral sources are available. Plants obtain nitrogen in the form of ammonia, ammonium ions, and nitrate ions. These nitrogen-containing compounds are formed by bacteria in soil, which convert molecular nitrogen into useful compounds--a process called nitrogen fixation--during metabolism. The process is mediated by an important enzyme called nitrogenase. The conversion of ammonia into amino acids and other biomolecules is controlled by the metabolism of the plant.

In order to obtain an energetically stable completely filled outer shell of electrons, nitrogen not only can gain three electrons by forming three covalent bonds but also can give up all five electrons in its outer shell. Therefore, the resulting oxidation states of nitrogen in its compounds lie between -3 and +5 (inclusive). In ammonia, the oxidation state of nitrogen is -3.

The positive oxidation states of nitrogen occur only in its compounds with oxygen and fluorine.

Nitrogen oxides are common substances, whereas the nitrogen fluorides are rare.

Each nitrogen atom in nitrogen gas has an oxidation state of zero. Nitrogen fixation by soil bacteria alone would not be able to sustain the demands of the world population on agricultural food production. Most of the nitrogen required is supplied by fertilizers, which rely on the Haber process as the source of nitrogen.

Ammonia, which contains nitrogen in the -3 oxidation state, is produced by the Haber process, which catalytically combines nitrogen from air with hydrogen.

Hydrazine contains two nitrogens, in the -2 oxidation state, bonded to each other and four hydrogens. This important compound has three properties that are typical of nitrogen compounds. First, it is a Lewis and Bronsted-Lowry base; second, it is a reducing agent; and third, it is an energy-rich compound. Therefore, hydrazine readily complexes with metal ions, becomes oxidized (as it reduces some other reactant) to nitrogen in basic solution, and has been used in rocket fuels (as its methyl derivatives) in Apollo Moon missions, in the steering rockets of the space shuttle, and in the lunar-lander rockets. In the latter case, dinitrogen tetroxide (an oxidizing agent) was mixed with methyl hydrazine in a hypergolic reaction (in which reactants ignite on contact).

Nitrogen in the +1 oxidation state is present in dinitrogen monoxide (also called nitrous oxide), which is a colorless gas with a pleasant smell and sweet taste. The gas acts as an intoxicant (the so-called laughing gas) when breathed and is used as a general anesthetic in minor surgery.

In nitrogen monoxide (also called nitric oxide) the oxidation state of nitrogen is +2.

This colorless gas is formed in air at high temperatures by combination of nitrogen and oxygen during lightning discharges and in automobile engines. Industrially, the same reaction, using catalysts, is used in the manufacture of nitric acid. Nitric oxide contributes to the depletion of the earth's protective ozone layer as it is oxidized by ozone to nitrogen dioxide.

The oxidation state of nitrogen in nitrogen dioxide is +4. This red-brown gas is often observed as a result of atmospheric pollution over large cities, where the large numbers of automobiles generate significant amounts of nitric oxide, which is oxidized to nitrogen dioxide.

The dioxide reacts with water vapor in the atmosphere to generate nitric acid, which is a contributor to the acid rain problem of industrialized nations.

Dinitrogen trioxide contains nitrogen in the +3 oxidation state, but the compound is not stable and readily decomposes to nitric oxide and nitrogen dioxide.

In nitric acid, nitrogen is in the +5 oxidation state. The acid is produced in the Ostwald process by the catalytic combination of nitrogen and oxygen to form nitrogen dioxide, which is then reacted with water. Nitric acid is important in the manufacture of fertilizers, explosives, polymers, and plastics.

In humans and other animals, the nitrogen compounds required for nucleic acid and proteins are obtained from food. Proteins and nucleic acids in food are broken down into amino acids by enzymes during digestion, absorbed, and reformed into proteins as directed by nucleic acids.

Enzymes form a special group of catalysts that catalyze specific metabolic processes for particular reactants. The specificity of enzymes originates in their structural makeup. The proteins that are the constituents of enzymes are called globular proteins because the helices are extensively folded around themselves. The helices are formed and stabilized by hydrogen bonds between the nitrogens and carbonyl groups of amino acids in the chains.

Of the nucleic acids, ribonucleic acids contain only A, C, G, and U bases, while deoxyribonucleic acids (DNA) contain only A, C, G, and T bases. In DNA, three hydrogen bonds between G-C pairs and two between A-T pairs occur between separate strands of the molecule, linking one strand to the other and forming the double helix that characterizes DNA structure.

The situation in RNA is complicated by the different RNAs possible. In general, however, three hydrogen bonds occur between G-C pairs and two between A-U pairs, and each member of the pair may be in the same strand or in a different one.

The active compounds in coffee, tea, and cocoa are purine bases, the main example being caffeine. The pyrimidine structural skeleton is present in some vitamins, such as vitamin B1 (thiamine). Many other natural products contain purine and pyrimidines. Pteridines are nitrogen-containing compounds in which the pyrimidine ring is fused to a pyrazine ring. The pteridines occur in folic acid, tetrahydrofolic acid, and riboflavin. Pteridines are also found in insects and in the eyes and skins of fish, amphibians, and reptiles. Biopterin is a pteridine that occurs in human urine, fruit flies, and the "royal jelly" of bees.

Alkaloids are a group of nitrogen-containing compounds found in the higher orders of the plant kingdom. They include many compounds with pharmacological activity, such as morphine (an analgesic, from the opium poppy), quinine (used in malaria treatment, from cinchona bark), colchicine (for gout treatment, from the seeds and roots of the autumn crocus), reserpine (a tranquilizer, from snake root), atropine (a vasodilator, from nightshade), mescaline (a hallucinogen, from peyote cactus), and (+)-lysergic acid diethylamide (commonly known as LSD, a hallucinogen from fungus that grows on rye and wheat). It has been suggested that alkaloids may function as chelating agents, where nitrogens complex specifically to a required metal ion in the soil, rejecting others. Another possibility is that alkaloids may serve to protect plants from animals and insects, because of their intense biological activity and bitter taste.

Other applications involving nitrogen includes its use as an inert gas "pad" for storage of foods. In laboratories, the Bronsted-Lowry property of simple amines promotes their use as solvents in reactions that produce acid to remove the acid from the reaction process.

Context

The use of chemicals as explosives has its origins in ancient China, Arabia, and India.

These ancient formulations of gunpowder were replaced by ammonium nitrate. Nitroglycerin is an unstable liquid that was prepared in 1866 and used as an explosive. The substance is produced by the reaction of glycerol with nitric acid. The instability of nitroglycerin caused handling difficulties that were overcome by the Swedish inventor, Alfred Nobel. Nobel used an absorbent clay to soak up nitroglycerin, making it less shock-sensitive. The resulting material was called dynamite, and its success provided the funds used by the inventor to found the Nobel Prizes in Chemistry, Literature, Peace, Physics, and Physiology or Medicine.

One of the major advances in the chemistry of nitrogen occurred in 1828, when Friedrich Wohler heated an inorganic compound, ammonium cyanate, and obtained urea, a known constituent of urine from mammals. This discovery was important, because previously it was thought that organic compounds could come only from living things and the "vital force" contained therein. Thus, the chemistry of nitrogen is intimately related with the advent of organic chemistry and with biochemistry.

In 1898, William Ramsay predicted that the middle of the twentieth century would bring world disaster because of the depletion of fixed nitrogen. One of the first successes in averting the disaster took place in the laboratories of Adolf Frank and Nikodem Caro. They discovered the preparation of cyanamide by the passage of nitrogen gas over calcium carbide at 1,000 degrees Celsius. Cyanamide decomposes slowly in the soil, releasing the ammonia required by plants. Yet, it was because of the discovery of the more efficient Haber process, by Fritz Haber, that the disaster did not occur. The use of a platinum catalyst allowed the reactions to occur at a much lower temperature and, therefore, more cheaply than that required in the cyanamide preparation. Haber received the 1918 Nobel Prize in Chemistry for his discovery of the ammonia process. The Haber process also allowed the large-scale manufacture of explosives based on ammonium nitrate.

Another German chemist, Wilhelm Ostwald, discovered the process for the industrial preparation of nitric acid in 1902. In this process, ammonia is burned in the presence of a platinum catalyst to give nitric oxide, which reacts further with oxygen to give nitrogen dioxide.

This gas reacts with water to produce nitric acid and nitric oxide, which is recirculated to the first step. Ostwald was awarded the 1909 Nobel Prize in Chemistry for his work in catalysis.

The combined work of Haber and Ostwald permitted Germany to produce its own explosives during World War I. (Previously, the required nitrates had to be imported from Chile.)

In fact, the Haber and Ostwald discoveries had a disastrous effect on the Chilean economy, which centered on the export of nitrates. Nitrates are used as the explosives for mining, building demolition, and fireworks.

Later in the twentieth century, research and advances in the area of nitrogen compounds occurred mainly in the organic and biochemical areas. Thus, an organic diamine was used in the manufacture of nylon in 1938, as a result of the work by Wallace H. Carothers.

Biochemical pathways involving amino acid, protein, and nucleic acid syntheses were revealed, and, in 1953, the complete structural analysis of DNA by James D. Watson and Francis Crick was completed. They were awarded the 1962 Nobel Prize in Physiology or Medicine for their work.

Principal terms

AMINE: an organic compound containing nitrogen

AMINO ACID: any one of twenty types of organic nitrogen-containing compounds that can be bonded together to form macromolecular chains called proteins

CATALYST: a substance that alters the rate of a chemical reaction and is not consumed in the process

ENZYMES: catalysts, consisting of proteins; which mediate the reactions occurring in cells

FIXATION: the process in which nitrogen compounds that can be utilized directly by plants are formed; these compounds usually contain nitrogen in the form of ammonia

METABOLISM: all the processes by which complex molecules, such as carbohydrates and proteins, are formed (anabolism) or broken down (catabolism) in plants and organisms

NUCLEIC ACIDS: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), the biomolecules that control all cellular functions, including growth, metabolism, and reproduction

NUCLEOTIDE: the basic building block of the nucleic acids; nucleotides consist of a nitrogenous base bonded to a simple sugar containing a phosphate group

PEPTIDE: any molecule resulting from the formation of a bond between the amino group of one amino acid and the carboxyl group of another

Bibliography

Baum, Rudy M. "Nobel Prize for Catalytic RNA Found Winners on Separate Tracks." CHEMICAL AND ENGINEERING NEWS 67 (December 4, 1989): 31-34. This article provides an excellent review of the research on ribozymes. References to other publications are provided.

Clements, Richard. MODERN CHEMICAL DISCOVERIES. New York: E. P. Dutton, 1954. This book provides some informative accounts of developments in the area of nitrogen compounds, particularly in chapter 34.

Ebbing, Darrell D., and Mark S. Wrighton. GENERAL CHEMISTRY. 3d ed. Boston: Houghton-Mifflin, 1990. This excellent text provides detailed discussions relating to nitrogen compounds, accompanied by many colorful illustrations, including the acid-base properties and fertilizer uses of ammonia (chapter 4), the Ostwald process (chapter 6), and acid rain (chapter 16).

Fieser, Louis F., and Mary Fieser. ORGANIC CHEMISTRY. 3d ed. Lexington, Mass.: D. C. Heath, 1956. Chapter 16 on proteins contains an informative account of the development of enzyme research and understanding from a historical perspective. Brief biographies of the major scientific figures are included.

Gillespie, Ronald J., David A. Humphreys, N. Colin Baird, and Edward A. Robinson. CHEMISTRY. 2d ed. Boston: Allyn & Bacon, 1989. Chapters 18 (on nitrogen), 23 (organic chemistry), and 24 (polymers) are recommended. Useful biographical information is included.

Kotz, John C., and Keith F. Purcell. CHEMISTRY AND CHEMICAL REACTIVITY. Philadelphia: Saunders College, 1987. An introductory college text. Chapter 22 contains an excellent description of nitrogen compounds and their properties. Biographical sketches are included in each chapter.

Radel, Stanley, and Marjorie H. Navidi. CHEMISTRY. St. Paul, Minn.: West, 1990. Chapter 11 contains a well-written summary of the use of nitrogen compounds in fireworks, rockets, and explosives.

Tedder, J. M., A. Nechvatal, A. W. Murray, and J. Carnduff. BASIC ORGANIC CHEMISTRY. Part 4. New York: John Wiley & Sons, 1972. Although this book is an advanced and detailed text, large sections of each chapter are excellent and are recommended for all readers. Chapters 6, 7, and 8 treat amino acids and proteins, alkaloids, and nucleic acids, respectively. Annotated references are included after each chapter.

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The Chemistry of Water Pollution

X-Ray Determination of Molecular Structure