Organic chemistry

cal and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study. The range of chemicals studied in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but also containing other elements,[1][2][3] especially oxygen, nitrogen, sulfur, phosphorus (included in many biochemicals) and the halogens. Organometallic chemistry is the study of compounds containing carbon–metal bonds. In addition, contemporary research focuses on organic chemistry involving other organometallics including the lanthanides, but especially the transition metals zinc, copper, palladium, nickel, cobalt, titanium and chromium. To be supplied
Line-angle representation
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Ball-and-stick representation
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Space-filling representation
Three representations of an organic compound, 5α-Dihydroprogesterone (5α-DHP), a steroid hormone. For molecules showing color, the carbon atoms are in black, hydrogens in gray, and oxygens in red. In the line angle representation, carbon atoms are implied at every terminus of a line and vertex of multiple lines, and hydrogen atoms are implied to fill the remaining needed valences (up to 4). Organic compounds form the basis of all earthly life and constitute the majority of known chemicals. The bonding patterns of carbon, with its valence of four—formal single, double, and triple bonds, plus structures with delocalized electrons—make the array of organic compounds structurally diverse, and their range of applications enormous. They form the basis of, or are constituents of, many commercial products including pharmaceuticals; petrochemicals and agrichemicals, and products made from them including lubricants, solvents; plastics; fuels and explosives. The study of organic chemistry overlaps organometallic chemistry and biochemistry, but also with meBefore the 18th century, chemists generally believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds. According to the concept of vitalism (vital force theory), organic matter was endowed with a "vital force".[4] During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis. He separated the acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from inorganic starting materials (the salts potassium cyanate and ammonium sulfate), in what is now called the Wöhler synthesis. Although Wöhler himself was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological (organic) starting materials. The event is now generally accepted as indeed disproving the doctrine of vitalism.[5]

In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkin's mauve. His discovery, made widely known through its financial success, greatly increased interest in organic chemistry.[6]

A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper.[7] Both researchers suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions.[8]

The era of the pharmaceutical industry began in the last decade of the 19th century when the manufacturing of acetylsalicylic acid—more commonly referred to as aspirin—in Germany was started by Bayer.[9] By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine, (Salvarsan), as the first effective medicinal treatment of syphilis, and thereby initiated the medical practice of chemotherapy. Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies.[10][11] His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums.[12]


An example of an organometallic molecule, a catalyst called Grubbs' catalyst. Its formula is often given as RuCl2(PCy3)2(=CHPh), where the ball-and-stick model is based on X-ray crystallography.[13] The single metal atom ruthenium (Ru), (in turquoise), is at the very center of the structure; two chlorines (green), are bonded to the ruthenium atom—carbon atoms are black, hydrogens gray-white, and phosphorus orange. A phosphorus-ligand bond, tricyclohexyl phosphine, PCy, is below center; (another PCy ligand appears at the top of the image where its rings are obscuring one another). The ring group projecting to the right, an alkylidene, contains a metal-carbon double bond to ruthenium. Early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer. In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals.[14]

In the early part of the 20th century, polymers and enzymes were shown to be large organic molecules, and petroleum was shown to be of biological origin. The multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to glucose and terpineol. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12.[15]


The total synthesis of vitamin B12 marked a major achievement in organic chemistry. The discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into types of compounds by various chemical processes led to organic reactions enabling a broad range of industrial and commercial products including, among (many) others: plastics, synthetic rubber, organic adhesives, and various property-modifying petroleum additives and catalysts. The majority of chemical compounds occurring in biological organisms are carbon compounds, so the association between organic chemistry and biochemistry is so close that biochemistry might be regarded as in essence a branch of organic chemistry. Although the history of biochemistry might be taken to span some four centuries, fundamental understanding of the field only began to develop in the late 19th century and the actual term biochemistry was coined around the start of 20th century. Research in the field increased throughout the twentieth century, without any indication of slackening in the rate of increase, as may be verified by inspection of abstraction and indexing services such as BIOSIS Previews and Biological Abstracts, which began in the 1920s as a single annual volume, but has grown so drastically that by the end of the 20th century it was only available to the everyday user as an online electronic database.[16]

Characterization
Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity; chromatography techniques are especially important for this application, and include HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, evaporation, magnetic separation and solvent extraction. Organic compounds were traditionally characterized by a variety of chemical tests, called "wet methods", but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis.[17] Listed in approximate order of utility, the chief analytical methods are:

Nuclear magnetic resonance (NMR) spectroscopy is the most commonly used technique, often permitting the complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principal constituent atoms of organic chemistry – hydrogen and carbon – exist naturally with NMR-responsive isotopes, respectively 1H and 13C. Elemental analysis: A destructive method used to determine the elemental composition of a molecule. Mass spectrometry indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High-resolution mass spectrometry can usually identify the exact formula of a compound and is used in place of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allow one to obtain the "mass spec" of virtually any organic compound. Crystallography can be useful for determining molecular geometry when a single crystal of the material is available. Highly efficient hardware and software allows a structure to be determined within hours of obtaining a suitable crystal. Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, and UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific applications. Refractive index and density can also be important for substance identification. Properties
The physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information includes a melting point, boiling point, and index of refraction. Qualitative properties include odor, consistency, solubility, and color. Melting and boiling properties
Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, and instead tend to degrade. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime. A well-known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of modern mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist. Solubility
Neutral organic compounds tend to be hydrophobic; that is, they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable groups as well as low molecular weight alcohols, amines, and carboxylic acids where hydrogen bonding occurs. Otherwise, organic compounds tend to dissolve in organic solvents. Solubility varies widely with the organic solute and with the organic solvent. Solid state properties
Various specialized properties of molecular crystals and organic polymers with conjugated systems are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see conductive polymers and organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science. Nomenclature
Main article: IUPAC nomenclature of organic chemistry

Various names and depictions for one organic compound. The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and mono functionalized derivatives thereof. Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. They are common for complex molecules, which include most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] qudicinal chemistry, polymer chemistry, and materials science